Raspbian Package Auto-Building

pymol → 1.7.2.1-2 → armhf → 2015-06-21 10:44:58

sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on testwandboard

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║ pymol 1.7.2.1-2 (armhf)                                    21 Jun 2015 10:18 ║
╚══════════════════════════════════════════════════════════════════════════════╝

Package: pymol
Version: 1.7.2.1-2
Source Version: 1.7.2.1-2
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'build/pymol-YJasgY/pymol-1.7.2.1' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/pymol-YJasgY' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-20de89bc-a9d5-40a7-9339-88ad6741666b' with '«CHROOT»'

┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot                                                                │
└──────────────────────────────────────────────────────────────────────────────┘

Get:1 http://172.17.0.1 stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1 stretch-staging/main Sources [7973 kB]
Get:3 http://172.17.0.1 stretch-staging/main armhf Packages [9768 kB]
Ign http://172.17.0.1 stretch-staging/main Translation-en
Fetched 17.8 MB in 36s (490 kB/s)
Reading package lists...

┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files                                                           │
└──────────────────────────────────────────────────────────────────────────────┘


Check APT
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Checking available source versions...

Download source files with APT
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Reading package lists...
Building dependency tree...
NOTICE: 'pymol' packaging is maintained in the 'Svn' version control system at:
svn://anonscm.debian.org/debichem/unstable/pymol/
Need to get 8792 kB of source archives.
Get:1 http://172.17.0.1/private/ stretch-staging/main pymol 1.7.2.1-2 (dsc) [2028 B]
Get:2 http://172.17.0.1/private/ stretch-staging/main pymol 1.7.2.1-2 (tar) [8745 kB]
Get:3 http://172.17.0.1/private/ stretch-staging/main pymol 1.7.2.1-2 (diff) [45.0 kB]
Fetched 8792 kB in 4s (1795 kB/s)
Download complete and in download only mode

Check architectures
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Check dependencies
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Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-n5CQet/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Ign file: ./ InRelease
Get:1 file: ./ Release.gpg [299 B]
Get:2 file: ./ Release [2119 B]
Ign file: ./ Translation-en
Reading package lists...
Reading package lists...

┌──────────────────────────────────────────────────────────────────────────────┐
│ Install core build dependencies (apt-based resolver)                         │
└──────────────────────────────────────────────────────────────────────────────┘

Installing build dependencies
Reading package lists...
Building dependency tree...
The following NEW packages will be installed:
  sbuild-build-depends-core-dummy
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 1 newly installed, 0 to remove and 76 not upgraded.
Need to get 0 B/816 B of archives.
After this operation, 0 B of additional disk space will be used.
Selecting previously unselected package sbuild-build-depends-core-dummy.
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(Reading database ... 11998 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
Merged Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>> 7.0.50~), freeglut3-dev, libfreetype6-dev, libglew1.5-dev, libpng12-0-dev, python, python-dev, python-numpy, python-support (>= 0.4), texlive-latex-base, tk-dev
Filtered Build-Depends: libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>> 7.0.50~), freeglut3-dev, libfreetype6-dev, libglew1.5-dev, libpng12-0-dev, python, python-dev, python-numpy, python-support (>= 0.4), texlive-latex-base, tk-dev
dpkg-deb: building package `sbuild-build-depends-pymol-dummy' in `/«BUILDDIR»/resolver-r4tG0d/apt_archive/sbuild-build-depends-pymol-dummy.deb'.
OK
Ign file: ./ InRelease
Get:1 file: ./ Release.gpg [299 B]
Get:2 file: ./ Release [2119 B]
Ign file: ./ Translation-en
Reading package lists...
Reading package lists...

┌──────────────────────────────────────────────────────────────────────────────┐
│ Install pymol build dependencies (apt-based resolver)                        │
└──────────────────────────────────────────────────────────────────────────────┘

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
  bsdmainutils debhelper file fontconfig-config fonts-dejavu-core freeglut3
  freeglut3-dev gcc-5-base gettext gettext-base groff-base intltool-debian
  libasprintf0c2 libavahi-client3 libavahi-common-data libavahi-common3
  libblas-common libblas3 libcroco3 libcups2 libcupsfilters1 libcupsimage2
  libdrm-dev libdrm-exynos1 libdrm-freedreno1 libdrm-nouveau2 libdrm-omap1
  libdrm-radeon1 libdrm-tegra0 libdrm2 libexpat1 libexpat1-dev libffi6
  libfontconfig1 libfontconfig1-dev libfreetype6 libfreetype6-dev libgfortran3
  libgl1-mesa-dev libgl1-mesa-glx libglapi-mesa libglew-dev libglew1.10
  libglib2.0-0 libglu1-mesa libglu1-mesa-dev libgnutls-deb0-28 libgraphite2-3
  libgs9 libgs9-common libgssapi-krb5-2 libharfbuzz-icu0 libharfbuzz0b
  libhogweed4 libice-dev libice6 libicu52 libidn11 libijs-0.35 libjasper1
  libjbig0 libjbig2dec0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkpathsea6
  libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libmagic1 libnettle6
  libopenjpeg5 libp11-kit0 libpaper-utils libpaper1 libpipeline1 libpixman-1-0
  libpng12-dev libpoppler46 libpotrace0 libptexenc1 libpthread-stubs0-dev
  libpython-dev libpython-stdlib libpython2.7 libpython2.7-dev
  libpython2.7-minimal libpython2.7-stdlib libsm-dev libsm6 libsqlite3-0
  libssl1.0.0 libsynctex1 libtasn1-6 libtcl8.6 libtiff5 libtk8.6 libunistring0
  libx11-6 libx11-data libx11-dev libx11-xcb-dev libx11-xcb1 libxau-dev
  libxau6 libxaw7 libxcb-dri2-0 libxcb-dri2-0-dev libxcb-dri3-0
  libxcb-dri3-dev libxcb-glx0 libxcb-glx0-dev libxcb-present-dev
  libxcb-present0 libxcb-randr0 libxcb-randr0-dev libxcb-render0
  libxcb-render0-dev libxcb-shape0 libxcb-shape0-dev libxcb-sync-dev
  libxcb-sync1 libxcb-xfixes0 libxcb-xfixes0-dev libxcb1 libxcb1-dev
  libxdamage-dev libxdamage1 libxdmcp-dev libxdmcp6 libxext-dev libxext6
  libxfixes-dev libxfixes3 libxft-dev libxft2 libxi6 libxml2 libxmu6 libxpm4
  libxrender-dev libxrender1 libxshmfence-dev libxshmfence1 libxss-dev libxss1
  libxt-dev libxt6 libxxf86vm-dev libxxf86vm1 libzzip-0-13 man-db
  mesa-common-dev mime-support pkg-config po-debconf poppler-data python
  python-dev python-minimal python-numpy python-support python2.7
  python2.7-dev python2.7-minimal tcl tcl-dev tcl8.6 tcl8.6-dev tex-common
  texlive-base texlive-binaries texlive-latex-base tk tk-dev tk8.6 tk8.6-dev
  ucf x11-common x11proto-core-dev x11proto-damage-dev x11proto-dri2-dev
  x11proto-fixes-dev x11proto-gl-dev x11proto-input-dev x11proto-kb-dev
  x11proto-render-dev x11proto-scrnsaver-dev x11proto-xext-dev
  x11proto-xf86vidmode-dev xdg-utils xorg-sgml-doctools xtrans-dev zlib1g-dev
Suggested packages:
  wamerican wordlist whois vacation dh-make gettext-doc groff cups-common
  glew-utils gnutls-bin krb5-doc krb5-user libice-doc libjasper-runtime
  liblcms2-utils libsm-doc libxcb-doc libxext-doc libxt-doc less www-browser
  libmail-box-perl poppler-utils ghostscript fonts-japanese-mincho
  fonts-ipafont-mincho fonts-japanese-gothic fonts-ipafont-gothic
  fonts-arphic-ukai fonts-arphic-uming fonts-nanum python-doc python-tk
  gfortran python-nose python-numpy-dbg python-numpy-doc python2.7-doc
  binfmt-support tcl-doc tcl-tclreadline tcl8.6-doc perl-tk gv
  postscript-viewer xpdf-reader pdf-viewer tk-doc tk8.6-doc gvfs-bin
Recommended packages:
  curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
  libgl1-mesa-dri libglib2.0-data shared-mime-info xdg-user-dirs fonts-droid
  krb5-locales libx11-doc xml-core libmail-sendmail-perl lmodern ruby wish
  texlive-latex-base-doc xterm x-terminal-emulator libfile-mimeinfo-perl
  libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils
The following NEW packages will be installed:
  bsdmainutils debhelper file fontconfig-config fonts-dejavu-core freeglut3
  freeglut3-dev gcc-5-base gettext gettext-base groff-base intltool-debian
  libasprintf0c2 libavahi-client3 libavahi-common-data libavahi-common3
  libblas-common libblas3 libcroco3 libcups2 libcupsfilters1 libcupsimage2
  libdrm-dev libdrm-exynos1 libdrm-freedreno1 libdrm-nouveau2 libdrm-omap1
  libdrm-radeon1 libdrm-tegra0 libexpat1 libexpat1-dev libffi6 libfontconfig1
  libfontconfig1-dev libfreetype6 libfreetype6-dev libgfortran3
  libgl1-mesa-dev libgl1-mesa-glx libglapi-mesa libglew-dev libglew1.10
  libglib2.0-0 libglu1-mesa libglu1-mesa-dev libgnutls-deb0-28 libgraphite2-3
  libgs9 libgs9-common libgssapi-krb5-2 libharfbuzz-icu0 libharfbuzz0b
  libhogweed4 libice-dev libice6 libicu52 libidn11 libijs-0.35 libjasper1
  libjbig0 libjbig2dec0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkpathsea6
  libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libmagic1 libnettle6
  libopenjpeg5 libp11-kit0 libpaper-utils libpaper1 libpipeline1 libpixman-1-0
  libpng12-dev libpoppler46 libpotrace0 libptexenc1 libpthread-stubs0-dev
  libpython-dev libpython-stdlib libpython2.7 libpython2.7-dev
  libpython2.7-minimal libpython2.7-stdlib libsm-dev libsm6 libsqlite3-0
  libssl1.0.0 libsynctex1 libtasn1-6 libtcl8.6 libtiff5 libtk8.6 libunistring0
  libx11-6 libx11-data libx11-dev libx11-xcb-dev libx11-xcb1 libxau-dev
  libxau6 libxaw7 libxcb-dri2-0 libxcb-dri2-0-dev libxcb-dri3-0
  libxcb-dri3-dev libxcb-glx0 libxcb-glx0-dev libxcb-present-dev
  libxcb-present0 libxcb-randr0 libxcb-randr0-dev libxcb-render0
  libxcb-render0-dev libxcb-shape0 libxcb-shape0-dev libxcb-sync-dev
  libxcb-sync1 libxcb-xfixes0 libxcb-xfixes0-dev libxcb1 libxcb1-dev
  libxdamage-dev libxdamage1 libxdmcp-dev libxdmcp6 libxext-dev libxext6
  libxfixes-dev libxfixes3 libxft-dev libxft2 libxi6 libxml2 libxmu6 libxpm4
  libxrender-dev libxrender1 libxshmfence-dev libxshmfence1 libxss-dev libxss1
  libxt-dev libxt6 libxxf86vm-dev libxxf86vm1 libzzip-0-13 man-db
  mesa-common-dev mime-support pkg-config po-debconf poppler-data python
  python-dev python-minimal python-numpy python-support python2.7
  python2.7-dev python2.7-minimal sbuild-build-depends-pymol-dummy tcl tcl-dev
  tcl8.6 tcl8.6-dev tex-common texlive-base texlive-binaries
  texlive-latex-base tk tk-dev tk8.6 tk8.6-dev ucf x11-common
  x11proto-core-dev x11proto-damage-dev x11proto-dri2-dev x11proto-fixes-dev
  x11proto-gl-dev x11proto-input-dev x11proto-kb-dev x11proto-render-dev
  x11proto-scrnsaver-dev x11proto-xext-dev x11proto-xf86vidmode-dev xdg-utils
  xorg-sgml-doctools xtrans-dev zlib1g-dev
The following packages will be upgraded:
  libdrm2
1 upgraded, 195 newly installed, 0 to remove and 75 not upgraded.
Need to get 93.7 MB/93.7 MB of archives.
After this operation, 299 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ stretch-staging/main libpipeline1 armhf 1.4.0-1 [24.0 kB]
Get:2 http://172.17.0.1/private/ stretch-staging/main groff-base armhf 1.22.3-1 [1085 kB]
Get:3 http://172.17.0.1/private/ stretch-staging/main bsdmainutils armhf 9.0.6 [177 kB]
Get:4 http://172.17.0.1/private/ stretch-staging/main man-db armhf 2.7.0.2-5 [972 kB]
Get:5 http://172.17.0.1/private/ stretch-staging/main libasprintf0c2 armhf 0.19.4-1 [31.5 kB]
Get:6 http://172.17.0.1/private/ stretch-staging/main libkeyutils1 armhf 1.5.9-5 [10.9 kB]
Get:7 http://172.17.0.1/private/ stretch-staging/main libkrb5support0 armhf 1.12.1+dfsg-20 [54.9 kB]
Get:8 http://172.17.0.1/private/ stretch-staging/main libk5crypto3 armhf 1.12.1+dfsg-20 [108 kB]
Get:9 http://172.17.0.1/private/ stretch-staging/main libkrb5-3 armhf 1.12.1+dfsg-20 [258 kB]
Get:10 http://172.17.0.1/private/ stretch-staging/main libgssapi-krb5-2 armhf 1.12.1+dfsg-20 [128 kB]
Get:11 http://172.17.0.1/private/ stretch-staging/main libidn11 armhf 1.30-1 [166 kB]
Get:12 http://172.17.0.1/private/ stretch-staging/main libmagic1 armhf 1:5.22+15-2 [244 kB]
Get:13 http://172.17.0.1/private/ stretch-staging/main libffi6 armhf 3.1-2 [18.1 kB]
Get:14 http://172.17.0.1/private/ stretch-staging/main libp11-kit0 armhf 0.23.1-2 [94.1 kB]
Get:15 http://172.17.0.1/private/ stretch-staging/main libpython2.7-minimal armhf 2.7.10-2 [380 kB]
Get:16 http://172.17.0.1/private/ stretch-staging/main mime-support all 3.58 [36.0 kB]
Get:17 http://172.17.0.1/private/ stretch-staging/main libexpat1 armhf 2.1.0-6 [60.2 kB]
Get:18 http://172.17.0.1/private/ stretch-staging/main libsqlite3-0 armhf 3.8.10.2-1 [389 kB]
Get:19 http://172.17.0.1/private/ stretch-staging/main libssl1.0.0 armhf 1.0.2c-1 [883 kB]
Get:20 http://172.17.0.1/private/ stretch-staging/main libpython2.7-stdlib armhf 2.7.10-2 [1814 kB]
Get:21 http://172.17.0.1/private/ stretch-staging/main libpython2.7 armhf 2.7.10-2 [933 kB]
Get:22 http://172.17.0.1/private/ stretch-staging/main libtasn1-6 armhf 4.5-2 [43.9 kB]
Get:23 http://172.17.0.1/private/ stretch-staging/main libxml2 armhf 2.9.1+dfsg1-5 [703 kB]
Get:24 http://172.17.0.1/private/ stretch-staging/main python2.7-minimal armhf 2.7.10-2 [1162 kB]
Get:25 http://172.17.0.1/private/ stretch-staging/main python-minimal armhf 2.7.9-1 [40.1 kB]
Get:26 http://172.17.0.1/private/ stretch-staging/main python2.7 armhf 2.7.10-2 [258 kB]
Get:27 http://172.17.0.1/private/ stretch-staging/main libpython-stdlib armhf 2.7.9-1 [19.6 kB]
Get:28 http://172.17.0.1/private/ stretch-staging/main python armhf 2.7.9-1 [151 kB]
Get:29 http://172.17.0.1/private/ stretch-staging/main libdrm2 armhf 2.4.60-3 [28.4 kB]
Get:30 http://172.17.0.1/private/ stretch-staging/main libglapi-mesa armhf 10.5.5-1 [67.4 kB]
Get:31 http://172.17.0.1/private/ stretch-staging/main libxau6 armhf 1:1.0.8-1 [19.9 kB]
Get:32 http://172.17.0.1/private/ stretch-staging/main libxdmcp6 armhf 1:1.1.2-1 [25.0 kB]
Get:33 http://172.17.0.1/private/ stretch-staging/main libxcb1 armhf 1.10-3 [38.1 kB]
Get:34 http://172.17.0.1/private/ stretch-staging/main libx11-data all 2:1.6.3-1 [128 kB]
Get:35 http://172.17.0.1/private/ stretch-staging/main libx11-6 armhf 2:1.6.3-1 [678 kB]
Get:36 http://172.17.0.1/private/ stretch-staging/main libx11-xcb1 armhf 2:1.6.3-1 [176 kB]
Get:37 http://172.17.0.1/private/ stretch-staging/main libxcb-dri2-0 armhf 1.10-3 [12.1 kB]
Get:38 http://172.17.0.1/private/ stretch-staging/main libxcb-dri3-0 armhf 1.10-3 [10.6 kB]
Get:39 http://172.17.0.1/private/ stretch-staging/main libxcb-glx0 armhf 1.10-3 [23.8 kB]
Get:40 http://172.17.0.1/private/ stretch-staging/main libxcb-present0 armhf 1.10-3 [10.8 kB]
Get:41 http://172.17.0.1/private/ stretch-staging/main libxcb-sync1 armhf 1.10-3 [13.2 kB]
Get:42 http://172.17.0.1/private/ stretch-staging/main libxfixes3 armhf 1:5.0.1-2 [19.6 kB]
Get:43 http://172.17.0.1/private/ stretch-staging/main libxdamage1 armhf 1:1.1.4-2 [13.9 kB]
Get:44 http://172.17.0.1/private/ stretch-staging/main libxext6 armhf 2:1.3.3-1 [48.1 kB]
Get:45 http://172.17.0.1/private/ stretch-staging/main libxshmfence1 armhf 1.2-1 [7642 B]
Get:46 http://172.17.0.1/private/ stretch-staging/main libxxf86vm1 armhf 1:1.1.4-1 [20.2 kB]
Get:47 http://172.17.0.1/private/ stretch-staging/main libgl1-mesa-glx armhf 10.5.5-1 [171 kB]
Get:48 http://172.17.0.1/private/ stretch-staging/main libxi6 armhf 2:1.7.4-1 [73.4 kB]
Get:49 http://172.17.0.1/private/ stretch-staging/main freeglut3 armhf 2.8.1-2 [111 kB]
Get:50 http://172.17.0.1/private/ stretch-staging/main libavahi-common-data armhf 0.6.31-5 [98.8 kB]
Get:51 http://172.17.0.1/private/ stretch-staging/main libavahi-common3 armhf 0.6.31-5 [48.0 kB]
Get:52 http://172.17.0.1/private/ stretch-staging/main libavahi-client3 armhf 0.6.31-5 [50.6 kB]
Get:53 http://172.17.0.1/private/ stretch-staging/main libglib2.0-0 armhf 2.44.1-1 [2314 kB]
Get:54 http://172.17.0.1/private/ stretch-staging/main libcroco3 armhf 0.6.8-3 [121 kB]
Get:55 http://172.17.0.1/private/ stretch-staging/main libdrm-exynos1 armhf 2.4.60-3 [16.3 kB]
Get:56 http://172.17.0.1/private/ stretch-staging/main libdrm-freedreno1 armhf 2.4.60-3 [20.6 kB]
Get:57 http://172.17.0.1/private/ stretch-staging/main libdrm-nouveau2 armhf 2.4.60-3 [21.1 kB]
Get:58 http://172.17.0.1/private/ stretch-staging/main libdrm-omap1 armhf 2.4.60-3 [14.3 kB]
Get:59 http://172.17.0.1/private/ stretch-staging/main libdrm-radeon1 armhf 2.4.60-3 [28.2 kB]
Get:60 http://172.17.0.1/private/ stretch-staging/main libdrm-tegra0 armhf 2.4.60-3 [13.6 kB]
Get:61 http://172.17.0.1/private/ stretch-staging/main libfreetype6 armhf 2.5.2-4 [412 kB]
Get:62 http://172.17.0.1/private/ stretch-staging/main ucf all 3.0030 [69.7 kB]
Get:63 http://172.17.0.1/private/ stretch-staging/main fonts-dejavu-core all 2.35-1 [1064 kB]
Get:64 http://172.17.0.1/private/ stretch-staging/main fontconfig-config all 2.11.0-6.3 [273 kB]
Get:65 http://172.17.0.1/private/ stretch-staging/main libfontconfig1 armhf 2.11.0-6.3 [311 kB]
Get:66 http://172.17.0.1/private/ stretch-staging/main gcc-5-base armhf 5.1.1-9+rpi1 [165 kB]
Get:67 http://172.17.0.1/private/ stretch-staging/main libgfortran3 armhf 5.1.1-9+rpi1 [154 kB]
Get:68 http://172.17.0.1/private/ stretch-staging/main x11-common all 1:7.7+9 [287 kB]
Get:69 http://172.17.0.1/private/ stretch-staging/main libice6 armhf 2:1.0.9-1 [51.2 kB]
Get:70 http://172.17.0.1/private/ stretch-staging/main libsm6 armhf 2:1.2.2-1 [31.2 kB]
Get:71 http://172.17.0.1/private/ stretch-staging/main libxt6 armhf 1:1.1.4-1 [183 kB]
Get:72 http://172.17.0.1/private/ stretch-staging/main libxmu6 armhf 2:1.1.2-1 [50.8 kB]
Get:73 http://172.17.0.1/private/ stretch-staging/main libglew1.10 armhf 1.10.0-3 [205 kB]
Get:74 http://172.17.0.1/private/ stretch-staging/main libglu1-mesa armhf 9.0.0-2 [166 kB]
Get:75 http://172.17.0.1/private/ stretch-staging/main libgraphite2-3 armhf 1.2.4-3 [48.2 kB]
Get:76 http://172.17.0.1/private/ stretch-staging/main libicu52 armhf 52.1-9 [6554 kB]
Get:77 http://172.17.0.1/private/ stretch-staging/main libijs-0.35 armhf 0.35-10 [18.5 kB]
Get:78 http://172.17.0.1/private/ stretch-staging/main libjpeg62-turbo armhf 1:1.4.0-7 [102 kB]
Get:79 http://172.17.0.1/private/ stretch-staging/main libjasper1 armhf 1.900.1-debian1-2.4 [109 kB]
Get:80 http://172.17.0.1/private/ stretch-staging/main libjbig0 armhf 2.1-3.1 [27.5 kB]
Get:81 http://172.17.0.1/private/ stretch-staging/main liblcms2-2 armhf 2.6-3 [113 kB]
Get:82 http://172.17.0.1/private/ stretch-staging/main libpaper1 armhf 1.1.24+nmu4 [21.4 kB]
Get:83 http://172.17.0.1/private/ stretch-staging/main libpixman-1-0 armhf 0.32.6-3 [422 kB]
Get:84 http://172.17.0.1/private/ stretch-staging/main libopenjpeg5 armhf 1:1.5.2-3.1 [93.6 kB]
Get:85 http://172.17.0.1/private/ stretch-staging/main libtiff5 armhf 4.0.3-13 [193 kB]
Get:86 http://172.17.0.1/private/ stretch-staging/main libpoppler46 armhf 0.26.5-2 [1092 kB]
Get:87 http://172.17.0.1/private/ stretch-staging/main libexpat1-dev armhf 2.1.0-6 [117 kB]
Get:88 http://172.17.0.1/private/ stretch-staging/main libpython2.7-dev armhf 2.7.10-2 [18.0 MB]
Get:89 http://172.17.0.1/private/ stretch-staging/main libtcl8.6 armhf 8.6.4+dfsg-2 [866 kB]
Get:90 http://172.17.0.1/private/ stretch-staging/main libxrender1 armhf 1:0.9.8-1 [30.4 kB]
Get:91 http://172.17.0.1/private/ stretch-staging/main libxft2 armhf 2.3.2-1 [48.3 kB]
Get:92 http://172.17.0.1/private/ stretch-staging/main libxss1 armhf 1:1.2.2-1 [16.8 kB]
Get:93 http://172.17.0.1/private/ stretch-staging/main libtk8.6 armhf 8.6.4+dfsg-2 [664 kB]
Get:94 http://172.17.0.1/private/ stretch-staging/main libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:95 http://172.17.0.1/private/ stretch-staging/main libxpm4 armhf 1:3.5.11-1 [41.7 kB]
Get:96 http://172.17.0.1/private/ stretch-staging/main libxaw7 armhf 2:1.0.12-2 [159 kB]
Get:97 http://172.17.0.1/private/ stretch-staging/main libxcb-randr0 armhf 1.10-3 [18.7 kB]
Get:98 http://172.17.0.1/private/ stretch-staging/main libxcb-render0 armhf 1.10-3 [16.0 kB]
Get:99 http://172.17.0.1/private/ stretch-staging/main libxcb-shape0 armhf 1.10-3 [11.0 kB]
Get:100 http://172.17.0.1/private/ stretch-staging/main libxcb-xfixes0 armhf 1.10-3 [13.8 kB]
Get:101 http://172.17.0.1/private/ stretch-staging/main libzzip-0-13 armhf 0.13.62-3 [51.3 kB]
Get:102 http://172.17.0.1/private/ stretch-staging/main poppler-data all 0.4.7-3 [1470 kB]
Get:103 http://172.17.0.1/private/ stretch-staging/main file armhf 1:5.22+15-2 [59.9 kB]
Get:104 http://172.17.0.1/private/ stretch-staging/main gettext-base armhf 0.19.4-1 [117 kB]
Get:105 http://172.17.0.1/private/ stretch-staging/main libnettle6 armhf 3.1.1-3 [200 kB]
Get:106 http://172.17.0.1/private/ stretch-staging/main libhogweed4 armhf 3.1.1-3 [126 kB]
Get:107 http://172.17.0.1/private/ stretch-staging/main libgnutls-deb0-28 armhf 3.3.15-6 [645 kB]
Get:108 http://172.17.0.1/private/ stretch-staging/main python-support all 1.0.15 [33.6 kB]
Get:109 http://172.17.0.1/private/ stretch-staging/main gettext armhf 0.19.4-1 [1168 kB]
Get:110 http://172.17.0.1/private/ stretch-staging/main intltool-debian all 0.35.0+20060710.2 [25.9 kB]
Get:111 http://172.17.0.1/private/ stretch-staging/main po-debconf all 1.0.18 [248 kB]
Get:112 http://172.17.0.1/private/ stretch-staging/main debhelper all 9.20150507 [824 kB]
Get:113 http://172.17.0.1/private/ stretch-staging/main xorg-sgml-doctools all 1:1.11-1 [21.9 kB]
Get:114 http://172.17.0.1/private/ stretch-staging/main x11proto-core-dev all 7.0.27-1 [729 kB]
Get:115 http://172.17.0.1/private/ stretch-staging/main libxau-dev armhf 1:1.0.8-1 [23.0 kB]
Get:116 http://172.17.0.1/private/ stretch-staging/main libxdmcp-dev armhf 1:1.1.2-1 [40.3 kB]
Get:117 http://172.17.0.1/private/ stretch-staging/main x11proto-input-dev all 2.3.1-1 [157 kB]
Get:118 http://172.17.0.1/private/ stretch-staging/main x11proto-kb-dev all 1.0.6-2 [269 kB]
Get:119 http://172.17.0.1/private/ stretch-staging/main xtrans-dev all 1.3.5-1 [100 kB]
Get:120 http://172.17.0.1/private/ stretch-staging/main libpthread-stubs0-dev armhf 0.3-4 [4042 B]
Get:121 http://172.17.0.1/private/ stretch-staging/main libxcb1-dev armhf 1.10-3 [78.1 kB]
Get:122 http://172.17.0.1/private/ stretch-staging/main libx11-dev armhf 2:1.6.3-1 [749 kB]
Get:123 http://172.17.0.1/private/ stretch-staging/main libdrm-dev armhf 2.4.60-3 [141 kB]
Get:124 http://172.17.0.1/private/ stretch-staging/main mesa-common-dev armhf 10.5.5-1 [335 kB]
Get:125 http://172.17.0.1/private/ stretch-staging/main libx11-xcb-dev armhf 2:1.6.3-1 [178 kB]
Get:126 http://172.17.0.1/private/ stretch-staging/main libxcb-dri3-dev armhf 1.10-3 [11.4 kB]
Get:127 http://172.17.0.1/private/ stretch-staging/main libxcb-render0-dev armhf 1.10-3 [21.7 kB]
Get:128 http://172.17.0.1/private/ stretch-staging/main libxcb-randr0-dev armhf 1.10-3 [25.6 kB]
Get:129 http://172.17.0.1/private/ stretch-staging/main libxcb-shape0-dev armhf 1.10-3 [12.6 kB]
Get:130 http://172.17.0.1/private/ stretch-staging/main libxcb-xfixes0-dev armhf 1.10-3 [17.1 kB]
Get:131 http://172.17.0.1/private/ stretch-staging/main libxcb-sync-dev armhf 1.10-3 [15.8 kB]
Get:132 http://172.17.0.1/private/ stretch-staging/main libxcb-present-dev armhf 1.10-3 [12.4 kB]
Get:133 http://172.17.0.1/private/ stretch-staging/main libxshmfence-dev armhf 1.2-1 [7152 B]
Get:134 http://172.17.0.1/private/ stretch-staging/main libxcb-dri2-0-dev armhf 1.10-3 [14.3 kB]
Get:135 http://172.17.0.1/private/ stretch-staging/main libxcb-glx0-dev armhf 1.10-3 [35.2 kB]
Get:136 http://172.17.0.1/private/ stretch-staging/main x11proto-xext-dev all 7.3.0-1 [212 kB]
Get:137 http://172.17.0.1/private/ stretch-staging/main x11proto-fixes-dev all 1:5.0-2 [19.2 kB]
Get:138 http://172.17.0.1/private/ stretch-staging/main libxfixes-dev armhf 1:5.0.1-2 [21.5 kB]
Get:139 http://172.17.0.1/private/ stretch-staging/main x11proto-damage-dev all 1:1.2.1-2 [11.8 kB]
Get:140 http://172.17.0.1/private/ stretch-staging/main libxdamage-dev armhf 1:1.1.4-2 [13.7 kB]
Get:141 http://172.17.0.1/private/ stretch-staging/main libxext-dev armhf 2:1.3.3-1 [102 kB]
Get:142 http://172.17.0.1/private/ stretch-staging/main x11proto-xf86vidmode-dev all 2.3.1-2 [6114 B]
Get:143 http://172.17.0.1/private/ stretch-staging/main libxxf86vm-dev armhf 1:1.1.4-1 [24.8 kB]
Get:144 http://172.17.0.1/private/ stretch-staging/main x11proto-dri2-dev all 2.8-2 [18.2 kB]
Get:145 http://172.17.0.1/private/ stretch-staging/main x11proto-gl-dev all 1.4.17-1 [28.0 kB]
Get:146 http://172.17.0.1/private/ stretch-staging/main libgl1-mesa-dev armhf 10.5.5-1 [38.3 kB]
Get:147 http://172.17.0.1/private/ stretch-staging/main libglu1-mesa-dev armhf 9.0.0-2 [238 kB]
Get:148 http://172.17.0.1/private/ stretch-staging/main libice-dev armhf 2:1.0.9-1 [58.1 kB]
Get:149 http://172.17.0.1/private/ stretch-staging/main libsm-dev armhf 2:1.2.2-1 [33.5 kB]
Get:150 http://172.17.0.1/private/ stretch-staging/main libxt-dev armhf 1:1.1.4-1 [447 kB]
Get:151 http://172.17.0.1/private/ stretch-staging/main freeglut3-dev armhf 2.8.1-2 [168 kB]
Get:152 http://172.17.0.1/private/ stretch-staging/main libblas-common armhf 1.2.20110419-10 [8494 B]
Get:153 http://172.17.0.1/private/ stretch-staging/main libblas3 armhf 1.2.20110419-10 [120 kB]
Get:154 http://172.17.0.1/private/ stretch-staging/main libcups2 armhf 1.7.5-12 [252 kB]
Get:155 http://172.17.0.1/private/ stretch-staging/main libcupsimage2 armhf 1.7.5-12 [115 kB]
Get:156 http://172.17.0.1/private/ stretch-staging/main libcupsfilters1 armhf 1.0.69-1 [101 kB]
Get:157 http://172.17.0.1/private/ stretch-staging/main zlib1g-dev armhf 1:1.2.8.dfsg-2 [199 kB]
Get:158 http://172.17.0.1/private/ stretch-staging/main libpng12-dev armhf 1.2.50-2 [236 kB]
Get:159 http://172.17.0.1/private/ stretch-staging/main libfreetype6-dev armhf 2.5.2-4 [586 kB]
Get:160 http://172.17.0.1/private/ stretch-staging/main pkg-config armhf 0.28-1 [55.1 kB]
Get:161 http://172.17.0.1/private/ stretch-staging/main libfontconfig1-dev armhf 2.11.0-6.3 [875 kB]
Get:162 http://172.17.0.1/private/ stretch-staging/main libglew-dev armhf 1.10.0-3 [160 kB]
Get:163 http://172.17.0.1/private/ stretch-staging/main libjbig2dec0 armhf 0.11+20120125-1 [46.4 kB]
Get:164 http://172.17.0.1/private/ stretch-staging/main libgs9-common all 9.06~dfsg-2 [1979 kB]
Get:165 http://172.17.0.1/private/ stretch-staging/main libgs9 armhf 9.06~dfsg-2 [1600 kB]
Get:166 http://172.17.0.1/private/ stretch-staging/main libharfbuzz0b armhf 0.9.40-3 [482 kB]
Get:167 http://172.17.0.1/private/ stretch-staging/main libharfbuzz-icu0 armhf 0.9.40-3 [375 kB]
Get:168 http://172.17.0.1/private/ stretch-staging/main libkpathsea6 armhf 2014.20140926.35254-6 [145 kB]
Get:169 http://172.17.0.1/private/ stretch-staging/main liblapack3 armhf 3.5.0-4 [1316 kB]
Get:170 http://172.17.0.1/private/ stretch-staging/main libpaper-utils armhf 1.1.24+nmu4 [17.2 kB]
Get:171 http://172.17.0.1/private/ stretch-staging/main libpotrace0 armhf 1.12-1 [22.9 kB]
Get:172 http://172.17.0.1/private/ stretch-staging/main libptexenc1 armhf 2014.20140926.35254-6 [52.1 kB]
Get:173 http://172.17.0.1/private/ stretch-staging/main libpython-dev armhf 2.7.9-1 [19.6 kB]
Get:174 http://172.17.0.1/private/ stretch-staging/main libsynctex1 armhf 2014.20140926.35254-6 [54.4 kB]
Get:175 http://172.17.0.1/private/ stretch-staging/main x11proto-render-dev all 2:0.11.1-2 [20.8 kB]
Get:176 http://172.17.0.1/private/ stretch-staging/main libxrender-dev armhf 1:0.9.8-1 [38.8 kB]
Get:177 http://172.17.0.1/private/ stretch-staging/main libxft-dev armhf 2.3.2-1 [59.1 kB]
Get:178 http://172.17.0.1/private/ stretch-staging/main x11proto-scrnsaver-dev all 1.2.2-1 [25.0 kB]
Get:179 http://172.17.0.1/private/ stretch-staging/main libxss-dev armhf 1:1.2.2-1 [22.7 kB]
Get:180 http://172.17.0.1/private/ stretch-staging/main python2.7-dev armhf 2.7.10-2 [279 kB]
Get:181 http://172.17.0.1/private/ stretch-staging/main python-dev armhf 2.7.9-1 [1188 B]
Get:182 http://172.17.0.1/private/ stretch-staging/main python-numpy armhf 1:1.8.2-2 [1498 kB]
Get:183 http://172.17.0.1/private/ stretch-staging/main tcl8.6 armhf 8.6.4+dfsg-2 [122 kB]
Get:184 http://172.17.0.1/private/ stretch-staging/main tcl armhf 8.6.0+8+b1 [5508 B]
Get:185 http://172.17.0.1/private/ stretch-staging/main tcl8.6-dev armhf 8.6.4+dfsg-2 [892 kB]
Get:186 http://172.17.0.1/private/ stretch-staging/main tcl-dev armhf 8.6.0+8+b1 [7874 B]
Get:187 http://172.17.0.1/private/ stretch-staging/main tex-common all 5.03 [625 kB]
Get:188 http://172.17.0.1/private/ stretch-staging/main xdg-utils all 1.1.0~rc1+git20111210-7.4 [65.0 kB]
Get:189 http://172.17.0.1/private/ stretch-staging/main texlive-binaries armhf 2014.20140926.35254-6 [5322 kB]
Get:190 http://172.17.0.1/private/ stretch-staging/main texlive-base all 2014.20141024-2 [17.7 MB]
Get:191 http://172.17.0.1/private/ stretch-staging/main texlive-latex-base all 2014.20141024-2 [858 kB]
Get:192 http://172.17.0.1/private/ stretch-staging/main tk8.6 armhf 8.6.4+dfsg-2 [71.2 kB]
Get:193 http://172.17.0.1/private/ stretch-staging/main tk armhf 8.6.0+8+b1 [5534 B]
Get:194 http://172.17.0.1/private/ stretch-staging/main tk8.6-dev armhf 8.6.4+dfsg-2 [667 kB]
Get:195 http://172.17.0.1/private/ stretch-staging/main tk-dev armhf 8.6.0+8+b1 [5312 B]
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Processing triggers for systemd (215-17) ...
Setting up libpipeline1:armhf (1.4.0-1) ...
Setting up groff-base (1.22.3-1) ...
Setting up bsdmainutils (9.0.6) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up man-db (2.7.0.2-5) ...
Not building database; man-db/auto-update is not 'true'.
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Setting up libkeyutils1:armhf (1.5.9-5) ...
Setting up libkrb5support0:armhf (1.12.1+dfsg-20) ...
Setting up libk5crypto3:armhf (1.12.1+dfsg-20) ...
Setting up libkrb5-3:armhf (1.12.1+dfsg-20) ...
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Setting up libidn11:armhf (1.30-1) ...
Setting up libmagic1:armhf (1:5.22+15-2) ...
Setting up libffi6:armhf (3.1-2) ...
Setting up libp11-kit0:armhf (0.23.1-2) ...
Setting up mime-support (3.58) ...
Setting up libexpat1:armhf (2.1.0-6) ...
Setting up libsqlite3-0:armhf (3.8.10.2-1) ...
Setting up libssl1.0.0:armhf (1.0.2c-1) ...
Setting up libpython2.7-stdlib:armhf (2.7.10-2) ...
Setting up libpython2.7:armhf (2.7.10-2) ...
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Setting up libxml2:armhf (2.9.1+dfsg1-5) ...
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Setting up python (2.7.9-1) ...
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Setting up libxau6:armhf (1:1.0.8-1) ...
Setting up libxdmcp6:armhf (1:1.1.2-1) ...
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Setting up libx11-data (2:1.6.3-1) ...
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Setting up libxcb-dri3-0:armhf (1.10-3) ...
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Setting up libxi6:armhf (2:1.7.4-1) ...
Setting up freeglut3:armhf (2.8.1-2) ...
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Setting up libavahi-client3:armhf (0.6.31-5) ...
Setting up libglib2.0-0:armhf (2.44.1-1) ...
No schema files found: doing nothing.
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Setting up libdrm-nouveau2:armhf (2.4.60-3) ...
Setting up libdrm-omap1:armhf (2.4.60-3) ...
Setting up libdrm-radeon1:armhf (2.4.60-3) ...
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Setting up libfreetype6:armhf (2.5.2-4) ...
Setting up ucf (3.0030) ...
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Setting up fontconfig-config (2.11.0-6.3) ...
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Setting up gcc-5-base:armhf (5.1.1-9+rpi1) ...
Setting up libgfortran3:armhf (5.1.1-9+rpi1) ...
Setting up x11-common (1:7.7+9) ...
update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
All runlevel operations denied by policy
invoke-rc.d: policy-rc.d denied execution of start.
Setting up libice6:armhf (2:1.0.9-1) ...
Setting up libsm6:armhf (2:1.2.2-1) ...
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Setting up libglew1.10:armhf (1.10.0-3) ...
Setting up libglu1-mesa:armhf (9.0.0-2) ...
Setting up libgraphite2-3:armhf (1.2.4-3) ...
Setting up libicu52:armhf (52.1-9) ...
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Setting up libjpeg62-turbo:armhf (1:1.4.0-7) ...
Setting up libjasper1:armhf (1.900.1-debian1-2.4) ...
Setting up libjbig0:armhf (2.1-3.1) ...
Setting up liblcms2-2:armhf (2.6-3) ...
Setting up libpaper1:armhf (1.1.24+nmu4) ...

Creating config file /etc/papersize with new version
Setting up libpixman-1-0:armhf (0.32.6-3) ...
Setting up libopenjpeg5:armhf (1:1.5.2-3.1) ...
Setting up libtiff5:armhf (4.0.3-13) ...
Setting up libpoppler46:armhf (0.26.5-2) ...
Setting up libexpat1-dev:armhf (2.1.0-6) ...
Setting up libpython2.7-dev:armhf (2.7.10-2) ...
Setting up libtcl8.6:armhf (8.6.4+dfsg-2) ...
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Setting up libtk8.6:armhf (8.6.4+dfsg-2) ...
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Setting up libxpm4:armhf (1:3.5.11-1) ...
Setting up libxaw7:armhf (2:1.0.12-2) ...
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Setting up libzzip-0-13:armhf (0.13.62-3) ...
Setting up poppler-data (0.4.7-3) ...
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Setting up x11proto-kb-dev (1.0.6-2) ...
Setting up xtrans-dev (1.3.5-1) ...
Setting up libpthread-stubs0-dev:armhf (0.3-4) ...
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Setting up libdrm-dev:armhf (2.4.60-3) ...
Setting up mesa-common-dev:armhf (10.5.5-1) ...
Setting up libx11-xcb-dev:armhf (2:1.6.3-1) ...
Setting up libxcb-dri3-dev:armhf (1.10-3) ...
Setting up libxcb-render0-dev:armhf (1.10-3) ...
Setting up libxcb-randr0-dev:armhf (1.10-3) ...
Setting up libxcb-shape0-dev:armhf (1.10-3) ...
Setting up libxcb-xfixes0-dev:armhf (1.10-3) ...
Setting up libxcb-sync-dev:armhf (1.10-3) ...
Setting up libxcb-present-dev:armhf (1.10-3) ...
Setting up libxshmfence-dev:armhf (1.2-1) ...
Setting up libxcb-dri2-0-dev:armhf (1.10-3) ...
Setting up libxcb-glx0-dev:armhf (1.10-3) ...
Setting up x11proto-xext-dev (7.3.0-1) ...
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Setting up libxdamage-dev:armhf (1:1.1.4-2) ...
Setting up libxext-dev:armhf (2:1.3.3-1) ...
Setting up x11proto-xf86vidmode-dev (2.3.1-2) ...
Setting up libxxf86vm-dev:armhf (1:1.1.4-1) ...
Setting up x11proto-dri2-dev (2.8-2) ...
Setting up x11proto-gl-dev (1.4.17-1) ...
Setting up libgl1-mesa-dev:armhf (10.5.5-1) ...
Setting up libglu1-mesa-dev (9.0.0-2) ...
Setting up libice-dev:armhf (2:1.0.9-1) ...
Setting up libsm-dev:armhf (2:1.2.2-1) ...
Setting up libxt-dev:armhf (1:1.1.4-1) ...
Setting up freeglut3-dev:armhf (2.8.1-2) ...
Setting up libblas-common (1.2.20110419-10) ...
Setting up libblas3 (1.2.20110419-10) ...
update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode
Setting up libcups2:armhf (1.7.5-12) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-2) ...
Setting up libpng12-dev:armhf (1.2.50-2) ...
Setting up libfreetype6-dev (2.5.2-4) ...
Setting up pkg-config (0.28-1) ...
Setting up libfontconfig1-dev:armhf (2.11.0-6.3) ...
Setting up libglew-dev:armhf (1.10.0-3) ...
Setting up libjbig2dec0 (0.11+20120125-1) ...
Setting up libgs9-common (9.06~dfsg-2) ...
Setting up libharfbuzz0b:armhf (0.9.40-3) ...
Setting up libharfbuzz-icu0:armhf (0.9.40-3) ...
Setting up libkpathsea6 (2014.20140926.35254-6) ...
Setting up liblapack3 (3.5.0-4) ...
update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode
Setting up libpaper-utils (1.1.24+nmu4) ...
Setting up libpotrace0 (1.12-1) ...
Setting up libptexenc1 (2014.20140926.35254-6) ...
Setting up libpython-dev:armhf (2.7.9-1) ...
Setting up libsynctex1 (2014.20140926.35254-6) ...
Setting up x11proto-render-dev (2:0.11.1-2) ...
Setting up libxrender-dev:armhf (1:0.9.8-1) ...
Setting up libxft-dev (2.3.2-1) ...
Setting up x11proto-scrnsaver-dev (1.2.2-1) ...
Setting up libxss-dev:armhf (1:1.2.2-1) ...
Setting up python2.7-dev (2.7.10-2) ...
Setting up python-dev (2.7.9-1) ...
Setting up python-numpy (1:1.8.2-2) ...
Setting up tcl8.6 (8.6.4+dfsg-2) ...
Setting up tcl (8.6.0+8+b1) ...
Setting up tcl8.6-dev:armhf (8.6.4+dfsg-2) ...
Setting up tcl-dev:armhf (8.6.0+8+b1) ...
Setting up tex-common (5.03) ...
Setting up xdg-utils (1.1.0~rc1+git20111210-7.4) ...
Setting up tk8.6 (8.6.4+dfsg-2) ...
Setting up tk (8.6.0+8+b1) ...
Setting up tk8.6-dev:armhf (8.6.4+dfsg-2) ...
Setting up tk-dev:armhf (8.6.0+8+b1) ...
Setting up libcupsimage2:armhf (1.7.5-12) ...
Setting up libcupsfilters1:armhf (1.0.69-1) ...
Setting up libgs9 (9.06~dfsg-2) ...
Setting up texlive-binaries (2014.20140926.35254-6) ...
update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode
update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode
Building format(s) --refresh.
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Setting up texlive-base (2014.20141024-2) ...
/usr/bin/tl-paper: setting paper size for dvips to a4.
/usr/bin/tl-paper: setting paper size for dvipdfmx to a4.
/usr/bin/tl-paper: setting paper size for xdvi to a4.
/usr/bin/tl-paper: setting paper size for pdftex to a4.
Running mktexlsr. This may take some time... done.
Building format(s) --all.
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Processing triggers for tex-common (5.03) ...
Running updmap-sys. This may take some time... done.
Running mktexlsr /var/lib/texmf ... done.
Setting up texlive-latex-base (2014.20141024-2) ...
Running mktexlsr. This may take some time... done.
Building format(s) --all --cnffile /etc/texmf/fmt.d/10texlive-latex-base.cnf.
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Processing triggers for tex-common (5.03) ...
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Running mktexlsr /var/lib/texmf ... done.
Setting up sbuild-build-depends-pymol-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.19-18) ...
Processing triggers for systemd (215-17) ...

┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment                                                            │
└──────────────────────────────────────────────────────────────────────────────┘

Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.25-5 dpkg-dev_1.17.25 g++-4.9_4.9.2-10 gcc-4.9_4.9.2-10 libc6-dev_2.19-18 libstdc++-4.9-dev_4.9.2-10 libstdc++6_4.9.2-10 linux-libc-dev_3.16.7-ckt4-1+rpi1
Package versions: acl_2.2.52-2 adduser_3.113+nmu3 apt_1.0.9.8 base-files_8+rpi1 base-passwd_3.5.37 bash_4.3-11 binutils_2.25-5 bsdmainutils_9.0.6 bsdutils_1:2.25.2-6 build-essential_11.7 bzip2_1.0.6-7 coreutils_8.23-4 cpio_2.11+dfsg-4.1 cpp_4:4.9.2-2 cpp-4.9_4.9.2-10 dash_0.5.7-4 debconf_1.5.56 debconf-i18n_1.5.56 debfoster_2.7-2 debhelper_9.20150507 debianutils_4.4 diffutils_1:3.3-1 dmsetup_2:1.02.90-2.2 dpkg_1.17.25 dpkg-dev_1.17.25 e2fslibs_1.42.12-1.1 e2fsprogs_1.42.12-1.1 fakeroot_1.20.2-1 file_1:5.22+15-2 findutils_4.4.2-9 fontconfig-config_2.11.0-6.3 fonts-dejavu-core_2.35-1 freeglut3_2.8.1-2 freeglut3-dev_2.8.1-2 g++_4:4.9.2-2 g++-4.9_4.9.2-10 gcc_4:4.9.2-2 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.4-1 gcc-4.9_4.9.2-10 gcc-4.9-base_4.9.2-10 gcc-5-base_5.1.1-9+rpi1 gettext_0.19.4-1 gettext-base_0.19.4-1 gnupg_1.4.18-7 gpgv_1.4.18-7 grep_2.20-4.1 groff-base_1.22.3-1 gzip_1.6-4 hostname_3.15 init_1.22 init-system-helpers_1.22 initramfs-tools_0.120 initscripts_2.88dsf-59 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.2 klibc-utils_2.0.4-2+rpi1 kmod_18-3 libacl1_2.2.52-2 libapt-pkg4.12_1.0.9.8 libasan1_4.9.2-10 libasprintf0c2_0.19.4-1 libatomic1_4.9.2-10 libattr1_1:2.4.47-2 libaudit-common_1:2.4-1 libaudit1_1:2.4-1 libavahi-client3_0.6.31-5 libavahi-common-data_0.6.31-5 libavahi-common3_0.6.31-5 libblas-common_1.2.20110419-10 libblas3_1.2.20110419-10 libblkid1_2.25.2-6 libbz2-1.0_1.0.6-7 libc-bin_2.19-18 libc-dev-bin_2.19-18 libc6_2.19-18 libc6-dev_2.19-18 libcap2_1:2.24-8 libcap2-bin_1:2.24-8 libcloog-isl4_0.18.2-1 libcomerr2_1.42.12-1.1 libcroco3_0.6.8-3 libcryptsetup4_2:1.6.6-5 libcups2_1.7.5-12 libcupsfilters1_1.0.69-1 libcupsimage2_1.7.5-12 libdb5.3_5.3.28-9 libdbus-1-3_1.8.16-1 libdebconfclient0_0.192 libdevmapper1.02.1_2:1.02.90-2.2 libdpkg-perl_1.17.25 libdrm-dev_2.4.60-3 libdrm-exynos1_2.4.60-3 libdrm-freedreno1_2.4.60-3 libdrm-nouveau2_2.4.60-3 libdrm-omap1_2.4.60-3 libdrm-radeon1_2.4.60-3 libdrm-tegra0_2.4.60-3 libdrm2_2.4.60-3 libexpat1_2.1.0-6 libexpat1-dev_2.1.0-6 libfakeroot_1.20.2-1 libffi6_3.1-2 libfontconfig1_2.11.0-6.3 libfontconfig1-dev_2.11.0-6.3 libfreetype6_2.5.2-4 libfreetype6-dev_2.5.2-4 libgc1c2_1:7.2d-6.4 libgcc-4.9-dev_4.9.2-10 libgcc1_1:4.9.2-10 libgcrypt20_1.6.3-2 libgdbm3_1.8.3-13.1 libgfortran3_5.1.1-9+rpi1 libgl1-mesa-dev_10.5.5-1 libgl1-mesa-glx_10.5.5-1 libglapi-mesa_10.5.5-1 libglew-dev_1.10.0-3 libglew1.10_1.10.0-3 libglib2.0-0_2.44.1-1 libglu1-mesa_9.0.0-2 libglu1-mesa-dev_9.0.0-2 libgmp10_2:6.0.0+dfsg-6+rpi1 libgnutls-deb0-28_3.3.15-6 libgomp1_4.9.2-10 libgpg-error0_1.17-3 libgraphite2-3_1.2.4-3 libgs9_9.06~dfsg-2 libgs9-common_9.06~dfsg-2 libgssapi-krb5-2_1.12.1+dfsg-20 libharfbuzz-icu0_0.9.40-3 libharfbuzz0b_0.9.40-3 libhogweed4_3.1.1-3 libice-dev_2:1.0.9-1 libice6_2:1.0.9-1 libicu52_52.1-9 libidn11_1.30-1 libijs-0.35_0.35-10 libisl10_0.12.2-2 libjasper1_1.900.1-debian1-2.4 libjbig0_2.1-3.1 libjbig2dec0_0.11+20120125-1 libjpeg62-turbo_1:1.4.0-7 libk5crypto3_1.12.1+dfsg-20 libkeyutils1_1.5.9-5 libklibc_2.0.4-2+rpi1 libkmod2_18-3 libkpathsea6_2014.20140926.35254-6 libkrb5-3_1.12.1+dfsg-20 libkrb5support0_1.12.1+dfsg-20 liblapack3_3.5.0-4 liblcms2-2_2.6-3 liblocale-gettext-perl_1.05-8+b1 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.22+15-2 libmount1_2.25.2-6 libmpc3_1.0.2-1 libmpfr4_3.1.2-2 libncurses5_5.9+20140913-1 libncursesw5_5.9+20140913-1 libnettle6_3.1.1-3 libnih-dbus1_1.0.3-4.3 libnih1_1.0.3-4.3 libopenjpeg5_1:1.5.2-3.1 libp11-kit0_0.23.1-2 libpam-modules_1.1.8-3.1 libpam-modules-bin_1.1.8-3.1 libpam-runtime_1.1.8-3.1 libpam0g_1.1.8-3.1 libpaper-utils_1.1.24+nmu4 libpaper1_1.1.24+nmu4 libpcre3_2:8.35-3.3 libpipeline1_1.4.0-1 libpixman-1-0_0.32.6-3 libpng12-0_1.2.50-2 libpng12-dev_1.2.50-2 libpoppler46_0.26.5-2 libpotrace0_1.12-1 libprocps3_2:3.3.9-9 libptexenc1_2014.20140926.35254-6 libpthread-stubs0-dev_0.3-4 libpython-dev_2.7.9-1 libpython-stdlib_2.7.9-1 libpython2.7_2.7.10-2 libpython2.7-dev_2.7.10-2 libpython2.7-minimal_2.7.10-2 libpython2.7-stdlib_2.7.10-2 libreadline6_6.3-8 libselinux1_2.3-2 libsemanage-common_2.3-1 libsemanage1_2.3-1 libsepol1_2.3-2 libslang2_2.3.0-2 libsm-dev_2:1.2.2-1 libsm6_2:1.2.2-1 libsmartcols1_2.25.2-6 libsqlite3-0_3.8.10.2-1 libss2_1.42.12-1.1 libssl1.0.0_1.0.2c-1 libstdc++-4.9-dev_4.9.2-10 libstdc++6_4.9.2-10 libsynctex1_2014.20140926.35254-6 libsystemd0_215-17 libtasn1-6_4.5-2 libtcl8.6_8.6.4+dfsg-2 libtext-charwidth-perl_0.04-7+b4 libtext-iconv-perl_1.7-5+b5 libtext-wrapi18n-perl_0.06-7 libtiff5_4.0.3-13 libtimedate-perl_2.3000-2 libtinfo5_5.9+20140913-1 libtk8.6_8.6.4+dfsg-2 libubsan0_4.9.2-10 libudev1_215-17 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-25 libustr-1.0-1_1.0.4-3 libuuid1_2.25.2-6 libx11-6_2:1.6.3-1 libx11-data_2:1.6.3-1 libx11-dev_2:1.6.3-1 libx11-xcb-dev_2:1.6.3-1 libx11-xcb1_2:1.6.3-1 libxau-dev_1:1.0.8-1 libxau6_1:1.0.8-1 libxaw7_2:1.0.12-2 libxcb-dri2-0_1.10-3 libxcb-dri2-0-dev_1.10-3 libxcb-dri3-0_1.10-3 libxcb-dri3-dev_1.10-3 libxcb-glx0_1.10-3 libxcb-glx0-dev_1.10-3 libxcb-present-dev_1.10-3 libxcb-present0_1.10-3 libxcb-randr0_1.10-3 libxcb-randr0-dev_1.10-3 libxcb-render0_1.10-3 libxcb-render0-dev_1.10-3 libxcb-shape0_1.10-3 libxcb-shape0-dev_1.10-3 libxcb-sync-dev_1.10-3 libxcb-sync1_1.10-3 libxcb-xfixes0_1.10-3 libxcb-xfixes0-dev_1.10-3 libxcb1_1.10-3 libxcb1-dev_1.10-3 libxdamage-dev_1:1.1.4-2 libxdamage1_1:1.1.4-2 libxdmcp-dev_1:1.1.2-1 libxdmcp6_1:1.1.2-1 libxext-dev_2:1.3.3-1 libxext6_2:1.3.3-1 libxfixes-dev_1:5.0.1-2 libxfixes3_1:5.0.1-2 libxft-dev_2.3.2-1 libxft2_2.3.2-1 libxi6_2:1.7.4-1 libxml2_2.9.1+dfsg1-5 libxmu6_2:1.1.2-1 libxpm4_1:3.5.11-1 libxrender-dev_1:0.9.8-1 libxrender1_1:0.9.8-1 libxshmfence-dev_1.2-1 libxshmfence1_1.2-1 libxss-dev_1:1.2.2-1 libxss1_1:1.2.2-1 libxt-dev_1:1.1.4-1 libxt6_1:1.1.4-1 libxxf86vm-dev_1:1.1.4-1 libxxf86vm1_1:1.1.4-1 libzzip-0-13_0.13.62-3 linux-libc-dev_3.16.7-ckt4-1+rpi1 login_1:4.2-3 lsb-base_4.1+Debian13+rpi1+nmu1 make_4.0-8.1 makedev_2.3.1-93 man-db_2.7.0.2-5 mawk_1.3.3-17 mesa-common-dev_10.5.5-1 mime-support_3.58 mount_2.25.2-6 mountall_2.54 multiarch-support_2.19-18 ncurses-base_5.9+20140913-1 ncurses-bin_5.9+20140913-1 passwd_1:4.2-3 patch_2.7.5-1 perl_5.20.2-3 perl-base_5.20.2-3 perl-modules_5.20.2-3 pkg-config_0.28-1 plymouth_0.9.0-9 po-debconf_1.0.18 poppler-data_0.4.7-3 procps_2:3.3.9-9 python_2.7.9-1 python-dev_2.7.9-1 python-minimal_2.7.9-1 python-numpy_1:1.8.2-2 python-support_1.0.15 python2.7_2.7.10-2 python2.7-dev_2.7.10-2 python2.7-minimal_2.7.10-2 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-pymol-dummy_0.invalid.0 sed_4.2.2-4 sensible-utils_0.0.9 startpar_0.59-3 systemd_215-17 systemd-sysv_215-17 sysv-rc_2.88dsf-59 sysvinit-utils_2.88dsf-59 tar_1.27.1-2 tcl_8.6.0+8+b1 tcl-dev_8.6.0+8+b1 tcl8.6_8.6.4+dfsg-2 tcl8.6-dev_8.6.4+dfsg-2 tex-common_5.03 texlive-base_2014.20141024-2 texlive-binaries_2014.20140926.35254-6 texlive-latex-base_2014.20141024-2 tk_8.6.0+8+b1 tk-dev_8.6.0+8+b1 tk8.6_8.6.4+dfsg-2 tk8.6-dev_8.6.4+dfsg-2 tzdata_2015c-1 ucf_3.0030 udev_215-17 util-linux_2.25.2-6 x11-common_1:7.7+9 x11proto-core-dev_7.0.27-1 x11proto-damage-dev_1:1.2.1-2 x11proto-dri2-dev_2.8-2 x11proto-fixes-dev_1:5.0-2 x11proto-gl-dev_1.4.17-1 x11proto-input-dev_2.3.1-1 x11proto-kb-dev_1.0.6-2 x11proto-render-dev_2:0.11.1-2 x11proto-scrnsaver-dev_1.2.2-1 x11proto-xext-dev_7.3.0-1 x11proto-xf86vidmode-dev_2.3.1-2 xdg-utils_1.1.0~rc1+git20111210-7.4 xorg-sgml-doctools_1:1.11-1 xtrans-dev_1.3.5-1 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.8.dfsg-2 zlib1g-dev_1:1.2.8.dfsg-2

┌──────────────────────────────────────────────────────────────────────────────┐
│ Build                                                                        │
└──────────────────────────────────────────────────────────────────────────────┘


Unpack source
─────────────

gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Sat Jun 13 14:23:46 2015 UTC using RSA key ID B43481B0
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./pymol_1.7.2.1-2.dsc
dpkg-source: info: extracting pymol in pymol-1.7.2.1
dpkg-source: info: unpacking pymol_1.7.2.1.orig.tar.bz2
dpkg-source: info: unpacking pymol_1.7.2.1-2.debian.tar.xz
dpkg-source: info: applying 02_test-suite.patch
dpkg-source: info: applying 03_povray.patch
dpkg-source: info: applying 22_fix_pymol_import.patch
dpkg-source: info: applying 27_fix_pymol_path_in_setup.patch
dpkg-source: info: applying 28_no_data_install_in_python_path.patch
dpkg-source: info: applying 29_fix_path_to_splash.patch
dpkg-source: info: applying 31_fix_format-security.patch

Check disc space
────────────────

Sufficient free space for build

User Environment
────────────────

DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-20de89bc-a9d5-40a7-9339-88ad6741666b
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd

dpkg-buildpackage
─────────────────

dpkg-buildpackage: source package pymol
dpkg-buildpackage: source version 1.7.2.1-2
dpkg-buildpackage: source distribution unstable
 dpkg-source --before-build pymol-1.7.2.1
dpkg-buildpackage: host architecture armhf
 fakeroot debian/rules clean
dh clean --with python2 --parallel
   dh_testdir -O--parallel
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/«PKGBUILDDIR»'
[ ! -f Makefile ] || /usr/bin/make distclean
dh_auto_clean -Spython_distutils
	python setup.py clean -a
running clean
'build/lib.linux-armv7l-2.7' does not exist -- can't clean it
'build/bdist.linux-armv7l' does not exist -- can't clean it
'build/scripts-2.7' does not exist -- can't clean it
	find . -name \*.pyc -exec rm {} \+
make[1]: Leaving directory '/«PKGBUILDDIR»'
   debian/rules override_dh_clean
make[1]: Entering directory '/«PKGBUILDDIR»'
rm -f -r build test/tmp test/cmp generated
dh_clean debian/pymol.launch debian/pymol-ref-card.* \
         Rules.make create_shadertext.pyc
make[1]: Leaving directory '/«PKGBUILDDIR»'
 debian/rules build-arch
dh build-arch --with python2 --parallel
   dh_testdir -a -O--parallel
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_configure -Spython_distutils
make[1]: Leaving directory '/«PKGBUILDDIR»'
   debian/rules override_dh_auto_build
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_build -Spython_distutils
	python setup.py build --force
running build
running build_py
creating build/lib.linux-armv7l-2.7
creating build/lib.linux-armv7l-2.7/pymol
creating build/lib.linux-armv7l-2.7/pymol/embed
creating build/lib.linux-armv7l-2.7/pymol/embed/epymol
copying modules/pymol/embed/epymol/__init__.py -> build/lib.linux-armv7l-2.7/pymol/embed/epymol
creating build/lib.linux-armv7l-2.7/chempy
creating build/lib.linux-armv7l-2.7/chempy/tinker
copying modules/chempy/tinker/__init__.py -> build/lib.linux-armv7l-2.7/chempy/tinker
copying modules/chempy/tinker/amber.py -> build/lib.linux-armv7l-2.7/chempy/tinker
copying modules/chempy/tinker/keyword.py -> build/lib.linux-armv7l-2.7/chempy/tinker
copying modules/chempy/tinker/realtime.py -> build/lib.linux-armv7l-2.7/chempy/tinker
copying modules/chempy/tinker/state.py -> build/lib.linux-armv7l-2.7/chempy/tinker
creating build/lib.linux-armv7l-2.7/pmg_tk
creating build/lib.linux-armv7l-2.7/pmg_tk/skins
creating build/lib.linux-armv7l-2.7/pmg_tk/skins/demo
copying modules/pmg_tk/skins/demo/__init__.py -> build/lib.linux-armv7l-2.7/pmg_tk/skins/demo
creating build/lib.linux-armv7l-2.7/pmg_tk/startup
copying modules/pmg_tk/startup/__init__.py -> build/lib.linux-armv7l-2.7/pmg_tk/startup
copying modules/pmg_tk/startup/remote_pdb_load.py -> build/lib.linux-armv7l-2.7/pmg_tk/startup
copying modules/pmg_tk/startup/apbs_tools.py -> build/lib.linux-armv7l-2.7/pmg_tk/startup
creating build/lib.linux-armv7l-2.7/pymol/opengl
creating build/lib.linux-armv7l-2.7/pymol/opengl/glu
copying modules/pymol/opengl/glu/__init__.py -> build/lib.linux-armv7l-2.7/pymol/opengl/glu
creating build/lib.linux-armv7l-2.7/pmg_wx
copying modules/pmg_wx/__init__.py -> build/lib.linux-armv7l-2.7/pmg_wx
creating build/lib.linux-armv7l-2.7/chempy/fast
copying modules/chempy/fast/__init__.py -> build/lib.linux-armv7l-2.7/chempy/fast
creating build/lib.linux-armv7l-2.7/chempy/fragments
copying modules/chempy/fragments/__init__.py -> build/lib.linux-armv7l-2.7/chempy/fragments
copying modules/pmg_tk/skins/__init__.py -> build/lib.linux-armv7l-2.7/pmg_tk/skins
creating build/lib.linux-armv7l-2.7/web
copying modules/web/__init__.py -> build/lib.linux-armv7l-2.7/web
copying modules/web/pymolhttpd.py -> build/lib.linux-armv7l-2.7/web
copying modules/pmg_tk/__init__.py -> build/lib.linux-armv7l-2.7/pmg_tk
copying modules/pmg_tk/PyMOLMapLoad.py -> build/lib.linux-armv7l-2.7/pmg_tk
copying modules/pmg_tk/Demo.py -> build/lib.linux-armv7l-2.7/pmg_tk
copying modules/pmg_tk/Setting.py -> build/lib.linux-armv7l-2.7/pmg_tk
copying modules/pmg_tk/volume.py -> build/lib.linux-armv7l-2.7/pmg_tk
copying modules/pmg_tk/SetEditor.py -> build/lib.linux-armv7l-2.7/pmg_tk
copying modules/pmg_tk/ColorEditor.py -> build/lib.linux-armv7l-2.7/pmg_tk
copying modules/pmg_tk/TextEditor.py -> build/lib.linux-armv7l-2.7/pmg_tk
copying modules/pmg_tk/PMGApp.py -> build/lib.linux-armv7l-2.7/pmg_tk
creating build/lib.linux-armv7l-2.7/pymol/contrib
copying modules/pymol/contrib/__init__.py -> build/lib.linux-armv7l-2.7/pymol/contrib
creating build/lib.linux-armv7l-2.7/pymol/opengl/glut
copying modules/pymol/opengl/glut/__init__.py -> build/lib.linux-armv7l-2.7/pymol/opengl/glut
creating build/lib.linux-armv7l-2.7/pymol2
copying modules/pymol2/__init__.py -> build/lib.linux-armv7l-2.7/pymol2
copying modules/pymol2/cmd2.py -> build/lib.linux-armv7l-2.7/pymol2
copying modules/pymol2/make_cmd2.py -> build/lib.linux-armv7l-2.7/pymol2
creating build/lib.linux-armv7l-2.7/web/examples
copying modules/web/examples/justhttpd.py -> build/lib.linux-armv7l-2.7/web/examples
copying modules/web/examples/__init__.py -> build/lib.linux-armv7l-2.7/web/examples
copying modules/pymol/embed/__init__.py -> build/lib.linux-armv7l-2.7/pymol/embed
creating build/lib.linux-armv7l-2.7/pmg_tk/skins/normal
copying modules/pmg_tk/skins/normal/__init__.py -> build/lib.linux-armv7l-2.7/pmg_tk/skins/normal
copying modules/pmg_tk/skins/normal/builder.py -> build/lib.linux-armv7l-2.7/pmg_tk/skins/normal
copying modules/pmg_tk/skins/normal/ModalWindow.py -> build/lib.linux-armv7l-2.7/pmg_tk/skins/normal
creating build/lib.linux-armv7l-2.7/chempy/champ
copying modules/chempy/champ/__init__.py -> build/lib.linux-armv7l-2.7/chempy/champ
copying modules/chempy/champ/assign.py -> build/lib.linux-armv7l-2.7/chempy/champ
copying modules/chempy/champ/formal_charges.py -> build/lib.linux-armv7l-2.7/chempy/champ
copying modules/chempy/champ/amber99.py -> build/lib.linux-armv7l-2.7/chempy/champ
creating build/lib.linux-armv7l-2.7/pymol/embed/wxpymol
copying modules/pymol/embed/wxpymol/__init__.py -> build/lib.linux-armv7l-2.7/pymol/embed/wxpymol
creating build/lib.linux-armv7l-2.7/pymol/wizard
copying modules/pymol/wizard/security.py -> build/lib.linux-armv7l-2.7/pymol/wizard
copying modules/pymol/wizard/box.py -> build/lib.linux-armv7l-2.7/pymol/wizard
copying modules/pymol/wizard/__init__.py -> build/lib.linux-armv7l-2.7/pymol/wizard
copying modules/pymol/wizard/distance.py -> build/lib.linux-armv7l-2.7/pymol/wizard
copying modules/pymol/wizard/pair_fit.py -> build/lib.linux-armv7l-2.7/pymol/wizard
copying modules/pymol/wizard/charge.py -> build/lib.linux-armv7l-2.7/pymol/wizard
copying modules/pymol/wizard/message.py -> build/lib.linux-armv7l-2.7/pymol/wizard
copying modules/pymol/wizard/density.py -> build/lib.linux-armv7l-2.7/pymol/wizard
copying modules/pymol/wizard/pseudoatom.py -> build/lib.linux-armv7l-2.7/pymol/wizard
copying modules/pymol/wizard/mutagenesis.py -> build/lib.linux-armv7l-2.7/pymol/wizard
copying modules/pymol/wizard/appearance.py -> build/lib.linux-armv7l-2.7/pymol/wizard
copying modules/pymol/wizard/filter.py -> build/lib.linux-armv7l-2.7/pymol/wizard
copying modules/pymol/wizard/fedora.py -> build/lib.linux-armv7l-2.7/pymol/wizard
copying modules/pymol/wizard/benchmark.py -> build/lib.linux-armv7l-2.7/pymol/wizard
copying modules/pymol/wizard/stereodemo.py -> build/lib.linux-armv7l-2.7/pymol/wizard
copying modules/pymol/wizard/label.py -> build/lib.linux-armv7l-2.7/pymol/wizard
copying modules/pymol/wizard/annotation.py -> build/lib.linux-armv7l-2.7/pymol/wizard
copying modules/pymol/wizard/sculpting.py -> build/lib.linux-armv7l-2.7/pymol/wizard
copying modules/pymol/wizard/cleanup.py -> build/lib.linux-armv7l-2.7/pymol/wizard
copying modules/pymol/wizard/demo.py -> build/lib.linux-armv7l-2.7/pymol/wizard
copying modules/pymol/wizard/dragging.py -> build/lib.linux-armv7l-2.7/pymol/wizard
copying modules/pymol/wizard/measurement.py -> build/lib.linux-armv7l-2.7/pymol/wizard
copying modules/pymol/wizard/renaming.py -> build/lib.linux-armv7l-2.7/pymol/wizard
copying modules/pymol/wizard/toggle.py -> build/lib.linux-armv7l-2.7/pymol/wizard
creating build/lib.linux-armv7l-2.7/pymol/opengl/gl
copying modules/pymol/opengl/gl/__init__.py -> build/lib.linux-armv7l-2.7/pymol/opengl/gl
copying modules/pymol/setting.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/editor.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/internal.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/keywords.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/constants_palette.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/querying.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/moving.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/importing.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/cmd.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/gui.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/parsing.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/m4x.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/menu.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/colorramping.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/fitting.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/editing.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/parser.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/shortcut.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/controlling.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/constants.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/preset.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/xray.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/invocation.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/checking.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/viewing.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/computing.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/experimenting.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/externing.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/selecting.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/selector.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/xwin.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/headering.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/helping.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/keyboard.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/movie.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/callback.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/completing.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/rpc.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/creating.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/feedingback.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/wizarding.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/cgo.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/exporting.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/monitoring.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/api.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/vfont.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/locking.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/util.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/povray.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/__init__.py -> build/lib.linux-armv7l-2.7/pymol
copying modules/pymol/commanding.py -> build/lib.linux-armv7l-2.7/pymol
creating build/lib.linux-armv7l-2.7/chempy/bmin
copying modules/chempy/bmin/commands.py -> build/lib.linux-armv7l-2.7/chempy/bmin
copying modules/chempy/bmin/__init__.py -> build/lib.linux-armv7l-2.7/chempy/bmin
copying modules/chempy/bmin/realtime.py -> build/lib.linux-armv7l-2.7/chempy/bmin
copying modules/chempy/bmin/state.py -> build/lib.linux-armv7l-2.7/chempy/bmin
copying modules/chempy/bmin/util.py -> build/lib.linux-armv7l-2.7/chempy/bmin
copying modules/chempy/neighbor.py -> build/lib.linux-armv7l-2.7/chempy
copying modules/chempy/cex.py -> build/lib.linux-armv7l-2.7/chempy
copying modules/chempy/arc.py -> build/lib.linux-armv7l-2.7/chempy
copying modules/chempy/protein_amber99.py -> build/lib.linux-armv7l-2.7/chempy
copying modules/chempy/__init__.py -> build/lib.linux-armv7l-2.7/chempy
copying modules/chempy/dictdb.py -> build/lib.linux-armv7l-2.7/chempy
copying modules/chempy/lst.py -> build/lib.linux-armv7l-2.7/chempy
copying modules/chempy/brick.py -> build/lib.linux-armv7l-2.7/chempy
copying modules/chempy/cif.py -> build/lib.linux-armv7l-2.7/chempy
copying modules/chempy/place.py -> build/lib.linux-armv7l-2.7/chempy
copying modules/chempy/charge.py -> build/lib.linux-armv7l-2.7/chempy
copying modules/chempy/io.py -> build/lib.linux-armv7l-2.7/chempy
copying modules/chempy/pdb.py -> build/lib.linux-armv7l-2.7/chempy
copying modules/chempy/bond_amber.py -> build/lib.linux-armv7l-2.7/chempy
copying modules/chempy/cc1.py -> build/lib.linux-armv7l-2.7/chempy
copying modules/chempy/water_amber.py -> build/lib.linux-armv7l-2.7/chempy
copying modules/chempy/mol.py -> build/lib.linux-armv7l-2.7/chempy
copying modules/chempy/gms.py -> build/lib.linux-armv7l-2.7/chempy
copying modules/chempy/hetatm.py -> build/lib.linux-armv7l-2.7/chempy
copying modules/chempy/mae.py -> build/lib.linux-armv7l-2.7/chempy
copying modules/chempy/protein.py -> build/lib.linux-armv7l-2.7/chempy
copying modules/chempy/mmd.py -> build/lib.linux-armv7l-2.7/chempy
copying modules/chempy/pkl.py -> build/lib.linux-armv7l-2.7/chempy
copying modules/chempy/water_residues.py -> build/lib.linux-armv7l-2.7/chempy
copying modules/chempy/bond_mmff.py -> build/lib.linux-armv7l-2.7/chempy
copying modules/chempy/protein_amber.py -> build/lib.linux-armv7l-2.7/chempy
copying modules/chempy/protein_mmff.py -> build/lib.linux-armv7l-2.7/chempy
copying modules/chempy/models.py -> build/lib.linux-armv7l-2.7/chempy
copying modules/chempy/xyz.py -> build/lib.linux-armv7l-2.7/chempy
copying modules/chempy/mass.py -> build/lib.linux-armv7l-2.7/chempy
copying modules/chempy/protein_residues.py -> build/lib.linux-armv7l-2.7/chempy
copying modules/chempy/bonds.py -> build/lib.linux-armv7l-2.7/chempy
copying modules/chempy/gamess1.py -> build/lib.linux-armv7l-2.7/chempy
copying modules/chempy/map.py -> build/lib.linux-armv7l-2.7/chempy
copying modules/chempy/cpv.py -> build/lib.linux-armv7l-2.7/chempy
copying modules/chempy/solvate.py -> build/lib.linux-armv7l-2.7/chempy
copying modules/chempy/sdf.py -> build/lib.linux-armv7l-2.7/chempy
copying modules/chempy/mol2.py -> build/lib.linux-armv7l-2.7/chempy
creating build/lib.linux-armv7l-2.7/pymol/plugins
copying modules/pymol/plugins/__init__.py -> build/lib.linux-armv7l-2.7/pymol/plugins
copying modules/pymol/plugins/repository.py -> build/lib.linux-armv7l-2.7/pymol/plugins
copying modules/pymol/plugins/managergui.py -> build/lib.linux-armv7l-2.7/pymol/plugins
copying modules/pymol/plugins/installation.py -> build/lib.linux-armv7l-2.7/pymol/plugins
copying modules/pymol/plugins/legacysupport.py -> build/lib.linux-armv7l-2.7/pymol/plugins
copying modules/pymol/opengl/__init__.py -> build/lib.linux-armv7l-2.7/pymol/opengl
running build_ext
building 'pymol._cmd' extension
creating build/temp.linux-armv7l-2.7
creating build/temp.linux-armv7l-2.7/ov
creating build/temp.linux-armv7l-2.7/ov/src
creating build/temp.linux-armv7l-2.7/layer0
creating build/temp.linux-armv7l-2.7/layer1
creating build/temp.linux-armv7l-2.7/layer2
creating build/temp.linux-armv7l-2.7/layer3
creating build/temp.linux-armv7l-2.7/layer4
creating build/temp.linux-armv7l-2.7/layer5
creating build/temp.linux-armv7l-2.7/modules
creating build/temp.linux-armv7l-2.7/modules/cealign
creating build/temp.linux-armv7l-2.7/modules/cealign/src
creating build/temp.linux-armv7l-2.7/build
creating build/temp.linux-armv7l-2.7/build/generated
creating build/temp.linux-armv7l-2.7/contrib
creating build/temp.linux-armv7l-2.7/contrib/uiuc
creating build/temp.linux-armv7l-2.7/contrib/uiuc/plugins
creating build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin
creating build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c ov/src/OVHeap.c -o build/temp.linux-armv7l-2.7/ov/src/OVHeap.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Tracker.c -o build/temp.linux-armv7l-2.7/layer0/Tracker.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/ShaderMgr.c -o build/temp.linux-armv7l-2.7/layer0/ShaderMgr.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/Text.c -o build/temp.linux-armv7l-2.7/layer1/Text.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c ov/src/OVRandom.c -o build/temp.linux-armv7l-2.7/ov/src/OVRandom.o -ffast-math -funroll-loops -O3 -fcommon
layer0/ShaderMgr.c: In function 'CShaderPrg_ReplaceStringsInPlace':
layer0/ShaderMgr.c:161:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
       while(rstr=strstr(dest_line, replaceStrings[i])){
       ^
layer0/ShaderMgr.c: In function 'CShaderMgr_Reload_Shader_Variables':
layer0/ShaderMgr.c:401:7: warning: variable 'bg_image_mode_solid' set but not used [-Wunused-but-set-variable]
   int bg_image_mode_solid;
       ^
layer0/ShaderMgr.c: In function 'CShaderPrg_BindAttribLocations':
layer0/ShaderMgr.c:509:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
     if (err = glGetError()){
     ^
layer0/ShaderMgr.c:513:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
     if (err = glGetError()){
     ^
layer0/ShaderMgr.c:517:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
     if (err = glGetError()){
     ^
layer0/ShaderMgr.c: In function 'CShaderPrg_BindLabelAttribLocations':
layer0/ShaderMgr.c:528:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   if (err = glGetError()){
   ^
layer0/ShaderMgr.c:535:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
     if (err = glGetError()){
     ^
layer0/ShaderMgr.c: In function 'CShaderPrg_BindCylinderAttribLocations':
layer0/ShaderMgr.c:549:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
     if (err = glGetError()){
     ^
layer0/ShaderMgr.c:553:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
     if (err = glGetError()){
     ^
layer0/ShaderMgr.c:557:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
     if (err = glGetError()){
     ^
layer0/ShaderMgr.c:561:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
     if (err = glGetError()){
     ^
layer0/ShaderMgr.c: In function 'CShaderPrg_Reload':
layer0/ShaderMgr.c:700:24: warning: unused variable 'needAttach' [-Wunused-variable]
   int status, howLong, needAttach = 0;
                        ^
layer0/ShaderMgr.c: In function 'ShaderMgrConfig':
layer0/ShaderMgr.c:836:14: warning: unused variable 'err' [-Wunused-variable]
       GLenum err ;
              ^
layer0/ShaderMgr.c:885:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
       if (err = glGetError()){
       ^
layer0/ShaderMgr.c:889:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
       if (err = glGetError()){
       ^
layer0/ShaderMgr.c: In function 'CShaderMgr_ReadShaderFromDisk':
layer0/ShaderMgr.c:1225:7: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat=]
       " PyMOLShader_NewFromFile-Error: size(%ld)!=res(%ld)\n", size,res ENDFB(G);
       ^
layer0/ShaderMgr.c: In function 'CShaderPrg_Enable_CylinderShader':
layer0/ShaderMgr.c:1882:10: warning: variable 'm' set but not used [-Wunused-but-set-variable]
   float *m;
          ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c ov/src/OVHeapArray.c -o build/temp.linux-armv7l-2.7/ov/src/OVHeapArray.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c ov/src/OVOneToOne.c -o build/temp.linux-armv7l-2.7/ov/src/OVOneToOne.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Triangle.c -o build/temp.linux-armv7l-2.7/layer0/Triangle.o -ffast-math -funroll-loops -O3 -fcommon
layer0/Triangle.c: In function 'TriangleBuildLast':
layer0/Triangle.c:1511:7: warning: variable 'both_active' set but not used [-Wunused-but-set-variable]
   int both_active;
       ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c ov/src/OVLexicon.c -o build/temp.linux-armv7l-2.7/ov/src/OVLexicon.o -ffast-math -funroll-loops -O3 -fcommon
ov/src/OVLexicon.c: In function 'OVLexicon_BorrowFromCString':
ov/src/OVLexicon.c:360:11: warning: variable 'cur_index' set but not used [-Wunused-but-set-variable]
   ov_word cur_index = 0;
           ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c ov/src/ov_utility.c -o build/temp.linux-armv7l-2.7/ov/src/ov_utility.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c ov/src/OVContext.c -o build/temp.linux-armv7l-2.7/ov/src/OVContext.o -ffast-math -funroll-loops -O3 -fcommon
ov/src/OVContext.c: In function 'OVContext_Del':
ov/src/OVContext.c:21:13: warning: variable 'heap' set but not used [-Wunused-but-set-variable]
     OVHeap *heap = I->heap;
             ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c ov/src/OVOneToAny.c -o build/temp.linux-armv7l-2.7/ov/src/OVOneToAny.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Crystal.c -o build/temp.linux-armv7l-2.7/layer0/Crystal.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Raw.c -o build/temp.linux-armv7l-2.7/layer0/Raw.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/os_gl.c -o build/temp.linux-armv7l-2.7/layer0/os_gl.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Debug.c -o build/temp.linux-armv7l-2.7/layer0/Debug.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Block.c -o build/temp.linux-armv7l-2.7/layer0/Block.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Isosurf.c -o build/temp.linux-armv7l-2.7/layer0/Isosurf.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Map.c -o build/temp.linux-armv7l-2.7/layer0/Map.o -ffast-math -funroll-loops -O3 -fcommon
layer0/Isosurf.c: In function 'IsosurfNewFromPyList':
layer0/Isosurf.c:168:7: warning: variable 'll' set but not used [-Wunused-but-set-variable]
   int ll;
       ^
layer0/Isosurf.c: In function 'IsofieldGetCorners':
layer0/Isosurf.c:2211:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Texture.c -o build/temp.linux-armv7l-2.7/layer0/Texture.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Queue.c -o build/temp.linux-armv7l-2.7/layer0/Queue.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/MemoryCache.c -o build/temp.linux-armv7l-2.7/layer0/MemoryCache.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Util.c -o build/temp.linux-armv7l-2.7/layer0/Util.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Err.c -o build/temp.linux-armv7l-2.7/layer0/Err.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Deferred.c -o build/temp.linux-armv7l-2.7/layer0/Deferred.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Matrix.c -o build/temp.linux-armv7l-2.7/layer0/Matrix.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Pixmap.c -o build/temp.linux-armv7l-2.7/layer0/Pixmap.o -ffast-math -funroll-loops -O3 -fcommon
layer0/Matrix.c: In function 'MatrixFitRMSTTTf':
layer0/Matrix.c:1180:18: warning: variable 'ix' set but not used [-Wunused-but-set-variable]
       int iters, ix, iy, iz, unchanged = 0;
                  ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Sphere.c -o build/temp.linux-armv7l-2.7/layer0/Sphere.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/FontGLUT8x13.c -o build/temp.linux-armv7l-2.7/layer1/FontGLUT8x13.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/Scene.c -o build/temp.linux-armv7l-2.7/layer1/Scene.o -ffast-math -funroll-loops -O3 -fcommon
layer1/Scene.c: In function 'SceneDrawImageOverlay':
layer1/Scene.c:3348:20: warning: variable 'color_word' set but not used [-Wunused-but-set-variable]
       unsigned int color_word;
                    ^
layer1/Scene.c: In function 'SceneReadTriplets':
layer1/Scene.c:3571:7: warning: variable 'dim' set but not used [-Wunused-but-set-variable]
   int dim[3];
       ^
layer1/Scene.c: In function 'SceneDrag':
layer1/Scene.c:5957:8: warning: variable 'result' set but not used [-Wunused-but-set-variable]
    int result, which_light;
        ^
layer1/Scene.c:6005:8: warning: variable 'result' set but not used [-Wunused-but-set-variable]
    int result, which_light;
        ^
layer1/Scene.c: In function 'SceneReshape':
layer1/Scene.c:6381:7: warning: variable 'y' set but not used [-Wunused-but-set-variable]
   int y = height;
       ^
layer1/Scene.c: In function 'SceneApplyImageGamma':
layer1/Scene.c:6538:7: warning: variable 'big_endian' set but not used [-Wunused-but-set-variable]
   int big_endian;
       ^
layer1/Scene.c: In function 'SceneRay':
layer1/Scene.c:6766:7: warning: variable 'curState' set but not used [-Wunused-but-set-variable]
   int curState;
       ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/MyPNG.c -o build/temp.linux-armv7l-2.7/layer0/MyPNG.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/View.c -o build/temp.linux-armv7l-2.7/layer1/View.o -ffast-math -funroll-loops -O3 -fcommon
layer1/View.c: In function 'matrix_interpolate':
layer1/View.c:657:23: warning: variable 'center' set but not used [-Wunused-but-set-variable]
   float p0[3], p1[3], center[3];
                       ^
layer1/View.c:657:16: warning: variable 'p1' set but not used [-Wunused-but-set-variable]
   float p0[3], p1[3], center[3];
                ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/Control.c -o build/temp.linux-armv7l-2.7/layer1/Control.o -ffast-math -funroll-loops -O3 -fcommon
layer1/Control.c: In function 'ControlDrag':
layer1/Control.c:252:7: warning: variable 'width' set but not used [-Wunused-but-set-variable]
   int width;
       ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/FontGLUTHel10.c -o build/temp.linux-armv7l-2.7/layer1/FontGLUTHel10.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/Rep.c -o build/temp.linux-armv7l-2.7/layer1/Rep.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/Basis.c -o build/temp.linux-armv7l-2.7/layer1/Basis.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/Pop.c -o build/temp.linux-armv7l-2.7/layer1/Pop.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/TypeFace.c -o build/temp.linux-armv7l-2.7/layer1/TypeFace.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/P.c -o build/temp.linux-armv7l-2.7/layer1/P.o -ffast-math -funroll-loops -O3 -fcommon
layer1/P.c: In function 'PLabelExprUsesVariable':
layer1/P.c:191:17: warning: variable 'buffer' set but not used [-Wunused-but-set-variable]
   OrthoLineType buffer;
                 ^
layer1/P.c: In function 'PLabelAtomAlt':
layer1/P.c:343:8: warning: the address of 'tok' will always evaluate as 'true' [-Waddress]
    if (tok && tok[0]){
        ^
layer1/P.c: In function 'PAlterAtomState':
layer1/P.c:824:59: warning: variable 'z_id1' set but not used [-Wunused-but-set-variable]
   PyObject *x_id1, *x_id2 = NULL, *y_id1, *y_id2 = NULL, *z_id1, *z_id2 = NULL;
                                                           ^
layer1/P.c:824:36: warning: variable 'y_id1' set but not used [-Wunused-but-set-variable]
   PyObject *x_id1, *x_id2 = NULL, *y_id1, *y_id2 = NULL, *z_id1, *z_id2 = NULL;
                                    ^
layer1/P.c:824:13: warning: variable 'x_id1' set but not used [-Wunused-but-set-variable]
   PyObject *x_id1, *x_id2 = NULL, *y_id1, *y_id2 = NULL, *z_id1, *z_id2 = NULL;
             ^
layer1/P.c: In function 'PUnlockAPIAsGlut':
layer1/P.c:1468:5: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'long int' [-Wformat=]
     ENDFD;
     ^
layer1/P.c: In function 'PUnlockAPIAsGlutNoFlush':
layer1/P.c:1482:5: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'long int' [-Wformat=]
     ENDFD;
     ^
layer1/P.c: In function 'PLockAPIAsGlut':
layer1/P.c:1533:5: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'long int' [-Wformat=]
     ENDFD;
     ^
layer1/P.c:1545:5: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'long int' [-Wformat=]
     ENDFD;
     ^
layer1/P.c:1563:7: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'long int' [-Wformat=]
       ENDFD;
       ^
layer1/P.c: In function 'PFlush':
layer1/P.c:2635:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
       while(size = OrthoCommandOutSize(G)){
       ^
layer1/P.c: In function 'PFlushFast':
layer1/P.c:2679:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   while(size = OrthoCommandOutSize(G)){
   ^
layer1/P.c:2693:7: warning: format '%x' expects argument of type 'unsigned int', but argument 4 has type 'long int' [-Wformat=]
       ENDFD;
       ^
layer1/P.c: In function 'PAutoBlock':
layer1/P.c:2789:9: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'long int' [-Wformat=]
         SavedThread[MAX_SAVED_THREAD - 2].id, SavedThread[MAX_SAVED_THREAD - 3].id ENDFD;
         ^
layer1/P.c:2798:5: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'long int' [-Wformat=]
     ENDFD;
     ^
layer1/P.c: In function 'PUnblock':
layer1/P.c:2818:5: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'long int' [-Wformat=]
     ENDFD;
     ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/MemoryDebug.c -o build/temp.linux-armv7l-2.7/layer0/MemoryDebug.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Match.c -o build/temp.linux-armv7l-2.7/layer0/Match.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Field.c -o build/temp.linux-armv7l-2.7/layer0/Field.o -ffast-math -funroll-loops -O3 -fcommon
layer0/Field.c: In function 'FieldNewFromPyList':
layer0/Field.c:126:7: warning: variable 'll' set but not used [-Wunused-but-set-variable]
   int ll;
       ^
layer0/Field.c:125:16: warning: variable 'n_elem' set but not used [-Wunused-but-set-variable]
   unsigned int n_elem;
                ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Feedback.c -o build/temp.linux-armv7l-2.7/layer0/Feedback.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Vector.c -o build/temp.linux-armv7l-2.7/layer0/Vector.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/Symmetry.c -o build/temp.linux-armv7l-2.7/layer1/Symmetry.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/RepDot.c -o build/temp.linux-armv7l-2.7/layer2/RepDot.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Parse.c -o build/temp.linux-armv7l-2.7/layer0/Parse.o -ffast-math -funroll-loops -O3 -fcommon
layer2/RepDot.c: In function 'RepDotRender':
layer2/RepDot.c:195:33: warning: "/*" within comment [-Wcomment]
            /*      if(normals)  /* NORMALS do not get set for points 
 ^
layer0/Parse.c: In function 'ParseFloat3List':
layer0/Parse.c:173:7: warning: array subscript has type 'char' [-Wchar-subscripts]
       buf[blen] = 0;
       ^
layer2/RepDot.c:220:6: warning: 'tmpCGO' may be used uninitialized in this function [-Wmaybe-uninitialized]
      CGOFreeWithoutVBOs(tmpCGO);
      ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Tetsurf.c -o build/temp.linux-armv7l-2.7/layer0/Tetsurf.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/RepWireBond.c -o build/temp.linux-armv7l-2.7/layer2/RepWireBond.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/PConv.c -o build/temp.linux-armv7l-2.7/layer1/PConv.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/ButMode.c -o build/temp.linux-armv7l-2.7/layer1/ButMode.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/Extrude.c -o build/temp.linux-armv7l-2.7/layer1/Extrude.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/Font.c -o build/temp.linux-armv7l-2.7/layer1/Font.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/Character.c -o build/temp.linux-armv7l-2.7/layer1/Character.o -ffast-math -funroll-loops -O3 -fcommon
layer1/Extrude.c: In function 'ExtrudeCGOSurfaceVariableTube':
layer1/Extrude.c:1124:14: warning: variable 'stop' set but not used [-Wunused-but-set-variable]
   int start, stop;
              ^
layer1/Extrude.c:1124:7: warning: variable 'start' set but not used [-Wunused-but-set-variable]
   int start, stop;
       ^
layer1/Character.c: In function 'CharacterRenderOpenGL':
layer1/Character.c:273:18: warning: unused variable 'texVals' [-Wunused-variable]
    const GLfloat texVals [] = {
                  ^
layer1/Character.c:267:18: warning: unused variable 'vertexVals' [-Wunused-variable]
    const GLfloat vertexVals [] = {
                  ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/CoordSet.c -o build/temp.linux-armv7l-2.7/layer2/CoordSet.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/ScrollBar.c -o build/temp.linux-armv7l-2.7/layer1/ScrollBar.o -ffast-math -funroll-loops -O3 -fcommon
layer2/CoordSet.c: In function 'CoordSetAtomToChemPyAtom':
layer2/CoordSet.c:1021:7: warning: variable 'ok' set but not used [-Wunused-but-set-variable]
   int ok = true;
       ^
In file included from layer0/OOMac.h:21:0,
                 from layer1/Extrude.c:25:
layer1/Extrude.c: In function 'ExtrudeCGOSurfaceTube':
layer0/Err.h:29:43: warning: 'TN' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define CHECKOK(ok, var) ok &= var ? true : false;
                                           ^
layer1/Extrude.c:690:47: note: 'TN' was declared here
   float *sv, *sn, *tv, *tn, *tv1, *tn1, *TV, *TN;
                                               ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/Color.c -o build/temp.linux-armv7l-2.7/layer1/Color.o -ffast-math -funroll-loops -O3 -fcommon
layer1/Color.c: In function 'ColorExtFromPyList':
layer1/Color.c:406:7: warning: variable 'll' set but not used [-Wunused-but-set-variable]
   int ll;
       ^
layer1/Color.c: In function 'ColorDef':
layer1/Color.c:576:7: warning: variable 'best' set but not used [-Wunused-but-set-variable]
   int best;
       ^
layer1/Color.c: In function 'Color3fToInt':
layer1/Color.c:3069:16: warning: unused variable 'result' [-Wunused-variable]
   unsigned int result;
                ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Word.c -o build/temp.linux-armv7l-2.7/layer0/Word.o -ffast-math -funroll-loops -O3 -fcommon
In file included from layer0/OOMac.h:21:0,
                 from layer1/Extrude.c:25:
layer1/Extrude.c: In function 'ExtrudeCGOSurfacePolygon':
layer0/Err.h:29:43: warning: 'TN' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define CHECKOK(ok, var) ok &= var ? true : false;
                                           ^
layer1/Extrude.c:1390:47: note: 'TN' was declared here
   float *sv, *sn, *tv, *tn, *tv1, *tn1, *TV, *TN;
                                               ^
In file included from layer0/OOMac.h:21:0,
                 from layer1/Extrude.c:25:
layer1/Extrude.c: In function 'ExtrudeCGOSurfaceStrand':
layer0/Err.h:29:43: warning: 'TN' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define CHECKOK(ok, var) ok &= var ? true : false;
                                           ^
layer1/Extrude.c:1708:47: note: 'TN' was declared here
   float *sv, *sn, *tv, *tn, *tv1, *tn1, *TV, *TN;
                                               ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/CGO.c -o build/temp.linux-armv7l-2.7/layer1/CGO.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/ObjectMolecule.c -o build/temp.linux-armv7l-2.7/layer2/ObjectMolecule.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/ObjectMolecule2.c -o build/temp.linux-armv7l-2.7/layer2/ObjectMolecule2.o -ffast-math -funroll-loops -O3 -fcommon
layer1/CGO.c: In function 'CGONewFromPyList':
layer1/CGO.c:329:7: warning: variable 'll' set but not used [-Wunused-but-set-variable]
   int ll;
       ^
layer1/CGO.c: In function 'CGOFromFloatArray':
layer1/CGO.c:530:7: warning: variable 'c' set but not used [-Wunused-but-set-variable]
   int c;
       ^
layer1/CGO.c: In function 'CGOCombineBeginEnd':
layer1/CGO.c:1935:11: warning: variable 'pickColorValsUC' set but not used [-Wunused-but-set-variable]
    uchar *pickColorValsUC;
           ^
layer1/CGO.c:1881:6: warning: unused variable 'ncolors' [-Wunused-variable]
  int ncolors = 0;
      ^
layer1/CGO.c: In function 'CGOCountNumVerticesForScreen':
layer1/CGO.c:2313:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   while(op = (CGO_MASK & CGO_read_int(pc))) {
   ^
layer1/CGO.c: In function 'OptimizePointsToVBO':
layer1/CGO.c:2642:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
     CHECK_GL_ERROR_OK("ERROR: OptimizePointsToVBO() BEFORE glGenBuffers returns err=%d\n");    
     ^
layer1/CGO.c:2645:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
       CHECK_GL_ERROR_OK("ERROR: OptimizePointsToVBO() glGenBuffers returns err=%d\n");
       ^
layer1/CGO.c:2649:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
       CHECK_GL_ERROR_OK("ERROR: OptimizePointsToVBO() glBindBuffer returns err=%d\n");
       ^
layer1/CGO.c:2657:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
       CHECK_GL_ERROR_OK("ERROR: OptimizePointsToVBO() glBufferData returns err=%d\n");
       ^
layer1/CGO.c:2671:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
       CHECK_GL_ERROR_OK("ERROR: OptimizePointsToVBO() glBindBuffer returns err=%d\n");
       ^
layer1/CGO.c:2682:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: OptimizePointsToVBO() glBufferData returns err=%d\n");
  ^
layer1/CGO.c:2688:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
       CHECK_GL_ERROR_OK("ERROR: OptimizePointsToVBO() glBindBuffer returns err=%d\n");
       ^
layer1/CGO.c:2699:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: OptimizePointsToVBO() glBufferData returns err=%d\n");
  ^
layer1/CGO.c:2450:9: warning: variable 'err' set but not used [-Wunused-but-set-variable]
   short err = 0;
         ^
layer1/CGO.c: In function 'CGOProcessCGOtoArrays':
layer1/CGO.c:2730:9: warning: variable 'err' set but not used [-Wunused-but-set-variable]
   short err = 0;
         ^
layer1/CGO.c: In function 'CGOProcessScreenCGOtoArrays':
layer1/CGO.c:3012:8: warning: variable 'has_texcoord' set but not used [-Wunused-but-set-variable]
  short has_texcoord = false;
        ^
layer1/CGO.c:2966:9: warning: variable 'err' set but not used [-Wunused-but-set-variable]
   short err = 0;
         ^
layer1/CGO.c: In function 'CGOOptimizeToVBONotIndexedWithReturnedData':
layer1/CGO.c:3220:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBONotIndexed() glGenBuffers returns err=%d\n");
  ^
layer1/CGO.c:3224:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBONotIndexed() glBindBuffer returns err=%d\n");
  ^
layer1/CGO.c:3232:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBONotIndexed() glBufferData returns err=%d\n");
  ^
layer1/CGO.c:3236:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBONotIndexed() glBindBuffer returns err=%d\n");
  ^
layer1/CGO.c:3248:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBONotIndexed() glBufferData returns err=%d\n");
  ^
layer1/CGO.c:3252:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBONotIndexed() glBindBuffer returns err=%d\n");
  ^
layer1/CGO.c:3264:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBONotIndexed() glBufferData returns err=%d\n");
  ^
layer1/CGO.c:3268:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBONotIndexed() glBindBuffer returns err=%d\n");
  ^
layer1/CGO.c:3275:4: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
    CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBONotIndexed() glBufferData returns err=%d\n");
    ^
layer1/CGO.c:3505:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
     CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBONotIndexed() glGenBuffers returns err=%d\n");
     ^
layer1/CGO.c:3509:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBONotIndexed() glBindBuffer returns err=%d\n");
  ^
layer1/CGO.c:3517:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBONotIndexed() glBufferData returns err=%d\n");
  ^
layer1/CGO.c:3521:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBONotIndexed() glBindBuffer returns err=%d\n");
  ^
layer1/CGO.c:3533:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBONotIndexed() glBufferData returns err=%d\n");
  ^
layer1/CGO.c:3537:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBONotIndexed() glBindBuffer returns err=%d\n");
  ^
layer1/CGO.c:3549:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBONotIndexed() glBufferData returns err=%d\n");
  ^
layer1/CGO.c:3141:9: warning: variable 'err' set but not used [-Wunused-but-set-variable]
   short err = 0;
         ^
layer1/CGO.c: In function 'CGOOptimizeToVBOIndexedWithColorImpl':
layer1/CGO.c:3890:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
       CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() BEFORE glGenBuffers returns err=%d\n");
       ^
layer1/CGO.c:3893:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() glGenBuffers returns err=%d\n");
  ^
layer1/CGO.c:3897:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() glBindBuffer returns err=%d\n");
  ^
layer1/CGO.c:3905:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() glBufferData returns err=%d\n");
  ^
layer1/CGO.c:3909:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() glBindBuffer returns err=%d\n");
  ^
layer1/CGO.c:3921:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() glBufferData returns err=%d\n");
  ^
layer1/CGO.c:3925:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() glBindBuffer returns err=%d\n");
  ^
layer1/CGO.c:3937:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() glBufferData returns err=%d\n");
  ^
layer1/CGO.c:3941:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() glBindBuffer returns err=%d\n");
  ^
layer1/CGO.c:3949:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() glBufferData returns err=%d\n");
  ^
layer1/CGO.c:3953:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() glBindBuffer returns err=%d\n");
  ^
layer1/CGO.c:3960:4: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
    CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() glBufferData returns err=%d\n");
    ^
layer1/CGO.c:4200:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
       CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() BEFORE glGenBuffers returns err=%d\n");
       ^
layer1/CGO.c:4203:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() glGenBuffers returns err=%d\n");
  ^
layer1/CGO.c:4207:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() glBindBuffer returns err=%d\n");
  ^
layer1/CGO.c:4215:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() glBufferData returns err=%d\n");
  ^
layer1/CGO.c:4219:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() glBindBuffer returns err=%d\n");
  ^
layer1/CGO.c:4231:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() glBufferData returns err=%d\n");
  ^
layer1/CGO.c:4235:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() glBindBuffer returns err=%d\n");
  ^
layer1/CGO.c:4247:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() glBufferData returns err=%d\n");
  ^
layer1/CGO.c:4251:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() glBindBuffer returns err=%d\n");
  ^
layer1/CGO.c:4259:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() glBufferData returns err=%d\n");
  ^
layer1/CGO.c:3631:9: warning: variable 'err' set but not used [-Wunused-but-set-variable]
   short err = 0;
         ^
layer1/CGO.c: In function 'CGOOptimizeGLSLCylindersToVBOIndexedImpl':
layer1/CGO.c:4621:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
       CHECK_GL_ERROR_OK("ERROR: CGOOptimizeGLSLCylindersToVBO() BEFORE glGenBuffers returns err=%d\n");
       ^
layer1/CGO.c:4624:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeGLSLCylindersToVBO() glGenBuffers returns err=%d\n");
  ^
layer1/CGO.c:4628:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeGLSLCylindersToVBO() glBindBuffer returns err=%d\n");
  ^
layer1/CGO.c:4661:4: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
    CHECK_GL_ERROR_OK("ERROR: CGOOptimizeGLSLCylindersToVBO() glBufferData returns err=%d\n");
    ^
layer1/CGO.c:4667:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeGLSLCylindersToVBO() glBindBuffer returns err=%d\n");
  ^
layer1/CGO.c:4671:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeGLSLCylindersToVBO() glBufferData returns err=%d\n");
  ^
layer1/CGO.c: In function 'CGOOptimizeSpheresToVBONonIndexedImpl':
layer1/CGO.c:4932:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
       CHECK_GL_ERROR_OK("ERROR: CGOOptimizeSpheresToVBONonIndexed() BEFORE glGenBuffers returns err=%d\n");
       ^
layer1/CGO.c:4935:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeSpheresToVBONonIndexed() glGenBuffers returns err=%d\n");
  ^
layer1/CGO.c:4939:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeSpheresToVBONonIndexed() glBindBuffer returns err=%d\n");
  ^
layer1/CGO.c:4963:4: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
    CHECK_GL_ERROR_OK("ERROR: CGOOptimizeSpheresToVBONonIndexed() glBufferData returns err=%d\n");
    ^
layer1/CGO.c: In function 'CGOSimplify':
layer1/CGO.c:5171:11: warning: variable 'pickColorValsUC' set but not used [-Wunused-but-set-variable]
    uchar *pickColorValsUC;
           ^
layer1/CGO.c: In function 'CGOOptimizeTextures':
layer1/CGO.c:5385:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
       CHECK_GL_ERROR_OK("ERROR: CGOOptimizeTextures() BEFORE glGenBuffers returns err=%d\n");
       ^
layer1/CGO.c:5389:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
       CHECK_GL_ERROR_OK("ERROR: CGOOptimizeTextures() glGenBuffers returns err=%d\n");
       ^
layer1/CGO.c:5392:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
       CHECK_GL_ERROR_OK("ERROR: CGOOptimizeTextures() glBindBuffer returns err=%d\n");
       ^
layer1/CGO.c:5400:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeTextures() glBufferData returns err=%d\n");
  ^
layer1/CGO.c:5405:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
       CHECK_GL_ERROR_OK("ERROR: CGOOptimizeTextures() glBindBuffer returns err=%d\n");
       ^
layer1/CGO.c:5412:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeTextures() glBufferData returns err=%d\n");
  ^
layer1/CGO.c:5416:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
       CHECK_GL_ERROR_OK("ERROR: CGOOptimizeTextures() glBindBuffer returns err=%d\n");
       ^
layer1/CGO.c:5423:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeTextures() glBufferData returns err=%d\n")
  ^
layer1/CGO.c: In function 'CGOOptimizeLabels':
layer1/CGO.c:5582:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
       CHECK_GL_ERROR_OK("ERROR: CGOOptimizeLabels() BEFORE glGenBuffers returns err=%d\n");
       ^
layer1/CGO.c:5586:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
       CHECK_GL_ERROR_OK("ERROR: CGOOptimizeLabels() glGenBuffers returns err=%d\n");
       ^
layer1/CGO.c:5589:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
       CHECK_GL_ERROR_OK("ERROR: CGOOptimizeLabels() glBindBuffer returns err=%d\n");
       ^
layer1/CGO.c:5597:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeLabels() glBufferData returns err=%d\n");
  ^
layer1/CGO.c:5602:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
       CHECK_GL_ERROR_OK("ERROR: CGOOptimizeLabels() glBindBuffer returns err=%d\n");
       ^
layer1/CGO.c:5609:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeLabels() glBufferData returns err=%d\n");
  ^
layer1/CGO.c:5613:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
       CHECK_GL_ERROR_OK("ERROR: CGOOptimizeLabels() glBindBuffer returns err=%d\n");
       ^
layer1/CGO.c:5620:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeLabels() glBufferData returns err=%d\n")
  ^
layer1/CGO.c:5624:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
       CHECK_GL_ERROR_OK("ERROR: CGOOptimizeLabels() glBindBuffer returns err=%d\n");
       ^
layer1/CGO.c:5631:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeLabels() glBufferData returns err=%d\n")
  ^
layer1/CGO.c: In function 'CGOExpandDrawTextures':
layer1/CGO.c:5679:30: warning: variable 'onvals' set but not used [-Wunused-but-set-variable]
  int nvals = narrays*nverts, onvals;
                              ^
layer1/CGO.c: In function 'CGORenderRay':
layer1/CGO.c:6220:42: warning: variable 'pickColorVals' set but not used [-Wunused-but-set-variable]
  float *normalVals = 0, *colorVals = 0, *pickColorVals;
                                          ^
layer2/ObjectMolecule.c: In function 'ObjectMoleculeFixSeleHydrogens':
layer2/ObjectMolecule.c:731:13: warning: variable 'cs' set but not used [-Wunused-but-set-variable]
   CoordSet *cs;
             ^
layer1/CGO.c: In function 'CGO_gl_draw_buffers_indexed':
layer1/CGO.c:6662:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   CHECK_GL_ERROR_OK("beginning of CGO_gl_draw_buffers_indexed returns err=%d\n");
   ^
layer1/CGO.c:6788:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   CHECK_GL_ERROR_OK("CGO_gl_draw_buffers_indexed: before glDrawElements returns err=%d\n");
   ^
layer1/CGO.c:6790:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   CHECK_GL_ERROR_OK("CGO_gl_draw_buffers_indexed: after glDrawElements returns err=%d\n");
   ^
layer1/CGO.c:6835:1: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
 CHECK_GL_ERROR_OK("CGO_gl_draw_buffers_indexed: end returns err=%d\n");
 ^
layer2/ObjectMolecule.c: In function 'ObjectMoleculeLoadTRJFile':
layer2/ObjectMolecule.c:886:7: warning: variable 'ok' set but not used [-Wunused-but-set-variable]
   int ok = true;
       ^
layer1/CGO.c: In function 'CGO_gl_draw_label':
layer1/CGO.c:7136:50: warning: variable 'textExtent' set but not used [-Wunused-but-set-variable]
   float worldPos[4], screenMin[3], screenMax[3], textExtent[4];
                                                  ^
layer1/CGO.c:7136:36: warning: variable 'screenMax' set but not used [-Wunused-but-set-variable]
   float worldPos[4], screenMin[3], screenMax[3], textExtent[4];
                                    ^
layer1/CGO.c:7136:22: warning: variable 'screenMin' set but not used [-Wunused-but-set-variable]
   float worldPos[4], screenMin[3], screenMax[3], textExtent[4];
                      ^
layer1/CGO.c: In function 'CGO_gl_draw_texture':
layer1/CGO.c:7177:50: warning: variable 'textExtent' set but not used [-Wunused-but-set-variable]
   float worldPos[4], screenMin[3], screenMax[3], textExtent[4];
                                                  ^
layer1/CGO.c:7177:36: warning: variable 'screenMax' set but not used [-Wunused-but-set-variable]
   float worldPos[4], screenMin[3], screenMax[3], textExtent[4];
                                    ^
layer1/CGO.c:7177:22: warning: variable 'screenMin' set but not used [-Wunused-but-set-variable]
   float worldPos[4], screenMin[3], screenMax[3], textExtent[4];
                      ^
layer1/CGO.c: In function 'CGORenderGLPicking':
layer1/CGO.c:7697:73: warning: variable 'pbnd' set but not used [-Wunused-but-set-variable]
        int nverts = CGO_get_int(pc+3), v, pl, idx = -1, pidx, bnd = -1, pbnd;
                                                                         ^
layer1/CGO.c:7697:57: warning: variable 'pidx' set but not used [-Wunused-but-set-variable]
        int nverts = CGO_get_int(pc+3), v, pl, idx = -1, pidx, bnd = -1, pbnd;
                                                         ^
layer1/CGO.c: In function 'CGOSimpleCone':
layer1/CGO.c:8765:15: warning: variable 'nub2' set but not used [-Wunused-but-set-variable]
   float nub1, nub2;
               ^
layer1/CGO.c:8765:9: warning: variable 'nub1' set but not used [-Wunused-but-set-variable]
   float nub1, nub2;
         ^
In file included from layer1/CGO.c:24:0:
layer1/CGO.c: In function 'CGOGetSizeWithoutStops':
layer1/CGO.h:35:26: warning: value computed is not used [-Wunused-value]
 #define CGO_read_int(p) (*((int*)((p)++)))
                          ^
layer1/CGO.c:9045:5: note: in expansion of macro 'CGO_read_int'
     CGO_read_int(pc);
     ^
layer2/ObjectMolecule.c: In function 'ObjectMoleculeLoadPMOFile':
layer2/ObjectMolecule.c:2855:7: warning: variable 'ok' set but not used [-Wunused-but-set-variable]
   int ok = true;
       ^
layer1/CGO.c: In function 'CGOChangeShadersTo':
layer1/CGO.c:9567:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   while(op = (CGO_MASK & CGO_read_int(pc))) {
   ^
layer1/CGO.c: In function 'CGOOptimizeScreenTexturesAndPolygons':
layer1/CGO.c:9685:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeScreenTexturesAndPolygons() glGenBuffers returns err=%d\n");
  ^
layer1/CGO.c:9689:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeScreenTexturesAndPolygons() glBindBuffer returns err=%d\n");
  ^
layer2/ObjectMolecule.c: In function 'ObjectMoleculeRenderSele':
layer2/ObjectMolecule.c:3290:51: warning: variable 'ai' set but not used [-Wunused-but-set-variable]
     register AtomInfoType *atInfo = I->AtomInfo, *ai;
                                                   ^
layer1/CGO.c:9697:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeScreenTexturesAndPolygons() glBufferData returns err=%d\n");
  ^
layer1/CGO.c:9701:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeScreenTexturesAndPolygons() glBindBuffer returns err=%d\n");
  ^
layer1/CGO.c:9709:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeScreenTexturesAndPolygons() glBufferData returns err=%d\n");
  ^
layer1/CGO.c:9713:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeScreenTexturesAndPolygons() glBindBuffer returns err=%d\n");
  ^
layer1/CGO.c:9724:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  CHECK_GL_ERROR_OK("ERROR: CGOOptimizeScreenTexturesAndPolygons() glBufferData returns err=%d\n");
  ^
layer2/ObjectMolecule.c: In function 'ObjectMoleculeLoadXYZFile':
layer2/ObjectMolecule.c:3881:7: warning: variable 'ok' set but not used [-Wunused-but-set-variable]
   int ok = true;
       ^
layer2/ObjectMolecule.c: In function 'ObjectMoleculeAttach':
layer2/ObjectMolecule.c:4477:10: warning: variable 'nn' set but not used [-Wunused-but-set-variable]
   int n, nn;
          ^
layer2/ObjectMolecule.c: In function 'ObjectMoleculeFindOpenValenceVector':
layer2/ObjectMolecule.c:4700:22: warning: variable 'ai1' set but not used [-Wunused-but-set-variable]
   AtomInfoType *ai, *ai1;
                      ^
layer2/ObjectMolecule.c: In function 'ObjectMoleculeCreateSpheroid':
layer2/ObjectMolecule.c:4881:10: warning: variable 'spl' set but not used [-Wunused-but-set-variable]
   float *spl;
          ^
layer2/ObjectMolecule.c: In function 'ObjectMoleculeGuessValences':
layer2/ObjectMolecule.c:6350:29: warning: variable 'bnd2' set but not used [-Wunused-but-set-variable]
                         int bnd2[5];
                             ^
layer2/ObjectMolecule.c:6124:38: warning: variable 'c2_len' set but not used [-Wunused-but-set-variable]
                 float c1_len = 0.0F, c2_len = 0.0F;
                                      ^
layer2/ObjectMolecule.c:6124:23: warning: variable 'c1_len' set but not used [-Wunused-but-set-variable]
                 float c1_len = 0.0F, c2_len = 0.0F;
                       ^
layer2/ObjectMolecule.c:6123:56: warning: variable 'c2_bd' set but not used [-Wunused-but-set-variable]
                 int c1_at = -1, c2_at = -1, c1_bd = 0, c2_bd = 0;
                                                        ^
layer2/ObjectMolecule.c:6123:45: warning: variable 'c1_bd' set but not used [-Wunused-but-set-variable]
                 int c1_at = -1, c2_at = -1, c1_bd = 0, c2_bd = 0;
                                             ^
layer2/ObjectMolecule.c:6118:68: warning: variable 'o4_len' set but not used [-Wunused-but-set-variable]
                 float o1_len = 0.0F, o2_len = 0.0F, o3_len = 0.0F, o4_len = 0.0F;
                                                                    ^
layer2/ObjectMolecule.c:6118:53: warning: variable 'o3_len' set but not used [-Wunused-but-set-variable]
                 float o1_len = 0.0F, o2_len = 0.0F, o3_len = 0.0F, o4_len = 0.0F;
                                                     ^
layer2/ObjectMolecule.c: In function 'ObjectMoleculeMOL2SetFormalCharges':
layer2/ObjectMolecule.c:8969:46: warning: variable 'n' set but not used [-Wunused-but-set-variable]
       int at, fcharge = 0, isProtein = 0, k, n;
                                              ^
layer2/ObjectMolecule.c: In function 'ObjectMoleculeMOL2Str2CoordSet':
layer2/ObjectMolecule.c:9368:38: warning: variable 'resv_flag' set but not used [-Wunused-but-set-variable]
           int chain_flag, resn_flag, resv_flag;
                                      ^
layer2/ObjectMolecule.c: In function 'ObjectMoleculeInvalidateAtomType':
layer2/ObjectMolecule.c:12194:16: warning: variable 'a' set but not used [-Wunused-but-set-variable]
   int ai, atm, a;
                ^
layer2/ObjectMolecule2.c:1639:17: warning: function declaration isn't a prototype [-Wstrict-prototypes]
 static SSHash * sshash_new() {
                 ^
layer2/ObjectMolecule2.c: In function 'ObjectMoleculePDBStr2CoordSet':
layer2/ObjectMolecule2.c:1793:7: warning: variable 'have_conect' set but not used [-Wunused-but-set-variable]
   int have_conect = false;
       ^
layer2/ObjectMolecule2.c:1792:7: warning: variable 'seen_conect' set but not used [-Wunused-but-set-variable]
   int seen_conect = false;
       ^
layer2/ObjectMolecule2.c:1758:10: warning: unused variable 'b' [-Wunused-variable]
   int a, b, c;
          ^
layer2/ObjectMolecule2.c: In function 'ObjectMoleculeNewFromPyList':
layer2/ObjectMolecule2.c:3702:7: warning: variable 'll' set but not used [-Wunused-but-set-variable]
   int ll;
       ^
layer1/CGO.c: In function 'CGO_gl_draw_buffers':
layer1/CGO.c:6649:5: warning: 'shaderPrg' may be used uninitialized in this function [-Wmaybe-uninitialized]
     CShaderPrg_Disable(shaderPrg);
     ^
layer1/CGO.c: In function 'CGO_gl_draw_arrays':
layer1/CGO.c:6510:12: warning: 'vertexVals' may be used uninitialized in this function [-Wmaybe-uninitialized]
     float *vertexVals;
            ^
layer1/CGO.c: In function 'CGOCombineBeginEnd':
layer1/CGO.c:1998:73: warning: 'normalVals' may be used uninitialized in this function [-Wmaybe-uninitialized]
   normalVals[pl] = tmp_ptr[0]; normalVals[pl+1] = tmp_ptr[1]; normalVals[pl+2] = tmp_ptr[2];  
                                                                         ^
layer1/CGO.c: In function 'OptimizePointsToVBO':
layer1/CGO.c:2607:8: warning: 'pickColorValsDA' may be used uninitialized in this function [-Wmaybe-uninitialized]
        SetVertexValuesForVBO(I->G, cgo, arrays, pl, plc, cnt, incr++, 
        ^
layer1/CGO.c: In function 'CGOProcessCGOtoArrays':
layer1/CGO.c:2907:8: warning: 'pickColorValsDA' may be used uninitialized in this function [-Wmaybe-uninitialized]
        SetVertexValuesForVBO(G, cgo, arrays, pl, plc, cnt, incr++, 
        ^
layer1/CGO.c:2927:8: warning: 'accessibilityValsDA' may be used uninitialized in this function [-Wmaybe-uninitialized]
        SetVertexValuesForVBO(G, cgo, arrays, pl, plc, cnt, incr++, 
        ^
layer1/CGO.c:2907:8: warning: 'normalValsDA' may be used uninitialized in this function [-Wmaybe-uninitialized]
        SetVertexValuesForVBO(G, cgo, arrays, pl, plc, cnt, incr++, 
        ^
layer1/CGO.c: In function 'CGOOptimizeToVBONotIndexedWithReturnedData':
layer1/CGO.c:3457:8: warning: 'pickColorValsDA' may be used uninitialized in this function [-Wmaybe-uninitialized]
        SetVertexValuesForVBO(I->G, cgo, arrays, pl, plc, cnt, incr++, 
        ^
layer1/CGO.c:3457:8: warning: 'normalValsDA' may be used uninitialized in this function [-Wmaybe-uninitialized]
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/Movie.c -o build/temp.linux-armv7l-2.7/layer1/Movie.o -ffast-math -funroll-loops -O3 -fcommon
In file included from layer0/OOMac.h:22:0,
                 from layer2/ObjectMolecule.c:25:
layer2/ObjectMolecule.c: In function 'ObjectMoleculeLoadRSTFile':
layer0/MemoryDebug.h:182:15: warning: 'buffer' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define mfree free
               ^
layer2/ObjectMolecule.c:1280:9: note: 'buffer' was declared here
   char *buffer, *p;
         ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/FontType.c -o build/temp.linux-armv7l-2.7/layer1/FontType.o -ffast-math -funroll-loops -O3 -fcommon
layer1/CGO.c: In function 'CGOSimplify':
layer1/CGO.c:5213:73: warning: 'normalVals' may be used uninitialized in this function [-Wmaybe-uninitialized]
   normalVals[pl] = tmp_ptr[0]; normalVals[pl+1] = tmp_ptr[1]; normalVals[pl+2] = tmp_ptr[2];  
                                                                         ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/Ray.c -o build/temp.linux-armv7l-2.7/layer1/Ray.o -ffast-math -funroll-loops -O3 -fcommon
In file included from layer1/Ray.c:44:0:
layer1/Basis.c: In function 'ConeLineToSphereCapped':
layer1/Basis.c:846:11: warning: variable 'base2orig_len' set but not used [-Wunused-but-set-variable]
     float base2orig_len, base2orig_len_sq;
           ^
layer1/Basis.c: In function 'BasisHitShadow':
layer1/Basis.c:2361:7: warning: variable 'check_interior_flag' set but not used [-Wunused-but-set-variable]
   int check_interior_flag;
       ^
layer1/Basis.c:2360:7: warning: variable 'excl_trans_flag' set but not used [-Wunused-but-set-variable]
   int excl_trans_flag;
       ^
layer1/Ray.c: In function 'RayRenderG3d':
layer1/Ray.c:967:36: warning: variable 'scale_z' set but not used [-Wunused-but-set-variable]
   register float scale_x, scale_y, scale_z;
                                    ^
layer1/Ray.c: In function 'RayRenderIDTF':
layer1/Ray.c:2132:11: warning: variable 'mesh_start' set but not used [-Wunused-but-set-variable]
       int mesh_start = 0;
           ^
layer1/Ray.c: In function 'RayRenderPOV':
layer1/Ray.c:2445:28: warning: variable 'bkrd_bottom' set but not used [-Wunused-but-set-variable]
   float *bkrd, *bkrd_top, *bkrd_bottom;
                            ^
layer1/Ray.c:2445:17: warning: variable 'bkrd_top' set but not used [-Wunused-but-set-variable]
   float *bkrd, *bkrd_top, *bkrd_bottom;
                 ^
layer1/Ray.c:2443:7: warning: variable 'fogRangeFlag' set but not used [-Wunused-but-set-variable]
   int fogRangeFlag = false;
       ^
layer1/Ray.c:2442:7: warning: variable 'fogFlag' set but not used [-Wunused-but-set-variable]
   int fogFlag = false;
       ^
layer1/Ray.c: In function 'RayRender':
layer1/Ray.c:6122:15: warning: variable 'dc' set but not used [-Wunused-but-set-variable]
           int dc = 0;
               ^
layer1/CGO.c: In function 'CGORenderRay':
layer1/CGO.c:6244:9: warning: 'vertexVals' may be used uninitialized in this function [-Wmaybe-uninitialized]
      v0 = &vertexVals[pl];
         ^
layer1/CGO.c: In function 'CGORenderGLPicking':
layer1/CGO.c:7753:13: warning: 'pca' may be used uninitialized in this function [-Wmaybe-uninitialized]
      float *pca;
             ^
layer1/CGO.c:7775:26: warning: 'nverts' may be used uninitialized in this function [-Wmaybe-uninitialized]
      pickColorVals = pca + nverts;
                          ^
layer1/CGO.c: In function 'CGORenderGL':
layer1/CGO.c:8085:12: warning: 'normalVals_tmp' may be used uninitialized in this function [-Wmaybe-uninitialized]
         n2 = normalVals_tmp + 3;
            ^
In file included from layer0/OOMac.h:22:0,
                 from layer1/CGO.c:26:
layer1/CGO.c: In function 'CGOOptimizeGLSLCylindersToVBOIndexedImpl':
layer0/MemoryDebug.h:182:15: warning: 'org_colorVals' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define mfree free
               ^
layer1/CGO.c:4373:12: note: 'org_colorVals' was declared here
     float *org_colorVals;
            ^
In file included from layer1/Ray.c:44:0:
layer1/Basis.c: In function 'BasisMakeMap':
layer1/Basis.c:3483:38: warning: 'tempRef' may be used uninitialized in this function [-Wmaybe-uninitialized]
                               tempRef[i] = 0;
                                      ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/Setting.c -o build/temp.linux-armv7l-2.7/layer1/Setting.o -ffast-math -funroll-loops -O3 -fcommon
In file included from layer0/OOMac.h:21:0,
                 from layer2/ObjectMolecule2.c:26:
layer2/ObjectMolecule2.c: In function 'ObjectMoleculeSort':
layer0/Err.h:29:43: warning: 'dAtmToIdx' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define CHECKOK(ok, var) ok &= var ? true : false;
                                           ^
layer2/ObjectMolecule2.c:4328:8: note: 'dAtmToIdx' was declared here
   int *dAtmToIdx;
        ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/RepMesh.c -o build/temp.linux-armv7l-2.7/layer2/RepMesh.o -ffast-math -funroll-loops -O3 -fcommon
layer2/RepMesh.c: In function 'RepMeshRender':
layer2/RepMesh.c:314:27: warning: 'origin' may be used uninitialized in this function [-Wmaybe-uninitialized]
    axis[1] = v[1] - origin[1];
                           ^
layer1/Ray.c: In function 'RayTraceThread':
layer1/Ray.c:3190:16: warning: 'back_mask' may be used uninitialized in this function [-Wmaybe-uninitialized]
   unsigned int back_mask;
                ^
layer2/RepMesh.c: In function 'RepMeshNew':
layer2/RepMesh.c:1175:8: warning: 'field' may be used uninitialized in this function [-Wmaybe-uninitialized]
     if (field)
        ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/FontGLUTHel12.c -o build/temp.linux-armv7l-2.7/layer1/FontGLUTHel12.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/Ortho.c -o build/temp.linux-armv7l-2.7/layer1/Ortho.o -ffast-math -funroll-loops -O3 -fcommon
layer1/Ortho.c: In function 'OrthoDoDraw':
layer1/Ortho.c:1520:10: warning: variable 'v' set but not used [-Wunused-but-set-variable]
   float *v;
          ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/RepSphere.c -o build/temp.linux-armv7l-2.7/layer2/RepSphere.o -ffast-math -funroll-loops -O3 -fcommon
layer1/Ortho.c: In function 'bg_grad':
layer1/Ortho.c:1430:7: warning: 'cgo2' may be used uninitialized in this function [-Wmaybe-uninitialized]
       CGOFree(cgo2);
       ^
layer2/RepSphere.c: In function 'RenderSphereMode_Direct':
layer2/RepSphere.c:855:13: warning: variable 'last_vdw' set but not used [-Wunused-but-set-variable]
       float last_vdw = -1.0F;
             ^
layer2/RepSphere.c: In function 'RepSphereComputeSphereNormals':
layer2/RepSphere.c:2176:15: warning: variable 'nbr_flag' set but not used [-Wunused-but-set-variable]
  register int nbr_flag;
               ^
layer2/RepSphere.c: In function 'RepSphereNew':
layer2/RepSphere.c:2529:17: warning: variable 'ai2' set but not used [-Wunused-but-set-variable]
   AtomInfoType *ai2;
                 ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/FontGLUT.c -o build/temp.linux-armv7l-2.7/layer1/FontGLUT.o -ffast-math -funroll-loops -O3 -fcommon
layer2/RepSphere.c: In function 'RepSphereRender':
layer2/RepSphere.c:2003:6: warning: 'radius' may be used uninitialized in this function [-Wmaybe-uninitialized]
      RenderSphereMode_Points(G, I, info, radius, c);
      ^
layer2/RepSphere.c:2009:6: warning: 'n_quad_verts' may be used uninitialized in this function [-Wmaybe-uninitialized]
      RenderSphereMode_9(G, I, info, n_quad_verts, &v, radius, c);
      ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/Shaker.c -o build/temp.linux-armv7l-2.7/layer1/Shaker.o -ffast-math -funroll-loops -O3 -fcommon
layer1/Shaker.c: In function 'ShakerGetPyra':
layer1/Shaker.c:73:16: warning: variable 't0' set but not used [-Wunused-but-set-variable]
   float av[3], t0[3];
                ^
layer2/RepSphere.c: In function 'RepSphereGenerateGeometryCullForSphere':
layer2/RepSphere.c:2356:13: warning: 'v1[0]' may be used uninitialized in this function [-Wmaybe-uninitialized]
       float v1[3];
             ^
layer1/Shaker.c: In function 'ShakerDoPyra':
layer1/Shaker.c:94:16: warning: variable 't0' set but not used [-Wunused-but-set-variable]
   float av[3], t0[3], push[3];
                ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/FontGLUT9x15.c -o build/temp.linux-armv7l-2.7/layer1/FontGLUT9x15.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/Wizard.c -o build/temp.linux-armv7l-2.7/layer1/Wizard.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/ObjectGroup.c -o build/temp.linux-armv7l-2.7/layer2/ObjectGroup.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/RepCartoon.c -o build/temp.linux-armv7l-2.7/layer2/RepCartoon.o -ffast-math -funroll-loops -O3 -fcommon
layer2/RepCartoon.c: In function 'do_ring':
layer2/RepCartoon.c:282:7: warning: variable 'cartoon_color' set but not used [-Wunused-but-set-variable]
   int cartoon_color;
       ^
layer2/RepCartoon.c: In function 'nuc_acid':
layer2/RepCartoon.c:1497:22: warning: variable 'v_n' set but not used [-Wunused-but-set-variable]
   float *v_o, *v_c, *v_n, t0[3];
                      ^
layer2/RepCartoon.c: In function 'GenerateRepCartoonCGO':
layer2/RepCartoon.c:1662:31: warning: variable 'ring_finder_eff' set but not used [-Wunused-but-set-variable]
   int ring_mode, ring_finder, ring_finder_eff;
                               ^
layer2/RepCartoon.c: In function 'RepCartoonNew':
layer2/RepCartoon.c:2889:9: warning: variable 'alpha' set but not used [-Wunused-but-set-variable]
   float alpha;
         ^
layer2/RepCartoon.c:2876:7: warning: variable 'skip_to' set but not used [-Wunused-but-set-variable]
   int skip_to;
       ^
layer2/RepCartoon.c:2865:7: warning: variable 'highlight_color' set but not used [-Wunused-but-set-variable]
   int highlight_color;
       ^
layer2/RepCartoon.c:2861:7: warning: variable 'cartoon_debug' set but not used [-Wunused-but-set-variable]
   int cartoon_debug;
       ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/FontGLUTHel18.c -o build/temp.linux-armv7l-2.7/layer1/FontGLUTHel18.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/ObjectGadget.c -o build/temp.linux-armv7l-2.7/layer2/ObjectGadget.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/PyMOLObject.c -o build/temp.linux-armv7l-2.7/layer1/PyMOLObject.o -ffast-math -funroll-loops -O3 -fcommon
layer2/ObjectGadget.c: In function 'ObjectGadgetInitFromPyList':
layer2/ObjectGadget.c:305:7: warning: variable 'll' set but not used [-Wunused-but-set-variable]
   int ll;
       ^
layer1/PyMOLObject.c: In function 'ObjectMotion':
layer1/PyMOLObject.c:384:13: warning: variable 'zero_flag' set but not used [-Wunused-but-set-variable]
         int zero_flag = -1;
             ^
layer1/PyMOLObject.c: In function 'ObjectStateFromPyList':
layer1/PyMOLObject.c:1469:7: warning: variable 'll' set but not used [-Wunused-but-set-variable]
   int ll = 0;
       ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/RepNonbondedSphere.c -o build/temp.linux-armv7l-2.7/layer2/RepNonbondedSphere.o -ffast-math -funroll-loops -O3 -fcommon
layer2/RepNonbondedSphere.c: In function 'RepNonbondedSphereRender':
layer2/RepNonbondedSphere.c:197:25: warning: variable 'use_default_shader' set but not used [-Wunused-but-set-variable]
       short use_shader, use_default_shader, use_sphere_shader, generate_shader_cgo = 0, use_display_lists = 0;
                         ^
layer2/ObjectMolecule.c: In function 'ObjectMoleculeMerge':
layer2/ObjectMolecule.c:9993:16: warning: 'i2a' may be used uninitialized in this function [-Wmaybe-uninitialized]
   cs->IdxToAtm = i2a;
                ^
layer2/ObjectMolecule.c:9989:12: warning: 'nAt' may be used uninitialized in this function [-Wmaybe-uninitialized]
   I->NAtom = nAt;
            ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/RepRibbon.c -o build/temp.linux-armv7l-2.7/layer2/RepRibbon.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/Seq.c -o build/temp.linux-armv7l-2.7/layer1/Seq.o -ffast-math -funroll-loops -O3 -fcommon
layer1/Seq.c: In function 'SeqDrag':
layer1/Seq.c:182:16: warning: variable 'col' set but not used [-Wunused-but-set-variable]
       CSeqCol *col;
                ^
layer1/Seq.c: In function 'SeqRelease':
layer1/Seq.c:213:16: warning: variable 'col' set but not used [-Wunused-but-set-variable]
       CSeqCol *col;
                ^
layer1/Seq.c: In function 'SeqClick':
layer1/Seq.c:267:16: warning: variable 'col' set but not used [-Wunused-but-set-variable]
       CSeqCol *col;
                ^
layer2/ObjectMolecule.c: In function 'ObjectMoleculeAddSeleHydrogens':
layer2/ObjectMolecule.c:4091:16: warning: 'cs' may be used uninitialized in this function [-Wmaybe-uninitialized]
           if(cs->fFree)
                ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer3/Editor.c -o build/temp.linux-armv7l-2.7/layer3/Editor.o -ffast-math -funroll-loops -O3 -fcommon
layer3/Editor.c: In function 'EditorDrawDihedral':
layer3/Editor.c:113:22: warning: variable 'sele3' set but not used [-Wunused-but-set-variable]
           int sele0, sele3;
                      ^
layer3/Editor.c:113:15: warning: variable 'sele0' set but not used [-Wunused-but-set-variable]
           int sele0, sele3;
               ^
layer3/Editor.c: In function 'EditorAttach':
layer3/Editor.c:934:7: warning: variable 'state' set but not used [-Wunused-but-set-variable]
   int state;
       ^
layer3/Editor.c: In function 'EditorReplace':
layer3/Editor.c:1115:7: warning: variable 'state' set but not used [-Wunused-but-set-variable]
   int state;
       ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/ObjectCGO.c -o build/temp.linux-armv7l-2.7/layer2/ObjectCGO.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/Sculpt.c -o build/temp.linux-armv7l-2.7/layer2/Sculpt.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer3/PlugIOManager.c -o build/temp.linux-armv7l-2.7/layer3/PlugIOManager.o -ffast-math -funroll-loops -O3 -fcommon
layer3/PlugIOManager.c: In function 'PlugIOManagerLoadTraj':
layer3/PlugIOManager.c:232:31: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
                   if(stop > 0 && cnt >= stop || max > 0 && ncnt >= max) {
                               ^
layer3/PlugIOManager.c: In function 'PlugIOManagerLoadVol':
layer3/PlugIOManager.c:349:17: warning: variable 'isNew' set but not used [-Wunused-but-set-variable]
             int isNew = false;
                 ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer3/Executive.c -o build/temp.linux-armv7l-2.7/layer3/Executive.o -ffast-math -funroll-loops -O3 -fcommon
layer2/ObjectMolecule.c: In function 'ObjectMoleculeFillOpenValences':
layer2/ObjectMolecule.c:4619:12: warning: 'cs' may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(cs->fFree)
            ^
layer3/Executive.c: In function 'ExecutiveGetHistogram':
layer3/Executive.c:4512:7: warning: too many arguments for format [-Wformat-extra-args]
       " GetHistogram-Error: wrong object type.", objName ENDFB(G);
       ^
In file included from layer0/OOMac.h:21:0,
                 from layer3/Executive.c:24:
layer3/Executive.c: In function 'ExecutiveSetSymmetry':
layer3/Executive.c:5899:19: warning: assignment makes integer from pointer without a cast
   ok_assert(1, ok = symmetry);
                   ^
layer0/Err.h:32:31: note: in definition of macro 'ok_assert'
 #define ok_assert(x, c) {if(!(c)) ok_raise(x);}
                               ^
layer3/Executive.c: In function 'ExecutiveMapSet':
layer3/Executive.c:6547:21: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
               float tmp[3];
                     ^
layer3/Executive.c: In function 'ExecutiveSculptIterate':
layer3/Executive.c:7022:7: warning: variable 'ok' set but not used [-Wunused-but-set-variable]
   int ok = true;
       ^
layer3/Executive.c: In function 'ExecutiveRemoveAtoms':
layer3/Executive.c:9382:7: warning: variable 'flag' set but not used [-Wunused-but-set-variable]
   int flag = false;
       ^
layer3/Executive.c: In function 'ExecutiveIterateList':
layer3/Executive.c:10699:14: warning: variable 'cs' set but not used [-Wunused-but-set-variable]
    CoordSet *cs = NULL;
              ^
layer3/Executive.c: In function 'ExecutiveCenter':
layer3/Executive.c:13688:23: warning: variable 'df' set but not used [-Wunused-but-set-variable]
   float mn[3], mx[3], df[3];
                       ^
layer3/Executive.c: In function 'ExecutiveRelease':
layer3/Executive.c:15726:7: warning: variable 'n' set but not used [-Wunused-but-set-variable]
   int n;
       ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/ObjectDist.c -o build/temp.linux-armv7l-2.7/layer2/ObjectDist.o -ffast-math -funroll-loops -O3 -fcommon
layer2/ObjectDist.c: In function 'ObjectDistGetDistSetFromM4XBond':
layer2/ObjectDist.c:187:25: warning: variable 'dist' set but not used [-Wunused-but-set-variable]
       float *vv0, *vv1, dist;
                         ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/ObjectVolume.c -o build/temp.linux-armv7l-2.7/layer2/ObjectVolume.o -ffast-math -funroll-loops -O3 -fcommon
layer2/ObjectVolume.c: In function 'ObjectVolumeNewFromPyList':
layer2/ObjectVolume.c:269:7: warning: variable 'll' set but not used [-Wunused-but-set-variable]
   int ll;
       ^
layer2/ObjectVolume.c: In function 'ObjectVolumeFree':
layer2/ObjectVolume.c:341:9: warning: unused variable 'i' [-Wunused-variable]
   int a,i;
         ^
layer2/ObjectVolume.c: In function 'ObjectVolumeUpdate':
layer2/ObjectVolume.c:451:50: warning: statement with no effect [-Wunused-value]
       a, vs->RefreshFlag, vs->ResurfaceFlag ENDFD(G);
                                                  ^
layer2/ObjectVolume.c:474:9: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
         && vs->Ramp[5 * (vs->RampSize - 1)] == 359.f) {
         ^
layer2/ObjectVolume.c:515:26: warning: variable 'max_ext' set but not used [-Wunused-but-set-variable]
         float *min_ext, *max_ext;
                          ^
layer2/ObjectVolume.c:515:16: warning: variable 'min_ext' set but not used [-Wunused-but-set-variable]
         float *min_ext, *max_ext;
                ^
layer2/ObjectVolume.c:569:39: warning: pointer targets in passing argument 2 of 'FieldNew' differ in signedness [-Wpointer-sign]
           vs->carvemask = FieldNew(G, vs->dim, 3, sizeof(GLubyte), cFieldOther);
                                       ^
In file included from layer0/Isosurf.h:24:0,
                 from layer2/ObjectMap.h:24,
                 from layer2/ObjectVolume.h:19,
                 from layer2/ObjectVolume.c:26:
layer0/Field.h:65:9: note: expected 'int *' but argument is of type 'unsigned int *'
 CField *FieldNew(PyMOLGlobals * G, int *dim, int n_dim, unsigned int base_size, int type);
         ^
layer2/ObjectVolume.c: At top level:
layer2/ObjectVolume.c:714:15: warning: function declaration isn't a prototype [-Wstrict-prototypes]
 static GLuint tex3dGenBind()
               ^
layer2/ObjectVolume.c: In function 'ObjectVolumeRender':
layer2/ObjectVolume.c:924:89: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
         CShaderPrg_Set1f(shaderPrg, "fogIsSolidColor", bg_gradient || bg_image_filename && bg_image_filename[0] ? 0.f : 1.f);
                                                                                         ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/ObjectCallback.c -o build/temp.linux-armv7l-2.7/layer2/ObjectCallback.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/RepDistLabel.c -o build/temp.linux-armv7l-2.7/layer2/RepDistLabel.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/RepEllipsoid.c -o build/temp.linux-armv7l-2.7/layer2/RepEllipsoid.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/GadgetSet.c -o build/temp.linux-armv7l-2.7/layer2/GadgetSet.o -ffast-math -funroll-loops -O3 -fcommon
layer2/RepDistLabel.c: In function 'RepDistLabelNew':
layer2/RepDistLabel.c:404:24: warning: variable 'v6' set but not used [-Wunused-but-set-variable]
       float *v4, *v5, *v6;
                        ^
layer2/RepDistLabel.c:404:19: warning: variable 'v5' set but not used [-Wunused-but-set-variable]
       float *v4, *v5, *v6;
                   ^
layer2/GadgetSet.c: In function 'GadgetSetFromPyList':
layer2/GadgetSet.c:93:7: warning: variable 'll' set but not used [-Wunused-but-set-variable]
   int ll;
       ^
layer2/GadgetSet.c: In function 'GadgetSetRender':
layer2/GadgetSet.c:303:13: warning: variable 'ok' set but not used [-Wunused-but-set-variable]
         int ok = true;
             ^
layer2/GadgetSet.c:290:9: warning: variable 'use_shader' set but not used [-Wunused-but-set-variable]
   short use_shader;
         ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/RepDistDash.c -o build/temp.linux-armv7l-2.7/layer2/RepDistDash.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/ObjectSlice.c -o build/temp.linux-armv7l-2.7/layer2/ObjectSlice.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/SculptCache.c -o build/temp.linux-armv7l-2.7/layer2/SculptCache.o -ffast-math -funroll-loops -O3 -fcommon
layer2/RepDistDash.c: In function 'RepDistDashNew':
layer2/RepDistDash.c:351:29: warning: variable 'd1' set but not used [-Wunused-but-set-variable]
   float *v, *v1, *v2, d[3], d1[3];
                             ^
layer2/ObjectSlice.c: In function 'ObjectSliceStateFromPyList':
layer2/ObjectSlice.c:103:7: warning: variable 'll' set but not used [-Wunused-but-set-variable]
   int ll;
       ^
layer2/ObjectSlice.c: In function 'ObjectSliceNewFromPyList':
layer2/ObjectSlice.c:172:7: warning: variable 'll' set but not used [-Wunused-but-set-variable]
   int ll;
       ^
layer2/ObjectSlice.c: In function 'ObjectSliceUpdate':
layer2/ObjectSlice.c:709:7: warning: variable 'ok' set but not used [-Wunused-but-set-variable]
   int ok = true;
       ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/RepLabel.c -o build/temp.linux-armv7l-2.7/layer2/RepLabel.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/ObjectSurface.c -o build/temp.linux-armv7l-2.7/layer2/ObjectSurface.o -ffast-math -funroll-loops -O3 -fcommon
layer2/ObjectSurface.c: In function 'ObjectSurfaceUpdate':
layer2/ObjectSurface.c:498:7: warning: variable 'ok' set but not used [-Wunused-but-set-variable]
   int ok = true;
       ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/RepNonbonded.c -o build/temp.linux-armv7l-2.7/layer2/RepNonbonded.o -ffast-math -funroll-loops -O3 -fcommon
layer2/ObjectSlice.c: In function 'GenerateOutlineOfSlice':
layer2/ObjectSlice.c:1120:5: warning: 'origin' may be used uninitialized in this function [-Wmaybe-uninitialized]
     CGOSphere(cgo, origin, 1.f);
     ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/AtomInfo.c -o build/temp.linux-armv7l-2.7/layer2/AtomInfo.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/DistSet.c -o build/temp.linux-armv7l-2.7/layer2/DistSet.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/RepDihedral.c -o build/temp.linux-armv7l-2.7/layer2/RepDihedral.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/VFont.c -o build/temp.linux-armv7l-2.7/layer2/VFont.o -ffast-math -funroll-loops -O3 -fcommon
layer2/RepDihedral.c: In function 'RepDihedralNew':
layer2/RepDihedral.c:527:15: warning: variable 'mod_pos' set but not used [-Wunused-but-set-variable]
         float mod_pos;
               ^
layer2/RepDihedral.c:383:37: warning: variable 'v6' set but not used [-Wunused-but-set-variable]
     float *v1, *v2, *v3, *v4, *v5, *v6;
                                     ^
layer2/VFont.c: In function 'VFontIndent':
layer2/VFont.c:145:10: warning: variable 'pc' set but not used [-Wunused-but-set-variable]
   float *pc;
          ^
layer2/VFont.c:144:9: warning: variable 'base' set but not used [-Wunused-but-set-variable]
   float base[3], pen[3];
         ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/ObjectMap.c -o build/temp.linux-armv7l-2.7/layer2/ObjectMap.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer3/Seeker.c -o build/temp.linux-armv7l-2.7/layer3/Seeker.o -ffast-math -funroll-loops -O3 -fcommon
layer3/Seeker.c: In function 'SeekerRefresh':
layer3/Seeker.c:505:22: warning: variable 'not_selected' set but not used [-Wunused-but-set-variable]
         register int not_selected;
                      ^
In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1761:0,
                 from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:17,
                 from layer2/ObjectMap.c:45:
/usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it by " \
  ^
layer2/ObjectMap.c: In function 'ObjectMapStateTrim':
layer2/ObjectMap.c:480:7: warning: variable 'max' set but not used [-Wunused-but-set-variable]
   int max[3];
       ^
layer2/ObjectMap.c: In function 'ObjectMapStateInterpolate':
layer2/ObjectMap.c:1110:10: warning: variable 'out' set but not used [-Wunused-but-set-variable]
   float *out;
          ^
layer2/ObjectMap.c: In function 'ObjectMapNewFromPyList':
layer2/ObjectMap.c:1589:7: warning: variable 'll' set but not used [-Wunused-but-set-variable]
   int ll;
       ^
layer2/ObjectMap.c: In function 'ObjectMapCCP4StrToMap':
layer2/ObjectMap.c:2727:41: warning: passing argument 2 of 'UtilNCopy' discards 'const' qualifier from pointer target type
     UtilNCopy(ms->Symmetry->SpaceGroup, space_group_numbers[ispg], WordLength);
                                         ^
In file included from layer2/ObjectMap.c:41:0:
layer0/Util.h:34:6: note: expected 'char *' but argument is of type 'const char *'
 void UtilNCopy(char *dst, char *src, ov_size n);        /* up to N-1 chars */
      ^
layer2/ObjectMap.c:2470:14: warning: variable 'xref' set but not used [-Wunused-but-set-variable]
   int cc[3], xref[3];
              ^
layer2/ObjectMap.c: In function 'ObjectMapLoadCCP4':
layer2/ObjectMap.c:4593:7: warning: variable 'ok' set but not used [-Wunused-but-set-variable]
   int ok = true;
       ^
layer2/ObjectMap.c: In function 'ObjectMapLoadPHI':
layer2/ObjectMap.c:4764:7: warning: variable 'ok' set but not used [-Wunused-but-set-variable]
   int ok = true;
       ^
layer2/ObjectMap.c: In function 'ObjectMapLoadDXFile':
layer2/ObjectMap.c:5119:7: warning: variable 'ok' set but not used [-Wunused-but-set-variable]
   int ok = true;
       ^
layer2/ObjectMap.c: In function 'ObjectMapLoadACNTFile':
layer2/ObjectMap.c:5367:7: warning: variable 'ok' set but not used [-Wunused-but-set-variable]
   int ok = true;
       ^
layer2/ObjectMap.c: In function 'ObjectMapLoadFLDFile':
layer2/ObjectMap.c:5420:7: warning: variable 'ok' set but not used [-Wunused-but-set-variable]
   int ok = true;
       ^
In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:26:0,
                 from layer2/ObjectMap.c:45:
layer2/ObjectMap.c: At top level:
/usr/lib/python2.7/dist-packages/numpy/core/include/numpy/__multiarray_api.h:1629:1: warning: '_import_array' defined but not used [-Wunused-function]
 _import_array(void)
 ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.o -ffast-math -funroll-loops -O3 -fcommon
contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c: In function 'read_molden_rundata':
contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:585:25: warning: variable 'hessian_data' set but not used [-Wunused-but-set-variable]
   molfile_qm_hessian_t *hessian_data;
                         ^
contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c: In function 'get_basis':
contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:828:36: warning: unused variable 's_coeff2' [-Wunused-variable]
  char s_expon[128], s_coeff1[128], s_coeff2[128];
                                    ^
contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:828:21: warning: unused variable 's_coeff1' [-Wunused-variable]
  char s_expon[128], s_coeff1[128], s_coeff2[128];
                     ^
contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:828:7: warning: unused variable 's_expon' [-Wunused-variable]
  char s_expon[128], s_coeff1[128], s_coeff2[128];
       ^
In file included from contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:37:0:
contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c: At top level:
contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:95:20: warning: 'get_pte_label' defined but not used [-Wunused-function]
 static const char *get_pte_label(const int idx)
                    ^
contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:102:14: warning: 'get_pte_mass' defined but not used [-Wunused-function]
 static float get_pte_mass(const int idx)
              ^
contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:109:14: warning: 'get_pte_vdw_radius' defined but not used [-Wunused-function]
 static float get_pte_vdw_radius(const int idx)
              ^
contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:133:12: warning: 'get_pte_idx' defined but not used [-Wunused-function]
 static int get_pte_idx(const char *label)
            ^
In file included from contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:38:0:
contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:706:12: warning: 'symmetry_expand' defined but not used [-Wunused-function]
 static int symmetry_expand(qm_atom_t **atoms, int numunique, int natoms, 
            ^
contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1001:12: warning: 'have_keyline' defined but not used [-Wunused-function]
 static int have_keyline(FILE *file, const char *keystring1,
            ^
contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1072:13: warning: 'thisline' defined but not used [-Wunused-function]
 static void thisline(FILE *file) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1092:13: warning: 'whereami' defined but not used [-Wunused-function]
 static void whereami(FILE *file) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:485:13: warning: 'replace_wavefunction' defined but not used [-Wunused-function]
 static void replace_wavefunction(qm_timestep_t *ts, int n) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:502:13: warning: 'del_wavefunction' defined but not used [-Wunused-function]
 static void del_wavefunction(qm_timestep_t *ts) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:580:13: warning: 'print_matrix4' defined but not used [-Wunused-function]
 static void print_matrix4(const float mat[16]) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h: In function 'eatline':
contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:835:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
     fgets(readbuf, 1024, fd);
     ^
contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c: In function 'open_molden_read':
contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:213:11: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
           fscanf(data->file, "%d", &natm);
           ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.o -ffast-math -funroll-loops -O3 -fcommon
contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c: In function 'open_rst_read':
contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c:43:11: warning: variable 'timesteprst' set but not used [-Wunused-but-set-variable]
   double  timesteprst;
           ^
contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c:57:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
   fgets(title, 82, fd);
   ^
contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c:60:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
   fgets(line, 82, fd);
   ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer3/Selector.c -o build/temp.linux-armv7l-2.7/layer3/Selector.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.o -ffast-math -funroll-loops -O3 -fcommon
contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c: In function 'vtf_parse_atom':
contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c:234:7: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'char (*)[16]' [-Wformat=]
       if (sscanf(s, "%16s %n", &atom.name, &n) < 1) {
       ^
contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c:243:7: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'char (*)[16]' [-Wformat=]
       if (sscanf(s, "%16s %n", &atom.type, &n) < 1) {
       ^
contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c:269:2: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'char (*)[8]' [-Wformat=]
  if (sscanf(s, "%8s %n", &atom.resname, &n) < 1) {
  ^
contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c:284:7: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'char (*)[8]' [-Wformat=]
       if (sscanf(s, "%8s %n", &atom.segid, &n) < 1) {
       ^
contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c:293:7: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'char (*)[2]' [-Wformat=]
       if (sscanf(s, "%2s %n", &atom.insertion, &n) < 1) {
       ^
contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c:305:2: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'char (*)[2]' [-Wformat=]
  if (sscanf(s, "%2s %n", &atom.chain, &n) < 1) {
  ^
contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c:339:2: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'char (*)[2]' [-Wformat=]
  if (sscanf(s, "%2s %n", &atom.altloc, &n) < 1) {
  ^
layer3/Selector.c: In function 'SelectorGetSpacialMapFromSeleCoord':
layer3/Selector.c:1491:23: warning: variable 'ai' set but not used [-Wunused-but-set-variable]
         AtomInfoType *ai;
                       ^
layer3/Selector.c: In function 'SelectorAssignSS':
layer3/Selector.c:2089:11: warning: variable 'c' set but not used [-Wunused-but-set-variable]
       int c, i, h, k, l;
           ^
layer3/Selector.c: In function 'SelectorGetPairIndices':
layer3/Selector.c:3563:23: warning: variable 'ai2' set but not used [-Wunused-but-set-variable]
   AtomInfoType *ai1, *ai2;
                       ^
layer3/Selector.c:3563:17: warning: variable 'ai1' set but not used [-Wunused-but-set-variable]
   AtomInfoType *ai1, *ai2;
                 ^
layer3/Selector.c: In function 'SelectorMapMaskVDW':
layer3/Selector.c:5356:11: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
   int n1, n2;
           ^
layer3/Selector.c: In function 'SelectorSelect0':
layer3/Selector.c:8623:15: warning: variable 's' set but not used [-Wunused-but-set-variable]
       int at, s;
               ^
layer3/Selector.c:8669:18: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
           b >  2 && b <  5 ||
                  ^
layer3/Selector.c:8671:18: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
           b > 18 && b < 32 ||
                  ^
layer3/Selector.c:8672:18: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
           b > 36 && b < 51 ||
                  ^
layer3/Selector.c:8673:18: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
           b > 54 && b < 85 ||
                  ^
layer3/Selector.c: In function 'SelectorSelect1':
layer3/Selector.c:9091:11: warning: variable 'prevmodel' set but not used [-Wunused-but-set-variable]
       int prevmodel;
           ^
layer3/Selector.c:9153:11: warning: variable 'prevmodel' set but not used [-Wunused-but-set-variable]
       int prevmodel;
           ^
layer3/Selector.c: In function 'SelectorLogic1':
layer3/Selector.c:10326:21: warning: variable 'ai' set but not used [-Wunused-but-set-variable]
       AtomInfoType *ai;
                     ^
layer3/Selector.c: In function 'SelectorEvaluate':
layer3/Selector.c:10858:19: warning: variable 'cc2' set but not used [-Wunused-but-set-variable]
   char *q, *cc1, *cc2;
                   ^
layer3/Selector.c:10857:15: warning: variable 'opFlag2' set but not used [-Wunused-but-set-variable]
   int opFlag, opFlag2, maxLevel;
               ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/psfplugin.o -ffast-math -funroll-loops -O3 -fcommon
contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c: In function 'write_psf_structure':
contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c:652:19: warning: variable 'atomname' set but not used [-Wunused-but-set-variable]
       const char *atomname; 
                   ^
In file included from contrib/uiuc/plugins/molfile_plugin/src/fortread.h:28:0,
                 from contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c:29:
contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c: At top level:
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: 'swap2_unaligned' defined but not used [-Wunused-function]
 static void swap2_unaligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: 'swap4_unaligned' defined but not used [-Wunused-function]
 static void swap4_unaligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: 'swap8_unaligned' defined but not used [-Wunused-function]
 static void swap8_unaligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: 'swap2_aligned' defined but not used [-Wunused-function]
 static void swap2_aligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: 'swap8_aligned' defined but not used [-Wunused-function]
 static void swap8_aligned(void *v, long ndata) {
             ^
In file included from contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c:29:0:
contrib/uiuc/plugins/molfile_plugin/src/fortread.h:36:12: warning: 'fort_eat_recmark' defined but not used [-Wunused-function]
 static int fort_eat_recmark(FILE *ifp, int recmarklen) {
            ^
contrib/uiuc/plugins/molfile_plugin/src/fortread.h:55:12: warning: 'fort_get_endian_reclen' defined but not used [-Wunused-function]
 static int fort_get_endian_reclen(int reclen, int word0, int word1, 
            ^
contrib/uiuc/plugins/molfile_plugin/src/fortread.h:103:12: warning: 'fortread_4' defined but not used [-Wunused-function]
 static int fortread_4(void *dest, int n, int swap, FILE *fd) {
            ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.o -ffast-math -funroll-loops -O3 -fcommon
contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: In function 'have_gamess':
contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1101:8: warning: variable 'word' set but not used [-Wunused-but-set-variable]
   char word[3][BUFSIZ];
        ^
contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: In function 'get_basis_stats':
contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:2258:8: warning: variable 'word' set but not used [-Wunused-but-set-variable]
   char word[7][BUFSIZ];
        ^
contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: In function 'get_wavefunction':
contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:3561:8: warning: variable 'word' set but not used [-Wunused-but-set-variable]
   char word[6][BUFSIZ];
        ^
In file included from contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:160:0:
contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: At top level:
contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:890:12: warning: 'iswhiteline' defined but not used [-Wunused-function]
 static int iswhiteline(char *s) {
            ^
contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:896:14: warning: 'strtoupper' defined but not used [-Wunused-function]
 static char *strtoupper(char *s) {
              ^
contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1072:13: warning: 'thisline' defined but not used [-Wunused-function]
 static void thisline(FILE *file) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1092:13: warning: 'whereami' defined but not used [-Wunused-function]
 static void whereami(FILE *file) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:580:13: warning: 'print_matrix4' defined but not used [-Wunused-function]
 static void print_matrix4(const float mat[16]) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1023:12: warning: 'fpexpftoc' defined but not used [-Wunused-function]
 static int fpexpftoc(char *ftocstr) {
            ^
In file included from contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:162:0:
contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:95:20: warning: 'get_pte_label' defined but not used [-Wunused-function]
 static const char *get_pte_label(const int idx)
                    ^
contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:102:14: warning: 'get_pte_mass' defined but not used [-Wunused-function]
 static float get_pte_mass(const int idx)
              ^
contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:109:14: warning: 'get_pte_vdw_radius' defined but not used [-Wunused-function]
 static float get_pte_vdw_radius(const int idx)
              ^
contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:133:12: warning: 'get_pte_idx' defined but not used [-Wunused-function]
 static int get_pte_idx(const char *label)
            ^
contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:997:13: warning: 'print_input_data' defined but not used [-Wunused-function]
 static void print_input_data(qmdata_t *data) {
             ^
In file included from contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:160:0:
contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h: In function 'eatline':
contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:835:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
     fgets(readbuf, 1024, fd);
     ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer4/Menu.c -o build/temp.linux-armv7l-2.7/layer4/Menu.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer4/Export.c -o build/temp.linux-armv7l-2.7/layer4/Export.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer4/Cmd.c -o build/temp.linux-armv7l-2.7/layer4/Cmd.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/RepAngle.c -o build/temp.linux-armv7l-2.7/layer2/RepAngle.o -ffast-math -funroll-loops -O3 -fcommon
layer4/Cmd.c: In function 'APIEnter':
layer4/Cmd.c:132:5: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'long int' [-Wformat=]
     ENDFD;
     ^
layer4/Cmd.c: In function 'APIEnterBlocked':
layer4/Cmd.c:167:5: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'long int' [-Wformat=]
     ENDFD;
     ^
layer4/Cmd.c: In function 'APIExit':
layer4/Cmd.c:203:5: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'long int' [-Wformat=]
     ENDFD;
     ^
layer4/Cmd.c: In function 'APIExitBlocked':
layer4/Cmd.c:213:5: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'long int' [-Wformat=]
     ENDFD;
     ^
layer4/Cmd.c: In function 'CmdAlign':
layer4/Cmd.c:2182:9: warning: variable 'result' set but not used [-Wunused-but-set-variable]
   float result = -1.0;
         ^
layer4/Cmd.c: In function 'Cmd_New':
layer4/Cmd.c:4172:11: warning: variable 'ok' set but not used [-Wunused-but-set-variable]
       int ok = true;
           ^
layer4/Cmd.c: In function 'CmdPNG':
layer4/Cmd.c:5964:29: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
       if(ray || !G->HaveGUI && (!SceneGetCopyType(G) || width || height)) {
                             ^
layer4/Cmd.c: In function 'CmdLoadObject':
layer4/Cmd.c:6916:9: warning: variable 'isTmp' set but not used [-Wunused-but-set-variable]
     int isTmp;
         ^
layer4/Cmd.c: In function 'CmdSetObjectColor':
layer4/Cmd.c:7870:7: warning: variable 'result' set but not used [-Wunused-but-set-variable]
   int result = -1;
       ^
layer2/RepAngle.c: In function 'RepAngleNew':
layer2/RepAngle.c:453:15: warning: variable 'mod_pos' set but not used [-Wunused-but-set-variable]
         float mod_pos;
               ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/ObjectGadgetRamp.c -o build/temp.linux-armv7l-2.7/layer2/ObjectGadgetRamp.o -ffast-math -funroll-loops -O3 -fcommon
layer2/ObjectGadgetRamp.c: In function 'ObjectGadgetRampUpdateCGO':
layer2/ObjectGadgetRamp.c:651:10: warning: variable 'p' set but not used [-Wunused-but-set-variable]
   float *p;
          ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.o -ffast-math -funroll-loops -O3 -fcommon
contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c: In function 'get_atom_radius':
contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c:166:16: warning: variable 'type' set but not used [-Wunused-but-set-variable]
   char *name, *type;
                ^
contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c:166:9: warning: variable 'name' set but not used [-Wunused-but-set-variable]
   char *name, *type;
         ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/carplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/carplugin.o -ffast-math -funroll-loops -O3 -fcommon
contrib/uiuc/plugins/molfile_plugin/src/carplugin.c: In function 'read_car_timestep':
contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:326:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
     fgets(line, LINESIZE, data->file);
     ^
contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:339:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
     fgets(line, LINESIZE, data->file);
     ^
contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:344:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
     fgets(line, LINESIZE, data->file);
     ^
contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:349:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
   fgets(line, LINESIZE, data->file);
   ^
contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:363:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
       fgets(line, LINESIZE, data->file);
       ^
contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:373:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
     fgets(line, LINESIZE, data->file);
     ^
contrib/uiuc/plugins/molfile_plugin/src/carplugin.c: In function 'read_car_structure':
contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:266:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
     fgets(line, LINESIZE, data->file);
     ^
contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:268:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
     fgets(line, LINESIZE, data->file);
     ^
contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:272:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
   fgets(line, LINESIZE, data->file);
   ^
contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:295:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
       fgets(line, LINESIZE, data->file);
       ^
contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:305:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
     fgets(line, LINESIZE, data->file);
     ^
contrib/uiuc/plugins/molfile_plugin/src/carplugin.c: In function 'open_car_read':
contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:169:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
   fgets(line, LINESIZE, fd);
   ^
contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:179:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
   fgets(line, LINESIZE, fd);
   ^
contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:182:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
     fgets(line, LINESIZE, fd);
     ^
contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:210:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
   fgets(line, LINESIZE, fd);
   ^
contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:213:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
   fgets(line, LINESIZE, fd);
   ^
contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:224:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
     fgets(line, LINESIZE, fd);
     ^
contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:226:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
     fgets(line, LINESIZE, fd);
     ^
contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:230:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
   fgets(line, LINESIZE, fd);
   ^
contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:234:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
       fgets(line, LINESIZE, fd);
       ^
contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:245:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
     fgets(line, LINESIZE, fd);
     ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/RepSurface.c -o build/temp.linux-armv7l-2.7/layer2/RepSurface.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/hash.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/hash.o -ffast-math -funroll-loops -O3 -fcommon
layer2/RepSurface.c: In function 'RepSurfaceRender':
layer2/RepSurface.c:1960:11: warning: variable 'col' set but not used [-Wunused-but-set-variable]
    float *col;
           ^
layer2/RepSurface.c:2221:28: warning: variable 'col' set but not used [-Wunused-but-set-variable]
                     float *col;
                            ^
layer2/RepSurface.c: In function 'RepSurfaceColor':
layer2/RepSurface.c:3714:22: warning: variable 'planew' set but not used [-Wunused-but-set-variable]
    float d[3], *vn0, planew, v0mod[3];
                      ^
layer2/RepSurface.c:3793:29: warning: variable 'planew' set but not used [-Wunused-but-set-variable]
    float d[3], *vn0, pt[3], planew, v0mod[3];
                             ^
layer2/RepSurface.c:3793:22: warning: variable 'pt' set but not used [-Wunused-but-set-variable]
    float d[3], *vn0, pt[3], planew, v0mod[3];
                      ^
layer2/RepSurface.c:3949:36: warning: variable 'pai2' set but not used [-Wunused-but-set-variable]
         AtomInfoType *pai = NULL, *pai2 = NULL; /* variables for color smoothing */
                                    ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.o -ffast-math -funroll-loops -O3 -fcommon
layer2/RepSurface.c: In function 'SolventDotNew':
layer2/RepSurface.c:5687:7: warning: variable 'maxDot' set but not used [-Wunused-but-set-variable]
   int maxDot = 0;
       ^
In file included from contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:51:0:
contrib/uiuc/plugins/molfile_plugin/src/fastio.h:468:12: warning: 'fio_read_int32' defined but not used [-Wunused-function]
 static int fio_read_int32(fio_fd fd, int *i) {
            ^
contrib/uiuc/plugins/molfile_plugin/src/fastio.h:472:12: warning: 'fio_write_str' defined but not used [-Wunused-function]
 static int fio_write_str(fio_fd fd, const char *str) {
            ^
In file included from contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:60:0:
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: 'swap2_unaligned' defined but not used [-Wunused-function]
 static void swap2_unaligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: 'swap2_aligned' defined but not used [-Wunused-function]
 static void swap2_aligned(void *v, long ndata) {
             ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.o -ffast-math -funroll-loops -O3 -fcommon
In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:40:0:
contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h:44:27: warning: function declaration isn't a prototype [-Wstrict-prototypes]
 static vasp_plugindata_t *vasp_plugindata_malloc()
                           ^
In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:41:0:
contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: 'get_pte_idx_from_string' defined but not used [-Wunused-function]
 static int get_pte_idx_from_string(const char *label) {
            ^
contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c: In function 'read_vaspxdatcar_timestep':
contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:284:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
   fgets(lineptr, LINESIZE, data->file);
   ^
contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c: In function 'read_vaspxdatcar_structure':
contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:229:27: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
   for (i = 0; i < 4; ++i) fgets(lineptr, LINESIZE, data->file);
                           ^
contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:234:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
     fgets(lineptr, LINESIZE, data->file);
     ^
contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:238:32: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
       for (i = 0; i < 2; ++i)  fgets(lineptr, LINESIZE, data->file);
                                ^
contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:253:44: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
   for (i = 0; i < 10 - data->version; ++i) fgets(lineptr, LINESIZE, data->file);
                                            ^
contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c: In function 'open_vaspxdatcar_read':
contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:90:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
   fgets(lineptr, LINESIZE, poscar);
   ^
contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:93:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
   fgets(lineptr, LINESIZE, poscar);
   ^
contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:98:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
     fgets(lineptr, LINESIZE, poscar);
     ^
contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:112:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
   fgets(lineptr, LINESIZE, poscar);
   ^
contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:122:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
       fgets(lineptr, LINESIZE, poscar);
       ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.o -ffast-math -funroll-loops -O3 -fcommon
In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:42:0:
contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h:44:27: warning: function declaration isn't a prototype [-Wstrict-prototypes]
 static vasp_plugindata_t *vasp_plugindata_malloc()
                           ^
contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h:111:13: warning: 'vasp_timestep_unitcell' defined but not used [-Wunused-function]
 static void vasp_timestep_unitcell(molfile_timestep_t *ts, vasp_plugindata_t *data)
             ^
contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c: In function 'read_vaspchgcar_data':
contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:238:60: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
   for (n = 0; n < data->numatoms + data->version + 5; ++n) fgets(lineptr, LINESIZE, data->file);
                                                            ^
contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:283:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
       fgets(lineptr, LINESIZE, data->file);
       ^
contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c: In function 'read_vaspchgcar_metadata':
contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:151:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
   fgets(lineptr, LINESIZE, data->file);
   ^
contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c: In function 'open_vaspchgcar_read':
contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:72:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
   fgets(lineptr, LINESIZE, data->file);
   ^
contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:76:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
   fgets(lineptr, LINESIZE, data->file);
   ^
contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:82:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
     fgets(lineptr, LINESIZE, data->file);
     ^
contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:93:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
   fgets(lineptr, LINESIZE, data->file);
   ^
contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:104:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
       fgets(lineptr, LINESIZE, data->file);
       ^
contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:132:44: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
   for (i = 0; i < data->numatoms + 2; ++i) fgets(lineptr, LINESIZE, data->file);
                                            ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.o -ffast-math -funroll-loops -O3 -fcommon
In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:42:0:
contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h:44:27: warning: function declaration isn't a prototype [-Wstrict-prototypes]
 static vasp_plugindata_t *vasp_plugindata_malloc()
                           ^
contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h:111:13: warning: 'vasp_timestep_unitcell' defined but not used [-Wunused-function]
 static void vasp_timestep_unitcell(molfile_timestep_t *ts, vasp_plugindata_t *data)
             ^
contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c: In function 'read_vaspparchg_data':
contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:239:60: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
   for (n = 0; n < data->numatoms + data->version + 5; ++n) fgets(lineptr, LINESIZE, data->file);
                                                            ^
contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c: In function 'read_vaspparchg_metadata':
contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:151:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
   fgets(lineptr, LINESIZE, data->file);
   ^
contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c: In function 'open_vaspparchg_read':
contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:72:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
   fgets(lineptr, LINESIZE, data->file);
   ^
contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:76:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
   fgets(lineptr, LINESIZE, data->file);
   ^
contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:82:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
     fgets(lineptr, LINESIZE, data->file);
     ^
contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:93:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
   fgets(lineptr, LINESIZE, data->file);
   ^
contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:104:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
       fgets(lineptr, LINESIZE, data->file);
       ^
contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:132:44: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
   for (i = 0; i < data->numatoms + 2; ++i) fgets(lineptr, LINESIZE, data->file);
                                            ^
layer2/RepSurface.c: In function 'SurfaceJobRun':
layer2/RepSurface.c:4648:11: warning: 'solv_map' may be used uninitialized in this function [-Wmaybe-uninitialized]
           MapFree(solv_map);
           ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.o -ffast-math -funroll-loops -O3 -fcommon
In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:40:0:
contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h:44:27: warning: function declaration isn't a prototype [-Wstrict-prototypes]
 static vasp_plugindata_t *vasp_plugindata_malloc()
                           ^
In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:41:0:
contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: 'get_pte_idx_from_string' defined but not used [-Wunused-function]
 static int get_pte_idx_from_string(const char *label) {
            ^
contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c: In function 'read_vaspoutcar_timestep':
contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:240:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
       fgets(lineptr, LINESIZE, data->file);
       ^
contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:243:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
  fgets(lineptr, LINESIZE, data->file);
  ^
contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c: In function 'read_vaspoutcar_structure':
contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:205:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
         fgets(lineptr, LINESIZE, data->file);
         ^
contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c: In function 'open_vaspoutcar_read':
contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:88:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
   fgets(lineptr, LINESIZE, data->file);
   ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.o -ffast-math -funroll-loops -O3 -fcommon
contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c: In function 'read_dlpoly_timestep':
contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c:420:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
   fgets(fbuffer, 1024, data->file);
   ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/corplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/corplugin.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.o -ffast-math -funroll-loops -O3 -fcommon
In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:40:0:
contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h:44:27: warning: function declaration isn't a prototype [-Wstrict-prototypes]
 static vasp_plugindata_t *vasp_plugindata_malloc()
                           ^
In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:41:0:
contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: 'get_pte_idx_from_string' defined but not used [-Wunused-function]
 static int get_pte_idx_from_string(const char *label) {
            ^
contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c: In function 'read_vaspposcar_timestep':
contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:232:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
   fgets(lineptr, LINESIZE, data->file);
   ^
contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:237:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
     fgets(lineptr, LINESIZE, data->file);
     ^
contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:246:43: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
   for (i = 0; i < data->version - 2; ++i) fgets(lineptr, LINESIZE, data->file);
                                           ^
contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:249:35: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
   if (tolower(lineptr[0]) == 's') fgets(lineptr, LINESIZE, data->file);
                                   ^
contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:256:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
     fgets(lineptr, LINESIZE, data->file);
     ^
contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c: In function 'read_vaspposcar_structure':
contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:195:42: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
  for (i = 0; i < data->version + 3; ++i) fgets(lineptr, LINESIZE, data->file);
                                          ^
contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:198:34: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
  if (tolower(lineptr[0]) == 's') fgets(lineptr, LINESIZE, data->file);
                                  ^
contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:203:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
    fgets(lineptr, LINESIZE, data->file);
    ^
contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c: In function 'open_vaspposcar_read':
contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:70:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
   fgets(lineptr, LINESIZE, data->file);
   ^
contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:74:27: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
   for (i = 0; i < 5; ++i) fgets(lineptr, LINESIZE, data->file);
                           ^
contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:87:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
       fgets(lineptr, LINESIZE, data->file);
       ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/binposplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/binposplugin.o -ffast-math -funroll-loops -O3 -fcommon
contrib/uiuc/plugins/molfile_plugin/src/binposplugin.c: In function 'open_binpos_read':
contrib/uiuc/plugins/molfile_plugin/src/binposplugin.c:64:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
   fread(magicchar,sizeof(char),4,fd);
   ^
contrib/uiuc/plugins/molfile_plugin/src/binposplugin.c:72:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
   fread(&igarb,sizeof(int),1,fd);
   ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.o -ffast-math -funroll-loops -O3 -fcommon
layer2/RepSurface.c: In function 'RepSurfaceRender':
layer2/RepSurface.c:3324:6: warning: 'simple' may be used uninitialized in this function [-Wmaybe-uninitialized]
      CGOFree(simple);
      ^
In file included from contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:43:0:
contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:706:12: warning: 'symmetry_expand' defined but not used [-Wunused-function]
 static int symmetry_expand(qm_atom_t **atoms, int numunique, int natoms, 
            ^
contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:830:13: warning: 'eatline' defined but not used [-Wunused-function]
 static void eatline(FILE * fd, int n)
             ^
contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:841:13: warning: 'eatwhitelines' defined but not used [-Wunused-function]
 static void eatwhitelines(FILE *file) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:890:12: warning: 'iswhiteline' defined but not used [-Wunused-function]
 static int iswhiteline(char *s) {
            ^
contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:896:14: warning: 'strtoupper' defined but not used [-Wunused-function]
 static char *strtoupper(char *s) {
              ^
contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:957:12: warning: 'goto_keyline' defined but not used [-Wunused-function]
 static int goto_keyline(FILE *file, ...) {
            ^
contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1001:12: warning: 'have_keyline' defined but not used [-Wunused-function]
 static int have_keyline(FILE *file, const char *keystring1,
            ^
contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1072:13: warning: 'thisline' defined but not used [-Wunused-function]
 static void thisline(FILE *file) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1092:13: warning: 'whereami' defined but not used [-Wunused-function]
 static void whereami(FILE *file) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:433:18: warning: 'init_qmdata' defined but not used [-Wunused-function]
 static qmdata_t* init_qmdata(qmdata_t *data) {
                  ^
contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:466:27: warning: 'add_wavefunction' defined but not used [-Wunused-function]
 static qm_wavefunction_t* add_wavefunction(qm_timestep_t *ts) {
                           ^
contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:485:13: warning: 'replace_wavefunction' defined but not used [-Wunused-function]
 static void replace_wavefunction(qm_timestep_t *ts, int n) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:502:13: warning: 'del_wavefunction' defined but not used [-Wunused-function]
 static void del_wavefunction(qm_timestep_t *ts) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:535:13: warning: 'angular_momentum_expon' defined but not used [-Wunused-function]
 static void angular_momentum_expon(int  *ang_mom_expon,
             ^
contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:580:13: warning: 'print_matrix4' defined but not used [-Wunused-function]
 static void print_matrix4(const float mat[16]) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1023:12: warning: 'fpexpftoc' defined but not used [-Wunused-function]
 static int fpexpftoc(char *ftocstr) {
            ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.o -ffast-math -funroll-loops -O3 -fcommon
In file included from contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:33:0:
contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:133:12: warning: 'get_pte_idx' defined but not used [-Wunused-function]
 static int get_pte_idx(const char *label)
            ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.o -ffast-math -funroll-loops -O3 -fcommon
In file included from contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.c:57:0:
contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: 'get_pte_idx_from_string' defined but not used [-Wunused-function]
 static int get_pte_idx_from_string(const char *label) {
            ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer4/PopUp.c -o build/temp.linux-armv7l-2.7/layer4/PopUp.o -ffast-math -funroll-loops -O3 -fcommon
contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c: In function 'open_namdbin_read':
contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c:70:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
   fread(&filen, sizeof(namdbin_int32), 1, fd);
   ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/jsplugin.o -ffast-math -funroll-loops -O3 -fcommon
contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c: In function 'read_js_structure':
contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c:403:16: warning: unused variable 'bszmask' [-Wunused-variable]
     fio_size_t bszmask;
                ^
In file included from contrib/uiuc/plugins/molfile_plugin/src/hash.h:37:0,
                 from contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c:87:
contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c: At top level:
contrib/uiuc/plugins/molfile_plugin/src/hash.c:183:21: warning: 'hash_delete' defined but not used [-Wunused-function]
 VMDEXTERNSTATIC int hash_delete(hash_t *tptr, const char *key) {
                     ^
contrib/uiuc/plugins/molfile_plugin/src/hash.c:270:24: warning: 'hash_stats' defined but not used [-Wunused-function]
 VMDEXTERNSTATIC char * hash_stats(hash_t *tptr) {
                        ^
In file included from contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c:88:0:
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: 'swap2_unaligned' defined but not used [-Wunused-function]
 static void swap2_unaligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: 'swap4_unaligned' defined but not used [-Wunused-function]
 static void swap4_unaligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: 'swap8_unaligned' defined but not used [-Wunused-function]
 static void swap8_unaligned(void *v, long ndata) {
             ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer5/PyMOL.c -o build/temp.linux-armv7l-2.7/layer5/PyMOL.o -ffast-math -funroll-loops -O3 -fcommon
layer5/PyMOL.c: In function 'PyMOL_CmdGetNames':
layer5/PyMOL.c:4588:15: warning: variable 'arg' set but not used [-Wunused-but-set-variable]
   char *res, *arg;
               ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.o -ffast-math -funroll-loops -O3 -fcommon
In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c:47:0:
contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h:44:27: warning: function declaration isn't a prototype [-Wstrict-prototypes]
 static vasp_plugindata_t *vasp_plugindata_malloc()
                           ^
In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c:48:0:
contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: 'get_pte_idx_from_string' defined but not used [-Wunused-function]
 static int get_pte_idx_from_string(const char *label) {
            ^
contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c: In function 'read_vaspxml_structure':
contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c:140:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
       fgets(lineptr, LINESIZE, data->file);
       ^
contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c:145:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
         fgets(lineptr, LINESIZE, data->file);
         ^
contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c: In function 'open_vaspxml_read':
contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c:87:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
        fgets(lineptr, LINESIZE, data->file);
        ^
contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c:93:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
        fgets(lineptr, LINESIZE, data->file);
        ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/crdplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/crdplugin.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/ObjectAlignment.c -o build/temp.linux-armv7l-2.7/layer2/ObjectAlignment.o -ffast-math -funroll-loops -O3 -fcommon
contrib/uiuc/plugins/molfile_plugin/src/crdplugin.c: In function 'write_crd_timestep':
contrib/uiuc/plugins/molfile_plugin/src/crdplugin.c:167:6: warning: 'lfdone' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if (!lfdone)
      ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/mapplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/mapplugin.o -ffast-math -funroll-loops -O3 -fcommon
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.o -ffast-math -funroll-loops -O3 -fcommon
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp: In function 'int read_xbgf_timestep(void*, int, molfile_timestep_t*)':
contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:288:37: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
     fgets(line, LINESIZE, bgf->file);
                                     ^
contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:297:37: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
     fgets(line, LINESIZE, bgf->file);
                                     ^
contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp: In function 'int read_xbgf_bonds_aux(void*, int*, int**, int**, float**)':
contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:365:37: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
     fgets(line, LINESIZE, bgf->file);
                                     ^
contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:387:35: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   fgets(line, LINESIZE, bgf->file);
                                   ^
contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:395:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
     fgets(nextline, LINESIZE, bgf->file);
                                         ^
contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:455:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
         fgets(line, LINESIZE, bgf->file);
                                         ^
contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp: In function 'int read_xbgf_structure(void*, int*, molfile_atom_t*)':
contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:241:37: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
     fgets(line, LINESIZE, bgf->file);
                                     ^
contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:250:37: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
     fgets(line, LINESIZE, bgf->file);
                                     ^
contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp: In function 'void* open_xbgf_read(const char*, const char*, int*)':
contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:72:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
     fgets(line, LINESIZE, fd);
                              ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.o -ffast-math -funroll-loops -O3 -fcommon
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp: In function 'int read_mol2_timestep(void*, int, molfile_timestep_t*)':
contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:275:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
     fgets(line, LINESIZE, mol2->file);
                                      ^
contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:289:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
     fgets(line, LINESIZE, mol2->file);
                                      ^
contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp: In function 'int read_mol2_bonds_aux(void*, int*, int**, int**, float**)':
contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:199:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
     fgets(line, LINESIZE, mol2->file);
                                      ^
contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:209:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
     fgets(line, LINESIZE, mol2->file);
                                      ^
contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp: In function 'int read_mol2(void*, int*, molfile_atom_t*)':
contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:127:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
     fgets(line, LINESIZE, mol2->file);
                                      ^
contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:138:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
     fgets(line, LINESIZE, mol2->file);
                                      ^
contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp: In function 'void* open_mol2_read(const char*, const char*, int*)':
contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:74:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
     fgets(line, LINESIZE, fd);
                              ^
contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:81:28: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   fgets(line, LINESIZE, fd);  // Read and ignore the mol_name
                            ^
contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:82:28: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   fgets(line, LINESIZE, fd);  // Read the molecule info
                            ^
contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:91:28: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   fgets(line, LINESIZE, fd);  // Read and ignore the mol_type
                            ^
contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:92:28: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   fgets(line, LINESIZE, fd);  // Read the charge_type
                            ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/gridplugin.o -ffast-math -funroll-loops -O3 -fcommon
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp: In function 'void* open_grid_read(const char*, const char*, int*)':
contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp:84:40: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   fread(&dataBegin, sizeof(int), 1, fd);
                                        ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.o -ffast-math -funroll-loops -O3 -fcommon
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp: In function 'void eatline(FILE*)':
contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:234:27: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   fgets(readbuf, 1024, fd);    // go on to next line
                           ^
contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp: In function 'void* open_xsf_read(const char*, const char*, int*)':
contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:405:37: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
         fgets(readbuf, 256, xsf->fd);
                                     ^
contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:439:43: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
               fgets(readbuf, 256, xsf->fd);
                                           ^
contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:441:43: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
               fgets(readbuf, 256, xsf->fd);
                                           ^
contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:443:43: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
               fgets(readbuf, 256, xsf->fd);
                                           ^
contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:445:43: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
               fgets(readbuf, 256, xsf->fd);
                                           ^
contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:447:43: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
               fgets(readbuf, 256, xsf->fd);
                                           ^
contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:467:45: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
                 fgets(readbuf, 256, xsf->fd);
                                             ^
contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:504:39: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
           fgets(readbuf, 256, xsf->fd);
                                       ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/ObjectMesh.c -o build/temp.linux-armv7l-2.7/layer2/ObjectMesh.o -ffast-math -funroll-loops -O3 -fcommon
In file included from contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp:59:0:
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope:
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: 'void swap2_unaligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap2_unaligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: 'void swap4_unaligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap4_unaligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: 'void swap8_unaligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap8_unaligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: 'void swap2_aligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap2_aligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: 'void swap8_aligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap8_aligned(void *v, long ndata) {
             ^
In file included from contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp:60:0:
contrib/uiuc/plugins/molfile_plugin/src/fortread.h:36:12: warning: 'int fort_eat_recmark(FILE*, int)' defined but not used [-Wunused-function]
 static int fort_eat_recmark(FILE *ifp, int recmarklen) {
            ^
contrib/uiuc/plugins/molfile_plugin/src/fortread.h:55:12: warning: 'int fort_get_endian_reclen(int, int, int, int*, int*)' defined but not used [-Wunused-function]
 static int fort_get_endian_reclen(int reclen, int word0, int word1, 
            ^
contrib/uiuc/plugins/molfile_plugin/src/fortread.h:133:13: warning: 'void strnwscpy(char*, const char*, int)' defined but not used [-Wunused-function]
 static void strnwscpy(char *target, const char *source, const int len) {
             ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.o -ffast-math -funroll-loops -O3 -fcommon
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp: In function 'int read_ccp4_data(void*, int, float*, float*)':
contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp:370:57: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if ( fread(rowdata, sizeof(float), extent[0], fd) != extent[0] ) {
                                                         ^
contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp: In function 'void* open_ccp4_read(const char*, const char*, int*)':
contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp:183:29: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
       fgets(symData, 81, fd);
                             ^
layer2/ObjectMesh.c: In function 'ObjectMeshNewFromPyList':
layer2/ObjectMesh.c:231:7: warning: variable 'll' set but not used [-Wunused-but-set-variable]
   int ll;
       ^
layer2/ObjectMesh.c: In function 'ObjectMeshUpdate':
layer2/ObjectMesh.c:604:7: warning: variable 'ok' set but not used [-Wunused-but-set-variable]
   int ok = true;
       ^
In file included from contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp:44:0:
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope:
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: 'void swap2_unaligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap2_unaligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: 'void swap4_unaligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap4_unaligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: 'void swap8_unaligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap8_unaligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: 'void swap2_aligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap2_aligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: 'void swap8_aligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap8_aligned(void *v, long ndata) {
             ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/dxplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/dxplugin.o -ffast-math -funroll-loops -O3 -fcommon
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
In file included from contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:37:0:
contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h: At global scope:
contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: 'int get_pte_idx_from_string(const char*)' defined but not used [-Wunused-function]
 static int get_pte_idx_from_string(const char *label) {
            ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/grdplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/grdplugin.o -ffast-math -funroll-loops -O3 -fcommon
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.o -ffast-math -funroll-loops -O3 -fcommon
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
In file included from contrib/uiuc/plugins/molfile_plugin/src/grdplugin.cpp:51:0:
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: 'void swap2_unaligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap2_unaligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: 'void swap4_unaligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap4_unaligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: 'void swap8_unaligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap8_unaligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: 'void swap2_aligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap2_aligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: 'void swap8_aligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap8_aligned(void *v, long ndata) {
             ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/pltplugin.o -ffast-math -funroll-loops -O3 -fcommon
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp: In function 'void line3(FILE*, GRASSP*)':
contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:186:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   fread(line3, 1, 80, infile);
                              ^
contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp: In function 'int read_rawgraphics(void*, int*, const molfile_graphics_t**)':
contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:284:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   TRASH; 
        ^
contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:285:29: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   fread(line, 1, 80, infile); 
                             ^
contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:291:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   TRASH;
        ^
contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:305:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   TRASH; 
        ^
contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:306:29: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   fread(line, 1, 80, infile); 
                             ^
contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:307:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   TRASH;
        ^
contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:311:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   TRASH; 
        ^
contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:313:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   TRASH;
        ^
contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:318:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   TRASH; 
        ^
contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:319:29: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   fread(line, 1, 80, infile); 
                             ^
contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:320:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   TRASH;
        ^
contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:328:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   TRASH; 
        ^
contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:329:29: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   fread(line, 1, 80, infile); 
                             ^
contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:330:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   TRASH;
        ^
contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:354:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   TRASH; 
        ^
contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:355:50: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   fread(vertex, 3 * sizeof(float), nvert, infile); 
                                                  ^
contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:356:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   TRASH;
        ^
contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:357:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   TRASH; 
        ^
contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:358:50: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   fread(access, 3 * sizeof(float), nvert, infile); 
                                                  ^
contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:359:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   TRASH;
        ^
contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:360:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   TRASH; 
        ^
contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:361:50: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   fread(normal, 3 * sizeof(float), nvert, infile); 
                                                  ^
contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:362:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   TRASH;
        ^
contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:371:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
     TRASH; 
          ^
contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:372:57: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
     fread(triangle, 3 * sizeof(int), ntriangles, infile); 
                                                         ^
contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:373:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
     TRASH;
          ^
contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:374:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
     TRASH;
          ^
contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:375:56: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
     fread(properties, 3 * sizeof(float), nvert, infile);
                                                        ^
contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:394:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
     TRASH;
          ^
contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:395:60: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
     fread(striangle, sizeof(short), 3 * ntriangles, infile);
                                                            ^
contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:396:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
     TRASH;
          ^
contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:397:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
     TRASH;
          ^
contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:398:56: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
     fread(properties, sizeof(float), 3 * nvert, infile);
                                                        ^
contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp: In function 'int read_plt_data(void*, int, float*, float*)':
contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp:143:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if ( fread(datablock, sizeof(float), ndata, fd) != ndata ) {
                                                   ^
contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp: In function 'void* open_plt_read(const char*, const char*, int*)':
contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp:69:39: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   fread(intHeader, sizeof(int), 5, fd);
                                       ^
contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp:82:43: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   fread(floatHeader, sizeof(float), 6, fd);
                                           ^
In file included from contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp:42:0:
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope:
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: 'void swap2_unaligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap2_unaligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: 'void swap4_unaligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap4_unaligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: 'void swap8_unaligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap8_unaligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: 'void swap2_aligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap2_aligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: 'void swap8_aligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap8_aligned(void *v, long ndata) {
             ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/msmsplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/msmsplugin.o -ffast-math -funroll-loops -O3 -fcommon
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.o -ffast-math -funroll-loops -O3 -fcommon
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
In file included from contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:40:0:
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope:
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: 'void swap2_unaligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap2_unaligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: 'void swap4_unaligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap4_unaligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: 'void swap8_unaligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap8_unaligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: 'void swap8_aligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap8_aligned(void *v, long ndata) {
             ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.o -ffast-math -funroll-loops -O3 -fcommon
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
In file included from contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.cpp:30:0:
contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h: In function 'int mdio_readline(md_file*, char*, int, int)':
contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h:426:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
  fgets(buf, n, mf->f);
                      ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/RepCylBond.c -o build/temp.linux-armv7l-2.7/layer2/RepCylBond.o -ffast-math -funroll-loops -O3 -fcommon
layer2/RepCylBond.c: In function 'RepCylBondPopulateAdjacentAtoms':
layer2/RepCylBond.c:1383:25: warning: variable 'h_scale' set but not used [-Wunused-but-set-variable]
   float radius, transp, h_scale;
                         ^
layer2/RepCylBond.c:1383:17: warning: variable 'transp' set but not used [-Wunused-but-set-variable]
   float radius, transp, h_scale;
                 ^
layer2/RepCylBond.c:1383:9: warning: variable 'radius' set but not used [-Wunused-but-set-variable]
   float radius, transp, h_scale;
         ^
layer2/RepCylBond.c:1380:10: warning: variable 'ord' set but not used [-Wunused-but-set-variable]
   int a, ord, a1, a2, stick_color, c1, c2, s1, s2, half_bonds, hide_long = false;
          ^
layer2/RepCylBond.c: In function 'RepCylBondNew':
layer2/RepCylBond.c:1543:16: warning: variable 'v_size' set but not used [-Wunused-but-set-variable]
   unsigned int v_size, vr_size;
                ^
layer2/RepCylBond.c:1536:7: warning: variable 'stick_round_nub' set but not used [-Wunused-but-set-variable]
   int stick_round_nub;
       ^
layer2/RepCylBond.c: At top level:
layer2/RepCylBond.c:2363:13: warning: 'subdivide' defined but not used [-Wunused-function]
 static void subdivide(int n, float *x, float *y)
             ^
contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In member function 'bool desres::molfile::Timekeys::init(const string&)':
contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:486:71: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t {aka unsigned int}' [-Wformat=]
             fprintf(stderr, "non-constant framesize at frame %ld\n", i);
                                                                       ^
contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:488:48: warning: format '%d' expects argument of type 'int', but argument 2 has type 'uint64_t {aka long long unsigned int}' [-Wformat=]
                     keys[i].size(), m_framesize);
                                                ^
contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:488:48: warning: format '%d' expects argument of type 'int', but argument 3 has type 'uint64_t {aka long long unsigned int}' [-Wformat=]
contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:494:67: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t {aka unsigned int}' [-Wformat=]
                     "non-constant time interval at frame %ld\n", i);
                                                                   ^
contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:499:67: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t {aka unsigned int}' [-Wformat=]
             fprintf(stderr, "unexpected offset for frame %ld\n", i);
                                                                   ^
contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function 'int handle_wrapped_v2({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)':
contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1302:28: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'uint64_t {aka long long unsigned int}' [-Wformat=]
         3*natoms, pos.count);
                            ^
contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1311:30: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'uint64_t {aka long long unsigned int}' [-Wformat=]
           3*natoms, vel.count);
                              ^
contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function 'int handle_wrapped_v1({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)':
contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1573:34: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'uint64_t {aka long long unsigned int}' [-Wformat=]
           velblob.count, 3*natoms);
                                  ^
contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h: In function 'int xtc_3dfcoord(md_file*, float*, int*, float*)':
contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h:1764:37: warning: 'bitsizeint[2]' may be used uninitialized in this function [-Wmaybe-uninitialized]
  unsigned sizeint[3], sizesmall[3], bitsizeint[3], size3;
                                     ^
contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h:1764:37: warning: 'bitsizeint[1]' may be used uninitialized in this function [-Wmaybe-uninitialized]
contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h:1764:37: warning: 'bitsizeint[0]' may be used uninitialized in this function [-Wmaybe-uninitialized]
contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h:1831:32: warning: 'smallidx' may be used uninitialized in this function [-Wmaybe-uninitialized]
  small = xtc_magicints[smallidx] / 2;
                                ^
contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h:1816:36: warning: '*((void*)& maxint +4)' may be used uninitialized in this function [-Wmaybe-uninitialized]
  sizeint[1] = maxint[1] - minint[1]+1;
                                    ^
contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h:1815:36: warning: 'maxint' may be used uninitialized in this function [-Wmaybe-uninitialized]
  sizeint[0] = maxint[0] - minint[0]+1;
                                    ^
contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h:1861:28: warning: '*((void*)& minint +8)' may be used uninitialized in this function [-Wmaybe-uninitialized]
   thiscoord[2] += minint[2];
                            ^
contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h:1860:28: warning: '*((void*)& minint +4)' may be used uninitialized in this function [-Wmaybe-uninitialized]
   thiscoord[1] += minint[1];
                            ^
contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h:1859:28: warning: 'minint' may be used uninitialized in this function [-Wmaybe-uninitialized]
   thiscoord[0] += minint[0];
                            ^
contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h:1817:36: warning: '*((void*)& maxint +8)' may be used uninitialized in this function [-Wmaybe-uninitialized]
  sizeint[2] = maxint[2] - minint[2]+1;
                                    ^
In file included from contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h:48:0,
                 from contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.cpp:30:
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope:
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: 'void swap2_unaligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap2_unaligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: 'void swap4_unaligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap4_unaligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: 'void swap8_unaligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap8_unaligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: 'void swap2_aligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap2_aligned(void *v, long ndata) {
             ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.o -ffast-math -funroll-loops -O3 -fcommon
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp: In function 'int read_spider_data(void*, int, float*, float*)':
contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp:277:7: warning: unused variable 'x' [-Wunused-variable]
   int x, y, z, xsize, ysize, zsize, xysize, total;
       ^
contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp:277:10: warning: unused variable 'y' [-Wunused-variable]
   int x, y, z, xsize, ysize, zsize, xysize, total;
          ^
contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp:277:13: warning: unused variable 'z' [-Wunused-variable]
   int x, y, z, xsize, ysize, zsize, xysize, total;
             ^
contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp:286:49: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   fread(datablock, total * sizeof(float), 1, fd);
                                                 ^
In file included from contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp:36:0:
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope:
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: 'void swap2_unaligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap2_unaligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: 'void swap4_unaligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap4_unaligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: 'void swap8_unaligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap8_unaligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: 'void swap2_aligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap2_aligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: 'void swap8_aligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap8_aligned(void *v, long ndata) {
             ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.o -ffast-math -funroll-loops -O3 -fcommon
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp: In function 'int read_bgf_timestep(void*, int, molfile_timestep_t*)':
contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:243:37: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
     fgets(line, LINESIZE, bgf->file);
                                     ^
contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:252:37: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
     fgets(line, LINESIZE, bgf->file);
                                     ^
contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp: In function 'int read_bgf_bonds_aux(void*, int*, int**, int**, float**)':
contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:328:37: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
     fgets(line, LINESIZE, bgf->file);
                                     ^
contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:346:35: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   fgets(line, LINESIZE, bgf->file);
                                   ^
contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:355:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
     fgets(nextline, LINESIZE, bgf->file);
                                         ^
contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:419:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
         fgets(line, LINESIZE, bgf->file);
                                         ^
contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp: In function 'int read_bgf_structure(void*, int*, molfile_atom_t*)':
contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:194:37: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
     fgets(line, LINESIZE, bgf->file);
                                     ^
contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:203:37: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
     fgets(line, LINESIZE, bgf->file);
                                     ^
contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp: In function 'void* open_bgf_read(const char*, const char*, int*)':
contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:59:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
     fgets(line, LINESIZE, fd);
                              ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.o -ffast-math -funroll-loops -O3 -fcommon
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/stlplugin.o -ffast-math -funroll-loops -O3 -fcommon
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp: In function 'void* open_fs4_read(const char*, const char*, int*)':
contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp:79:40: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   fread(&dataBegin, sizeof(int), 1, fd);
                                        ^
contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp: In function 'int read_rawgraphics(void*, int*, const molfile_graphics_t**)':
contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:96:28: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
     fgets(line, 80, infile);
                            ^
contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:104:28: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
     fgets(line, 80, infile);
                            ^
contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:119:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
       fgets(line, 80, infile);
                              ^
contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:131:32: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
         fgets(line, 80, infile);
                                ^
contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:153:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
       fgets(line, 80, infile);
                              ^
contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:162:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
       fgets(line, 80, infile);
                              ^
contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:171:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
       fgets(line, 80, infile);
                              ^
In file included from contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp:47:0:
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope:
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: 'void swap2_unaligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap2_unaligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: 'void swap4_unaligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap4_unaligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: 'void swap8_unaligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap8_unaligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: 'void swap2_aligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap2_aligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: 'void swap8_aligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap8_aligned(void *v, long ndata) {
             ^
In file included from contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp:48:0:
contrib/uiuc/plugins/molfile_plugin/src/fortread.h:36:12: warning: 'int fort_eat_recmark(FILE*, int)' defined but not used [-Wunused-function]
 static int fort_eat_recmark(FILE *ifp, int recmarklen) {
            ^
contrib/uiuc/plugins/molfile_plugin/src/fortread.h:55:12: warning: 'int fort_get_endian_reclen(int, int, int, int*, int*)' defined but not used [-Wunused-function]
 static int fort_get_endian_reclen(int reclen, int word0, int word1, 
            ^
contrib/uiuc/plugins/molfile_plugin/src/fortread.h:133:13: warning: 'void strnwscpy(char*, const char*, int)' defined but not used [-Wunused-function]
 static void strnwscpy(char *target, const char *source, const int len) {
             ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.o -ffast-math -funroll-loops -O3 -fcommon
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp: In function 'int read_parm7_structure(void*, int*, molfile_atom_t*)':
contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp:76:30: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
     fscanf(file, "%s\n", buf);    // format
                              ^
In file included from contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp:25:0:
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h: In function 'int parse_parm7_atoms(const char*, int, molfile_atom_t*, FILE*)':
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:202:27: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
       fgets(buf, 85, file);
                           ^
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h: In function 'int parse_parm7_atype(const char*, int, molfile_atom_t*, FILE*)':
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:254:27: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
       fgets(buf, 85, file);
                           ^
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h: In function 'int parse_parm7_resnames(const char*, int, char*, FILE*)':
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:272:27: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
       fgets(buf, 85, file);
                           ^
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h: In function 'int parse_parm7_respointers(const char*, int, molfile_atom_t*, int, const char*, FILE*)':
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:286:28: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
   fscanf(file, " %d", &cur);
                            ^
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h: In function 'parmstruct* read_parm7_header(FILE*)':
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:365:25: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   fgets(sdum, 512, file);
                         ^
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:379:46: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   fgets(prm->title, sizeof(prm->title), file);
                                              ^
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:407:36: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
     fgets(sdum, sizeof(sdum), file);
                                    ^
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:422:36: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
          &prm->Jparm,  &prm->Nparm);
                                    ^
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:426:34: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
          &prm->Natyp, &prm->Nphb);
                                  ^
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:429:49: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
          &prm->IfBox, &prm->Nmxrs,  &prm->IfCap);
                                                 ^
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:431:36: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
   fscanf(file,"%8d",&prm->Numextra); //BB
                                    ^
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h: In function 'int read_parm7_flag(FILE*, const char*, const char*)':
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:78:28: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
   fscanf(file, "%s\n", buf);
                            ^
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:86:28: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
   fscanf(file, "%s\n", buf);
                            ^
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:96:28: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
   fscanf(file, "%s\n", buf);
                            ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/raster3dplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/raster3dplugin.o -ffast-math -funroll-loops -O3 -fcommon
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer5/main.c -o build/temp.linux-armv7l-2.7/layer5/main.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/biomoccaplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/biomoccaplugin.o -ffast-math -funroll-loops -O3 -fcommon
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.o -ffast-math -funroll-loops -O3 -fcommon
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.cpp: In function 'int read_pbeq_data(void*, int, float*, float*)':
contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.cpp:262:55: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long int' [-Wformat=]
           printf("pbeqplugin) offset: %d\n", ftell(fd));
                                                       ^
In file included from contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.cpp:53:0:
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope:
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: 'void swap2_unaligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap2_unaligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: 'void swap4_unaligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap4_unaligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: 'void swap8_unaligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap8_unaligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: 'void swap2_aligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap2_aligned(void *v, long ndata) {
             ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer5/TestPyMOL.c -o build/temp.linux-armv7l-2.7/layer5/TestPyMOL.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.o -ffast-math -funroll-loops -O3 -fcommon
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp: In function 'void* open_cube_read(const char*, const char*, int*)':
contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:181:32: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   fgets(readbuf, 256, cube->fd);    // go on to next line
                                ^
contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:351:41: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
     fscanf(cube->fd, "%d", &cube->nsets);
                                         ^
contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:356:35: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
       fscanf(cube->fd, "%d", &orb);
                                   ^
contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp: In function 'void eatline(FILE*)':
contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:141:27: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   fgets(readbuf, 1024, fd);    // go on to next line
                           ^
layer5/TestPyMOL.c: In function 'get_st':
layer5/TestPyMOL.c:76:25: warning: variable 'p' set but not used [-Wunused-but-set-variable]
   char *result = NULL, *p;
                         ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c modules/cealign/src/ccealignmodule.cpp -o build/temp.linux-armv7l-2.7/modules/cealign/src/ccealignmodule.o -ffast-math -funroll-loops -O3 -fcommon
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
In file included from contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:42:0:
contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h: At global scope:
contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:133:12: warning: 'int get_pte_idx(const char*)' defined but not used [-Wunused-function]
 static int get_pte_idx(const char *label)
            ^
contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: 'int get_pte_idx_from_string(const char*)' defined but not used [-Wunused-function]
 static int get_pte_idx_from_string(const char *label) {
            ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/edmplugin.o -ffast-math -funroll-loops -O3 -fcommon
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp: In function 'int read_edm_data(void*, int, float*, float*)':
contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp:207:10: warning: unused variable 'l' [-Wunused-variable]
   int z, l, sentinel, convcnt;
          ^
contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp:220:7: warning: unused variable 'leftover' [-Wunused-variable]
   int leftover = (nperslice - (nlines - 1) * 6);
       ^
contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp:270:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   fgets(readbuf, 13, edm->fd);
                              ^
contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp: In function 'void eatline(FILE*)':
contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp:44:27: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   fgets(readbuf, 1024, fd);    // go on to next line
                           ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/situsplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/situsplugin.o -ffast-math -funroll-loops -O3 -fcommon
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/mmcif.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/mmcif.o -ffast-math -funroll-loops -O3 -fcommon
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
contrib/uiuc/plugins/molfile_plugin/src/mmcif.cpp: In function 'int read_mmcif_timestep(void*, int, molfile_timestep_t*)':
contrib/uiuc/plugins/molfile_plugin/src/mmcif.cpp:85:14: warning: unused variable 'data' [-Wunused-variable]
   mmcifdata *data = (mmcifdata *)mydata;
              ^
In file included from contrib/uiuc/plugins/molfile_plugin/src/mmcif.cpp:64:0:
contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h: At global scope:
contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:95:20: warning: 'const char* get_pte_label(int)' defined but not used [-Wunused-function]
 static const char *get_pte_label(const int idx)
                    ^
contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:102:14: warning: 'float get_pte_mass(int)' defined but not used [-Wunused-function]
 static float get_pte_mass(const int idx)
              ^
contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:109:14: warning: 'float get_pte_vdw_radius(int)' defined but not used [-Wunused-function]
 static float get_pte_vdw_radius(const int idx)
              ^
contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:133:12: warning: 'int get_pte_idx(const char*)' defined but not used [-Wunused-function]
 static int get_pte_idx(const char *label)
            ^
contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: 'int get_pte_idx_from_string(const char*)' defined but not used [-Wunused-function]
 static int get_pte_idx_from_string(const char *label) {
            ^
contrib/uiuc/plugins/molfile_plugin/src/mmcif.cpp:98:14: warning: 'void* open_mmcif_write(const char*, const char*, int)' defined but not used [-Wunused-function]
 static void *open_mmcif_write(const char *filename, const char *filetype, 
              ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.o -ffast-math -funroll-loops -O3 -fcommon
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp: In function 'int read_dsn6_data(void*, int, float*, float*)':
contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp:233:44: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
         fread(brick, sizeof(char), 512, fd);
                                            ^
contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp: In function 'void* open_dsn6_read(const char*, const char*, int*)':
contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp:91:43: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   fread(fileHeader, sizeof(short), 19, fd);
                                           ^
In file included from contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp:63:0:
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope:
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: 'void swap4_unaligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap4_unaligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: 'void swap8_unaligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap8_unaligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:110:13: warning: 'void swap4_aligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap4_aligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: 'void swap8_aligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap8_aligned(void *v, long ndata) {
             ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.o -ffast-math -funroll-loops -O3 -fcommon
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp: In function 'int {anonymous}::write_structure(void*, int, const molfile_atom_t*)':
contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp:1883:9: warning: unused variable 'last_ctnumber' [-Wunused-variable]
     int last_ctnumber = -1;
         ^
In file included from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:70:0:
contrib/uiuc/plugins/molfile_plugin/src/vmddir.h: At global scope:
contrib/uiuc/plugins/molfile_plugin/src/vmddir.h:137:12: warning: 'int vmd_file_is_executable(const char*)' defined but not used [-Wunused-function]
 static int vmd_file_is_executable(const char * filename) {
            ^
In file included from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:71:0:
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: 'void swap2_unaligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap2_unaligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: 'void swap2_aligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap2_aligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:110:13: warning: 'void swap4_aligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap4_aligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: 'void swap8_aligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap8_aligned(void *v, long ndata) {
             ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/parmplugin.o -ffast-math -funroll-loops -O3 -fcommon
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
In file included from contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp:24:0:
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h: In member function 'int {anonymous}::ReadPARM::readparm(FILE*)':
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:435:53: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
           fscanf(file, " " DBLFMT, &prm->Charges[i]);
                                                     ^
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:444:45: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
    fscanf(file, " " DBLFMT, &prm->Masses[i]);
                                             ^
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:510:48: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
           fscanf(file, " " DBLFMT, &prm->Rk[i]);
                                                ^
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:517:49: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
           fscanf(file, " " DBLFMT, &prm->Req[i]);
                                                 ^
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:524:48: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
           fscanf(file, " " DBLFMT, &prm->Tk[i]);
                                                ^
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:531:49: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
           fscanf(file, " " DBLFMT, &prm->Teq[i]);
                                                 ^
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:538:48: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
           fscanf(file, " " DBLFMT, &prm->Pk[i]);
                                                ^
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:545:48: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
           fscanf(file, " " DBLFMT, &prm->Pn[i]);
                                                ^
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:552:51: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
           fscanf(file, " " DBLFMT, &prm->Phase[i]);
                                                   ^
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:559:51: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
           fscanf(file, " " DBLFMT, &prm->Solty[i]);
                                                   ^
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:567:49: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
           fscanf(file, " " DBLFMT, &prm->Cn1[i]);
                                                 ^
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:575:49: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
           fscanf(file, " " DBLFMT, &prm->Cn2[i]);
                                                 ^
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:756:50: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
           fscanf(file, " " DBLFMT, &prm->HB12[i]);
                                                  ^
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:763:49: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
           fscanf(file, " " DBLFMT, &prm->HB6[i]);
                                                 ^
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:771:42: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
           fscanf(file, " " DBLFMT, &H[i]);
                                          ^
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:854:46: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
     &prm->Box[0], &prm->Box[1], &prm->Box[2]);
                                              ^
contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:869:40: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
     &prm->Xcap, &prm->Ycap, &prm->Zcap);
                                        ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c build/generated/ShaderText.c -o build/temp.linux-armv7l-2.7/build/generated/ShaderText.o -ffast-math -funroll-loops -O3 -fcommon
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.o -ffast-math -funroll-loops -O3 -fcommon
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp: In function 'int count_mdf_bonds(const char*)':
contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:135:7: warning: unused variable 'retval' [-Wunused-variable]
   int retval;
       ^
contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp: In function 'int read_mdf_bonds(void*, int*, int**, int**, float**, int**, int*, char***)':
contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:280:37: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
     fgets(line, LINESIZE, mdf->file);
                                     ^
contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:299:39: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
       fgets(line, LINESIZE, mdf->file);
                                       ^
contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:321:37: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
     fgets(line, LINESIZE, mdf->file);
                                     ^
contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:359:39: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
       fgets(line, LINESIZE, mdf->file);
                                       ^
contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp: In function 'int read_mdf_structure(void*, int*, molfile_atom_t*)':
contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:225:37: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
     fgets(line, LINESIZE, mdf->file);
                                     ^
contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:243:39: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
       fgets(line, LINESIZE, mdf->file);
                                       ^
contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp: In function 'void* open_mdf_read(const char*, const char*, int*)':
contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:166:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
     fgets(line, LINESIZE, fd);
                              ^
contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:178:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
     fgets(line, LINESIZE, fd);
                              ^
contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:185:32: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
       fgets(line, LINESIZE, fd);
                                ^
In file included from contrib/uiuc/plugins/molfile_plugin/src/hash.h:37:0,
                 from contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:45:
contrib/uiuc/plugins/molfile_plugin/src/hash.c: At global scope:
contrib/uiuc/plugins/molfile_plugin/src/hash.c:183:21: warning: 'int hash_delete(hash_t*, const char*)' defined but not used [-Wunused-function]
 VMDEXTERNSTATIC int hash_delete(hash_t *tptr, const char *key) {
                     ^
contrib/uiuc/plugins/molfile_plugin/src/hash.c:270:24: warning: 'char* hash_stats(hash_t*)' defined but not used [-Wunused-function]
 VMDEXTERNSTATIC char * hash_stats(hash_t *tptr) {
                        ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/phiplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/phiplugin.o -ffast-math -funroll-loops -O3 -fcommon
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/brixplugin.o -ffast-math -funroll-loops -O3 -fcommon
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp: In function 'int read_brix_data(void*, int, float*, float*)':
contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:247:44: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
         fread(brick, sizeof(char), 512, fd);
                                            ^
contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp: In function 'void* open_brix_read(const char*, const char*, int*)':
contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:79:29: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
   fscanf(fd, "%3s", keyWord);
                             ^
contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:86:62: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
   fscanf(fd, " %s %d %d %d", keyWord, &org_x, &org_y, &org_z);
                                                              ^
contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:93:62: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
   fscanf(fd, " %s %d %d %d", keyWord, &ext_x, &ext_y, &ext_z);
                                                              ^
contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:100:65: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
   fscanf(fd, " %s %f %f %f", keyWord, &grid_x, &grid_y, &grid_z);
                                                                 ^
contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:110:74: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
          &cell_x, &cell_y, &cell_z, &cell_alpha, &cell_beta, &cell_gamma);
                                                                          ^
contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:123:39: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
   fscanf(fd, " %s %f", keyWord, &prod);
                                       ^
contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:128:39: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
   fscanf(fd, " %s %f", keyWord, &plus);
                                       ^
contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:135:40: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
   fscanf(fd, " %s %f", keyWord, &sigma);
                                        ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.o -ffast-math -funroll-loops -O3 -fcommon
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp: In function 'void* open_uhbd_read(const char*, const char*, int*)':
contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp:90:22: warning: variable 'o' set but not used [-Wunused-but-set-variable]
   float orig[3], ra, o[3], s[3]; //xdelta[3], ydelta[3], zdelta[3];
                      ^
contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp:90:28: warning: variable 's' set but not used [-Wunused-but-set-variable]
   float orig[3], ra, o[3], s[3]; //xdelta[3], ydelta[3], zdelta[3];
                            ^
contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp: In function 'int read_uhbd_data(void*, int, float*, float*)':
contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp:254:66: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (fread(datablock + z*xysize, sizeof(float), xysize, fd) != xysize) {
                                                                  ^
contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp: In function 'void* open_uhbd_read(const char*, const char*, int*)':
contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp:102:41: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   fread(&headersize, sizeof(int), 1, fd);
                                         ^
In file included from contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp:47:0:
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope:
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: 'void swap2_unaligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap2_unaligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: 'void swap8_unaligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap8_unaligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: 'void swap2_aligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap2_aligned(void *v, long ndata) {
             ^
contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: 'void swap8_aligned(void*, long int)' defined but not used [-Wunused-function]
 static void swap8_aligned(void *v, long ndata) {
             ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/avsplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/avsplugin.o -ffast-math -funroll-loops -O3 -fcommon
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
c++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security build/temp.linux-armv7l-2.7/ov/src/OVHeap.o build/temp.linux-armv7l-2.7/ov/src/OVRandom.o build/temp.linux-armv7l-2.7/ov/src/OVHeapArray.o build/temp.linux-armv7l-2.7/ov/src/OVOneToOne.o build/temp.linux-armv7l-2.7/ov/src/OVLexicon.o build/temp.linux-armv7l-2.7/ov/src/ov_utility.o build/temp.linux-armv7l-2.7/ov/src/OVContext.o build/temp.linux-armv7l-2.7/ov/src/OVOneToAny.o build/temp.linux-armv7l-2.7/layer0/Crystal.o build/temp.linux-armv7l-2.7/layer0/Raw.o build/temp.linux-armv7l-2.7/layer0/Isosurf.o build/temp.linux-armv7l-2.7/layer0/MyPNG.o build/temp.linux-armv7l-2.7/layer0/Tracker.o build/temp.linux-armv7l-2.7/layer0/Triangle.o build/temp.linux-armv7l-2.7/layer0/Err.o build/temp.linux-armv7l-2.7/layer0/Matrix.o build/temp.linux-armv7l-2.7/layer0/MemoryDebug.o build/temp.linux-armv7l-2.7/layer0/Match.o build/temp.linux-armv7l-2.7/layer0/Field.o build/temp.linux-armv7l-2.7/layer0/Feedback.o build/temp.linux-armv7l-2.7/layer0/Vector.o build/temp.linux-armv7l-2.7/layer0/Parse.o build/temp.linux-armv7l-2.7/layer0/Tetsurf.o build/temp.linux-armv7l-2.7/layer0/Word.o build/temp.linux-armv7l-2.7/layer0/ShaderMgr.o build/temp.linux-armv7l-2.7/layer0/os_gl.o build/temp.linux-armv7l-2.7/layer0/Debug.o build/temp.linux-armv7l-2.7/layer0/Block.o build/temp.linux-armv7l-2.7/layer0/Map.o build/temp.linux-armv7l-2.7/layer0/Texture.o build/temp.linux-armv7l-2.7/layer0/Queue.o build/temp.linux-armv7l-2.7/layer0/MemoryCache.o build/temp.linux-armv7l-2.7/layer0/Util.o build/temp.linux-armv7l-2.7/layer0/Deferred.o build/temp.linux-armv7l-2.7/layer0/Pixmap.o build/temp.linux-armv7l-2.7/layer0/Sphere.o build/temp.linux-armv7l-2.7/layer1/Text.o build/temp.linux-armv7l-2.7/layer1/ButMode.o build/temp.linux-armv7l-2.7/layer1/Extrude.o build/temp.linux-armv7l-2.7/layer1/CGO.o build/temp.linux-armv7l-2.7/layer1/Setting.o build/temp.linux-armv7l-2.7/layer1/FontGLUTHel12.o build/temp.linux-armv7l-2.7/layer1/Ortho.o build/temp.linux-armv7l-2.7/layer1/FontGLUT.o build/temp.linux-armv7l-2.7/layer1/Shaker.o build/temp.linux-armv7l-2.7/layer1/FontGLUT9x15.o build/temp.linux-armv7l-2.7/layer1/Wizard.o build/temp.linux-armv7l-2.7/layer1/FontGLUTHel18.o build/temp.linux-armv7l-2.7/layer1/FontGLUT8x13.o build/temp.linux-armv7l-2.7/layer1/Scene.o build/temp.linux-armv7l-2.7/layer1/PConv.o build/temp.linux-armv7l-2.7/layer1/Font.o build/temp.linux-armv7l-2.7/layer1/Character.o build/temp.linux-armv7l-2.7/layer1/ScrollBar.o build/temp.linux-armv7l-2.7/layer1/Color.o build/temp.linux-armv7l-2.7/layer1/Movie.o build/temp.linux-armv7l-2.7/layer1/FontType.o build/temp.linux-armv7l-2.7/layer1/Ray.o build/temp.linux-armv7l-2.7/layer1/PyMOLObject.o build/temp.linux-armv7l-2.7/layer1/Seq.o build/temp.linux-armv7l-2.7/layer1/View.o build/temp.linux-armv7l-2.7/layer1/Control.o build/temp.linux-armv7l-2.7/layer1/FontGLUTHel10.o build/temp.linux-armv7l-2.7/layer1/Rep.o build/temp.linux-armv7l-2.7/layer1/Basis.o build/temp.linux-armv7l-2.7/layer1/Pop.o build/temp.linux-armv7l-2.7/layer1/TypeFace.o build/temp.linux-armv7l-2.7/layer1/P.o build/temp.linux-armv7l-2.7/layer1/Symmetry.o build/temp.linux-armv7l-2.7/layer2/RepDot.o build/temp.linux-armv7l-2.7/layer2/RepWireBond.o build/temp.linux-armv7l-2.7/layer2/CoordSet.o build/temp.linux-armv7l-2.7/layer2/ObjectMolecule.o build/temp.linux-armv7l-2.7/layer2/GadgetSet.o build/temp.linux-armv7l-2.7/layer2/ObjectSlice.o build/temp.linux-armv7l-2.7/layer2/DistSet.o build/temp.linux-armv7l-2.7/layer2/VFont.o build/temp.linux-armv7l-2.7/layer2/ObjectMap.o build/temp.linux-armv7l-2.7/layer2/RepAngle.o build/temp.linux-armv7l-2.7/layer2/ObjectGadgetRamp.o build/temp.linux-armv7l-2.7/layer2/RepSurface.o build/temp.linux-armv7l-2.7/layer2/ObjectAlignment.o build/temp.linux-armv7l-2.7/layer2/ObjectMesh.o build/temp.linux-armv7l-2.7/layer2/RepCylBond.o build/temp.linux-armv7l-2.7/layer2/ObjectMolecule2.o build/temp.linux-armv7l-2.7/layer2/RepMesh.o build/temp.linux-armv7l-2.7/layer2/RepSphere.o build/temp.linux-armv7l-2.7/layer2/ObjectGroup.o build/temp.linux-armv7l-2.7/layer2/RepCartoon.o build/temp.linux-armv7l-2.7/layer2/ObjectDist.o build/temp.linux-armv7l-2.7/layer2/ObjectVolume.o build/temp.linux-armv7l-2.7/layer2/RepEllipsoid.o build/temp.linux-armv7l-2.7/layer2/RepDistDash.o build/temp.linux-armv7l-2.7/layer2/RepLabel.o build/temp.linux-armv7l-2.7/layer2/RepNonbonded.o build/temp.linux-armv7l-2.7/layer2/AtomInfo.o build/temp.linux-armv7l-2.7/layer2/ObjectGadget.o build/temp.linux-armv7l-2.7/layer2/RepNonbondedSphere.o build/temp.linux-armv7l-2.7/layer2/RepRibbon.o build/temp.linux-armv7l-2.7/layer2/ObjectCGO.o build/temp.linux-armv7l-2.7/layer2/Sculpt.o build/temp.linux-armv7l-2.7/layer2/ObjectCallback.o build/temp.linux-armv7l-2.7/layer2/RepDistLabel.o build/temp.linux-armv7l-2.7/layer2/SculptCache.o build/temp.linux-armv7l-2.7/layer2/ObjectSurface.o build/temp.linux-armv7l-2.7/layer2/RepDihedral.o build/temp.linux-armv7l-2.7/layer3/Seeker.o build/temp.linux-armv7l-2.7/layer3/Selector.o build/temp.linux-armv7l-2.7/layer3/Editor.o build/temp.linux-armv7l-2.7/layer3/PlugIOManager.o build/temp.linux-armv7l-2.7/layer3/Executive.o build/temp.linux-armv7l-2.7/layer4/Menu.o build/temp.linux-armv7l-2.7/layer4/Export.o build/temp.linux-armv7l-2.7/layer4/Cmd.o build/temp.linux-armv7l-2.7/layer4/PopUp.o build/temp.linux-armv7l-2.7/layer5/PyMOL.o build/temp.linux-armv7l-2.7/layer5/main.o build/temp.linux-armv7l-2.7/layer5/TestPyMOL.o build/temp.linux-armv7l-2.7/modules/cealign/src/ccealignmodule.o build/temp.linux-armv7l-2.7/build/generated/ShaderText.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/psfplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/carplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/hash.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/corplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/binposplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/jsplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/crdplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/mapplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/gridplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/dxplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/grdplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/pltplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/msmsplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/parmplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/phiplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/brixplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/avsplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/stlplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/raster3dplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/biomoccaplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/edmplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/situsplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/mmcif.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.o -lpng -lfreetype -lGLEW -lGL -lGLU -lglut -o build/lib.linux-armv7l-2.7/pymol/_cmd.so
building 'chempy.champ._champ' extension
creating build/temp.linux-armv7l-2.7/contrib/champ
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Icontrib/champ -I/usr/include/python2.7 -c contrib/champ/champ.c -o build/temp.linux-armv7l-2.7/contrib/champ/champ.o
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Icontrib/champ -I/usr/include/python2.7 -c contrib/champ/list.c -o build/temp.linux-armv7l-2.7/contrib/champ/list.o
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Icontrib/champ -I/usr/include/python2.7 -c contrib/champ/strblock.c -o build/temp.linux-armv7l-2.7/contrib/champ/strblock.o
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Icontrib/champ -I/usr/include/python2.7 -c contrib/champ/os_memory.c -o build/temp.linux-armv7l-2.7/contrib/champ/os_memory.o
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Icontrib/champ -I/usr/include/python2.7 -c contrib/champ/feedback2.c -o build/temp.linux-armv7l-2.7/contrib/champ/feedback2.o
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Icontrib/champ -I/usr/include/python2.7 -c contrib/champ/champ_module.c -o build/temp.linux-armv7l-2.7/contrib/champ/champ_module.o
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Icontrib/champ -I/usr/include/python2.7 -c contrib/champ/vla.c -o build/temp.linux-armv7l-2.7/contrib/champ/vla.o
contrib/champ/champ.c: In function 'ChampSmiToPat':
contrib/champ/champ.c:5005:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int' [-Wformat=]
         ENDFB;
         ^
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Icontrib/champ -I/usr/include/python2.7 -c contrib/champ/sort.c -o build/temp.linux-armv7l-2.7/contrib/champ/sort.o
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Icontrib/champ -I/usr/include/python2.7 -c contrib/champ/chiral.c -o build/temp.linux-armv7l-2.7/contrib/champ/chiral.o
arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Icontrib/champ -I/usr/include/python2.7 -c contrib/champ/err2.c -o build/temp.linux-armv7l-2.7/contrib/champ/err2.o
arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security build/temp.linux-armv7l-2.7/contrib/champ/champ.o build/temp.linux-armv7l-2.7/contrib/champ/list.o build/temp.linux-armv7l-2.7/contrib/champ/strblock.o build/temp.linux-armv7l-2.7/contrib/champ/os_memory.o build/temp.linux-armv7l-2.7/contrib/champ/feedback2.o build/temp.linux-armv7l-2.7/contrib/champ/champ_module.o build/temp.linux-armv7l-2.7/contrib/champ/vla.o build/temp.linux-armv7l-2.7/contrib/champ/sort.o build/temp.linux-armv7l-2.7/contrib/champ/chiral.o build/temp.linux-armv7l-2.7/contrib/champ/err2.o -o build/lib.linux-armv7l-2.7/chempy/champ/_champ.so
make[1]: Leaving directory '/«PKGBUILDDIR»'
   debian/rules override_dh_auto_test
make[1]: Entering directory '/«PKGBUILDDIR»'
#dh_auto_test
chmod +x test/pymol-test
(cd test && python run)
 run_tests: C0001quit...
 run_tests: C0001quit.log DIFFERS over about 4 lines:
['1,8d0\n', '< PyMOL>quit\n', '< ================================= HEAP =================================\n', '< OVHeap: Summary: Blocks expected 0, found 0, peaked at 79.\n', '< OVHeap: Summary: Total bytes allocated 0x0 (0.000 MB).\n', '< ========================================================================\n', '< Memory: 0 blocks expected, 0 found, 118 maximum allocated.\n', '< Memory: current memory allocated 0 bytes (0.0 MB).\n', '<  PyMOL: normal program termination.\n']
 run_tests: C0010hello...
 run_tests: C0010hello.log DIFFERS over about 1 lines:
['1,2d0\n', '< PyMOL>print "hello"\n', '< hello\n']
 run_tests: C0020pdb...
 run_tests: C0020pdb.pdb is missing.
 run_tests: C0020pdb.log DIFFERS over about 4 lines:
['1,8d0\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>print cmd.get_names()\n', "< ['pept']\n", '< PyMOL>print cmd.select("(all)")\n', '< 107\n', '< PyMOL>save cmp/C0020pdb.pdb\n', '<  Save: wrote "cmp/C0020pdb.pdb".\n']
 run_tests: C0021pdbstr...
 run_tests: C0021pdbstr.log DIFFERS over about 3 lines:
['1,6d0\n', '< PyMOL>f=open("dat/pept.pdb","rb")\n', '< PyMOL>l=f.read()\n', '< PyMOL>f.close()\n', '< PyMOL>cmd.read_pdbstr(l,"test")\n', '< PyMOL>print cmd.count_atoms()\n', '< 107\n']
 run_tests: C0025mol...
 run_tests: C0025mol.log DIFFERS over about 3 lines:
['1,6d0\n', '< PyMOL>load dat/small01.mol\n', '<  ExecutiveLoad: "dat/small01.mol" loaded as "small01", through state 1.\n', '< PyMOL>print cmd.get_names()\n', "< ['small01']\n", '< PyMOL>print cmd.select("(all)")\n', '< 36\n']
 run_tests: C0026sdf...
 run_tests: C0026sdf.log DIFFERS over about 17 lines:
['1,34d0\n', '< PyMOL>load dat/ligs3d.sdf\n', '<  ObjectMoleculeReadStr: read through molecule 1.\n', '<  ObjectMoleculeReadStr: read through molecule 2.\n', '<  ObjectMoleculeReadStr: read through molecule 3.\n', '<  ObjectMoleculeReadStr: read through molecule 4.\n', '<  ObjectMoleculeReadStr: read through molecule 5.\n', '<  ObjectMoleculeReadStr: read through molecule 6.\n', '<  ObjectMoleculeReadStr: read through molecule 7.\n', '<  ObjectMoleculeReadStr: read through molecule 8.\n', '<  ObjectMoleculeReadStr: read through molecule 9.\n', '<  ObjectMoleculeReadStr: read through molecule 10.\n', '<  ExecutiveLoad: "dat/ligs3d.sdf" loaded as "ligs3d", through state 10.\n', '< PyMOL>print cmd.get_names()\n', "< ['ligs3d']\n", '< PyMOL>print cmd.select("(all)")\n', '< 337\n', '< PyMOL>set ray_default_renderer=2\n', '<  Setting: ray_default_renderer set to 2.\n', '< PyMOL>set valence\n', '<  Setting: valence set to on.\n', '< PyMOL>frame 1\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 91 graphics primitives.\n', '< PyMOL>frame 10\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 70 graphics primitives.\n', '< PyMOL>hide\n', '< PyMOL>show sticks\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 70 graphics primitives.\n', '< PyMOL>unset valence\n', '<  Setting: valence set to off.\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 42 graphics primitives.\n']
 run_tests: C0027mol2...
 run_tests: C0027mol2.log DIFFERS over about 36 lines:
['1,71d0\n', '< PyMOL>load dat/small03.mol2\n', '<  ObjectMoleculeReadStr: read through molecule 1.\n', '<  ObjectMoleculeReadStr: read through molecule 2.\n', '<  ObjectMoleculeReadStr: read through molecule 3.\n', '<  ObjectMoleculeReadStr: read through molecule 4.\n', '<  ObjectMoleculeReadStr: read through molecule 5.\n', '<  ObjectMoleculeReadStr: read through molecule 6.\n', '<  ObjectMoleculeReadStr: read through molecule 7.\n', '<  ObjectMoleculeReadStr: read through molecule 8.\n', '<  ObjectMoleculeReadStr: read through molecule 9.\n', '<  ObjectMoleculeReadStr: read through molecule 10.\n', '<  ExecutiveLoad: "dat/small03.mol2" loaded as "small03", through state 16.\n', '< PyMOL>print cmd.get_names()\n', "< ['small03']\n", '< PyMOL>print cmd.count_states()\n', '< 16\n', '< PyMOL>print cmd.select("(all)")\n', '< 389\n', '< PyMOL>set ray_default_renderer=2\n', '<  Setting: ray_default_renderer set to 2.\n', '< PyMOL>set valence\n', '<  Setting: valence set to on.\n', '< PyMOL>frame 1\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 19 graphics primitives.\n', '< PyMOL>frame 10\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 41 graphics primitives.\n', '< PyMOL>hide\n', '< PyMOL>show sticks\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 41 graphics primitives.\n', '< PyMOL>unset valence\n', '<  Setting: valence set to off.\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 37 graphics primitives.\n', '< PyMOL>dele all\n', '< PyMOL>load dat/small03.mol2, discrete=0\n', '<  ObjectMoleculeReadStr: read through molecule 1.\n', '<  ObjectMoleculeReadStr: read through molecule 2.\n', '<  ObjectMoleculeReadStr: read through molecule 3.\n', '<  ObjectMoleculeReadStr: read through molecule 4.\n', '<  ObjectMoleculeReadStr: read through molecule 5.\n', '<  ObjectMoleculeReadStr: read through molecule 6.\n', '<  ObjectMoleculeReadStr: read through molecule 7.\n', '<  ObjectMoleculeReadStr: read through molecule 8.\n', '<  ObjectMoleculeReadStr: read through molecule 9.\n', '<  ObjectMoleculeReadStr: read through molecule 10.\n', '<  ExecutiveLoad: "dat/small03.mol2" loaded as "small03", through state 16.\n', '< PyMOL>count_atoms\n', '<  count_atoms: 369 atoms\n', '< PyMOL>dele all\n', '< PyMOL>load dat/small03.mol2, multiplex=1\n', '<  ExecutiveLoad: loaded 16 objects from "dat/small03.mol2".\n', '< PyMOL>print cmd.get_names()\n', "< ['AGLYSL01', 'AMHTAR01', 'AMPTRB10', 'ARGIND11', 'BAOXLM01', 'BBSPRT10', 'BEVJER10', 'BEWCUB', 'BEWKUJ04', 'BIHKEI01', 'BIPDEJ02', 'BIPJUF10', 'BIPYCL01', 'BITNAT10', 'BIYBIU10', 'BODKOU']\n", '< PyMOL>print cmd.count_states()\n', '< 1\n', '< PyMOL>print cmd.select("(all)")\n', '< 389\n', '< PyMOL>dele all\n', '< PyMOL>set multiplex, 1\n', '<  Setting: multiplex set to 1.\n', '< PyMOL>load dat/small03.mol2\n', '<  ExecutiveLoad: loaded 16 objects from "dat/small03.mol2".\n', '< PyMOL>print cmd.get_names()\n', "< ['AGLYSL01', 'AMHTAR01', 'AMPTRB10', 'ARGIND11', 'BAOXLM01', 'BBSPRT10', 'BEVJER10', 'BEWCUB', 'BEWKUJ04', 'BIHKEI01', 'BIPDEJ02', 'BIPJUF10', 'BIPYCL01', 'BITNAT10', 'BIYBIU10', 'BODKOU']\n", '< PyMOL>print cmd.count_states()\n', '< 1\n', '< PyMOL>print cmd.select("(all)")\n', '< 389\n']
 run_tests: C0030pkl...
 run_tests: C0030pkl.pdb is missing.
 run_tests: C0030pkl.log DIFFERS over about 4 lines:
['1,8d0\n', '< PyMOL>load dat/pept.pkl\n', '<  Executive: object "pept" created.\n', '< PyMOL>print cmd.get_names()\n', "< ['pept']\n", '< PyMOL>print cmd.select("(all)")\n', '< 198\n', '< PyMOL>save cmp/C0030pkl.pdb\n', '<  Save: wrote "cmp/C0030pkl.pdb".\n']
 run_tests: C0050multi...
 run_tests: C0050multi.log DIFFERS over about 4 lines:
['1,8d0\n', '< PyMOL>load dat/pept.pkl\n', '<  Executive: object "pept" created.\n', '< PyMOL>load dat/il2.pdb\n', '<  CmdLoad: "dat/il2.pdb" loaded as "il2".\n', '< PyMOL>load dat/tiny.pdb\n', '<  CmdLoad: "dat/tiny.pdb" loaded as "tiny".\n', '< PyMOL>load dat/water.pdb\n', '<  CmdLoad: "dat/water.pdb" loaded as "water".\n']
 run_tests: C0060delete...
 run_tests: C0060delete.log DIFFERS over about 19 lines:
['1,37d0\n', '< PyMOL>load dat/pept.pkl\n', '<  Executive: object "pept" created.\n', '< PyMOL>print cmd.get_names()\n', "< ['pept']\n", '< PyMOL>delete pept\n', '< PyMOL>print cmd.get_names()\n', '< []\n', '< PyMOL>load dat/pept.pkl\n', '<  Executive: object "pept" created.\n', '< PyMOL>delete pept\n', '< PyMOL>load dat/pept.pkl\n', '<  Executive: object "pept" created.\n', '< PyMOL>delete pept\n', '< PyMOL>load dat/il2.pdb\n', '<  CmdLoad: "dat/il2.pdb" loaded as "il2".\n', '< PyMOL>load dat/pept.pkl\n', '<  Executive: object "pept" created.\n', '< PyMOL>print cmd.get_names()\n', "< ['il2', 'pept']\n", '< PyMOL>delete il2\n', '< PyMOL>delete pept\n', '< PyMOL>print cmd.get_names()\n', '< []\n', '< PyMOL>load dat/il2.pdb\n', '<  CmdLoad: "dat/il2.pdb" loaded as "il2".\n', '< PyMOL>load dat/pept.pkl\n', '<  Executive: object "pept" created.\n', '< PyMOL>delete il2\n', '< PyMOL>delete pept\n', '< PyMOL>load dat/il2.pdb\n', '<  CmdLoad: "dat/il2.pdb" loaded as "il2".\n', '< PyMOL>load dat/pept.pkl\n', '<  Executive: object "pept" created.\n', '< PyMOL>delete il2\n', '< PyMOL>delete pept\n', '< PyMOL>print cmd.get_names()\n', '< []\n']
 run_tests: C0070rep...
 run_tests: C0070rep.log DIFFERS over about 9 lines:
['1,17d0\n', '< PyMOL>load dat/tiny.pdb\n', '<  CmdLoad: "dat/tiny.pdb" loaded as "tiny".\n', '< PyMOL>print cmd.get_names()\n', "< ['tiny']\n", '< PyMOL>show sticks\n', '< PyMOL>refresh\n', '< PyMOL>show spheres\n', '< PyMOL>refresh\n', '< PyMOL>show dots\n', '< PyMOL>refresh\n', '< PyMOL>show surface\n', '< PyMOL>refresh\n', '<  RepSurface: 318 surface points.\n', '<  RepSurface: 632 triangles.\n', '< PyMOL>show mesh\n', '< PyMOL>refresh\n', '<  IsosurfVolume: Surface generated using 1747 lines.\n']
 run_tests: C0080create...
 run_tests: C0080create.log DIFFERS over about 61 lines:
['1,121d0\n', '< PyMOL>load dat/pept.pkl\n', '<  Executive: object "pept" created.\n', '< PyMOL>print cmd.get_names()\n', "< ['pept']\n", '< PyMOL>create cpy=(pept)\n', '<  Selector: found 198 atoms.\n', '<  Executive: object "cpy" created.\n', '< PyMOL>create pc1=(resi 1 and pept)\n', '<  Selector: found 12 atoms.\n', '<  Executive: object "pc1" created.\n', '< PyMOL>create pc2=(resi 2 and pept)\n', '<  Selector: found 10 atoms.\n', '<  Executive: object "pc2" created.\n', '< PyMOL>create pc3=(resi 3 and pept)\n', '<  Selector: found 10 atoms.\n', '<  Executive: object "pc3" created.\n', '< PyMOL>create pc4=(resi 4 and pept)\n', '<  Selector: found 24 atoms.\n', '<  Executive: object "pc4" created.\n', '< PyMOL>create pc5=(resi 5 and pept)\n', '<  Selector: found 17 atoms.\n', '<  Executive: object "pc5" created.\n', '< PyMOL>create pc6=(resi 6 and pept)\n', '<  Selector: found 19 atoms.\n', '<  Executive: object "pc6" created.\n', '< PyMOL>create pc7=(resi 7 and pept)\n', '<  Selector: found 7 atoms.\n', '<  Executive: object "pc7" created.\n', '< PyMOL>create pc8=(resi 8 and pept)\n', '<  Selector: found 15 atoms.\n', '<  Executive: object "pc8" created.\n', '< PyMOL>create pc9=(resi 9 and pept)\n', '<  Selector: found 19 atoms.\n', '<  Executive: object "pc9" created.\n', '< PyMOL>create pc10=(resi 10 and pept)\n', '<  Selector: found 16 atoms.\n', '<  Executive: object "pc10" created.\n', '< PyMOL>create pc11=(resi 11 and pept)\n', '<  Selector: found 24 atoms.\n', '<  Executive: object "pc11" created.\n', '< PyMOL>create pc12=(resi 12 and pept)\n', '<  Selector: found 10 atoms.\n', '<  Executive: object "pc12" created.\n', '< PyMOL>create pc13=(resi 13 and pept)\n', '<  Selector: found 15 atoms.\n', '<  Executive: object "pc13" created.\n', '< PyMOL>create chk = (pc1 | pc2 | pc3 | pc4 | pc5 | pc6 | pc7 | pc8 | pc9 | pc10 | pc11 | pc12 | pc13 )\n', '<  Selector: found 198 atoms.\n', '<  Executive: object "chk" created.\n', '< PyMOL>print cmd.get_names()\n', "< ['pept', 'cpy', 'pc1', 'pc2', 'pc3', 'pc4', 'pc5', 'pc6', 'pc7', 'pc8', 'pc9', 'pc10', 'pc11', 'pc12', 'pc13', 'chk']\n", '< PyMOL>delete pc*\n', '< PyMOL>print cmd.get_names()\n', "< ['pept', 'cpy', 'chk']\n", '< PyMOL>save cmp/C0080create.1.pdb,(cpy and resi 4:6)\n', '<  Save: wrote "cmp/C0080create.1.pdb".\n', '< PyMOL>save cmp/C0080create.2.pdb,(chk and resi 4:6)\n', '<  Save: wrote "cmp/C0080create.2.pdb".\n', '< PyMOL>dele all\n', '< PyMOL>load dat/ligs3d.sdf\n', '<  ObjectMoleculeReadStr: read through molecule 1.\n', '<  ObjectMoleculeReadStr: read through molecule 2.\n', '<  ObjectMoleculeReadStr: read through molecule 3.\n', '<  ObjectMoleculeReadStr: read through molecule 4.\n', '<  ObjectMoleculeReadStr: read through molecule 5.\n', '<  ObjectMoleculeReadStr: read through molecule 6.\n', '<  ObjectMoleculeReadStr: read through molecule 7.\n', '<  ObjectMoleculeReadStr: read through molecule 8.\n', '<  ObjectMoleculeReadStr: read through molecule 9.\n', '<  ObjectMoleculeReadStr: read through molecule 10.\n', '<  ExecutiveLoad: "dat/ligs3d.sdf" loaded as "ligs3d", through state 10.\n', '< PyMOL>load dat/il2.pdb\n', '<  CmdLoad: "dat/il2.pdb" loaded as "il2".\n', '< PyMOL>create cpy,il2\n', '<  Selector: found 2084 atoms.\n', '<  Executive: object "cpy" created.\n', '< PyMOL>print cmd.count_states("il2")\n', '< 1\n', '< PyMOL>print cmd.count_states("ligs3d")\n', '< 10\n', '< PyMOL>print cmd.count_states("cpy")\n', '< 1\n', '< PyMOL>create tst2,ligs3d, 5, 3\n', '<  Selector: found 32 atoms.\n', '<  Executive: object "tst2" created.\n', '< PyMOL>print cmd.count_states("tst2")\n', '< 3\n', '< PyMOL>print cmd.count_atoms("tst2 and state 1")\n', '< 0\n', '< PyMOL>print cmd.count_atoms("tst2 and state 2")\n', '< 0\n', '< PyMOL>print cmd.count_atoms("tst2 and state 3")\n', '< 32\n', '< PyMOL>print cmd.count_atoms("ligs3d and state 3")\n', '< 33\n', '< PyMOL>print cmd.count_atoms("ligs3d and state 5")\n', '< 32\n', '< PyMOL>print cmd.count_atoms("tst2 and state 5")\n', '< 0\n', '< PyMOL>dele all\n', '< PyMOL>load dat/ligs3d.sdf\n', '<  ObjectMoleculeReadStr: read through molecule 1.\n', '<  ObjectMoleculeReadStr: read through molecule 2.\n', '<  ObjectMoleculeReadStr: read through molecule 3.\n', '<  ObjectMoleculeReadStr: read through molecule 4.\n', '<  ObjectMoleculeReadStr: read through molecule 5.\n', '<  ObjectMoleculeReadStr: read through molecule 6.\n', '<  ObjectMoleculeReadStr: read through molecule 7.\n', '<  ObjectMoleculeReadStr: read through molecule 8.\n', '<  ObjectMoleculeReadStr: read through molecule 9.\n', '<  ObjectMoleculeReadStr: read through molecule 10.\n', '<  ExecutiveLoad: "dat/ligs3d.sdf" loaded as "ligs3d", through state 10.\n', '< PyMOL>create tmp, ligs3d, 0, 4\n', '<  Selector: found 337 atoms.\n', '<  Executive: object "tmp" created.\n', '< PyMOL>count_states\n', '<  cmd.count_states: 13 states.\n', '< PyMOL>disable\n', '< PyMOL>enable tmp\n', '< PyMOL>count_states\n', '<  cmd.count_states: 13 states.\n']
 run_tests: C0080create.2.pdb is missing.
 run_tests: C0080create.1.pdb is missing.
 run_tests: C0100select...
 run_tests: C0100select.log DIFFERS over about 90 lines:
['1,180d0\n', '< PyMOL>load dat/tiny.pdb\n', '<  CmdLoad: "dat/tiny.pdb" loaded as "tiny".\n', '< PyMOL>load dat/il2.pdb\n', '<  CmdLoad: "dat/il2.pdb" loaded as "il2".\n', '< PyMOL>print cmd.get_names()\n', "< ['tiny', 'il2']\n", '< PyMOL>select tst = (all)\n', '<  Selector: selection "tst" defined with 2121 atoms.\n', '< PyMOL>select tst = (none)\n', '<  Selector: selection "tst" defined with 0 atoms.\n', '< PyMOL>select tst = (name c)\n', '<  Selector: selection "tst" defined with 129 atoms.\n', '< PyMOL>dele tst\n', '< PyMOL>select tst = (segi e)\n', '<  Selector: selection "tst" defined with 9 atoms.\n', '< PyMOL>select tst = (all)\n', '<  Selector: selection "tst" defined with 2121 atoms.\n', "< PyMOL>select (segi '')\n", '<  Selector: selection "sel01" defined with 2112 atoms.\n', '< PyMOL>select (name ca,c,n,o)\n', '<  Selector: selection "sel02" defined with 515 atoms.\n', '< PyMOL>select (n;ca,c)\n', '<  Selector: selection "sel03" defined with 257 atoms.\n', '< PyMOL>select (resn pro)\n', '<  Selector: selection "sel04" defined with 56 atoms.\n', '< PyMOL>select (r;pro)\n', '<  Selector: selection "sel05" defined with 56 atoms.\n', '< PyMOL>select (chain c,e)\n', '<  Selector: selection "sel06" defined with 36 atoms.\n', '< PyMOL>select (c;c,e)\n', '<  Selector: selection "sel07" defined with 36 atoms.\n', '< PyMOL>select (resi 100)\n', '<  Selector: selection "sel08" defined with 15 atoms.\n', '< PyMOL>select (i;100)\n', '<  Selector: selection "sel09" defined with 15 atoms.\n', '< PyMOL>select (id 50)\n', '<  Selector: selection "sel10" defined with 1 atoms.\n', '< PyMOL>select (byres id 50)\n', '<  Selector: selection "sel11" defined with 22 atoms.\n', "< PyMOL>select (alt '')\n", '<  Selector: selection "sel12" defined with 2121 atoms.\n', '< PyMOL>select (tiny)\n', '<  Selector: selection "sel13" defined with 37 atoms.\n', '< PyMOL>select (tiny or il2)\n', '<  Selector: selection "sel14" defined with 2121 atoms.\n', '< PyMOL>select (tiny | il2)\n', '<  Selector: selection "sel15" defined with 2121 atoms.\n', '< PyMOL>select (vis)\n', '<  Selector: selection "sel16" defined with 2121 atoms.\n', '< PyMOL>hide (tiny)\n', '< PyMOL>select (vis)\n', '<  Selector: selection "sel17" defined with 2084 atoms.\n', "< PyMOL>print cmd.get_names('all')\n", "< ['tiny', 'il2', 'tst', 'sel01', 'sel02', 'sel03', 'sel04', 'sel05', 'sel06', 'sel07', 'sel08', 'sel09', 'sel10', 'sel11', 'sel12', 'sel13', 'sel14', 'sel15', 'sel16', 'sel17']\n", '< PyMOL>delete sel*\n', "< PyMOL>print cmd.get_names('all')\n", "< ['tiny', 'il2', 'tst']\n", '< PyMOL>select foo = (name c)\n', '<  Selector: selection "foo" defined with 129 atoms.\n', '< PyMOL>select fie = (name n,c)\n', '<  Selector: selection "fie" defined with 257 atoms.\n', '< PyMOL>select (foo and not fie)\n', '<  Selector: selection "sel18" defined with 0 atoms.\n', '< PyMOL>select (fie &! foo)\n', '<  Selector: selection "sel19" defined with 128 atoms.\n', '< PyMOL>select foe = (tiny a; 30)\n', '<  Selector: selection "foe" defined with 105 atoms.\n', '< PyMOL>select fum = (il2 and not foe)\n', '<  Selector: selection "fum" defined with 1979 atoms.\n', '< PyMOL>select (hydro)\n', '<  Selector: selection "sel20" defined with 1075 atoms.\n', '< PyMOL>select (b<30 and b>0.1)\n', '<  Selector: selection "sel21" defined with 362 atoms.\n', '< PyMOL>select (q=0.0)\n', '<  Selector: selection "sel22" defined with 9 atoms.\n', '< PyMOL>select (q=1.0)\n', '<  Selector: selection "sel23" defined with 2112 atoms.\n', '< PyMOL>select (b=0.0)\n', '<  Selector: selection "sel24" defined with 1080 atoms.\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>select tst,pept within 5 of tiny\n', '<  Selector: selection "tst" defined with 0 atoms.\n', '< PyMOL>select tst,pept within 50 of tiny\n', '<  Selector: selection "tst" defined with 67 atoms.\n', '< PyMOL>select tst, pept w. 1 of pept\n', '<  Selector: selection "tst" defined with 107 atoms.\n', '< PyMOL>print cmd.select("(none)")\n', '< 0\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb,mult\n', '<  CmdLoad: "dat/pept.pdb" loaded as "mult".\n', '< PyMOL>load dat/il2.pdb,mult\n', '<  CmdLoad: "dat/il2.pdb" appended into object "mult", state 2.\n', '< PyMOL>frame 1\n', '< PyMOL>select tst,mult and present\n', '<  Selector: selection "tst" defined with 107 atoms.\n', '< PyMOL>frame 2\n', '< PyMOL>select tst,mult and present\n', '<  Selector: selection "tst" defined with 2084 atoms.\n', '< PyMOL>select tst,state 1\n', '<  Selector: selection "tst" defined with 107 atoms.\n', '< PyMOL>select tst,state 2\n', '<  Selector: selection "tst" defined with 2084 atoms.\n', '< PyMOL>hide\n', '< PyMOL>show sph,name c\n', '< PyMOL>select tst,present and vis\n', '<  Selector: selection "tst" defined with 126 atoms.\n', '< PyMOL>frame 1\n', '< PyMOL>select tst,present and vis\n', '<  Selector: selection "tst" defined with 13 atoms.\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>indicate name ca\n', '< PyMOL>count_atoms indicate\n', '<  count_atoms: 13 atoms\n', '< PyMOL>indicate name *c*\n', '< PyMOL>count_atoms indicate\n', '<  count_atoms: 69 atoms\n', '< PyMOL>indicate (name *c*,*n*)\n', '< PyMOL>count_atoms indicate\n', '<  count_atoms: 86 atoms\n', '< PyMOL>indicate (name *c*+*n*)\n', '< PyMOL>count_atoms indicate\n', '<  count_atoms: 86 atoms\n', '< PyMOL>indicate name *G\n', '< PyMOL>count_atoms indicate\n', '<  count_atoms: 9 atoms\n', '< PyMOL>indicate */*G\n', '< PyMOL>count_atoms indicate\n', '<  count_atoms: 9 atoms\n', '< PyMOL>indicate rank -3+5+10-23+7+40-\n', '< PyMOL>count_atoms indicate\n', '<  count_atoms: 87 atoms\n', '< PyMOL>indicate id -3+5+10-23+7+40-\n', '< PyMOL>count_atoms indicate\n', '<  count_atoms: 87 atoms\n', '< PyMOL>indicate index -3+5+10-23+7+40-\n', '< PyMOL>count_atoms indicate\n', '<  count_atoms: 87 atoms\n', '< PyMOL>dele all\n', '< PyMOL>load dat/1tii.pdb\n', '< HEADER    ENTEROTOXIN                             20-MAR-96   1TII\n', '< TITLE     ESCHERICHIA COLI HEAT LABILE ENTEROTOXIN TYPE IIB\n', '< COMPND    MOL_ID: 1;\n', '< COMPND   2 MOLECULE: HEAT LABILE ENTEROTOXIN TYPE IIB;\n', '< COMPND   3 CHAIN: D, E, F, G, H, A, C;\n', '< COMPND   4 SYNONYM: LT-IIB;\n', '< COMPND   5 ENGINEERED: YES;\n', '< COMPND   6 OTHER_DETAILS: LATENT/INACTIVE FORM\n', '<  ObjectMolecule: Read secondary structure assignments.\n', '<  ObjectMolecule: Read crystal symmetry information.\n', '<  Symmetry: Found 6 symmetry operators.\n', '<  CmdLoad: "dat/1tii.pdb" loaded as "1tii".\n', '< PyMOL>indicate A:C+F/10+90+100-/ca+c+n*\n', '< PyMOL>count_atoms indicate\n', '<  count_atoms: 435 atoms\n', '< PyMOL>count_atoms 1TII\n', '<  count_atoms: 5684 atoms\n', '< PyMOL>count_atoms 1tii\n', '<  count_atoms: 5684 atoms\n', '< PyMOL>count_atoms HOH`307/ expand 5\n', '<  count_atoms: 12 atoms\n', '< PyMOL>count_atoms a// c//\n', '<  count_atoms: 1769 atoms\n', '< PyMOL>count_atoms a// c// d//\n', '<  count_atoms: 2509 atoms\n', '< PyMOL>count_atoms (a// c//) d//\n', '<  count_atoms: 2509 atoms\n', '< PyMOL>count_atoms a// c//&none\n', '<  count_atoms: 1479 atoms\n', '< PyMOL>count_atoms c//&none a//\n', '<  count_atoms: 1479 atoms\n', '< PyMOL>count_atoms c//&none (a//&none a//)\n', '<  count_atoms: 1479 atoms\n', '< PyMOL>count_atoms (c//&none) a// (a//&none)\n', '<  count_atoms: 1479 atoms\n', '< PyMOL>count_atoms (a// (d// c//)) & (e// (b// a//))\n', '<  count_atoms: 1479 atoms\n']
 run_tests: C0105names...
 run_tests: C0105names.log DIFFERS over about 27 lines:
['1,54d0\n', '< PyMOL>load dat/names.pdb\n', '<  CmdLoad: "dat/names.pdb" loaded as "names".\n', "< PyMOL>select test,name O4'\n", '<  Selector: selection "test" defined with 2 atoms.\n', "< PyMOL>select test,*/O4'\n", '<  Selector: selection "test" defined with 2 atoms.\n', "< PyMOL>select test,*/O4'+O3'\n", '<  Selector: selection "test" defined with 4 atoms.\n', "< PyMOL>select test,(*/O4',O3')\n", '<  Selector: selection "test" defined with 4 atoms.\n', "< PyMOL>select test,name O4'+O3'\n", '<  Selector: selection "test" defined with 4 atoms.\n', '< PyMOL>select test,name "O4\'+O3\'"\n', '<  Selector: selection "test" defined with 4 atoms.\n', "< PyMOL>select test,name O4'+Na\\+\n", '<  Selector: selection "test" defined with 4 atoms.\n', "< PyMOL>select test,(name Na\\+,O4')\n", '<  Selector: selection "test" defined with 4 atoms.\n', "< PyMOL>select test,name Na\\++O4'\n", '<  Selector: selection "test" defined with 4 atoms.\n', "< PyMOL>select test,*/Na\\++O4'\n", '<  Selector: selection "test" defined with 4 atoms.\n', "< PyMOL>select test,*/O4'+O4\n", '<  Selector: selection "test" defined with 3 atoms.\n', '< PyMOL>select test,*/O2\\*+O2\n', '<  Selector: selection "test" defined with 4 atoms.\n', "< PyMOL>select test,*/O2\\*+O2'\n", '<  Selector: selection "test" defined with 4 atoms.\n', "< PyMOL>select test,name 'O4''\n", '<  Selector: selection "test" defined with 2 atoms.\n', '< PyMOL>select test,name "O4\'"+O2\'\n', '<  Selector: selection "test" defined with 4 atoms.\n', "< PyMOL>select test,name 'O4''+O2'\n", '<  Selector: selection "test" defined with 4 atoms.\n', "< PyMOL>select test,name O4'+C2+C4+Na\\++Cl\\-\n", '<  Selector: selection "test" defined with 13 atoms.\n', "< PyMOL>select test,*/O4'+C2+C4+Na\\++Cl\\-\n", '<  Selector: selection "test" defined with 13 atoms.\n', "< PyMOL>select test,names////O4'\n", '<  Selector: selection "test" defined with 2 atoms.\n', "< PyMOL>select test,names and */O4'+'Na\\+'+'C2'+'C4'\n", '<  Selector: selection "test" defined with 12 atoms.\n', "< PyMOL>select test,chain ''\n", '<  Selector: selection "test" defined with 0 atoms.\n', "< PyMOL>select test,segi ''\n", '<  Selector: selection "test" defined with 86 atoms.\n', "< PyMOL>select test,chain R+''\n", '<  Selector: selection "test" defined with 82 atoms.\n', "< PyMOL>select test,chain ''+R\n", '<  Selector: selection "test" defined with 82 atoms.\n', '< PyMOL>select test,name Na\\+\n', '<  Selector: selection "test" defined with 2 atoms.\n', '< PyMOL>select test,name "Na\\+"\n', '<  Selector: selection "test" defined with 2 atoms.\n']
 run_tests: C0106order...
 run_tests: C0106order.log DIFFERS over about 49 lines:
['1,98d0\n', '< PyMOL>order does_not_exist\n', '< PyMOL>print cmd.get_names()\n', '< []\n', '< PyMOL>order *\n', '< PyMOL>print cmd.get_names()\n', '< []\n', '< PyMOL>order *,location=top\n', '< PyMOL>print cmd.get_names()\n', '< []\n', '< PyMOL>order *,location=bottom\n', '< PyMOL>print cmd.get_names()\n', '< []\n', '< PyMOL>order *,location=current\n', '< PyMOL>print cmd.get_names()\n', '< []\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>order pept\n', '< PyMOL>print cmd.get_names()\n', "< ['pept']\n", '< PyMOL>order *\n', '< PyMOL>print cmd.get_names()\n', "< ['pept']\n", '< PyMOL>order *,location=top\n', '< PyMOL>print cmd.get_names()\n', "< ['pept']\n", '< PyMOL>order *,location=bottom\n', '< PyMOL>print cmd.get_names()\n', "< ['pept']\n", '< PyMOL>order *,location=current\n', '< PyMOL>print cmd.get_names()\n', "< ['pept']\n", '< PyMOL>load dat/il2.pdb\n', '<  CmdLoad: "dat/il2.pdb" loaded as "il2".\n', '< PyMOL>print cmd.get_names()\n', "< ['pept', 'il2']\n", '< PyMOL>order *\n', '< PyMOL>print cmd.get_names()\n', "< ['pept', 'il2']\n", '< PyMOL>order il2,location=current\n', '< PyMOL>print cmd.get_names()\n', "< ['pept', 'il2']\n", '< PyMOL>order il2,location=top\n', '< PyMOL>print cmd.get_names()\n', "< ['il2', 'pept']\n", '< PyMOL>order il2,location=bottom\n', '< PyMOL>print cmd.get_names()\n', "< ['pept', 'il2']\n", '< PyMOL>order il2 pept\n', '< PyMOL>print cmd.get_names()\n', "< ['il2', 'pept']\n", '< PyMOL>load dat/small01.mol\n', '<  ExecutiveLoad: "dat/small01.mol" loaded as "small01", through state 1.\n', '< PyMOL>print cmd.get_names()\n', "< ['il2', 'pept', 'small01']\n", '< PyMOL>order small01 pept\n', '< PyMOL>print cmd.get_names()\n', "< ['il2', 'small01', 'pept']\n", '< PyMOL>order small01 pept il2\n', '< PyMOL>print cmd.get_names()\n', "< ['small01', 'pept', 'il2']\n", '< PyMOL>order *\n', '< PyMOL>print cmd.get_names()\n', "< ['small01', 'pept', 'il2']\n", '< PyMOL>create aaa,pept\n', '<  Selector: found 107 atoms.\n', '<  Executive: object "aaa" created.\n', '< PyMOL>order *,sort=1\n', '< PyMOL>print cmd.get_names()\n', "< ['aaa', 'il2', 'pept', 'small01']\n", '< PyMOL>create zzz,pept\n', '<  Selector: found 107 atoms.\n', '<  Executive: object "zzz" created.\n', '< PyMOL>order *,sort=1\n', '< PyMOL>print cmd.get_names()\n', "< ['aaa', 'il2', 'pept', 'small01', 'zzz']\n", '< PyMOL>create pept2, pept\n', '<  Selector: found 107 atoms.\n', '<  Executive: object "pept2" created.\n', '< PyMOL>create pept1, pept\n', '<  Selector: found 107 atoms.\n', '<  Executive: object "pept1" created.\n', '< PyMOL>order pept*\n', '< PyMOL>print cmd.get_names()\n', "< ['aaa', 'il2', 'pept', 'pept2', 'pept1', 'small01', 'zzz']\n", '< PyMOL>order pept*,sort=1\n', '< PyMOL>print cmd.get_names()\n', "< ['aaa', 'il2', 'pept', 'pept1', 'pept2', 'small01', 'zzz']\n", '< PyMOL>order pept*,location=top\n', '< PyMOL>print cmd.get_names()\n', "< ['pept', 'pept1', 'pept2', 'aaa', 'il2', 'small01', 'zzz']\n", '< PyMOL>order pept*,location=bottom\n', '< PyMOL>print cmd.get_names()\n', "< ['aaa', 'il2', 'small01', 'zzz', 'pept', 'pept1', 'pept2']\n", '< PyMOL>order aaa,location=bottom\n', '< PyMOL>order zzz,location=top\n', '< PyMOL>print cmd.get_names()\n', "< ['zzz', 'il2', 'small01', 'pept', 'pept1', 'pept2', 'aaa']\n"]
 run_tests: C0140iterate...
 run_tests: C0140iterate.log DIFFERS over about 23 lines:
['1,45d0\n', '< PyMOL>load dat/tiny.pdb\n', '<  CmdLoad: "dat/tiny.pdb" loaded as "tiny".\n', '< PyMOL>names = []\n', '< PyMOL>iterate (all),names.append(name)\n', '<  Iterate: iterated over 37 atoms.\n', '< PyMOL>print names\n', "< ['C', 'O', 'N', 'CA', 'C', 'O', 'CB', 'CG', 'CD', 'HA', '2HB', '3HB', '2HG', '3HG', '2HD', '3HD', 'N', 'CA', 'C', 'O', 'CB', 'OG', 'H', 'HA', '2HB', '3HB', 'HG', 'O', 'O01', 'C02', 'C03', 'C04', 'C05', 'H01', 'H04', 'H05', 'H06']\n", '< PyMOL>bfct = []\n', '< PyMOL>iterate (resn pro),bfct.append(b)\n', '<  Iterate: iterated over 14 atoms.\n', '<  50.7800\n', '<  48.1600\n', '<  43.9800\n', '<  44.4900\n', '<  38.5700\n', '<  54.5800\n', '<  46.5900\n', '<   0.0000\n', '<   0.0000\n', '<   0.0000\n', '<   0.0000\n', '<   0.0000\n', '<   0.0000\n', '<   0.0000\n', "< PyMOL>iterate (all),resn = 'NON'\n", '<  Iterate: iterated over 37 atoms.\n', '< PyMOL>iterate (all),b = b + 10\n', '<  Iterate: iterated over 37 atoms.\n', '< PyMOL>bfct = []\n', '< PyMOL>iterate (resn pro),bfct.append(b)\n', '<  Iterate: iterated over 14 atoms.\n', '<  50.7800\n', '<  48.1600\n', '<  43.9800\n', '<  44.4900\n', '<  38.5700\n', '<  54.5800\n', '<  46.5900\n', '<   0.0000\n', '<   0.0000\n', '<   0.0000\n', '<   0.0000\n', '<   0.0000\n', '<   0.0000\n', '<   0.0000\n']
 run_tests: C0150alter...
 run_tests: C0150alter.log DIFFERS over about 11 lines:
['1,22d0\n', '< PyMOL>load dat/tiny.pdb\n', '<  CmdLoad: "dat/tiny.pdb" loaded as "tiny".\n', '< PyMOL>alter (all),resn = name\n', '<  Alter: modified 37 atoms.\n', '< PyMOL>alter (all),b = b + 10\n', '<  Alter: modified 37 atoms.\n', '< PyMOL>alter (all),q = 0.95\n', '<  Alter: modified 37 atoms.\n', '< PyMOL>alter (all),name = name[0:2]\n', '<  Alter: modified 37 atoms.\n', "< PyMOL>alter (het),type = 'ATOM'\n", '<  Alter: modified 10 atoms.\n', "< PyMOL>alter (resi 9),type ='HETATM'\n", '<  Alter: modified 11 atoms.\n', "< PyMOL>alter (e;c),elem = 'X'\n", '<  Alter: modified 13 atoms.\n', '< PyMOL>alter (resi 8),resi=str(int(resi)+10)\n', '<  Alter: modified 14 atoms.\n', "< PyMOL>alter (resi 7),alt='B'\n", '<  Alter: modified 2 atoms.\n', '< PyMOL>save cmp/C0150alter.1.pdb\n', '<  Save: wrote "cmp/C0150alter.1.pdb".\n']
 run_tests: C0150alter.1.pdb is missing.
 run_tests: C0160get...
 run_tests: C0160get.log DIFFERS over about 42 lines:
['1,84d0\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" appended into object "pept", state 2.\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" appended into object "pept", state 3.\n', '< PyMOL>get line_width\n', '<  get: line_width = 1.49000\n', '< PyMOL>get line_width,doesnotexist\n', '<  SettingGet-Error: object "doesnotexist" not found.\n', '< PyMOL>get line_width,doesnotexist,5\n', '<  SettingGet-Error: object "doesnotexist" not found.\n', '< PyMOL>get line_width,pept\n', '<  get: line_width = 1.49000 in object pept\n', '< PyMOL>get line_width,pept,0\n', '<  get: line_width = 1.49000 in object pept\n', '< PyMOL>get line_width,pept,1\n', '<  get: line_width = 1.49000 in object pept state 1\n', '< PyMOL>get line_width,pept,2\n', '<  get: line_width = 1.49000 in object pept state 2\n', '< PyMOL>get line_width,pept,3\n', '<  get: line_width = 1.49000 in object pept state 3\n', '< PyMOL>get line_width,pept,4\n', '<  SettingGet-Error: object "pept" lacks state 4.\n', '< PyMOL>set line_width,2.0,pept\n', '<  Setting: line_width set to 2.00000 in object "pept".\n', '< PyMOL>get line_width,pept\n', '<  get: line_width = 2.00000 in object pept\n', '< PyMOL>get line_width,pept,1\n', '<  get: line_width = 2.00000 in object pept state 1\n', '< PyMOL>get line_width,pept,2\n', '<  get: line_width = 2.00000 in object pept state 2\n', '< PyMOL>get line_width,pept,3\n', '<  get: line_width = 2.00000 in object pept state 3\n', '< PyMOL>set line_width,4.0,pept,1\n', '<  Setting: line_width set to 4.00000 in object "pept", state 1.\n', '< PyMOL>get line_width,pept\n', '<  get: line_width = 2.00000 in object pept\n', '< PyMOL>get line_width,pept,1\n', '<  get: line_width = 4.00000 in object pept state 1\n', '< PyMOL>get line_width,pept,2\n', '<  get: line_width = 2.00000 in object pept state 2\n', '< PyMOL>get line_width,pept,3\n', '<  get: line_width = 2.00000 in object pept state 3\n', '< PyMOL>set line_width,6.0,pept,2\n', '<  Setting: line_width set to 6.00000 in object "pept", state 2.\n', '< PyMOL>get line_width,pept\n', '<  get: line_width = 2.00000 in object pept\n', '< PyMOL>get line_width,pept,1\n', '<  get: line_width = 4.00000 in object pept state 1\n', '< PyMOL>get line_width,pept,2\n', '<  get: line_width = 6.00000 in object pept state 2\n', '< PyMOL>get line_width,pept,3\n', '<  get: line_width = 2.00000 in object pept state 3\n', '< PyMOL>unset line_width,pept,2\n', '<  Setting: line_width unset in object "pept", state 2.\n', '< PyMOL>get line_width,pept\n', '<  get: line_width = 2.00000 in object pept\n', '< PyMOL>get line_width,pept,1\n', '<  get: line_width = 4.00000 in object pept state 1\n', '< PyMOL>get line_width,pept,2\n', '<  get: line_width = 2.00000 in object pept state 2\n', '< PyMOL>get line_width,pept,3\n', '<  get: line_width = 2.00000 in object pept state 3\n', '< PyMOL>unset line_width,pept\n', '<  Setting: line_width unset in object "pept".\n', '< PyMOL>get line_width,pept\n', '<  get: line_width = 1.49000 in object pept\n', '< PyMOL>get line_width,pept,1\n', '<  get: line_width = 4.00000 in object pept state 1\n', '< PyMOL>get line_width,pept,2\n', '<  get: line_width = 1.49000 in object pept state 2\n', '< PyMOL>get line_width,pept,3\n', '<  get: line_width = 1.49000 in object pept state 3\n', '< PyMOL>unset line_width,pept,1\n', '<  Setting: line_width unset in object "pept", state 1.\n', '< PyMOL>get line_width,pept\n', '<  get: line_width = 1.49000 in object pept\n', '< PyMOL>get line_width,pept,1\n', '<  get: line_width = 1.49000 in object pept state 1\n', '< PyMOL>get line_width,pept,2\n', '<  get: line_width = 1.49000 in object pept state 2\n', '< PyMOL>get line_width,pept,3\n', '<  get: line_width = 1.49000 in object pept state 3\n']
 run_tests: C0170scene...
 run_tests: C0170scene.log DIFFERS over about 125 lines:
['1,250d0\n', '< PyMOL>scene -10\n', "< Error: unknown scene: '-10'. Choices:\n", '< PyMOL>scene 9999\n', "< Error: unknown scene: '9999'. Choices:\n", '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '<   1.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   1.000\n', '<   0.000   0.000 -50.000   0.000   0.000   0.000  40.000 100.000 -20.000\n', '< PyMOL>scene 1,store\n', '<  scene: scene stored as "1".\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 166 graphics primitives.\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '<   1.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   1.000\n', '<   0.000   0.000 -63.191   1.224 -10.279  20.545  49.820  76.561 -20.000\n', '< PyMOL>scene 2,store\n', '<  scene: scene stored as "2".\n', '< PyMOL>scene 1,recall\n', '<  Scene: view updated.\n', '<  scene: "1" recalled.\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 0 graphics primitives.\n', '< PyMOL>scene 2\n', '<  Scene: view updated.\n', '<  scene: "2" recalled.\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 166 graphics primitives.\n', '< PyMOL>dist tst,5/ca,8/ca\n', '<  Executive: object "tst" created.\n', '< PyMOL>turn x,5\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '<   1.000   0.000   0.000   0.000   0.996   0.087   0.000  -0.087   0.996\n', '<   0.000   0.000 -63.191   1.224 -10.279  20.545  49.820  76.561 -20.000\n', '< PyMOL>scene 3,store\n', '<  scene: scene stored as "3".\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 180 graphics primitives.\n', '< PyMOL>hide dashes,tst\n', '< PyMOL>turn y,5\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '<   0.996   0.000  -0.087   0.008   0.996   0.087   0.087  -0.087   0.992\n', '<   0.000   0.000 -63.191   1.224 -10.279  20.545  49.820  76.561 -20.000\n', '< PyMOL>scene 4,store\n', '<  scene: scene stored as "4".\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 172 graphics primitives.\n', '< PyMOL>scene 3\n', '<  Scene: view updated.\n', '<  scene: "3" recalled.\n', '< PyMOL>disable tst\n', '< PyMOL>turn z,20\n', '< PyMOL>scene 5,store\n', '<  scene: scene stored as "5".\n', '< PyMOL>scene 1\n', '<  Scene: view updated.\n', '<  scene: "1" recalled.\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '<   1.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   1.000\n', '<   0.000   0.000 -50.000   0.000   0.000   0.000  40.000 100.000 -20.000\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 0 graphics primitives.\n', '< PyMOL>scene 2\n', '<  Scene: view updated.\n', '<  scene: "2" recalled.\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '<   1.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   1.000\n', '<   0.000   0.000 -63.191   1.224 -10.279  20.545  49.820  76.561 -20.000\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 166 graphics primitives.\n', '< PyMOL>scene 3\n', '<  Scene: view updated.\n', '<  scene: "3" recalled.\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '<   1.000   0.000   0.000   0.000   0.996   0.087   0.000  -0.087   0.996\n', '<   0.000   0.000 -63.191   1.224 -10.279  20.545  49.820  76.561 -20.000\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 180 graphics primitives.\n', '< PyMOL>scene 4\n', '<  Scene: view updated.\n', '<  scene: "4" recalled.\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '<   0.996   0.000  -0.087   0.008   0.996   0.087   0.087  -0.087   0.992\n', '<   0.000   0.000 -63.191   1.224 -10.279  20.545  49.820  76.561 -20.000\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 172 graphics primitives.\n', '< PyMOL>scene 5\n', '<  Scene: view updated.\n', '<  scene: "5" recalled.\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '<   0.940   0.342   0.000  -0.341   0.936   0.087   0.030  -0.082   0.996\n', '<   0.000   0.000 -63.191   1.224 -10.279  20.545  49.820  76.561 -20.000\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 166 graphics primitives.\n', '< PyMOL>scene 0\n', "< Error: unknown scene: '0'. Choices:\n", '<   1  2  3  4  5\n', '< PyMOL>scene 6\n', "< Error: unknown scene: '6'. Choices:\n", '<   1  2  3  4  5\n', '< PyMOL>scene 1000\n', "< Error: unknown scene: '1000'. Choices:\n", '<   1  2  3  4  5\n', '< PyMOL>scene 4,clear\n', "<  scene: '4' deleted.\n", '< PyMOL>scene 4\n', "< Error: unknown scene: '4'. Choices:\n", '<   1  2  3  5\n', '< PyMOL>scene *\n', '<  scene: current order:\n', '<   1  2  3  5\n', '< PyMOL>scene *,clear\n', '< PyMOL>scene *\n', '<  scene: current order:\n', '< PyMOL>scene 1\n', "< Error: unknown scene: '1'. Choices:\n", '< PyMOL>hide\n', '< PyMOL>show lines\n', '< PyMOL>color red\n', '<  Executive: Colored 107 atoms.\n', '< PyMOL>scene 1, store\n', '<  scene: scene stored as "1".\n', '< PyMOL>count_atoms color red\n', '<  count_atoms: 107 atoms\n', '< PyMOL>count_atoms color blue\n', '<  count_atoms: 0 atoms\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 112 graphics primitives.\n', '< PyMOL>hide\n', '< PyMOL>show sticks\n', '< PyMOL>color blue\n', '<  Executive: Colored 107 atoms.\n', '< PyMOL>scene 2, store\n', '<  scene: scene stored as "2".\n', '< PyMOL>count_atoms color red\n', '<  count_atoms: 0 atoms\n', '< PyMOL>count_atoms color blue\n', '<  count_atoms: 107 atoms\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 112 graphics primitives.\n', '< PyMOL>scene 1\n', '<  Scene: view updated.\n', '<  scene: "1" recalled.\n', '< PyMOL>count_atoms color red\n', '<  count_atoms: 107 atoms\n', '< PyMOL>count_atoms color blue\n', '<  count_atoms: 0 atoms\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 112 graphics primitives.\n', '< PyMOL>scene 2\n', '<  Scene: view updated.\n', '<  scene: "2" recalled.\n', '< PyMOL>count_atoms color red\n', '<  count_atoms: 0 atoms\n', '< PyMOL>count_atoms color blue\n', '<  count_atoms: 107 atoms\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 112 graphics primitives.\n', '< PyMOL>scene 2,rename,new_key=3\n', "<  scene: '2' renamed to '3'.\n", '< PyMOL>scene 1\n', '<  Scene: view updated.\n', '<  scene: "1" recalled.\n', '< PyMOL>count_atoms rep lines\n', '<  count_atoms: 107 atoms\n', '< PyMOL>count_atoms color red\n', '<  count_atoms: 107 atoms\n', '< PyMOL>count_atoms rep sticks\n', '<  count_atoms: 0 atoms\n', '< PyMOL>count_atoms color blue\n', '<  count_atoms: 0 atoms\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 112 graphics primitives.\n', '< PyMOL>scene 3\n', '<  Scene: view updated.\n', '<  scene: "3" recalled.\n', '< PyMOL>count_atoms rep lines\n', '<  count_atoms: 0 atoms\n', '< PyMOL>count_atoms color red\n', '<  count_atoms: 0 atoms\n', '< PyMOL>count_atoms rep sticks\n', '<  count_atoms: 107 atoms\n', '< PyMOL>count_atoms color blue\n', '<  count_atoms: 107 atoms\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 112 graphics primitives.\n', '< PyMOL>scene 2\n', "< Error: unknown scene: '2'. Choices:\n", '<   1  3\n', '< PyMOL>count_atoms rep lines\n', '<  count_atoms: 0 atoms\n', '< PyMOL>count_atoms color red\n', '<  count_atoms: 0 atoms\n', '< PyMOL>count_atoms rep sticks\n', '<  count_atoms: 107 atoms\n', '< PyMOL>count_atoms color blue\n', '<  count_atoms: 107 atoms\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 112 graphics primitives.\n', '< PyMOL>scene 3\n', '<  Scene: view updated.\n', '<  scene: "3" recalled.\n', '< PyMOL>hide\n', '< PyMOL>color green\n', '<  Executive: Colored 107 atoms.\n', '< PyMOL>show spheres\n', '< PyMOL>scene auto, update\n', '<  scene: scene updated as "3".\n', '< PyMOL>count_atoms rep spheres\n', '<  count_atoms: 107 atoms\n', '< PyMOL>count_atoms color green\n', '<  count_atoms: 107 atoms\n', '< PyMOL>count_atoms rep lines\n', '<  count_atoms: 0 atoms\n', '< PyMOL>count_atoms color red\n', '<  count_atoms: 0 atoms\n', '< PyMOL>count_atoms rep sticks\n', '<  count_atoms: 0 atoms\n', '< PyMOL>count_atoms color blue\n', '<  count_atoms: 0 atoms\n', '< PyMOL>scene 1\n', '<  Scene: view updated.\n', '<  scene: "1" recalled.\n', '< PyMOL>count_atoms rep spheres\n', '<  count_atoms: 0 atoms\n', '< PyMOL>count_atoms color green\n', '<  count_atoms: 0 atoms\n', '< PyMOL>count_atoms rep lines\n', '<  count_atoms: 107 atoms\n', '< PyMOL>count_atoms color red\n', '<  count_atoms: 107 atoms\n', '< PyMOL>count_atoms rep sticks\n', '<  count_atoms: 0 atoms\n', '< PyMOL>count_atoms color blue\n', '<  count_atoms: 0 atoms\n', '< PyMOL>scene 3\n', '<  Scene: view updated.\n', '<  scene: "3" recalled.\n', '< PyMOL>count_atoms rep spheres\n', '<  count_atoms: 107 atoms\n', '< PyMOL>count_atoms color green\n', '<  count_atoms: 107 atoms\n', '< PyMOL>count_atoms rep lines\n', '<  count_atoms: 0 atoms\n', '< PyMOL>count_atoms color red\n', '<  count_atoms: 0 atoms\n', '< PyMOL>count_atoms rep sticks\n', '<  count_atoms: 0 atoms\n', '< PyMOL>count_atoms color blue\n', '<  count_atoms: 0 atoms\n']
 run_tests: C0180embed...
 run_tests: C0180embed.log DIFFERS over about 45 lines:
['1,90d0\n', '< PyMOL>load dat/embed01.p1m\n', '< PyMOL>embed peptide\n', '<  Embed: read 108 lines.\n', '< PyMOL>load_embedded peptide\n', '<  CmdLoad: PDB-string loaded into object "peptide", state 1.\n', '< PyMOL>count_atoms\n', '<  count_atoms: 107 atoms\n', '< PyMOL>hide everything, peptide\n', '< PyMOL>show sticks, peptide\n', '< PyMOL>set valence\n', '<  Setting: valence set to on.\n', '< PyMOL>set ray_default_renderer,2\n', '<  Setting: ray_default_renderer set to 2.\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 207 graphics primitives.\n', '< PyMOL>load dat/embed02.p1m\n', '< PyMOL>embed sm, mol\n', '<  Embed: read 78 lines.\n', '< PyMOL>load_embedded sm\n', '<  ExecutiveLoad: content loaded into object "sm", through state 1.\n', '< PyMOL>hide everything, sm\n', '< PyMOL>show sticks, sm\n', '< PyMOL>set valence\n', '<  Setting: valence set to on.\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 269 graphics primitives.\n', '< PyMOL>load dat/embed03.p1m\n', '< PyMOL>embed ligands,sdf\n', '<  Embed: read 923 lines.\n', '< PyMOL>load_embedded ligands\n', '<  ObjectMoleculeReadStr: read through molecule 1.\n', '<  ObjectMoleculeReadStr: read through molecule 2.\n', '<  ObjectMoleculeReadStr: read through molecule 3.\n', '<  ObjectMoleculeReadStr: read through molecule 4.\n', '<  ObjectMoleculeReadStr: read through molecule 5.\n', '<  ObjectMoleculeReadStr: read through molecule 6.\n', '<  ObjectMoleculeReadStr: read through molecule 7.\n', '<  ObjectMoleculeReadStr: read through molecule 8.\n', '<  ObjectMoleculeReadStr: read through molecule 9.\n', '<  ObjectMoleculeReadStr: read through molecule 10.\n', '<  ExecutiveLoad: content loaded into object "ligands", through state 10.\n', '< PyMOL>hide everything, ligands\n', '< PyMOL>show sticks, ligands\n', '< PyMOL>set valence\n', '<  Setting: valence set to on.\n', '< PyMOL>frame 5\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 343 graphics primitives.\n', '< PyMOL>load dat/embed04.p1m\n', '< PyMOL>embed m2, mol2\n', '<  Embed: read 963 lines.\n', '< PyMOL>load_embedded m2\n', '<  ObjectMoleculeReadStr: read through molecule 1.\n', '<  ObjectMoleculeReadStr: read through molecule 2.\n', '<  ObjectMoleculeReadStr: read through molecule 3.\n', '<  ObjectMoleculeReadStr: read through molecule 4.\n', '<  ObjectMoleculeReadStr: read through molecule 5.\n', '<  ObjectMoleculeReadStr: read through molecule 6.\n', '<  ObjectMoleculeReadStr: read through molecule 7.\n', '<  ObjectMoleculeReadStr: read through molecule 8.\n', '<  ObjectMoleculeReadStr: read through molecule 9.\n', '<  ObjectMoleculeReadStr: read through molecule 10.\n', '<  ExecutiveLoad: content loaded into object "m2", through state 16.\n', '< PyMOL>hide everything, m2\n', '< PyMOL>show sticks, m2\n', '< PyMOL>set valence\n', '<  Setting: valence set to on.\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 356 graphics primitives.\n', '< PyMOL>load dat/embed05.p1m\n', '< PyMOL>embed ligand, mol\n', '<  Embed: read 77 lines.\n', '< PyMOL>embed protein\n', '<  Embed: read 227 lines.\n', '< PyMOL>load_embedded ligand\n', '<  ExecutiveLoad: content loaded into object "ligand", through state 1.\n', '< PyMOL>load_embedded protein\n', '<  CmdLoad: PDB-string loaded into object "protein", state 1.\n', '< PyMOL>hide lines, ligand\n', '< PyMOL>show sticks, ligand\n', '< PyMOL>set valence\n', '<  Setting: valence set to on.\n', '< PyMOL>dist hbond, protein, ligand, mode=2\n', '<  Executive: object "hbond" created.\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 868 graphics primitives.\n', '< PyMOL>print cmd.get_state()\n', '< 5\n', '< PyMOL>print cmd.get_names()\n', "< ['peptide', 'sm', 'ligands', 'm2', 'ligand', 'protein', 'hbond']\n"]
 run_tests: C0181embed...
 run_tests: C0181embed.log DIFFERS over about 10 lines:
['1,20d0\n', '< PyMOL>load dat/embed06.p1m\n', '< PyMOL>embed\n', '<  Embed: read 108 lines.\n', '< PyMOL>load_embedded\n', '<  CmdLoad: PDB-string loaded into object "embed06", state 1.\n', '< PyMOL>hide\n', '< PyMOL>show surface\n', '< PyMOL>set transparency, 0.5\n', '<  Setting: transparency set to 0.50000.\n', '< PyMOL>set surface_color, white\n', '<  Setting: surface_color set to white.\n', '< PyMOL>show sticks\n', '< PyMOL>set ray_default_renderer,2\n', '<  Setting: ray_default_renderer set to 2.\n', '< PyMOL>ray\n', '<  RepSurface: 1319 surface points.\n', '<  RepSurface: 2634 triangles.\n', '<  RayRenderTest: obtained 2800 graphics primitives.\n', '< PyMOL>print cmd.get_names()\n', "< ['embed06']\n"]
 run_tests: C0200feedback...
 run_tests: C0200feedback.log DIFFERS over about 127 lines:
['1,253d0\n', '< PyMOL>feedback\n', '<  feedback: possible actions: \n', '< set, enable, disable\n', '<  feedback: Please specify module names:\n', '<     all\n', '<     api\n', '<     ccmd\n', '<     cgo\n', '<     cmd\n', '<     color\n', '<     coordset\n', '<     distset\n', '<     editor\n', '<     executive\n', '<     export\n', '<     extrude\n', '<     feedback\n', '<     gadgetset\n', '<     isomesh\n', '<     isosurface\n', '<     main\n', '<     map\n', '<     match\n', '<     matrix\n', '<     movie\n', '<     mypng\n', '<     nag\n', '<     object\n', '<     objectcallback\n', '<     objectcgo\n', '<     objectdist\n', '<     objectgadget\n', '<     objectmap\n', '<     objectmesh\n', '<     objectmolecule\n', '<     objectslice\n', '<     objectsurface\n', '<     opengl\n', '<     ortho\n', '<     parser\n', '<     python\n', '<     raw\n', '<     ray\n', '<     rep\n', '<     repangle\n', '<     repcartoon\n', '<     repcylbond\n', '<     repdihederal\n', '<     repdistdash\n', '<     repdistlabel\n', '<     repdot\n', '<     replabel\n', '<     repmesh\n', '<     repnonbonded\n', '<     repnonbondedsphere\n', '<     repribbon\n', '<     repsphere\n', '<     repsurface\n', '<     repwirebond\n', '<     scene\n', '<     sculpt\n', '<     selector\n', '<     setting\n', '<     shaker\n', '<     symmetry\n', '<     threads\n', '<     triangle\n', '<     vfont\n', '<  feedback: Please specify masks:\n', '<     actions\n', '<     blather\n', '<     debugging\n', '<     details\n', '<     errors\n', '<     everything\n', '<     output\n', '<     results\n', '<     warnings\n', '< PyMOL>feedback ?\n', '< Usage: feedback [ action [, module [, mask ]]]\n', '< PyMOL>feedback enable\n', '<  feedback: Please specify module names:\n', '<     all\n', '<     api\n', '<     ccmd\n', '<     cgo\n', '<     cmd\n', '<     color\n', '<     coordset\n', '<     distset\n', '<     editor\n', '<     executive\n', '<     export\n', '<     extrude\n', '<     feedback\n', '<     gadgetset\n', '<     isomesh\n', '<     isosurface\n', '<     main\n', '<     map\n', '<     match\n', '<     matrix\n', '<     movie\n', '<     mypng\n', '<     nag\n', '<     object\n', '<     objectcallback\n', '<     objectcgo\n', '<     objectdist\n', '<     objectgadget\n', '<     objectmap\n', '<     objectmesh\n', '<     objectmolecule\n', '<     objectslice\n', '<     objectsurface\n', '<     opengl\n', '<     ortho\n', '<     parser\n', '<     python\n', '<     raw\n', '<     ray\n', '<     rep\n', '<     repangle\n', '<     repcartoon\n', '<     repcylbond\n', '<     repdihederal\n', '<     repdistdash\n', '<     repdistlabel\n', '<     repdot\n', '<     replabel\n', '<     repmesh\n', '<     repnonbonded\n', '<     repnonbondedsphere\n', '<     repribbon\n', '<     repsphere\n', '<     repsurface\n', '<     repwirebond\n', '<     scene\n', '<     sculpt\n', '<     selector\n', '<     setting\n', '<     shaker\n', '<     symmetry\n', '<     threads\n', '<     triangle\n', '<     vfont\n', '<  feedback: Please specify masks:\n', '<     actions\n', '<     blather\n', '<     debugging\n', '<     details\n', '<     errors\n', '<     everything\n', '<     output\n', '<     results\n', '<     warnings\n', '< PyMOL>feedback enable, selector\n', '<  feedback: Please specify masks:\n', '<     actions\n', '<     blather\n', '<     debugging\n', '<     details\n', '<     errors\n', '<     everything\n', '<     output\n', '<     results\n', '<     warnings\n', '< PyMOL>feedback enable, selector, everything\n', '< PyMOL>feedback enable, repcartoon extrude, everything\n', '< PyMOL>load dat/pept.pdb\n', '< SelectorCreate-Debug: entered...\n', '< SelectorUpdateTableSingleObject-Debug: entered for pept...\n', '< SelectorUpdateTableSingleObject-Debug: leaving...\n', '<  Selector: Embedded pept, 107 atoms.\n', '<  SelectorCreate: "pept" created with 107 atoms.\n', '< SelectorUpdateTableSingleObject-Debug: entered for pept...\n', '< SelectorUpdateTableSingleObject-Debug: leaving...\n', '< SelectorUpdateTableSingleObject-Debug: entered for pept...\n', '< SelectorUpdateTableSingleObject-Debug: leaving...\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>show cartoon\n', '<  SelectorGetTmp-Debug: entered with "all".\n', '<  SelectorGetTmp-Debug: leaving with "all".\n', '< PyMOL>refresh\n', '<  RepCartoonNew-Debug: entered.\n', '<  RepCartoon: found CA in 1; a2 -1\n', '<  RepCartoon: found CA in 1; a2 -1\n', '<  RepCartoon: found CA in 2; a2 1\n', '<  RepCartoon: found CA in 2; a2 1\n', '<  RepCartoon: found CA in 3; a2 9\n', '<  RepCartoon: found CA in 3; a2 9\n', '<  RepCartoon: found CA in 4; a2 15\n', '<  RepCartoon: found CA in 4; a2 15\n', '<  RepCartoon: found CA in 5; a2 20\n', '<  RepCartoon: found CA in 5; a2 20\n', '<  RepCartoon: found CA in 6; a2 34\n', '<  RepCartoon: found CA in 6; a2 34\n', '<  RepCartoon: found CA in 7; a2 44\n', '<  RepCartoon: found CA in 7; a2 44\n', '<  RepCartoon: found CA in 8; a2 52\n', '<  RepCartoon: found CA in 8; a2 52\n', '<  RepCartoon: found CA in 9; a2 56\n', '<  RepCartoon: found CA in 9; a2 56\n', '<  RepCartoon: found CA in 10; a2 65\n', '<  RepCartoon: found CA in 10; a2 65\n', '<  RepCartoon: found CA in 11; a2 73\n', '<  RepCartoon: found CA in 11; a2 73\n', '<  RepCartoon: found CA in 12; a2 80\n', '<  RepCartoon: found CA in 12; a2 80\n', '<  RepCartoon: found CA in 13; a2 94\n', '<  RepCartoon: found CA in 13; a2 94\n', '<  RepCartoon-Debug: path outlined, interpolating...\n', '<  RepCartoon: seg 0 *s 1 , *(s+1) 1\n', '<  RepCartoon: seg 1 *s 1 , *(s+1) 1\n', '<  RepCartoon: seg 2 *s 1 , *(s+1) 1\n', '<  RepCartoon: seg 3 *s 1 , *(s+1) 1\n', '<  RepCartoon: seg 4 *s 1 , *(s+1) 1\n', '<  RepCartoon: seg 5 *s 1 , *(s+1) 1\n', '<  RepCartoon: seg 6 *s 1 , *(s+1) 1\n', '<  RepCartoon: seg 7 *s 1 , *(s+1) 1\n', '<  RepCartoon: seg 8 *s 1 , *(s+1) 1\n', '<  RepCartoon: seg 9 *s 1 , *(s+1) 1\n', '<  RepCartoon: seg 10 *s 1 , *(s+1) 1\n', '<  RepCartoon: seg 11 *s 1 , *(s+1) 1\n', '<  RepCartoon-Debug: generating coordinate systems...\n', '<  RepCartoon-Debug: creating 3D scaffold...\n', '<  ExtrudeComputeTangents-DEBUG: entered.\n', '<  ExtrudeComputeTangents-DEBUG: exiting...\n', '<  ExtrudeRectangle-DEBUG: entered...\n', '<  ExtrudeRectangle-DEBUG: exiting...\n', '<  ExtrudeBuildNormals2f-DEBUG: entered.\n', '<  ExtrudeBuildNormals2f-DEBUG: entering...\n', '<  ExtrudeCGOSurfaceStrand-DEBUG: entered.\n', '<  ExtrudeCGOSurfaceStrand-DEBUG: exiting...\n', '<  ExtrudeComputeTangents-DEBUG: entered.\n', '<  ExtrudeComputeTangents-DEBUG: exiting...\n', '<  ExtrudeCircle-DEBUG: entered.\n', '<  ExtrudeCircle-DEBUG: exiting...\n', '<  ExtrudeBuildNormals1f-DEBUG: entered.\n', '<  ExtrudeBuildNormals1f-DEBUG: exiting...\n', '<  ExtrudeCGOSurfaceTube-DEBUG: entered.\n', '<  ExtrudeCGOSurfaceTube-DEBUG: exiting...\n', '<  ExtrudeComputeTangents-DEBUG: entered.\n', '<  ExtrudeComputeTangents-DEBUG: exiting...\n', '<  ExtrudeRectangle-DEBUG: entered...\n', '<  ExtrudeRectangle-DEBUG: exiting...\n', '<  ExtrudeBuildNormals2f-DEBUG: entered.\n', '<  ExtrudeBuildNormals2f-DEBUG: entering...\n', '<  ExtrudeCGOSurfaceStrand-DEBUG: entered.\n', '<  ExtrudeCGOSurfaceStrand-DEBUG: exiting...\n', '< PyMOL>feedback disable, repcartoon extrude, everything\n', '< PyMOL>rebuild\n', '< PyMOL>refresh\n']
 run_tests: C0201extend...
 run_tests: C0201extend.log DIFFERS over about 11 lines:
['1,22d0\n', '< PyMOL>def foo(moo=2): print moo\n', "< PyMOL>cmd.extend('foo',foo)\n", '< PyMOL>foo\n', '< 2\n', '< PyMOL>foo 3\n', '< 3\n', '< PyMOL>foo moo=5\n', '< 5\n', '< PyMOL>foo ?\n', '< Usage: foo [ moo ]\n', '< PyMOL>def fie(moo=3):\\\n', '< PyMOL>"help for fie" \\\n', '< PyMOL>print moo\n', '< PyMOL>print fie.__doc__\n', '< help for fie\n', '< PyMOL>help fie\n', "< Error: unknown topic: 'fie'.\n", "< PyMOL>cmd.extend('fie',fie)\n", '< PyMOL>help fie\n', '< \n', '< help for fie \n', '< \n']
 run_tests: C0202help_python...
 run_tests: C0202help_python.log DIFFERS over about 50 lines:
['1,99d0\n', '< PyMOL>help def\n', '< \n', '< DESCRIPTION\n', '< \n', '<     You have asked for help on a Python keyword which is available\n', '<     from within the PyMOL command language.  Please consult the\n', '<     official Python documentation at http://www.python.org for\n', '<     detailed information on Python keywords.\n', '< \n', '<     You may include Python blocks in your PyMOL command scripts, but do\n', '<     note that multi-line blocks of Python in PyMOL command files will\n', '<     require explicit continuation syntax in order to execute properly\n', '<     (see below).\n', '< \n', '<     Generally, if you want to write Python block which span multiple\n', '<     lines, you will want to use ".py" file, and then use "extend" in\n', '<     order to expose your new code to the PyMOL command language.  This\n', '<     will give you better error checking and more predictable results.\n', '< \n', '< EXAMPLES\n', '< \n', '<     a=1\n', '<     while a<10: \\\n', '<         print a \\\n', '<         a=a+1\n', '< \n', '< SEE ALSO\n', '< \n', '<     extend, run, @ \n', '< \n', "< PyMOL>cmd.python_help.__doc__='python help'\n", '< PyMOL>help for\n', '< \n', '< python help \n', '< \n', '< PyMOL>help pass\n', '< \n', '< python help \n', '< \n', '< PyMOL>help raise\n', '< \n', '< python help \n', '< \n', '< PyMOL>help return\n', '< \n', '< python help \n', '< \n', '< PyMOL>help try\n', '< \n', '< python help \n', '< \n', '< PyMOL>help except\n', '< \n', '< python help \n', '< \n', '< PyMOL>help finally\n', '< \n', '< python help \n', '< \n', '< PyMOL>help while\n', '< \n', '< python help \n', '< \n', '< PyMOL>help assert\n', '< \n', '< python help \n', '< \n', '< PyMOL>help class\n', '< \n', '< python help \n', '< \n', '< PyMOL>help continue\n', '< \n', '< python help \n', '< \n', '< PyMOL>help del\n', '< \n', '< python help \n', '< \n', '< PyMOL>help elif\n', '< \n', '< python help \n', '< \n', '< PyMOL>help else\n', '< \n', '< python help \n', '< \n', '< PyMOL>help global\n', '< \n', '< python help \n', '< \n', '< PyMOL>help if\n', '< \n', '< python help \n', '< \n', '< PyMOL>help import\n', '< \n', '< python help \n', '< \n']
 run_tests: C0300session...
 run_tests: C0300session.log DIFFERS over about 13 lines:
['1,26d0\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>select cas,name ca\n', '<  Selector: selection "cas" defined with 13 atoms.\n', '< PyMOL>set line_width,5\n', '<  Setting: line_width set to 5.00000.\n', '< PyMOL>show spheres,name n\n', '< PyMOL>save tmp/session.pse\n', '<  Save: wrote "tmp/session.pse".\n', '< PyMOL>reinitialize\n', '< PyMOL>print cmd.get_names()\n', '< []\n', '< PyMOL>get line_width\n', '<  get: line_width = 1.49000\n', '< PyMOL>count_atoms rep spheres\n', '<  count_atoms: 0 atoms\n', '< PyMOL>load tmp/session.pse\n', '<  Executive: Loading version 1.20 session...\n', '< PyMOL>print cmd.get_names()\n', "< ['pept']\n", '< PyMOL>get line_width\n', '<  get: line_width = 5.00000\n', '< PyMOL>count_atoms rep spheres\n', '<  count_atoms: 13 atoms\n', '< PyMOL>count_atoms cas\n', '<  count_atoms: 13 atoms\n']
 run_tests: C0500misc...
 run_tests: C0500misc.log DIFFERS over about 129 lines:
['1,258d0\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>cls\n', '< \n', '< PyMOL>print cmd.count_states()\n', '< 1\n', '< PyMOL>print cmd.count_states("pept")\n', '< 1\n', '< PyMOL>cmd.do("print \'it be done\'")\n', "< PyMOL>print 'it be done'\n", '< it be done\n', '< PyMOL>viewport 200,150\n', '< PyMOL>stereo on\n', '< PyMOL>turn x,90\n', '< PyMOL>origin\n', '< PyMOL>origin (i;11)\n', '< PyMOL>origin pept\n', '< PyMOL>zoom (i;11)\n', '< PyMOL>zoom pept\n', '< PyMOL>zoom\n', '< PyMOL>frame 1\n', '< PyMOL>frame 2\n', '< PyMOL>move x,2\n', '< PyMOL>clip near,2\n', '< PyMOL>clip far,2\n', '< PyMOL>refresh\n', '< PyMOL>reset\n', '< PyMOL>meter_reset\n', '< PyMOL>mclear\n', '< PyMOL>mset 1 x10\n', '< PyMOL>mdo 1:turn x,5\n', '< PyMOL>mdo 2:turn y,10\n', '< PyMOL>rock\n', '< PyMOL>rock\n', '< PyMOL>forward\n', '< PyMOL>backward\n', '< PyMOL>rewind\n', '< PyMOL>ending\n', '< PyMOL>middle\n', '< PyMOL>mplay\n', '< PyMOL>mstop\n', '< PyMOL>color red\n', '<  Executive: Colored 107 atoms.\n', '< PyMOL>color blue,(name n)\n', '<  Executive: Colored 13 atoms.\n', '< PyMOL>flag 3=(resn his)\n', '<  Flag: flag 3 is set in 10 of 107 atoms.\n', '< PyMOL>set_color dude = [ 1.0,0.6,0.3]\n', '<  Color: "dude" defined as [ 1.000, 0.600, 0.300 ].\n', '< PyMOL>color dude,(name o)\n', '<  Executive: Colored 13 atoms.\n', '< PyMOL>show sticks,(all)\n', '< PyMOL>hide\n', '< PyMOL>show lines\n', '< PyMOL>mmatrix store\n', '< PyMOL>turn x,45\n', '< PyMOL>mmatrix recall\n', '< PyMOL>disable\n', '< PyMOL>enable\n', '< PyMOL>mmatrix clear\n', '< PyMOL>refresh\n', '< PyMOL>rebuild\n', '< PyMOL>refresh\n', '< PyMOL>set line_smooth=1\n', '<  Setting: line_smooth set to on.\n', '< PyMOL>label (all),chain\n', '<  Label: labelled 107 atoms.\n', "< PyMOL>label (all),''\n", '<  Label: labelled 107 atoms.\n', '< PyMOL>stored.cnt = 0\n', '< PyMOL>iterate (all),stored.cnt=stored.cnt+1\n', '<  Iterate: iterated over 107 atoms.\n', '< PyMOL>print stored.cnt\n', '< 107\n', '< PyMOL>stored.x = 0\n', '< PyMOL>iterate_state 1,(all),stored.x=stored.x+x\n', '<  IterateState: iterated over 107 atom coordinate states.\n', '< PyMOL>print "%8.4f"%stored.x\n', '< 130.9720\n', "< PyMOL>alter (all),segi='PEPT'\n", '<  Alter: modified 107 atoms.\n', '< PyMOL>alter_state 1,(all),x = x + 1.0\n', '<  AlterState: modified 107 atom coordinate states.\n', '< PyMOL>print "%8.4f"%cmd.get_dihedral("(i;11&n;n)","(i;11&n;ca)","(i;11&n;cb)","(i;11&n;cg)")\n', '< -160.7909\n', '< PyMOL>edit (i;11&n;n), (i;11&n;c), pkbond=0\n', '<  Selector: selection "pk1" defined with 1 atoms.\n', '<  Selector: selection "pk2" defined with 1 atoms.\n', '< PyMOL>dist\n', '<  Executive: object "dist01" created.\n', '< PyMOL>dist (pk1),(pk2)\n', '<  Executive: object "dist02" created.\n', '< PyMOL>dist tst\n', '<  Executive: object "tst" created.\n', '< PyMOL>dist tst2 = (pk1),(pk2)\n', '<  Executive: object "tst2" created.\n', '< PyMOL>bond\n', '<  Bond: 1 bonds added to model "pept".\n', '< PyMOL>unbond\n', '<  Unbond: 1 bonds removed from model "pept".\n', '< PyMOL>bond (pk1),(pk2),2\n', '<  Bond: 1 bonds added to model "pept".\n', '< PyMOL>unbond (pk1),(pk2)\n', '<  Unbond: 1 bonds removed from model "pept".\n', '< PyMOL>copy cpy=pept\n', '<  Executive: object "cpy" created.\n', '<  Executive: object cpy created.\n', '< PyMOL>select cpy_sel = (cpy)\n', '<  Selector: selection "cpy_sel" defined with 107 atoms.\n', '< PyMOL>alter_state 1,(cpy),x=x+math.cos(y+z)\n', '<  AlterState: modified 107 atom coordinate states.\n', '< PyMOL>rms cpy,pept\n', '<  Executive: RMS =    0.695 (107 to 107 atoms)\n', '< PyMOL>rms (cpy and name ca),pept\n', '<  Executive: RMS =    0.639 (13 to 13 atoms)\n', '< PyMOL>rms (cpy and name ca),(pept &n;ca)\n', '<  Executive: RMS =    0.639 (13 to 13 atoms)\n', '< PyMOL>rms_cur cpy,pept\n', '<  Executive: RMS =    0.700 (107 to 107 atoms)\n', '< PyMOL>rms_cur (cpy and name ca),pept\n', '<  Executive: RMS =    0.722 (13 to 13 atoms)\n', '< PyMOL>rms_cur (cpy and name ca),(pept &n;ca)\n', '<  Executive: RMS =    0.722 (13 to 13 atoms)\n', '< PyMOL>fit cpy,pept\n', '<  Executive: RMS =    0.695 (107 to 107 atoms)\n', '< PyMOL>fit (cpy),(pept)\n', '<  Executive: RMS =    0.695 (107 to 107 atoms)\n', '< PyMOL>fit (cpy and name ca),(pept &n;ca)\n', '<  Executive: RMS =    0.639 (13 to 13 atoms)\n', '< PyMOL>pair_fit (cpy&i;11&n;ca),(pept&i;11&n;ca),\\\n', '< PyMOL>(cpy&i;5&n;ca),(pept&i;5&n;ca),\\\n', '< PyMOL>(cpy&i;1&n;ca),(pept&i;1&n;ca),\\\n', '< PyMOL>(cpy&i;8&n;ca),(pept&i;8&n;ca)\n', '<  ExecutiveRMS: RMS =    0.478 (4 to 4 atoms)\n', '< PyMOL>update (cpy),(pept)\n', '<  Update: coordinates updated for 107 atoms.\n', '< PyMOL>remove (cpy and name c)\n', '<  Remove: eliminated 13 atoms in model "cpy".\n', '< PyMOL>edit (cpy and i;11 & n;ca)\n', '<  Selector: selection "pk1" defined with 1 atoms.\n', '< PyMOL>remove_picked\n', '<  Remove: eliminated 1 atoms in model "cpy".\n', '< PyMOL>edit (cpy and i;5 & n;ca),(cpy and i;5 and n;cb)\n', '<  Selector: selection "pk1" defined with 1 atoms.\n', '<  Selector: selection "pk2" defined with 1 atoms.\n', "< PyMOL>alter (cpy),name=''\n", '<  Alter: modified 93 atoms.\n', '< PyMOL>rename cpy\n', '<  Rename: renamed 93 atoms.\n', '< PyMOL>rename cpy,1\n', '<  Rename: renamed 93 atoms.\n', '< PyMOL>cycle_valence\n', '< PyMOL>cycle_valence\n', '<  Remove: eliminated 1 atoms in model "cpy".\n', '<  Remove: eliminated 1 atoms in model "cpy".\n', '< PyMOL>cycle_valence\n', '< PyMOL>remove_picked\n', '< PyMOL>edit (cpy and i;11 &n;n)\n', '< Editor-Error: Invalid input selection(s).\n', '< PyMOL>cmd.attach("H",1,1)\n', '< PyMOL>create tmp = (cpy&i;5)\n', '<  Selector: found 13 atoms.\n', '<  Executive: object "tmp" created.\n', '< PyMOL>fuse (cpy&i;11&n;cb),(tmp&n;cb)\n', '< PyMOL>edit (cpy and i;10 & n;n)\n', '< Editor-Error: Invalid input selection(s).\n', '< PyMOL>h_fill\n', '< PyMOL>h_fill\n', '< PyMOL>h_add (cpy)\n', '< PyMOL>edit (cpy and i;8 &n;o)\n', '< Editor-Error: Invalid input selection(s).\n', '< PyMOL>cmd.replace("S",3,1)\n', '<  Error: you must first pick an atom to replace.\n', '< PyMOL>delete tmp\n', '< PyMOL>delete cpy\n', '< PyMOL>delete cpy_sel\n', '< PyMOL>edit (i;11&n;ca)\n', '<  Selector: selection "pk1" defined with 1 atoms.\n', '< PyMOL>unpick\n', '< PyMOL>protect (pept and n;ca)\n', '<  Protect: 13 atoms protected from movement.\n', '< PyMOL>protect pept\n', '<  Protect: 107 atoms protected from movement.\n', '< PyMOL>protect\n', '<  Protect: 107 atoms protected from movement.\n', '< PyMOL>deprotect (pept and n;ca)\n', '<  Protect: 13 atoms deprotected.\n', '< PyMOL>deprotect\n', '<  Protect: 107 atoms deprotected.\n', '< PyMOL>mask (pept and n;ca)\n', '<  Mask: 13 atoms masked (cannot be picked or selected).\n', '< PyMOL>mask pept\n', '<  Mask: 107 atoms masked (cannot be picked or selected).\n', '< PyMOL>mask\n', '<  Mask: 107 atoms masked (cannot be picked or selected).\n', '< PyMOL>unmask (pept and n;ca)\n', '<  Mask: 13 atoms unmasked.\n', '< PyMOL>unmask\n', '<  Mask: 107 atoms unmasked.\n', '< PyMOL>edit (i;11&n;ca),(i;11&n;n),(i;11&n;c)\n', '<  Selector: selection "pk1" defined with 1 atoms.\n', '<  Selector: selection "pk2" defined with 1 atoms.\n', '<  Selector: selection "pk3" defined with 1 atoms.\n', '< PyMOL>invert\n', '<  Editor: Inverted atom.\n', '< PyMOL>invert\n', '<  Editor: Inverted atom.\n', '< PyMOL>edit (i;11&n;ca),(i;11&n;cb)\n', '<  Selector: selection "pk1" defined with 1 atoms.\n', '<  Selector: selection "pk2" defined with 1 atoms.\n', '< PyMOL>torsion 10\n', '< PyMOL>torsion -10\n', '< PyMOL>torsion 180\n', '< PyMOL>torsion 180\n', '< PyMOL>print cmd.get_model().__class__\n', '< chempy.models.Indexed\n', '< PyMOL>print "%8.3f"%cmd.get_area()\n', '< 1381.186\n', '< PyMOL>print "%8.3f"%cmd.get_area("(name ca)")\n', '<  112.133\n', '< PyMOL>print cmd.get_names()\n', "< ['pept', 'dist01', 'dist02', 'tst', 'tst2']\n", "< PyMOL>print cmd.get_type('pept')\n", '< object:molecule\n', '< PyMOL>print cmd.identify("(i;7)")\n', '< [52, 53, 54, 55]\n', '< PyMOL>print "%8.4f %8.4f %8.4f %8.4f %8.4f %8.4f"%(ext[0][0],ext[0][1],ext[0][2],ext[1][0],ext[1][1],ext[1][2])\n', '<  -4.1880 -20.3310  13.1570   9.9190   0.8630  27.0580\n', '< PyMOL>sort\n', '< PyMOL>sort pept\n', '< PyMOL>spheroid\n', "< Warning: 'spheroid' is experimental, incomplete, and unstable.\n", '<  ObjectMolecule: computing spheroid from states 1 to 1.\n', '< PyMOL>spheroid pept\n', "< Warning: 'spheroid' is experimental, incomplete, and unstable.\n", '<  ObjectMolecule: computing spheroid from states 1 to 1.\n', '< PyMOL>cmd.config_mouse(quiet=0)\n', '<  config_mouse: three_button\n', '< PyMOL>rewind\n', '< PyMOL>dele all\n', '< PyMOL>load dat/ligs3d.sdf\n', '<  ObjectMoleculeReadStr: read through molecule 1.\n', '<  ObjectMoleculeReadStr: read through molecule 2.\n', '<  ObjectMoleculeReadStr: read through molecule 3.\n', '<  ObjectMoleculeReadStr: read through molecule 4.\n', '<  ObjectMoleculeReadStr: read through molecule 5.\n', '<  ObjectMoleculeReadStr: read through molecule 6.\n', '<  ObjectMoleculeReadStr: read through molecule 7.\n', '<  ObjectMoleculeReadStr: read through molecule 8.\n', '<  ObjectMoleculeReadStr: read through molecule 9.\n', '<  ObjectMoleculeReadStr: read through molecule 10.\n', '<  ExecutiveLoad: "dat/ligs3d.sdf" loaded as "ligs3d", through state 10.\n', '< PyMOL>split_states ligs3d\n', '< PyMOL>print cmd.get_names()\n', "< ['ligs3d', 'MFCD02681585', 'MFCD01567969', 'MFCD00023789', 'MFCD02579443', 'MFCD02579410', 'MFCD02579135', 'MFCD02681468', 'MFCD00141070', 'MFCD02983625', 'MFCD00115818']\n", '< PyMOL>rewind\n', '< PyMOL>ray renderer=2\n', '<  RayRenderTest: obtained 564 graphics primitives.\n']
 run_tests: C0550pseudo...
 run_tests: C0550pseudo.log DIFFERS over about 36 lines:
['1,72d0\n', '< PyMOL>pseudoatom test\n', '<  ObjMol: created test/PSDO/P/PSD`1/PS1\n', '< PyMOL>move x,10\n', '< PyMOL>pseudoatom test\n', '<  ObjMol: created test/PSDO/P/PSD`1/PS2\n', '< PyMOL>count_atoms\n', '<  count_atoms: 2 atoms\n', '< PyMOL>ray renderer=2\n', '<  RayRenderTest: obtained 6 graphics primitives.\n', '< PyMOL>iterate all,print name+ " %0.2f"%vdw\n', '< PS1 1.00\n', '< PS2 1.00\n', '<  Iterate: iterated over 2 atoms.\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>pseudoatom test, pept and resi 1\n', '<  ObjMol: created test/PSDO/P/PSD`1/PS1\n', '< PyMOL>pseudoatom test, pept and resi 2\n', '<  ObjMol: created test/PSDO/P/PSD`1/PS2\n', '< PyMOL>pseudoatom test, pept and resi 10\n', '<  ObjMol: created test/PSDO/P/PSD`1/PS3\n', '< PyMOL>iterate name PS*, print name+ " %0.2f"%vdw\n', '< PS1 1.81\n', '< PS2 1.79\n', '< PS3 1.81\n', '<  Iterate: iterated over 3 atoms.\n', '< PyMOL>hide\n', '< PyMOL>as spheres, test\n', '< PyMOL>ray renderer=2\n', '<  RayRenderTest: obtained 3 graphics primitives.\n', '< PyMOL>bond name PS2, name PS3\n', '<  Bond: 1 bonds added to model "test".\n', '< PyMOL>show sticks, test\n', '< PyMOL>ray renderer=2\n', '<  RayRenderTest: obtained 4 graphics primitives.\n', '< PyMOL>pseudoatom test, vdw=5.0\n', '<  ObjMol: created test/PSDO/P/PSD`1/PS4\n', '< PyMOL>ray renderer=2\n', '<  RayRenderTest: obtained 7 graphics primitives.\n', '< PyMOL>pseudoatom test, color=blue\n', '<  ObjMol: created test/PSDO/P/PSD`1/PS5\n', '< PyMOL>ray renderer=2\n', '<  RayRenderTest: obtained 10 graphics primitives.\n', '< PyMOL>pseudoatom test, label=Hello world\n', '<  ObjMol: created test/PSDO/P/PSD`1/PS6\n', '< PyMOL>ray renderer=2\n', '<  RayRenderTest: obtained 32 graphics primitives.\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>pseudoatom pept, pept and resi 1\n', '<  ObjMol: created pept/PSDO/P/PSD`1/PS1\n', '< PyMOL>pseudoatom pept, pept and resi 2\n', '<  ObjMol: created pept/PSDO/P/PSD`1/PS2\n', '< PyMOL>pseudoatom pept, pept and resi 10\n', '<  ObjMol: created pept/PSDO/P/PSD`1/PS3\n', '< PyMOL>count_atoms pept\n', '<  count_atoms: 110 atoms\n', '< PyMOL>bond name PS2, name PS3\n', '<  Bond: 1 bonds added to model "pept".\n', '< PyMOL>hide nonbonded\n', '< PyMOL>ray renderer=2\n', '<  RayRenderTest: obtained 167 graphics primitives.\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', "< PyMOL>pseudoatom test, all, b=1.5, q=1.6, resn=abc, resi=10, name=ilk, elem=s, vdw=5, segi=asdf, chain=''\n", '<  ObjMol: created test/asdf//abc`10/ilk\n', '< PyMOL>iterate name ilk,print "%8.3f %8.3f %8.3f"%(b,q,vdw)\n', '<    1.500    1.600    5.000\n', '<  Iterate: iterated over 1 atoms.\n']
 run_tests: C0600util...
 run_tests: C0600util.log DIFFERS over about 27 lines:
['1,54d0\n', '< PyMOL>load dat/il2.pdb\n', '<  CmdLoad: "dat/il2.pdb" loaded as "il2".\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>load dat/3al1.pdb\n', '< HEADER    STRUCTURAL PROTEIN                      26-OCT-98   3AL1\n', '< TITLE     DESIGNED PEPTIDE ALPHA-1, RACEMIC P1BAR FORM\n', '< COMPND    MOL_ID: 1;\n', '< COMPND   2 MOLECULE: D, L-ALPHA-1;\n', '< COMPND   3 CHAIN: A, B;\n', '< COMPND   4 ENGINEERED: YES;\n', '< COMPND   5 OTHER_DETAILS: N TERMINI ARE ACETYLATED\n', '<  ObjectMolecule: Read secondary structure assignments.\n', '<  ObjectMolecule: Read crystal symmetry information.\n', '<  Symmetry: Found 2 symmetry operators.\n', '<  CmdLoad: "dat/3al1.pdb" loaded as "3al1".\n', '< PyMOL>util.ss\n', '<  util.ss: WARNING: This is not a "correct" secondary structure\n', '<  util.ss: assignment algorithm!  Please use only as a last resort.\n', '<  util.ss: initiating secondary structure assignment on 163 residues.\n', '<  util.ss: extracting sequence and relationships...\n', '<  util.ss: analyzing phi/psi angles (slow)...\n', '<  util.ss: finding hydrogen bonds...\n', '<  util.ss: verifying beta sheets...\n', '<  util.ss: assignment complete.\n', '< PyMOL>util.cbac\n', '<  Executive: Colored 1948 atoms.\n', '<  Executive: Colored 922 atoms.\n', '< PyMOL>util.cbay\n', '<  Executive: Colored 1948 atoms.\n', '<  Executive: Colored 922 atoms.\n', '< PyMOL>util.cbaw\n', '<  Executive: Colored 1948 atoms.\n', '<  Executive: Colored 922 atoms.\n', '< PyMOL>util.cbas\n', '<  Executive: Colored 1948 atoms.\n', '<  Executive: Colored 922 atoms.\n', '< PyMOL>util.cbc\n', '<  util.cbc: color 26,(chain A)\n', '<  Executive: Colored 279 atoms.\n', '<  util.cbc: color 5,(chain B)\n', '<  Executive: Colored 310 atoms.\n', '<  util.cbc: color 154,(chain E)\n', '<  Executive: Colored 107 atoms.\n', "<  util.cbc: color 6,(chain '')\n", '<  Executive: Colored 2174 atoms.\n', '< PyMOL>hide\n', '< PyMOL>show car\n', '< PyMOL>zoom\n', '< PyMOL>set ray_default_renderer=2\n', '<  Setting: ray_default_renderer set to 2.\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 19492 graphics primitives.\n', '< PyMOL>util.rainbow("pept")\n']
 run_tests: C0700odd...
 run_tests: C0700odd.2.pdb is missing.
 run_tests: C0700odd.5.pdb is missing.
 run_tests: C0700odd.7.pdb is missing.
 run_tests: C0700odd.4.pdb is missing.
 run_tests: C0700odd.1.pdb is missing.
 run_tests: C0700odd.D.pdb is missing.
 run_tests: C0700odd.log DIFFERS over about 204 lines:
['1,408d0\n', '< PyMOL>unset pdb_hetatm_guess_valences\n', '<  Setting: pdb_hetatm_guess_valences set to off.\n', '< PyMOL>reinitialize store_defaults\n', '< PyMOL>load dat/odd01.pdb\n', '<  CmdLoad: "dat/odd01.pdb" loaded as "odd01".\n', '< PyMOL>iterate all, print name\n', '< CZ\n', '< NH1\n', '< NH2\n', '< HE\n', '< HH11\n', '< HH12\n', '< HH21\n', '< HH22\n', '< CA\n', '< CA\n', '< OA22\n', '< OA23\n', '< ABCD\n', '< LMN\n', '< XYZ\n', '< PE\n', '< O1B\n', '< AC5\n', '<  Iterate: iterated over 18 atoms.\n', '< PyMOL>save cmp/C0700odd.1.pdb\n', '<  Save: wrote "cmp/C0700odd.1.pdb".\n', '< PyMOL>set retain_order\n', '<  Setting: retain_order set to 1.\n', '< PyMOL>iterate all, print name\n', '< HE\n', '< CZ\n', '< NH1\n', '< HH11\n', '< HH12\n', '< NH2\n', '< HH21\n', '< HH22\n', '< CA\n', '< CA\n', '< OA22\n', '< OA23\n', '< ABCD\n', '< XYZ\n', '< LMN\n', '< PE\n', '< O1B\n', '< AC5\n', '<  Iterate: iterated over 18 atoms.\n', '< PyMOL>save cmp/C0700odd.2.pdb\n', '<  Save: wrote "cmp/C0700odd.2.pdb".\n', '< PyMOL>set pdb_no_end_record\n', '<  Setting: pdb_no_end_record set to on.\n', '< PyMOL>save cmp/C0700odd.3.pdb\n', '<  Save: wrote "cmp/C0700odd.3.pdb".\n', '< PyMOL>set pdb_retain_ids\n', '<  Setting: pdb_retain_ids set to on.\n', '< PyMOL>save cmp/C0700odd.4.pdb\n', '<  Save: wrote "cmp/C0700odd.4.pdb".\n', '< PyMOL>reinit\n', '< PyMOL>set retain_order\n', '<  Setting: retain_order set to 1.\n', '< PyMOL>load dat/odd01.pdb\n', '<  CmdLoad: "dat/odd01.pdb" loaded as "odd01".\n', '< PyMOL>iterate all,print name\n', '< HE\n', '< CZ\n', '< NH1\n', '< HH11\n', '< HH12\n', '< NH2\n', '< HH21\n', '< HH22\n', '< CA\n', '< CA\n', '< OA22\n', '< OA23\n', '< ABCD\n', '< XYZ\n', '< LMN\n', '< PE\n', '< O1B\n', '< AC5\n', '<  Iterate: iterated over 18 atoms.\n', '< PyMOL>set pdb_reformat_names_mode, 1\n', '<  Setting: pdb_reformat_names_mode set to 1.\n', '< PyMOL>save cmp/C0700odd.5.pdb\n', '<  Save: wrote "cmp/C0700odd.5.pdb".\n', '< PyMOL>dele all\n', '< PyMOL>load cmp/C0700odd.3.pdb\n', '<  CmdLoad: "cmp/C0700odd.3.pdb" loaded as "C0700odd.3".\n', '< PyMOL>set pdb_reformat_names_mode, 0\n', '<  Setting: pdb_reformat_names_mode set to 0.\n', '< PyMOL>save cmp/C0700odd.6.pdb\n', '<  Save: wrote "cmp/C0700odd.6.pdb".\n', '< PyMOL>iterate all,print name\n', '< HE\n', '< CZ\n', '< NH1\n', '< 1HH1\n', '< 2HH1\n', '< NH2\n', '< 1HH2\n', '< 2HH2\n', '< CA\n', '< CA\n', '< 2OA2\n', '< 3OA2\n', '< ABCD\n', '< XYZ\n', '< LMN\n', '< PE\n', '< O1B\n', '< AC5\n', '<  Iterate: iterated over 18 atoms.\n', '< PyMOL>reinit\n', '< PyMOL>set pdb_reformat_names_mode, 1\n', '<  Setting: pdb_reformat_names_mode set to 1.\n', '< PyMOL>load cmp/C0700odd.3.pdb\n', '<  CmdLoad: "cmp/C0700odd.3.pdb" loaded as "C0700odd.3".\n', '< PyMOL>iterate all,print name\n', '< CZ\n', '< NH1\n', '< NH2\n', '< HE\n', '< 1HH1\n', '< 2HH1\n', '< 1HH2\n', '< 2HH2\n', '< CA\n', '< CA\n', '< 2OA2\n', '< 3OA2\n', '< ABCD\n', '< LMN\n', '< XYZ\n', '< PE\n', '< O1B\n', '< AC5\n', '<  Iterate: iterated over 18 atoms.\n', '< PyMOL>save cmp/C0700odd.7.pdb\n', '<  Save: wrote "cmp/C0700odd.7.pdb".\n', '< PyMOL>set pdb_reformat_names_mode,2\n', '<  Setting: pdb_reformat_names_mode set to 2.\n', '< PyMOL>save cmp/C0700odd.8.pdb\n', '<  Save: wrote "cmp/C0700odd.8.pdb".\n', '< PyMOL>dele all\n', '< PyMOL>load cmp/C0700odd.5.pdb\n', '<  CmdLoad: "cmp/C0700odd.5.pdb" loaded as "C0700odd.5".\n', '< PyMOL>iterate all,print name\n', '< CZ\n', '< NH1\n', '< NH2\n', '< HE\n', '< HH11\n', '< HH12\n', '< HH21\n', '< HH22\n', '< CA\n', '< CA\n', '< OA22\n', '< OA23\n', '< ABCD\n', '< LMN\n', '< XYZ\n', '< PE\n', '< O1B\n', '< AC5\n', '<  Iterate: iterated over 18 atoms.\n', '< PyMOL>set pdb_reformat_names_mode,0\n', '<  Setting: pdb_reformat_names_mode set to 0.\n', '< PyMOL>save cmp/C0700odd.9.pdb\n', '<  Save: wrote "cmp/C0700odd.9.pdb".\n', '< PyMOL>set pdb_reformat_names_mode,1\n', '<  Setting: pdb_reformat_names_mode set to 1.\n', '< PyMOL>save cmp/C0700odd.A.pdb\n', '<  Save: wrote "cmp/C0700odd.A.pdb".\n', '< PyMOL>set pdb_literal_names, 1\n', '<  Setting: pdb_literal_names set to on.\n', '< PyMOL>save cmp/C0700odd.B.pdb\n', '<  Save: wrote "cmp/C0700odd.B.pdb".\n', '< PyMOL>dele all\n', '< PyMOL>load cmp/C0700odd.3.pdb\n', '<  CmdLoad: "cmp/C0700odd.3.pdb" loaded as "C0700odd.3".\n', '< PyMOL>iterate all,print name\n', '<  CZ \n', '<  HE \n', '<  NH1\n', '<  NH2\n', '< HH11\n', '< HH12\n', '< HH21\n', '< HH22\n', '< CA  \n', '<  CA \n', '< OA22\n', '< OA23\n', '<  LMN\n', '<  XYZ\n', '< ABCD\n', '<  O1B\n', '<  PE \n', '< AC5 \n', '<  Iterate: iterated over 18 atoms.\n', '< PyMOL>dele all\n', '< PyMOL>load cmp/C0700odd.5.pdb\n', '<  CmdLoad: "cmp/C0700odd.5.pdb" loaded as "C0700odd.5".\n', '< PyMOL>iterate all,print name\n', '<  CZ \n', '<  HE \n', '<  NH1\n', '<  NH2\n', '< 1HH1\n', '< 2HH1\n', '< 1HH2\n', '< 2HH2\n', '< CA  \n', '<  CA \n', '< 2OA2\n', '< 3OA2\n', '<  LMN\n', '<  XYZ\n', '< ABCD\n', '<  O1B\n', '<  PE \n', '< AC5 \n', '<  Iterate: iterated over 18 atoms.\n', '< PyMOL>reinit\n', '< PyMOL>load dat/small02.pdb\n', '<  CmdLoad: "dat/small02.pdb" loaded as "small02".\n', '< PyMOL>save cmp/C0700odd.C.pdb\n', '<  Save: wrote "cmp/C0700odd.C.pdb".\n', '< PyMOL>reinit\n', '< PyMOL>set pdb_reformat_names_mode, 1\n', '<  Setting: pdb_reformat_names_mode set to 1.\n', '< PyMOL>load dat/small02.pdb\n', '<  CmdLoad: "dat/small02.pdb" loaded as "small02".\n', '< PyMOL>iterate all, print name\n', '< CL16\n', '< C1\n', '< C4\n', '< C6\n', '< C9\n', '< N12\n', '< C13\n', '< C17\n', '< C19\n', '< C20\n', '< C22\n', '< C25\n', '< C28\n', '< C29\n', '< C30\n', '< N32\n', '< C33\n', '< C35\n', '< C39\n', '< C40\n', '< C41\n', '< C42\n', '< C43\n', '< C46\n', '< C49\n', '< C51\n', '< N54\n', '< C55\n', '< N56\n', '< O57\n', '< C58\n', '< C61\n', '< O64\n', '< C65\n', '< BR37\n', '< BR38\n', '<  Iterate: iterated over 36 atoms.\n', '< PyMOL>save cmp/C0700odd.D.pdb\n', '<  Save: wrote "cmp/C0700odd.D.pdb".\n', '< PyMOL>set pdb_reformat_names_mode, 2\n', '<  Setting: pdb_reformat_names_mode set to 2.\n', '< PyMOL>load dat/small02.pdb\n', '<  CmdLoad: "dat/small02.pdb" appended into object "small02", state 2.\n', '< PyMOL>iterate all, print name\n', '< CL16\n', '< C1\n', '< C4\n', '< C6\n', '< C9\n', '< N12\n', '< C13\n', '< C17\n', '< C19\n', '< C20\n', '< C22\n', '< C25\n', '< C28\n', '< C29\n', '< C30\n', '< N32\n', '< C33\n', '< C35\n', '< C39\n', '< C40\n', '< C41\n', '< C42\n', '< C43\n', '< C46\n', '< C49\n', '< C51\n', '< N54\n', '< C55\n', '< N56\n', '< O57\n', '< C58\n', '< C61\n', '< O64\n', '< C65\n', '< BR37\n', '< BR38\n', '<  Iterate: iterated over 36 atoms.\n', '< PyMOL>save cmp/C0700odd.E.pdb\n', '<  Save: wrote "cmp/C0700odd.E.pdb".\n', '< PyMOL>reinit\n', '< PyMOL>set pdb_literal_names\n', '<  Setting: pdb_literal_names set to on.\n', '< PyMOL>set retain_order\n', '<  Setting: retain_order set to 1.\n', '< PyMOL>set pdb_retain_ids\n', '<  Setting: pdb_retain_ids set to on.\n', '< PyMOL>set pdb_no_end_record\n', '<  Setting: pdb_no_end_record set to on.\n', '< PyMOL>unset pdb_use_ter_records\n', '<  Setting: pdb_use_ter_records set to 0.\n', '< PyMOL>load dat/odd01.pdb\n', '<  CmdLoad: "dat/odd01.pdb" loaded as "odd01".\n', '< PyMOL>save cmp/C0700odd.F.pdb\n', '<  Save: wrote "cmp/C0700odd.F.pdb".\n', '< PyMOL>reinit\n', '< PyMOL>load dat/helix_amber.pdb\n', '<  CmdLoad: "dat/helix_amber.pdb" loaded as "helix_amber".\n', '< PyMOL>iterate resi 2, print name, elem\n', '< N N\n', '< CA C\n', '< C C\n', '< O O\n', '< CB C\n', '< SG S\n', '< H H\n', '< HA H\n', '< HB2 H\n', '< HB3 H\n', '< N N\n', '< CA C\n', '< C C\n', '< O O\n', '< CB C\n', '< H H\n', '< HA H\n', '< HB1 H\n', '< HB2 H\n', '< HB3 H\n', '<  Iterate: iterated over 20 atoms.\n', '< PyMOL>reinit\n', '< PyMOL>load dat/odd02.pdb\n', '<  CmdLoad: "dat/odd02.pdb" loaded as "odd02".\n', '< PyMOL>iterate all, print name, elem\n', '< C C\n', '< O O\n', '< CG C\n', '< CD C\n', '< NE N\n', '< CZ C\n', '< NH1 N\n', '< NH2 N\n', '< HG1 H\n', '< HG2 H\n', '< HD1 H\n', '< HD2 H\n', '< HE H\n', '< HH11 H\n', '< HH12 H\n', '< HH21 H\n', '< Hh22 Hh\n', '< N N\n', '< CA C\n', '< C C\n', '< O O\n', '< CB C\n', '< CG1 C\n', '< CG2 C\n', '< HN H\n', '< HA H\n', '< HB H\n', '< HG11 H\n', '< HG12 H\n', '< HG21 H\n', '< HG22 H\n', '< HG23 H\n', '< Hg13 Hg\n', '< N N\n', '< CA C\n', '< HN H\n', '<  Iterate: iterated over 36 atoms.\n', '< PyMOL>save cmp/C0700.odd.G.pdb\n', '<  Save: wrote "cmp/C0700.odd.G.pdb".\n', '< PyMOL>set pdb_reformat_names_mode,1\n', '<  Setting: pdb_reformat_names_mode set to 1.\n', '< PyMOL>save cmp/C0700.odd.H.pdb\n', '<  Save: wrote "cmp/C0700.odd.H.pdb".\n']
 run_tests: C0700odd.E.pdb is missing.
 run_tests: C0700odd.A.pdb is missing.
 run_tests: C0700odd.B.pdb is missing.
 run_tests: C0700odd.F.pdb is missing.
 run_tests: C0700odd.6.pdb is missing.
 run_tests: C0700odd.3.pdb is missing.
 run_tests: C0700odd.8.pdb is missing.
 run_tests: C0700odd.9.pdb is missing.
 run_tests: C0700odd.C.pdb is missing.
 run_tests: C0740multipdb...
 run_tests: C0740multipdb.log DIFFERS over about 45 lines:
['1,89d0\n', '< PyMOL>ATOM      1  N   GLY A 252      39.368  46.327  27.875  1.00 46.28           N  \\\n', '< PyMOL>ATOM      2  CA  GLY A 252      39.565  46.477  29.344  1.00 46.89           C  \\\n', '< PyMOL>ATOM      3  C   GLY A 252      40.602  45.521  29.907  1.00 48.55           C  \\\n', '< PyMOL>ATOM      4  O   GLY A 252      40.907  44.497  29.293  1.00 46.16           O  \\\n', '< PyMOL>ATOM      5  N   SER A 253      41.144  45.862  31.078  1.00 45.72           N  \\\n', '< PyMOL>ATOM      6  CA  SER A 253      42.152  45.043  31.757  1.00 46.42           C  \\\n', '< PyMOL>ATOM      7  C   SER A 253      41.824  44.945  33.254  1.00 47.72           C  \\\n', '< PyMOL>ATOM      8  O   SER A 253      41.053  45.756  33.778  1.00 46.62           O  \\\n', '< PyMOL>ATOM      9  CB  SER A 253      43.543  45.667  31.587  1.00 45.55           C  \\\n', '< PyMOL>HEADER STEP\\\n', '< PyMOL>ATOM      1  N   SER E 258      55.863  54.272  24.437  1.00 37.51           N  \\\n', '< PyMOL>ATOM      2  CA  SER E 258      56.590  54.677  23.240  1.00 36.33           C  \\\n', '< PyMOL>ATOM      3  C   SER E 258      58.022  54.180  23.260  1.00 35.14           C  \\\n', '< PyMOL>ATOM      4  O   SER E 258      58.647  54.090  24.306  1.00 34.89           O  \\\n', '< PyMOL>ATOM      5  CB  SER E 258      56.566  56.199  23.083  1.00 35.95           C  \\\n', '< PyMOL>ATOM      6  OG  SER E 258      57.340  56.607  21.975  1.00 36.25           O  \\\n', '< PyMOL>ATOM      7  N   ARG E 259      58.546  53.842  22.088  1.00 34.24           N  """\n', '< PyMOL>cmd.read_pdbstr(pdbstr,"test")\n', '< PyMOL>print cmd.get_names()\n', "< ['PTPBR7', 'STEP']\n", '< PyMOL>count_atoms\n', '<  count_atoms: 16 atoms\n', '< PyMOL>reinit\n', '< PyMOL>cmd.read_pdbstr("""\\\n', '< PyMOL>HEADER    OXIDOREDUCTASE                          13-JUL-94   3MDD      3MDD   2\\\n', '< PyMOL>ATOM      1  N   GLY A  11      22.422  32.842 -15.744  1.00 24.74      3MDD 172\\\n', '< PyMOL>ATOM      2  CA  GLY A  11      21.837  32.022 -14.672  1.00 24.52      3MDD 173\\\n', '< PyMOL>ATOM      3  C   GLY A  11      21.575  30.609 -15.194  1.00 24.62      3MDD 174\\\n', '< PyMOL>ATOM      4  O   GLY A  11      22.036  30.238 -16.285  1.00 24.99      3MDD 175\\\n', '< PyMOL>ATOM      5  N   PHE A  12      20.843  29.864 -14.390  1.00 24.29      3MDD 176\\\n', '< PyMOL>ATOM      6  CA  PHE A  12      20.481  28.469 -14.679  1.00 24.00      3MDD 177\\\n', '< PyMOL>ATOM      7  C   PHE A  12      19.514  28.397 -15.861  1.00 23.38      3MDD 178\\\n', '< PyMOL>ATOM   6017  NZ  LYS B 395      -4.299  -6.687  15.377  1.00 35.83      3MDD6188\\\n', '< PyMOL>ATOM   6018  OXT LYS B 395      -0.899 -11.439  20.683  1.00 35.32      3MDD6189\\\n', '< PyMOL>END                                                                     3MDD6517\\\n', '< PyMOL>HEADER    ELECTRON TRANSPORT                      02-MAR-92   1MDA      1MDA   2\\\n', '< PyMOL>ATOM      1  N   GLU H   1      15.906  81.036  72.025  1.00 50.00      1MDA 307\\\n', '< PyMOL>ATOM      2  CA  GLU H   1      17.350  81.236  71.880  1.00 50.00      1MDA 308\\\n', '< PyMOL>ATOM      3  C   GLU H   1      17.854  81.695  70.506  1.00 50.00      1MDA 309\\\n', '< PyMOL>ATOM      4  O   GLU H   1      17.668  80.983  69.518  1.00 50.00      1MDA 310\\\n', '< PyMOL>ATOM      5  CB  GLU H   1      18.222  80.229  72.680  1.00 50.00      1MDA 311\\\n', '< PyMOL>ATOM      6  CG  GLU H   1      17.540  78.863  72.954  1.00 50.00      1MDA 312\\\n', '< PyMOL>ATOM      7  CD  GLU H   1      17.831  77.718  72.017  1.00 43.59      1MDA 313\\\n', '< PyMOL>ATOM      8  OE1 GLU H   1      18.953  77.453  71.614  1.00 47.42      1MDA 314\\\n', '< PyMOL>ATOM      9  OE2 GLU H   1      16.759  77.049  71.674  1.00 37.68      1MDA 315\\\n', '< PyMOL>ATOM   8568  CG  GLU B 105      37.556  38.617  32.271  1.00 15.99      1MDA8874\\\n', '< PyMOL>ATOM   8569  CD  GLU B 105      36.485  37.572  32.282  1.00 36.23      1MDA8875\\\n', '< PyMOL>ATOM   8570  OE1 GLU B 105      36.488  36.782  31.231  1.00 50.00      1MDA8876\\\n', '< PyMOL>ATOM   8571  OE2 GLU B 105      35.647  37.508  33.152  1.00 50.00      1MDA8877\\\n', '< PyMOL>ATOM   8572  OXT GLU B 105      41.453  38.354  30.968  1.00 50.00      1MDA8878\\\n', '< PyMOL>END                                                                     1MDA8924\\\n', '< PyMOL>""","test")\n', '< PyMOL>print cmd.get_names()\n', "< ['3MDD', '1MDA']\n", '< PyMOL>count_atoms\n', '<  count_atoms: 23 atoms\n', '< PyMOL>reinit\n', '< PyMOL>cmd.read_pdbstr("""\\\n', '< PyMOL>ATOM      1  N   GLY A  11      22.422  32.842 -15.744  1.00 24.74      3MDD 172\\\n', '< PyMOL>ATOM      2  CA  GLY A  11      21.837  32.022 -14.672  1.00 24.52      3MDD 173\\\n', '< PyMOL>ATOM      3  C   GLY A  11      21.575  30.609 -15.194  1.00 24.62      3MDD 174\\\n', '< PyMOL>ATOM      4  O   GLY A  11      22.036  30.238 -16.285  1.00 24.99      3MDD 175\\\n', '< PyMOL>ATOM      5  N   PHE A  12      20.843  29.864 -14.390  1.00 24.29      3MDD 176\\\n', '< PyMOL>ATOM      6  CA  PHE A  12      20.481  28.469 -14.679  1.00 24.00      3MDD 177\\\n', '< PyMOL>ATOM      7  C   PHE A  12      19.514  28.397 -15.861  1.00 23.38      3MDD 178\\\n', '< PyMOL>ATOM   6017  NZ  LYS B 395      -4.299  -6.687  15.377  1.00 35.83      3MDD6188\\\n', '< PyMOL>ATOM   6018  OXT LYS B 395      -0.899 -11.439  20.683  1.00 35.32      3MDD6189\\\n', '< PyMOL>END                                                                     3MDD6517\\\n', '< PyMOL>ATOM      1  N   GLU H   1      15.906  81.036  72.025  1.00 50.00      1MDA 307\\\n', '< PyMOL>ATOM      2  CA  GLU H   1      17.350  81.236  71.880  1.00 50.00      1MDA 308\\\n', '< PyMOL>ATOM      3  C   GLU H   1      17.854  81.695  70.506  1.00 50.00      1MDA 309\\\n', '< PyMOL>ATOM      4  O   GLU H   1      17.668  80.983  69.518  1.00 50.00      1MDA 310\\\n', '< PyMOL>ATOM      5  CB  GLU H   1      18.222  80.229  72.680  1.00 50.00      1MDA 311\\\n', '< PyMOL>ATOM      6  CG  GLU H   1      17.540  78.863  72.954  1.00 50.00      1MDA 312\\\n', '< PyMOL>ATOM      7  CD  GLU H   1      17.831  77.718  72.017  1.00 43.59      1MDA 313\\\n', '< PyMOL>ATOM      8  OE1 GLU H   1      18.953  77.453  71.614  1.00 47.42      1MDA 314\\\n', '< PyMOL>ATOM      9  OE2 GLU H   1      16.759  77.049  71.674  1.00 37.68      1MDA 315\\\n', '< PyMOL>ATOM   8568  CG  GLU B 105      37.556  38.617  32.271  1.00 15.99      1MDA8874\\\n', '< PyMOL>ATOM   8569  CD  GLU B 105      36.485  37.572  32.282  1.00 36.23      1MDA8875\\\n', '< PyMOL>ATOM   8570  OE1 GLU B 105      36.488  36.782  31.231  1.00 50.00      1MDA8876\\\n', '< PyMOL>ATOM   8571  OE2 GLU B 105      35.647  37.508  33.152  1.00 50.00      1MDA8877\\\n', '< PyMOL>ATOM   8572  OXT GLU B 105      41.453  38.354  30.968  1.00 50.00      1MDA8878\\\n', '< PyMOL>END                                                                     1MDA8924\\\n', '< PyMOL>""","test")\n', '< PyMOL>print cmd.get_names()\n', "< ['test_0001', 'test_0002']\n", '< PyMOL>count_atoms\n', '<  count_atoms: 23 atoms\n', '< PyMOL>reinit\n']
 run_tests: C0800matrices...
 run_tests: C0800matrices.log DIFFERS over about 141 lines:
['1,282d0\n', '< PyMOL>load dat/pept.pdb, mol1\n', '<  CmdLoad: "dat/pept.pdb" loaded as "mol1".\n', '< PyMOL>load dat/pept.pdb, mol2\n', '<  CmdLoad: "dat/pept.pdb" loaded as "mol2".\n', '< PyMOL>load dat/pept.pdb, mol3\n', '<  CmdLoad: "dat/pept.pdb" loaded as "mol3".\n', '< PyMOL>dump_lst((cmd.get_distance("mol1///5/ca","mol2///5/ca"), \\\n', '< PyMOL>cmd.get_distance("mol1///5/ca","mol3///5/ca"), \\\n', '< PyMOL>cmd.get_distance("mol2///5/ca","mol3///5/ca")))\n', '< [  0.00  0.00  0.00 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("mol1"))\n', '< [  1.00  0.00  0.00  0.00  \n', '<    0.00  1.00  0.00  0.00  \n', '<    0.00  0.00  1.00  0.00  \n', '<    0.00  0.00  0.00  1.00 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("mol2"))\n', '< [  1.00  0.00  0.00  0.00  \n', '<    0.00  1.00  0.00  0.00  \n', '<    0.00  0.00  1.00  0.00  \n', '<    0.00  0.00  0.00  1.00 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("mol3"))\n', '< [  1.00  0.00  0.00  0.00  \n', '<    0.00  1.00  0.00  0.00  \n', '<    0.00  0.00  1.00  0.00  \n', '<    0.00  0.00  0.00  1.00 ]\n', '< PyMOL>translate [2,3,4], object=mol2, object_mode=1\n', '< PyMOL>dump_lst((cmd.get_distance("mol1///5/ca","mol2///5/ca"), \\\n', '< PyMOL>cmd.get_distance("mol1///5/ca","mol3///5/ca"), \\\n', '< PyMOL>cmd.get_distance("mol2///5/ca","mol3///5/ca")))\n', '< [  5.38  0.00  5.38 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("mol1"))\n', '< [  1.00  0.00  0.00  0.00  \n', '<    0.00  1.00  0.00  0.00  \n', '<    0.00  0.00  1.00  0.00  \n', '<    0.00  0.00  0.00  1.00 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("mol2"))\n', '< [  1.00  0.00  0.00  2.00  \n', '<    0.00  1.00  0.00  3.00  \n', '<    0.00  0.00  1.00  4.00  \n', '<    0.00  0.00  0.00  1.00 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("mol3"))\n', '< [  1.00  0.00  0.00  0.00  \n', '<    0.00  1.00  0.00  0.00  \n', '<    0.00  0.00  1.00  0.00  \n', '<    0.00  0.00  0.00  1.00 ]\n', '< PyMOL>matrix= cmd.get_object_matrix("mol2")\n', '< PyMOL>cmd.transform_object("mol3",matrix, homogenous=1)\n', '< PyMOL>dump_lst((cmd.get_distance("mol1///5/ca","mol2///5/ca"), \\\n', '< PyMOL>cmd.get_distance("mol1///5/ca","mol3///5/ca"), \\\n', '< PyMOL>cmd.get_distance("mol2///5/ca","mol3///5/ca")))\n', '< [  5.38  5.38  0.00 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("mol1"))\n', '< [  1.00  0.00  0.00  0.00  \n', '<    0.00  1.00  0.00  0.00  \n', '<    0.00  0.00  1.00  0.00  \n', '<    0.00  0.00  0.00  1.00 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("mol2"))\n', '< [  1.00  0.00  0.00  2.00  \n', '<    0.00  1.00  0.00  3.00  \n', '<    0.00  0.00  1.00  4.00  \n', '<    0.00  0.00  0.00  1.00 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("mol3"))\n', '< [  1.00  0.00  0.00  2.00  \n', '<    0.00  1.00  0.00  3.00  \n', '<    0.00  0.00  1.00  4.00  \n', '<    0.00  0.00  0.00  1.00 ]\n', '< PyMOL>dele mol3\n', '< PyMOL>load dat/pept.pdb,mol3\n', '<  CmdLoad: "dat/pept.pdb" loaded as "mol3".\n', '< PyMOL>dump_lst((cmd.get_distance("mol1///5/ca","mol2///5/ca"), \\\n', '< PyMOL>cmd.get_distance("mol1///5/ca","mol3///5/ca"), \\\n', '< PyMOL>cmd.get_distance("mol2///5/ca","mol3///5/ca")))\n', '< [  5.38  0.00  5.38 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("mol1"))\n', '< [  1.00  0.00  0.00  0.00  \n', '<    0.00  1.00  0.00  0.00  \n', '<    0.00  0.00  1.00  0.00  \n', '<    0.00  0.00  0.00  1.00 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("mol2"))\n', '< [  1.00  0.00  0.00  2.00  \n', '<    0.00  1.00  0.00  3.00  \n', '<    0.00  0.00  1.00  4.00  \n', '<    0.00  0.00  0.00  1.00 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("mol3"))\n', '< [  1.00  0.00  0.00  0.00  \n', '<    0.00  1.00  0.00  0.00  \n', '<    0.00  0.00  1.00  0.00  \n', '<    0.00  0.00  0.00  1.00 ]\n', '< PyMOL>matrix_transfer mol1, mol3\n', '< PyMOL>dump_mat(cmd.get_object_matrix("mol1"))\n', '< [  1.00  0.00  0.00  0.00  \n', '<    0.00  1.00  0.00  0.00  \n', '<    0.00  0.00  1.00  0.00  \n', '<    0.00  0.00  0.00  1.00 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("mol2"))\n', '< [  1.00  0.00  0.00  2.00  \n', '<    0.00  1.00  0.00  3.00  \n', '<    0.00  0.00  1.00  4.00  \n', '<    0.00  0.00  0.00  1.00 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("mol3"))\n', '< [  1.00  0.00  0.00  0.00  \n', '<    0.00  1.00  0.00  0.00  \n', '<    0.00  0.00  1.00  0.00  \n', '<    0.00  0.00  0.00  1.00 ]\n', '< PyMOL>dump_lst((cmd.get_distance("mol1///5/ca","mol2///5/ca"), \\\n', '< PyMOL>cmd.get_distance("mol1///5/ca","mol3///5/ca"), \\\n', '< PyMOL>cmd.get_distance("mol2///5/ca","mol3///5/ca")))\n', '< [  5.38  0.00  5.38 ]\n', '< PyMOL>matrix_transfer mol2, mol3\n', '< PyMOL>dump_lst((cmd.get_distance("mol1///5/ca","mol2///5/ca"), \\\n', '< PyMOL>cmd.get_distance("mol1///5/ca","mol3///5/ca"), \\\n', '< PyMOL>cmd.get_distance("mol2///5/ca","mol3///5/ca")))\n', '< [  5.38  5.38  0.00 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("mol1"))\n', '< [  1.00  0.00  0.00  0.00  \n', '<    0.00  1.00  0.00  0.00  \n', '<    0.00  0.00  1.00  0.00  \n', '<    0.00  0.00  0.00  1.00 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("mol2"))\n', '< [  1.00  0.00  0.00  2.00  \n', '<    0.00  1.00  0.00  3.00  \n', '<    0.00  0.00  1.00  4.00  \n', '<    0.00  0.00  0.00  1.00 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("mol3"))\n', '< [  1.00  0.00  0.00  2.00  \n', '<    0.00  1.00  0.00  3.00  \n', '<    0.00  0.00  1.00  4.00  \n', '<    0.00  0.00  0.00  1.00 ]\n', '< PyMOL>dele all\n', '< PyMOL>load ../data/tut/1hpv.pdb\n', '< HEADER    HYDROLASE (ACID PROTEINASE)             18-NOV-94   1HPV      1HPV   2\n', '< COMPND    HIV-1 PROTEASE (E.C.3.4.23.-) COMPLEXED WITH VX-478           1HPV   3\n', '< COMPND   2 (3(S)-N-(3-TETRAHYDROFURANYLOXYCARBONYL) AMINO-1-            1HPV   4\n', '< COMPND   3 (N,N-ISOBUTYL,4-AMINOBENZENESULFONYL) AMINO-2-(S)-HYDROXY-   1HPV   5\n', '< COMPND   4 4-PHENYLBUTANE)                                              1HPV   6\n', '<  ObjectMolecule: Read secondary structure assignments.\n', '<  ObjectMolecule: Read crystal symmetry information.\n', '<  Symmetry: Found 6 symmetry operators.\n', '<  CmdLoad: "../data/tut/1hpv.pdb" loaded as "1hpv".\n', '< PyMOL>create ligand, organic\n', '<  Selector: found 35 atoms.\n', '<  Executive: object "ligand" created.\n', '< PyMOL>create protein, polymer\n', '<  Selector: found 1516 atoms.\n', '<  Executive: object "protein" created.\n', '< PyMOL>delete 1hpv\n', '< PyMOL>dump_lst((cmd.get_distance("ligand////s1","/protein/1HPV/B/ILE`84/CB"), \\\n', '< PyMOL>cmd.get_distance("/ligand/1HPV//478`200/C4","/protein/1HPV/B/ILE`50/CB"), \\\n', '< PyMOL>cmd.get_distance("/ligand/1HPV//478`200/O3"," /protein/1HPV/B/VAL`82/CB")))\n', '< [  6.86  5.47  8.86 ]\n', '< PyMOL>translate [2,3,4], object=protein, object_mode=1\n', '< PyMOL>rotate x, 20, object=protein, object_mode=1\n', '< PyMOL>rotate y, 40, object=protein, object_mode=1\n', '< PyMOL>rotate z, 90, object=protein, object_mode=1\n', '< PyMOL>translate [4,5,6], object=protein, object_mode=1\n', '< PyMOL>dump_lst((cmd.get_distance("ligand////s1","/protein/1HPV/B/ILE`84/CB"), \\\n', '< PyMOL>cmd.get_distance("/ligand/1HPV//478`200/C4","/protein/1HPV/B/ILE`50/CB"), \\\n', '< PyMOL>cmd.get_distance("/ligand/1HPV//478`200/O3"," /protein/1HPV/B/VAL`82/CB")))\n', '< [ 22.69 18.69 18.07 ]\n', '< PyMOL>matrix_transfer protein, ligand\n', '< PyMOL>dump_mat(cmd.get_object_matrix("protein"))\n', '< [  0.00 -0.94  0.34 30.89  \n', '<    0.77  0.22  0.60 11.28  \n', '<   -0.64  0.26  0.72 13.10  \n', '<    0.00  0.00  0.00  1.00 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("ligand"))\n', '< [  0.00 -0.94  0.34 30.89  \n', '<    0.77  0.22  0.60 11.28  \n', '<   -0.64  0.26  0.72 13.10  \n', '<    0.00  0.00  0.00  1.00 ]\n', '< PyMOL>dump_lst((cmd.get_distance("ligand////s1","/protein/1HPV/B/ILE`84/CB"), \\\n', '< PyMOL>cmd.get_distance("/ligand/1HPV//478`200/C4","/protein/1HPV/B/ILE`50/CB"), \\\n', '< PyMOL>cmd.get_distance("/ligand/1HPV//478`200/O3"," /protein/1HPV/B/VAL`82/CB")))\n', '< [  6.86  5.47  8.86 ]\n', '< PyMOL>load ../data/tut/1hpv.pdb, copy\n', '< HEADER    HYDROLASE (ACID PROTEINASE)             18-NOV-94   1HPV      1HPV   2\n', '< COMPND    HIV-1 PROTEASE (E.C.3.4.23.-) COMPLEXED WITH VX-478           1HPV   3\n', '< COMPND   2 (3(S)-N-(3-TETRAHYDROFURANYLOXYCARBONYL) AMINO-1-            1HPV   4\n', '< COMPND   3 (N,N-ISOBUTYL,4-AMINOBENZENESULFONYL) AMINO-2-(S)-HYDROXY-   1HPV   5\n', '< COMPND   4 4-PHENYLBUTANE)                                              1HPV   6\n', '<  ObjectMolecule: Read secondary structure assignments.\n', '<  ObjectMolecule: Read crystal symmetry information.\n', '<  Symmetry: Found 6 symmetry operators.\n', '<  CmdLoad: "../data/tut/1hpv.pdb" loaded as "copy".\n', '< PyMOL>create copy_ligand, copy and organic\n', '<  Selector: found 35 atoms.\n', '<  Executive: object "copy_ligand" created.\n', '< PyMOL>create copy_protein, copy and polymer\n', '<  Selector: found 1516 atoms.\n', '<  Executive: object "copy_protein" created.\n', '< PyMOL>create copy_protein2, copy and polymer\n', '<  Selector: found 1516 atoms.\n', '<  Executive: object "copy_protein2" created.\n', '< PyMOL>delete copy\n', '< PyMOL>matrix_transfer protein, copy_protein2\n', '< PyMOL>fit copy_protein, protein\n', '<  Executive: RMS =    0.000 (1516 to 1516 atoms)\n', '< PyMOL>dump_mat(cmd.get_object_matrix("protein"))\n', '< [  0.00 -0.94  0.34 30.89  \n', '<    0.77  0.22  0.60 11.28  \n', '<   -0.64  0.26  0.72 13.10  \n', '<    0.00  0.00  0.00  1.00 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("copy_protein"))\n', '< [  0.00 -0.94  0.34 30.89  \n', '<    0.77  0.22  0.60 11.28  \n', '<   -0.64  0.26  0.72 13.10  \n', '<    0.00  0.00  0.00  1.00 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("copy_protein2"))\n', '< [  0.00 -0.94  0.34 30.89  \n', '<    0.77  0.22  0.60 11.28  \n', '<   -0.64  0.26  0.72 13.10  \n', '<    0.00  0.00  0.00  1.00 ]\n', '< PyMOL>load ../data/tut/1hpv.pdb, target\n', '< HEADER    HYDROLASE (ACID PROTEINASE)             18-NOV-94   1HPV      1HPV   2\n', '< COMPND    HIV-1 PROTEASE (E.C.3.4.23.-) COMPLEXED WITH VX-478           1HPV   3\n', '< COMPND   2 (3(S)-N-(3-TETRAHYDROFURANYLOXYCARBONYL) AMINO-1-            1HPV   4\n', '< COMPND   3 (N,N-ISOBUTYL,4-AMINOBENZENESULFONYL) AMINO-2-(S)-HYDROXY-   1HPV   5\n', '< COMPND   4 4-PHENYLBUTANE)                                              1HPV   6\n', '<  ObjectMolecule: Read secondary structure assignments.\n', '<  ObjectMolecule: Read crystal symmetry information.\n', '<  Symmetry: Found 6 symmetry operators.\n', '<  CmdLoad: "../data/tut/1hpv.pdb" loaded as "target".\n', '< PyMOL>dump_lst((cmd.get_distance("ligand////s1","/target/1HPV/B/ILE`84/CB"), \\\n', '< PyMOL>cmd.get_distance("/ligand/1HPV//478`200/C4","/target/1HPV/B/ILE`50/CB"), \\\n', '< PyMOL>cmd.get_distance("/ligand/1HPV//478`200/O3"," /target/1HPV/B/VAL`82/CB")))\n', '< [ 14.32 17.77 18.33 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("ligand"))\n', '< [  0.00 -0.94  0.34 30.89  \n', '<    0.77  0.22  0.60 11.28  \n', '<   -0.64  0.26  0.72 13.10  \n', '<    0.00  0.00  0.00  1.00 ]\n', '< PyMOL>matrix_transfer target, ligand\n', '< PyMOL>dump_mat(cmd.get_object_matrix("ligand"))\n', '< [  1.00  0.00  0.00  0.00  \n', '<    0.00  1.00  0.00  0.00  \n', '<    0.00  0.00  1.00  0.00  \n', '<    0.00  0.00  0.00  1.00 ]\n', '< PyMOL>dump_lst((cmd.get_distance("ligand////s1","/target/1HPV/B/ILE`84/CB"), \\\n', '< PyMOL>cmd.get_distance("/ligand/1HPV//478`200/C4","/target/1HPV/B/ILE`50/CB"), \\\n', '< PyMOL>cmd.get_distance("/ligand/1HPV//478`200/O3"," /target/1HPV/B/VAL`82/CB")))\n', '< [  6.86  5.47  8.86 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("protein"))\n', '< [  0.00 -0.94  0.34 30.89  \n', '<    0.77  0.22  0.60 11.28  \n', '<   -0.64  0.26  0.72 13.10  \n', '<    0.00  0.00  0.00  1.00 ]\n', '< PyMOL>fit protein, target\n', '<  Executive: RMS =    0.000 (1516 to 1516 atoms)\n', '< PyMOL>dump_mat(cmd.get_object_matrix("protein"))\n', '< [  1.00  0.00  0.00  0.00  \n', '<    0.00  1.00  0.00  0.00  \n', '<    0.00  0.00  1.00  0.00  \n', '<    0.00  0.00  0.00  1.00 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("ligand"))\n', '< [  1.00  0.00  0.00  0.00  \n', '<    0.00  1.00  0.00  0.00  \n', '<    0.00  0.00  1.00  0.00  \n', '<    0.00  0.00  0.00  1.00 ]\n', '< PyMOL>dump_lst((cmd.get_distance("ligand////s1","/protein/1HPV/B/ILE`84/CB"), \\\n', '< PyMOL>cmd.get_distance("/ligand/1HPV//478`200/C4","/protein/1HPV/B/ILE`50/CB"), \\\n', '< PyMOL>cmd.get_distance("/ligand/1HPV//478`200/O3"," /protein/1HPV/B/VAL`82/CB")))\n', '< [  6.86  5.47  8.86 ]\n', '< PyMOL>matrix_transfer protein, ligand\n', '< PyMOL>dump_lst((cmd.get_distance("ligand////s1","/protein/1HPV/B/ILE`84/CB"), \\\n', '< PyMOL>cmd.get_distance("/ligand/1HPV//478`200/C4","/protein/1HPV/B/ILE`50/CB"), \\\n', '< PyMOL>cmd.get_distance("/ligand/1HPV//478`200/O3"," /protein/1HPV/B/VAL`82/CB")))\n', '< [  6.86  5.47  8.86 ]\n', '< PyMOL>dump_lst((cmd.get_distance("/target/1HPV/B/ILE`84/CB","/copy_protein2/1HPV/B/ILE`84/CB"),))\n', '< [ 19.55 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("copy_protein2"))\n', '< [  0.00 -0.94  0.34 30.89  \n', '<    0.77  0.22  0.60 11.28  \n', '<   -0.64  0.26  0.72 13.10  \n', '<    0.00  0.00  0.00  1.00 ]\n', '< PyMOL>matrix_reset copy_protein2\n', '< PyMOL>dump_mat(cmd.get_object_matrix("copy_protein2"))\n', '< [  1.00  0.00  0.00  0.00  \n', '<    0.00  1.00  0.00  0.00  \n', '<    0.00  0.00  1.00  0.00  \n', '<    0.00  0.00  0.00  1.00 ]\n', '< PyMOL>dump_lst((cmd.get_distance("/target/1HPV/B/ILE`84/CB","/copy_protein2/1HPV/B/ILE`84/CB"),))\n', '< [  0.00 ]\n']
 run_tests: C1000viewing...
 run_tests: C1000viewing.log DIFFERS over about 264 lines:
['1,527d0\n', '< PyMOL>bg white\n', '< PyMOL>bg_color black\n', '< PyMOL>bg_color 0\n', '< PyMOL>bg_color 1\n', '< PyMOL>bg_color blue\n', '< PyMOL>bg_color -28374283\n', '< Color-Error: Bad color name.\n', '< PyMOL>bg_color 239283498\n', '< Color-Error: Bad color name.\n', '< PyMOL>bg_color asdfasdf\n', '< Color-Error: Bad color name.\n', '< PyMOL>dele all\n', '< PyMOL>reset\n', '< PyMOL>clip\n', '< Parsing-Error: missing required argument: mode\n', '< PyMOL>clip near\n', '< Parsing-Error: missing required argument: distance\n', '< PyMOL>clip near,-5\n', '< PyMOL>clip far,10\n', '< PyMOL>clip near,2\n', '< PyMOL>clip far,-3\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '<   1.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   1.000\n', '<   0.000   0.000 -50.000   0.000   0.000   0.000  43.000  93.000 -20.000\n', '< PyMOL>dele all\n', '< PyMOL>load dat/1tii.pdb\n', '< HEADER    ENTEROTOXIN                             20-MAR-96   1TII\n', '< TITLE     ESCHERICHIA COLI HEAT LABILE ENTEROTOXIN TYPE IIB\n', '< COMPND    MOL_ID: 1;\n', '< COMPND   2 MOLECULE: HEAT LABILE ENTEROTOXIN TYPE IIB;\n', '< COMPND   3 CHAIN: D, E, F, G, H, A, C;\n', '< COMPND   4 SYNONYM: LT-IIB;\n', '< COMPND   5 ENGINEERED: YES;\n', '< COMPND   6 OTHER_DETAILS: LATENT/INACTIVE FORM\n', '<  ObjectMolecule: Read secondary structure assignments.\n', '<  ObjectMolecule: Read crystal symmetry information.\n', '<  Symmetry: Found 6 symmetry operators.\n', '<  CmdLoad: "dat/1tii.pdb" loaded as "1tii".\n', '< PyMOL>hide\n', '< PyMOL>show cartoon\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 67216 graphics primitives.\n', '< PyMOL>cartoon rect\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 39552 graphics primitives.\n', '< PyMOL>cartoon loop\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 59232 graphics primitives.\n', '< PyMOL>cartoon tube\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 88720 graphics primitives.\n', '< PyMOL>cartoon oval\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 98720 graphics primitives.\n', '< PyMOL>cartoon arrow\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 39552 graphics primitives.\n', '< PyMOL>cartoon dumbbell\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 138176 graphics primitives.\n', '< PyMOL>cartoon automatic\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 67216 graphics primitives.\n', '< PyMOL>cartoon loop,ss h\n', '< PyMOL>cartoon tube,ss s\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 66876 graphics primitives.\n', '< PyMOL>cartoon skip,resi 1-100\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 10678 graphics primitives.\n', '< PyMOL>dele all\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>color\n', '< Parsing-Error: missing required argument: color\n', '< PyMOL>color -123454\n', '< Color-Error: Unknown color.\n', '< PyMOL>color 1023912\n', '< Color-Error: Unknown color.\n', '< PyMOL>color blue\n', '<  Executive: Colored 107 atoms.\n', '< PyMOL>color red\n', '<  Executive: Colored 107 atoms.\n', '< PyMOL>color 99\n', '<  Executive: Colored 107 atoms.\n', '< PyMOL>color blue,pept\n', '<  Executive: Colored 107 atoms and 1 object.\n', '< PyMOL>color green,cgo\n', '<  Executive: Colored 1 object.\n', '< PyMOL>color red,(all)\n', '<  Executive: Colored 107 atoms.\n', '< PyMOL>dele all\n', '< PyMOL>cgo_tuple = (SPHERE, 0.0, 0.0, 0.0, 1.0)\n', "< PyMOL>cmd.load_cgo(cgo_tuple,'cgo')\n", '< PyMOL>ray renderer=2\n', '<  RayRenderTest: obtained 1 graphics primitives.\n', '< PyMOL>dele all\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>load dat/3al1.pdb\n', '< HEADER    STRUCTURAL PROTEIN                      26-OCT-98   3AL1\n', '< TITLE     DESIGNED PEPTIDE ALPHA-1, RACEMIC P1BAR FORM\n', '< COMPND    MOL_ID: 1;\n', '< COMPND   2 MOLECULE: D, L-ALPHA-1;\n', '< COMPND   3 CHAIN: A, B;\n', '< COMPND   4 ENGINEERED: YES;\n', '< COMPND   5 OTHER_DETAILS: N TERMINI ARE ACETYLATED\n', '<  ObjectMolecule: Read secondary structure assignments.\n', '<  ObjectMolecule: Read crystal symmetry information.\n', '<  Symmetry: Found 2 symmetry operators.\n', '<  CmdLoad: "dat/3al1.pdb" loaded as "3al1".\n', '< PyMOL>disable\n', '< PyMOL>enable pept\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 166 graphics primitives.\n', '< PyMOL>disable\n', '< PyMOL>enable 3al1\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 1266 graphics primitives.\n', '< PyMOL>disable\n', '< PyMOL>enable\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 1432 graphics primitives.\n', '< PyMOL>disable\n', '< PyMOL>enable all\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 1432 graphics primitives.\n', '< PyMOL>disable\n', '< PyMOL>enable 3al1\n', '< PyMOL>enable pept\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 1432 graphics primitives.\n', '< PyMOL>dele all\n', '< PyMOL>reset\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '<   1.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   1.000\n', '<   0.000   0.000 -50.000   0.000   0.000   0.000  40.000 100.000 -20.000\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>hide\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 0 graphics primitives.\n', '< PyMOL>show (name ca)\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 0 graphics primitives.\n', '< PyMOL>show (name c)\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 13 graphics primitives.\n', '< PyMOL>show (all)\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 166 graphics primitives.\n', '< PyMOL>hide (name ca)\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 115 graphics primitives.\n', '< PyMOL>hide\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 0 graphics primitives.\n', '< PyMOL>show sticks\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 166 graphics primitives.\n', '< PyMOL>show spheres,(name ca)\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 179 graphics primitives.\n', '< PyMOL>show surface,(not name n)\n', '< PyMOL>hide (name o)\n', '< PyMOL>ray\n', '<  RepSurface: 1319 surface points.\n', '<  RepSurface: 2634 triangles.\n', '<  RayRenderTest: obtained 2412 graphics primitives.\n', '< PyMOL>hide surf\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 153 graphics primitives.\n', '< PyMOL>hide sph\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 140 graphics primitives.\n', '< PyMOL>hide sticks\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 0 graphics primitives.\n', '< PyMOL>dele all\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>label (all),resi\n', '<  Label: labelled 107 atoms.\n', '< PyMOL>label (name ca),"ca"\n', '<  Label: labelled 13 atoms.\n', '< PyMOL>label (name n),"%s-%s-%s"%(chain,resi,resn)\n', '<  Label: labelled 13 atoms.\n', "< PyMOL>label (all),''\n", '<  Label: labelled 107 atoms.\n', '< PyMOL>label (all)\n', '<  Label: labelled 107 atoms.\n', '< PyMOL>dele all\n', '< PyMOL>dele all\n', '< PyMOL>reset\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '<   1.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   1.000\n', '<   0.000   0.000 -50.000   0.000   0.000   0.000  40.000 100.000 -20.000\n', '< PyMOL>move\n', '< Parsing-Error: missing required argument: axis\n', '< PyMOL>move x\n', '< Parsing-Error: missing required argument: distance\n', '< PyMOL>move y\n', '< Parsing-Error: missing required argument: distance\n', '< PyMOL>move z\n', '< Parsing-Error: missing required argument: distance\n', '< PyMOL>move x,10\n', '< PyMOL>move y,5\n', '< PyMOL>move z,2\n', '< PyMOL>move z,-1\n', '< PyMOL>move x,-10\n', '< PyMOL>move y,2\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '<   1.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   1.000\n', '<   0.000   7.000 -49.000   0.000   0.000   0.000  39.000  99.000 -20.000\n', '< PyMOL>dele all\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>orient\n', '< PyMOL>orient (none)\n', '< PyMOL>orient (name ca)\n', '< PyMOL>orient (resi 10)\n', '< PyMOL>orient (name ca and i. 10)\n', '< PyMOL>dele all\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>origin\n', '< PyMOL>origin (none)\n', '< PyMOL>origin (name ca)\n', '< PyMOL>origin (resi 10)\n', '< PyMOL>origin (name ca and i. 10)\n', '< PyMOL>dele all\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>show dots\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 6837 graphics primitives.\n', '< PyMOL>alter (all),vdw=5.0\n', '<  Alter: modified 107 atoms.\n', '< PyMOL>refresh\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 6837 graphics primitives.\n', '< PyMOL>rebuild\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 1960 graphics primitives.\n', '< PyMOL>dele all\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>color shoot\n', '< Color-Error: Unknown color.\n', '< PyMOL>set_color shoot,[1.0,0.9,1.0]\n', '<  Color: "shoot" defined as [ 1.000, 0.900, 1.000 ].\n', '< PyMOL>color shoot\n', '<  Executive: Colored 107 atoms.\n', '< PyMOL>refresh\n', '< PyMOL>set_color shoot,[1.0,0.0,1.0]\n', '<  Color: "shoot" defined as [ 1.000, 0.000, 1.000 ].\n', '< PyMOL>recolor\n', '< PyMOL>refresh\n', '< PyMOL>dele all\n', '< PyMOL>dele all\n', '< PyMOL>reset\n', '< PyMOL>cmd._dump_floats(v1)\n', '<   1.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   1.000\n', '<   0.000   0.000 -50.000   0.000   0.000   0.000  40.000 100.000 -20.000\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '<   1.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   1.000\n', '<   0.000   0.000 -63.191   1.224 -10.279  20.545  49.820  76.561 -20.000\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '<   1.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   1.000\n', '<   0.000   0.000 -50.000   0.000   0.000   0.000  40.000 100.000 -20.000\n', '< PyMOL>dele all\n', '< PyMOL>dele all\n', '< PyMOL>reset\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '<   1.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   1.000\n', '<   0.000   0.000 -50.000   0.000   0.000   0.000  40.000 100.000 -20.000\n', '< PyMOL>turn\n', '< Parsing-Error: missing required argument: axis\n', '< PyMOL>turn x\n', '< Parsing-Error: missing required argument: angle\n', '< PyMOL>turn y\n', '< Parsing-Error: missing required argument: angle\n', '< PyMOL>turn z\n', '< Parsing-Error: missing required argument: angle\n', '< PyMOL>turn x,10\n', '< PyMOL>turn y,5\n', '< PyMOL>turn z,2\n', '< PyMOL>turn z,-1\n', '< PyMOL>turn x,-10\n', '< PyMOL>turn y,2\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '<   0.992   0.002  -0.124  -0.002   1.000  -0.001   0.124   0.001   0.992\n', '<   0.000   0.000 -50.000   0.000   0.000   0.000  40.000 100.000 -20.000\n', '< PyMOL>dele all\n', '< PyMOL>dele all\n', '< PyMOL>reset\n', '< PyMOL>view\n', '< Parsing-Error: missing required argument: key\n', '< PyMOL>view 1,store\n', '<  view: view stored as "1".\n', '< PyMOL>view 2,store\n', '<  view: view stored as "2".\n', '< PyMOL>move x,10\n', '< PyMOL>view 2,st\n', '<  view: view stored as "2".\n', '< PyMOL>reset\n', '< PyMOL>move y,-10\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '<   1.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   1.000\n', '<   0.000 -10.000 -50.000   0.000   0.000   0.000  40.000 100.000 -20.000\n', '< PyMOL>view 1,recall\n', '<  view: "1" recalled.\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '<   1.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   1.000\n', '<   0.000   0.000 -50.000   0.000   0.000   0.000  40.000 100.000 -20.000\n', '< PyMOL>view 2,rec\n', '<  view: "2" recalled.\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '<   1.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   1.000\n', '<  10.000   0.000 -50.000   0.000   0.000   0.000  40.000 100.000 -20.000\n', '< PyMOL>turn x,10\n', '< PyMOL>view test,store\n', '<  view: view stored as "test".\n', '< PyMOL>turn x,20\n', '< PyMOL>view rest,store\n', '<  view: view stored as "rest".\n', '< PyMOL>view test\n', '<  view: "test" recalled.\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '<   1.000   0.000   0.000   0.000   0.985   0.174   0.000  -0.174   0.985\n', '<  10.000   0.000 -50.000   0.000   0.000   0.000  40.000 100.000 -20.000\n', '< PyMOL>view rest\n', '<  view: "rest" recalled.\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '<   1.000   0.000   0.000   0.000   0.866   0.500   0.000  -0.500   0.866\n', '<  10.000   0.000 -50.000   0.000   0.000   0.000  40.000 100.000 -20.000\n', '< PyMOL>view rest,clear\n', "<  view: 'rest' deleted.\n", '< PyMOL>view rest\n', "< Error: unknown view: 'rest'. Choices:\n", '<   1     2     test\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '<   1.000   0.000   0.000   0.000   0.866   0.500   0.000  -0.500   0.866\n', '<  10.000   0.000 -50.000   0.000   0.000   0.000  40.000 100.000 -20.000\n', '< PyMOL>view test\n', '<  view: "test" recalled.\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '<   1.000   0.000   0.000   0.000   0.985   0.174   0.000  -0.174   0.985\n', '<  10.000   0.000 -50.000   0.000   0.000   0.000  40.000 100.000 -20.000\n', '< PyMOL>viewport\n', '< PyMOL>viewport 300\n', '< PyMOL>viewport 100,100\n', '< PyMOL>viewport 300,300\n', '< PyMOL>viewport 640,480\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '<   1.000   0.000   0.000   0.000   0.985   0.174   0.000  -0.174   0.985\n', '<   0.000   0.000 -63.191   1.224 -10.279  20.545  49.820  76.561 -20.000\n', '< PyMOL>zoom\n', '< PyMOL>zoom resi 10\n', '< PyMOL>zoom resi 4,5,6\n', "< ExecutiveWindowZoom-Warning: selection doesn't specify any coordinates.\n", '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '<   1.000   0.000   0.000   0.000   0.985   0.174   0.000  -0.174   0.985\n', '<   0.000   0.000 -14.178   2.395  -9.290  18.016  11.178  17.178 -20.000\n', '< PyMOL>dele all\n', '< PyMOL>load dat/1tii.pdb,m1\n', '< HEADER    ENTEROTOXIN                             20-MAR-96   1TII\n', '< TITLE     ESCHERICHIA COLI HEAT LABILE ENTEROTOXIN TYPE IIB\n', '< COMPND    MOL_ID: 1;\n', '< COMPND   2 MOLECULE: HEAT LABILE ENTEROTOXIN TYPE IIB;\n', '< COMPND   3 CHAIN: D, E, F, G, H, A, C;\n', '< COMPND   4 SYNONYM: LT-IIB;\n', '< COMPND   5 ENGINEERED: YES;\n', '< COMPND   6 OTHER_DETAILS: LATENT/INACTIVE FORM\n', '<  ObjectMolecule: Read secondary structure assignments.\n', '<  ObjectMolecule: Read crystal symmetry information.\n', '<  Symmetry: Found 6 symmetry operators.\n', '<  CmdLoad: "dat/1tii.pdb" loaded as "m1".\n', '< PyMOL>load dat/il2.pdb,m1\n', '<  CmdLoad: "dat/il2.pdb" appended into object "m1", state 2.\n', '< PyMOL>load dat/pept.pdb,m1\n', '<  CmdLoad: "dat/pept.pdb" appended into object "m1", state 3.\n', '< PyMOL>zoom m1\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '<   1.000   0.000   0.000   0.000   0.985   0.174   0.000  -0.174   0.985\n', '<   0.000   0.000 -269.487  39.950   5.709  13.189 212.466 326.509 -20.000\n', '< PyMOL>zoom m1,state=0\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '<   1.000   0.000   0.000   0.000   0.985   0.174   0.000  -0.174   0.985\n', '<   0.000   0.000 -269.487  39.950   5.709  13.189 212.466 326.509 -20.000\n', '< PyMOL>zoom m1,state=1\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '<   1.000   0.000   0.000   0.000   0.985   0.174   0.000  -0.174   0.985\n', '<   0.000   0.000 -227.278  51.665  11.519  10.196 179.188 275.368 -20.000\n', '< PyMOL>zoom m1,state=2\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '<   1.000   0.000   0.000   0.000   0.985   0.174   0.000  -0.174   0.985\n', '<   0.000   0.000 -149.541   9.985  -9.318  20.976 117.899 181.182 -20.000\n', '< PyMOL>zoom m1,state=3\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '<   1.000   0.000   0.000   0.000   0.985   0.174   0.000  -0.174   0.985\n', '<   0.000   0.000 -63.191   1.224 -10.279  20.545  49.820  76.561 -20.000\n', '< PyMOL>zoom m1,state=4\n', "< ExecutiveWindowZoom-Warning: selection doesn't specify any coordinates.\n", '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '<   1.000   0.000   0.000   0.000   0.985   0.174   0.000  -0.174   0.985\n', '<   0.000   0.000 -63.191   1.224 -10.279  20.545  49.820  76.561 -20.000\n', '< PyMOL>origin m1\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '<   1.000   0.000   0.000   0.000   0.985   0.174   0.000  -0.174   0.985\n', '<  38.726  17.022 -67.659  39.950   5.709  13.189  49.820  76.561 -20.000\n', '< PyMOL>origin m1,state=0\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '<   1.000   0.000   0.000   0.000   0.985   0.174   0.000  -0.174   0.985\n', '<  38.726  17.022 -67.659  39.950   5.709  13.189  49.820  76.561 -20.000\n', '< PyMOL>origin m1,state=1\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '<   1.000   0.000   0.000   0.000   0.985   0.174   0.000  -0.174   0.985\n', '<  50.441  23.264 -69.598  51.665  11.519  10.196  49.820  76.561 -20.000\n', '< PyMOL>origin m1,state=2\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '<   1.000   0.000   0.000   0.000   0.985   0.174   0.000  -0.174   0.985\n', '<   8.761   0.872 -62.600   9.985  -9.318  20.976  49.820  76.561 -20.000\n', '< PyMOL>origin m1,state=3\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '<   1.000   0.000   0.000   0.000   0.985   0.174   0.000  -0.174   0.985\n', '<   0.000   0.000 -63.191   1.224 -10.279  20.545  49.820  76.561 -20.000\n', '< PyMOL>origin m1,state=4\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '<   1.000   0.000   0.000   0.000   0.985   0.174   0.000  -0.174   0.985\n', '<   0.000   0.000 -63.191   1.224 -10.279  20.545  49.820  76.561 -20.000\n', '< PyMOL>orient m1\n', '< PyMOL>cmd._dump_ufloats(cmd.get_view(0))\n', '<   0.924   0.347   0.160   0.338   0.550   0.763   0.177   0.760   0.626\n', '<   0.000   0.000 269.487  39.950   5.709  13.189 212.466 326.509  20.000\n', '< PyMOL>orient m1,state=0\n', '< PyMOL>cmd._dump_ufloats(cmd.get_view(0))\n', '<   0.924   0.347   0.160   0.338   0.550   0.763   0.177   0.760   0.626\n', '<   0.000   0.000 269.487  39.950   5.709  13.189 212.466 326.509  20.000\n', '< PyMOL>orient m1,state=1\n', '< PyMOL>cmd._dump_ufloats(cmd.get_view(0))\n', '<   0.899   0.239   0.366   0.288   0.306   0.907   0.329   0.921   0.206\n', '<   0.000   0.000 227.278  51.665  11.519  10.196 179.188 275.368  20.000\n', '< PyMOL>orient m1,state=2\n', '< PyMOL>cmd._dump_ufloats(cmd.get_view(0))\n', '<   0.288   0.019   0.958   0.301   0.951   0.072   0.909   0.309   0.279\n', '<   0.000   0.000 149.541   9.985   9.318  20.976 117.899 181.182  20.000\n', '< PyMOL>orient m1,state=3\n', '< PyMOL>cmd._dump_ufloats(cmd.get_view(0))\n', '<   0.537   0.312   0.784   0.841   0.118   0.529   0.072   0.943   0.325\n', '<   0.000   0.000  63.191   1.224  10.279  20.545  49.820  76.561  20.000\n', '< PyMOL>orient m1,state=4\n', '< PyMOL>cmd._dump_ufloats(cmd.get_view(0))\n', '<   0.537   0.312   0.784   0.841   0.118   0.529   0.072   0.943   0.325\n', '<   0.000   0.000  63.191   1.224  10.279  20.545  49.820  76.561  20.000\n', '< PyMOL>zoom m1,state=-5000\n', '< PyMOL>zoom (none),state=5\n', "< ExecutiveWindowZoom-Warning: selection doesn't specify any coordinates.\n", '< PyMOL>zoom (all),state=-1\n', '< PyMOL>zoom (all),state=0\n', '< PyMOL>cmd._dump_ufloats(cmd.get_view(0))\n', '<   0.537   0.312   0.784   0.841   0.118   0.529   0.072   0.943   0.325\n', '<   0.000   0.000 269.487  39.950   5.709  13.189 212.466 326.509  20.000\n', '< PyMOL>dele all\n', '< PyMOL>load dat/1tii.pdb\n', '< HEADER    ENTEROTOXIN                             20-MAR-96   1TII\n', '< TITLE     ESCHERICHIA COLI HEAT LABILE ENTEROTOXIN TYPE IIB\n', '< COMPND    MOL_ID: 1;\n', '< COMPND   2 MOLECULE: HEAT LABILE ENTEROTOXIN TYPE IIB;\n', '< COMPND   3 CHAIN: D, E, F, G, H, A, C;\n', '< COMPND   4 SYNONYM: LT-IIB;\n', '< COMPND   5 ENGINEERED: YES;\n', '< COMPND   6 OTHER_DETAILS: LATENT/INACTIVE FORM\n', '<  ObjectMolecule: Read secondary structure assignments.\n', '<  ObjectMolecule: Read crystal symmetry information.\n', '<  Symmetry: Found 6 symmetry operators.\n', '<  CmdLoad: "dat/1tii.pdb" loaded as "1tii".\n', '< PyMOL>cmd._dump_floats(cmd.get_extent("1tii")[0])\n', '<  11.590 -22.877 -28.270\n', '< PyMOL>cmd._dump_floats(cmd.get_extent("1tii")[1])\n', '<  84.681  40.101  47.233\n', '< PyMOL>cmd._dump_floats(cmd.get_extent("1TII")[0])\n', '<  11.590 -22.877 -28.270\n', '< PyMOL>cmd._dump_floats(cmd.get_extent("1TII")[1])\n', '<  84.681  40.101  47.233\n', '< PyMOL>cmd._dump_floats(cmd.get_extent("1Tii")[0])\n', '<  11.590 -22.877 -28.270\n', '< PyMOL>cmd._dump_floats(cmd.get_extent("1Tii")[1])\n', '<  84.681  40.101  47.233\n', '< PyMOL>cmd._dump_floats(cmd.get_extent("1tii////cA")[0])\n', '<  12.578 -21.622 -23.339\n', '< PyMOL>cmd._dump_floats(cmd.get_extent("1tii////ca")[1])\n', '<  81.195  38.760  45.050\n', '< PyMOL>cmd._dump_floats(cmd.get_extent("1TII////cA")[0])\n', '<  12.578 -21.622 -23.339\n', '< PyMOL>cmd._dump_floats(cmd.get_extent("1TII////ca")[1])\n', '<  81.195  38.760  45.050\n', '< PyMOL>cmd._dump_floats(cmd.get_extent("1Tii////cA")[0])\n', '<  12.578 -21.622 -23.339\n', '< PyMOL>cmd._dump_floats(cmd.get_extent("1Tii////ca")[1])\n', '<  81.195  38.760  45.050\n', '< PyMOL>dist TSt,/1tii//A/TYR`3/CD1, /1tii//F/ARG`12/NE\n', '<  Executive: object "TSt" created.\n', '< PyMOL>cmd._dump_floats(cmd.get_extent("tst")[0])\n', '<  35.306  24.391  -8.737\n', '< PyMOL>cmd._dump_floats(cmd.get_extent("tst")[1])\n', '<  77.385  25.286   6.130\n', '< PyMOL>cmd._dump_floats(cmd.get_extent("TST")[0])\n', '<  35.306  24.391  -8.737\n', '< PyMOL>cmd._dump_floats(cmd.get_extent("TST")[1])\n', '<  77.385  25.286   6.130\n', '< PyMOL>cmd._dump_floats(cmd.get_extent("tSt")[0])\n', '<  35.306  24.391  -8.737\n', '< PyMOL>cmd._dump_floats(cmd.get_extent("tSt")[1])\n', '<  77.385  25.286   6.130\n']
 run_tests: C1010helping...
 run_tests: C1010helping.log DIFFERS over about 27 lines:
['1,53d0\n', '< PyMOL>help\n', '< \n', '< COMMANDS\n', '< \n', '<     INPUT/OUTPUT  load      save      delete    quit\n', '<     VIEW          turn      move      clip      rock\n', '<                   show      hide      enable    disable\n', '<                   reset     refresh   rebuild   \n', '<                   zoom      origin    orient   \n', '<                   view      get_view  set_view\n', '<     MOVIES        mplay     mstop     mset      mdo\n', '<                   mpng      mmatrix   frame\n', '<                   rewind    middle    ending\n', '<                   forward   backward\n', '<     IMAGING       png       mpng\n', '<     RAY TRACING   ray       \n', '<     MAPS          isomesh   isodot\n', '<     DISPLAY       cls       viewport  splash    \n', '<     SELECTIONS    select    mask   \n', '<     SETTINGS      set       button\n', '<     ATOMS         alter     alter_state \n', '<     EDITING       create    replace   remove    h_fill   remove_picked\n', '<                   edit      bond      unbond    h_add    fuse       \n', '<                   undo      redo      protect   cycle_valence  attach\n', '<     FITTING       fit       rms       rms_cur   pair_fit  \n', '<                   intra_fit intra_rms intra_rms_cur   \n', '<     COLORS        color     set_color\n', '<     HELP          help      commands\n', '<     DISTANCES     dist      \n', '<     STEREO        stereo\n', '<     SYMMETRY      symexp\n', '<     SCRIPTS       @         run\n', '<     LANGUAGE      alias     extend\n', '< \n', '< Try "help <command-name>".  Also see the following extra topics:\n', '< \n', '<     "movies", "keyboard", "mouse", "selections",\n', '<     "examples", "launching", "editing", and "api". \n', '< \n', '< PyMOL>help dummy\n', '< \n', '< DESCRIPTION\n', '< \n', '<     This is a dummy function which returns None. \n', '< \n', "< PyMOL>cmd.show_help('dummy')\n", '< PyMOL>help dummy\n', '< \n', '< DESCRIPTION\n', '< \n', '<     This is a dummy function which returns None. \n', '< \n', '< (Hit ESC to hide)\n']
 run_tests: C1020querying...
 run_tests: C1020querying.log DIFFERS over about 123 lines:
['1,245d0\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>count_atoms\n', '<  count_atoms: 107 atoms\n', '< PyMOL>count_atoms name ca\n', '<  count_atoms: 13 atoms\n', '< PyMOL>count_states\n', '<  cmd.count_states: 1 states.\n', '< PyMOL>create pept,(all),1,2\n', '<  Selector: found 107 atoms.\n', '< PyMOL>create pept,(all),1,3\n', '<  Selector: found 107 atoms.\n', '< PyMOL>create pept,(none),1,2\n', '<  Selector: found 0 atoms.\n', '< PyMOL>create cpy,(all),1,1\n', '<  Selector: found 107 atoms.\n', '<  Executive: object "cpy" created.\n', '< PyMOL>count_states\n', '<  cmd.count_states: 3 states.\n', '< PyMOL>count_states pept\n', '<  cmd.count_states: 3 states.\n', '< PyMOL>count_states cpy\n', '<  cmd.count_states: 1 states.\n', '< PyMOL>count_frames\n', '<  cmd.count_frames: 3 frames\n', '< PyMOL>mset 1 x10\n', '< PyMOL>count_frames\n', '<  cmd.count_frames: 10 frames\n', '< PyMOL>cmd.count_frames()\n', '< PyMOL>cmd.count_states()\n', '< PyMOL>cmd.count_atoms()\n', '< PyMOL>dist\n', "< cmd-Error: The 'pk1' selection is undefined.\n", "< cmd-Error: The 'pk2' selection is undefined.\n", '< PyMOL>distance\n', "< cmd-Error: The 'pk1' selection is undefined.\n", "< cmd-Error: The 'pk2' selection is undefined.\n", '< PyMOL>select lb,resi 5 and name ca\n', '<  Selector: selection "lb" defined with 2 atoms.\n', '< PyMOL>dist\n', "< cmd-Error: The 'pk1' selection is undefined.\n", "< cmd-Error: The 'pk2' selection is undefined.\n", '< PyMOL>select rb,resi 8 and name ca\n', '<  Selector: selection "rb" defined with 2 atoms.\n', '< PyMOL>dist\n', "< cmd-Error: The 'pk1' selection is undefined.\n", "< cmd-Error: The 'pk2' selection is undefined.\n", '< PyMOL>dist (lb),resi 10 and name ca\n', '<  Executive: object "dist01" created.\n', '< PyMOL>distance resi 6 and name n,resi 9\n', '<  Executive: object "dist02" created.\n', '< PyMOL>distance resi 7 and name ca,all,3.0,zoom=1\n', '<  Executive: object "dist03" created.\n', '< PyMOL>print "%6.3f"%cmd.distance("resi 1 and name ca","resi 13 and name ca")\n', '<  5.762\n', '< PyMOL>print "%6.3f"%cmd.distance("resi 1 and name ca","resi 14 and name ca")\n', '< -1.000\n', '< PyMOL>print cmd.find_pairs("name o","name n",mode=1,cutoff=3.4)\n', "< [(('cpy', 103), ('pept', 1)), (('pept', 103), ('pept', 1)), (('cpy', 83), ('pept', 15)), (('pept', 83), ('pept', 15)), (('cpy', 59), ('pept', 34)), (('pept', 59), ('pept', 34)), (('cpy', 47), ('pept', 56)), (('cpy', 37), ('pept', 56)), (('pept', 47), ('pept', 56)), (('pept', 37), ('pept', 56)), (('cpy', 18), ('pept', 73)), (('pept', 18), ('pept', 73)), (('cpy', 4), ('pept', 100)), (('pept', 4), ('pept', 100)), (('cpy', 103), ('cpy', 1)), (('pept', 103), ('cpy', 1)), (('cpy', 83), ('cpy', 15)), (('pept', 83), ('cpy', 15)), (('cpy', 59), ('cpy', 34)), (('pept', 59), ('cpy', 34)), (('cpy', 47), ('cpy', 56)), (('cpy', 37), ('cpy', 56)), (('pept', 47), ('cpy', 56)), (('pept', 37), ('cpy', 56)), (('cpy', 18), ('cpy', 73)), (('pept', 18), ('cpy', 73)), (('cpy', 4), ('cpy', 100)), (('pept', 4), ('cpy', 100))]\n", '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>get_area (none)\n', '<  cmd.get_area: 0.000 Angstroms^2.\n', '< PyMOL>get_area\n', '<  cmd.get_area: 1381.186 Angstroms^2.\n', '< PyMOL>get_area state=2\n', '< Area-Error: Invalid state.\n', '< PyMOL>get_area name ca\n', '<  cmd.get_area: 112.133 Angstroms^2.\n', '< PyMOL>load dat/3al1.pdb\n', '< HEADER    STRUCTURAL PROTEIN                      26-OCT-98   3AL1\n', '< TITLE     DESIGNED PEPTIDE ALPHA-1, RACEMIC P1BAR FORM\n', '< COMPND    MOL_ID: 1;\n', '< COMPND   2 MOLECULE: D, L-ALPHA-1;\n', '< COMPND   3 CHAIN: A, B;\n', '< COMPND   4 ENGINEERED: YES;\n', '< COMPND   5 OTHER_DETAILS: N TERMINI ARE ACETYLATED\n', '<  ObjectMolecule: Read secondary structure assignments.\n', '<  ObjectMolecule: Read crystal symmetry information.\n', '<  Symmetry: Found 2 symmetry operators.\n', '<  CmdLoad: "dat/3al1.pdb" loaded as "3al1".\n', '< PyMOL>get_area\n', '< Area-Error: Selection must be within a single object.\n', '< PyMOL>dele all\n', '< PyMOL>print lst\n', "< [('white', 0), ('black', 1), ('blue', 2), ('green', 3), ('red', 4), ('cyan', 5), ('yellow', 6), ('dash', 7), ('magenta', 8), ('salmon', 9)]\n", '< PyMOL>print cmd.get_color_tuple("red")\n', '< (1.0, 0.0, 0.0)\n', '< PyMOL>print cmd.get_color_tuple("blue")\n', '< (0.0, 0.0, 1.0)\n', '< PyMOL>print cmd.get_color_tuple("green")\n', '< (0.0, 1.0, 0.0)\n', '< PyMOL>print cmd.get_color_tuple("white")\n', '< (1.0, 1.0, 1.0)\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>get_dihedral 1/n,1/ca,1/c,1/o\n', '<  cmd.get_dihedral: -8.586 degrees.\n', '<  -5.188 -20.331  13.157   8.919   0.863  27.058\n', '<  -5.063 -17.973  17.858   7.053  -2.295  25.698\n', '< PyMOL>print len(cmd.get_model().atom)\n', '< 107\n', '< PyMOL>print len(cmd.get_model("resi 1").bond)\n', '< 7\n', '< PyMOL>dele all\n', '< PyMOL>print cmd.get_names()\n', '< []\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>print cmd.get_names()\n', "< ['pept']\n", '< PyMOL>edit 4/ca\n', '<  Selector: selection "pk1" defined with 1 atoms.\n', '< PyMOL>print cmd.get_names("all")\n', "< ['pept', 'pk1', '_pkbase1', '_pkfrag1', '_pkbase2', '_pkfrag2', 'pkmol']\n", '< PyMOL>print cmd.get_names("selections")\n', "< ['pk1', '_pkbase1', '_pkfrag1', '_pkbase2', '_pkfrag2', 'pkmol']\n", '< PyMOL>print cmd.get_names("objects")\n', "< ['pept']\n", '< PyMOL>print cmd.get_names_of_type("object:molecule")\n', "< ['pept']\n", '< PyMOL>print cmd.get_names_of_type("object:map")\n', '< []\n', '< PyMOL>kee = pp.keys()[0]\n', '< PyMOL>print kee\n', "< ('pept', 10)\n", '< PyMOL>cmd._dump_floats(pp[kee])\n', '< -124.163 170.604\n', '< PyMOL>reset\n', '< PyMOL>get_position\n', '<  cmd.get_position: [   1.224, -10.279,  20.545]\n', '< PyMOL>zoom resi 10\n', '< PyMOL>get_position\n', '<  cmd.get_position: [   2.395,  -9.290,  18.016]\n', '< PyMOL>get_type\n', '< Parsing-Error: missing required argument: name\n', '< PyMOL>get_type nonexistent\n', '< cmd-Error: unrecognized name.\n', '< PyMOL>get_type pept\n', '< object:molecule\n', '< PyMOL>id_atom none\n', '< cmd-Error: atom none not found by id_atom.\n', '< PyMOL>id_atom all\n', '< cmd-Error: multiple atoms all found by id_atom.\n', '< PyMOL>id_atom 5/ca\n', '<  cmd.id_atom: (id 35)\n', '< PyMOL>identify name ca\n', '<  cmd.identify: (id 2)\n', '<  cmd.identify: (id 10)\n', '<  cmd.identify: (id 16)\n', '<  cmd.identify: (id 21)\n', '<  cmd.identify: (id 35)\n', '<  cmd.identify: (id 45)\n', '<  cmd.identify: (id 53)\n', '<  cmd.identify: (id 57)\n', '<  cmd.identify: (id 66)\n', '<  cmd.identify: (id 74)\n', '<  cmd.identify: (id 81)\n', '<  cmd.identify: (id 95)\n', '<  cmd.identify: (id 101)\n', '< PyMOL>index name ca\n', '<  cmd.index: (pept`2)\n', '<  cmd.index: (pept`10)\n', '<  cmd.index: (pept`16)\n', '<  cmd.index: (pept`21)\n', '<  cmd.index: (pept`35)\n', '<  cmd.index: (pept`45)\n', '<  cmd.index: (pept`53)\n', '<  cmd.index: (pept`57)\n', '<  cmd.index: (pept`66)\n', '<  cmd.index: (pept`74)\n', '<  cmd.index: (pept`81)\n', '<  cmd.index: (pept`95)\n', '<  cmd.index: (pept`101)\n', '< PyMOL>overlap pept,pept\n', '<  cmd.overlap: 549.083 Angstroms.\n', '< PyMOL>alter (all),vdw=0.0\n', '<  Alter: modified 107 atoms.\n', '< PyMOL>overlap pept,pept\n', '<  cmd.overlap: 0.000 Angstroms.\n', '< PyMOL>alter (all),vdw=0.5\n', '<  Alter: modified 107 atoms.\n', '< PyMOL>overlap pept,pept\n', '<  cmd.overlap: 53.500 Angstroms.\n', '< PyMOL>phi_psi all\n', '<  CYS-2:    ( -124.2,  170.6 )\n', '<  ALA-3:    ( -128.4,  140.0 )\n', '<  TRP-4:    ( -128.5,  135.2 )\n', '<  HIS-5:    ( -114.1,  109.1 )\n', '<  LEU-6:    (   53.9,   41.8 )\n', '<  GLY-7:    (   90.4,  -28.0 )\n', '<  GLU-8:    (  -75.5,  138.7 )\n', '<  LEU-9:    (  -73.5,  125.3 )\n', '<  VAL-10:   (  -91.9,  -61.0 )\n', '<  TRP-11:   ( -168.2,  159.0 )\n', '<  CYS-12:   ( -138.9,  133.5 )\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>get_symmetry\n', '<  get_symmetry: No symmetry defined.\n', '< PyMOL>get_symmetry pept\n', '<  get_symmetry: No symmetry defined.\n', '< PyMOL>get_symmetry none\n', '< Error: selection must refer to exactly one object.\n', '< PyMOL>load dat/3al1.pdb\n', '< HEADER    STRUCTURAL PROTEIN                      26-OCT-98   3AL1\n', '< TITLE     DESIGNED PEPTIDE ALPHA-1, RACEMIC P1BAR FORM\n', '< COMPND    MOL_ID: 1;\n', '< COMPND   2 MOLECULE: D, L-ALPHA-1;\n', '< COMPND   3 CHAIN: A, B;\n', '< COMPND   4 ENGINEERED: YES;\n', '< COMPND   5 OTHER_DETAILS: N TERMINI ARE ACETYLATED\n', '<  ObjectMolecule: Read secondary structure assignments.\n', '<  ObjectMolecule: Read crystal symmetry information.\n', '<  Symmetry: Found 2 symmetry operators.\n', '<  CmdLoad: "dat/3al1.pdb" loaded as "3al1".\n', '< PyMOL>get_symmetry\n', '< Error: selection must refer to exactly one object.\n', '< PyMOL>get_symmetry 3al1\n', '<  get_symmetry: A     =  20.544 B    =  20.859 C     =  26.055\n', '<  get_symmetry: Alpha = 101.160 Beta =  97.030 Gamma = 118.060\n', '<  get_symmetry: SpaceGroup = P -1\n', '< PyMOL>get_symmetry pept\n', '<  get_symmetry: No symmetry defined.\n', '< PyMOL>hide\n', '< PyMOL>show cell,pept\n', '< PyMOL>ray renderer=2\n', '<  RayRenderTest: obtained 0 graphics primitives.\n', '< PyMOL>apply(cmd.set_symmetry,["pept"]+cmd.get_symmetry("3al1"))\n', '<  Symmetry: Found 2 symmetry operators.\n', '< PyMOL>get_symmetry pept\n', '<  get_symmetry: A     =  20.544 B    =  20.859 C     =  26.055\n', '<  get_symmetry: Alpha = 101.160 Beta =  97.030 Gamma = 118.060\n', '<  get_symmetry: SpaceGroup = P -1\n', '< PyMOL>get_symmetry 3al1\n', '<  get_symmetry: A     =  20.544 B    =  20.859 C     =  26.055\n', '<  get_symmetry: Alpha = 101.160 Beta =  97.030 Gamma = 118.060\n', '<  get_symmetry: SpaceGroup = P -1\n', '< PyMOL>show cell,pept\n', '< PyMOL>ray renderer=2\n', '<  RayRenderTest: obtained 12 graphics primitives.\n']
 run_tests: C1030selecting...
 run_tests: C1030selecting.log DIFFERS over about 62 lines:
['1,123d0\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>select (resi trp)\n', '<  Selector: selection "sel01" defined with 0 atoms.\n', '< PyMOL>indicate (name ca)\n', '< PyMOL>deselect\n', '< PyMOL>select 1/o\n', '<  Selector: selection "sel02" defined with 1 atoms.\n', '< PyMOL>select 1/o+ca+n\n', '<  Selector: selection "sel03" defined with 3 atoms.\n', '< PyMOL>select /pept\n', '<  Selector: selection "sel04" defined with 107 atoms.\n', '< PyMOL>select bb = (name ca or name c or name n)\n', '<  Selector: selection "bb" defined with 39 atoms.\n', '< PyMOL>select bb = (name ca,c,n)\n', '<  Selector: selection "bb" defined with 39 atoms.\n', '< PyMOL>select bb = */ca+c+n\n', '<  Selector: selection "bb" defined with 39 atoms.\n', '< PyMOL>select bb = (*/ca,c,n)\n', '<  Selector: selection "bb" defined with 39 atoms.\n', '< PyMOL>select bb = (not (not (name ca or name c or name n)))\n', '<  Selector: selection "bb" defined with 39 atoms.\n', '< PyMOL>select bb = (not (not (n. c|n. ca|n. n)))\n', '<  Selector: selection "bb" defined with 39 atoms.\n', '< PyMOL>select bb = (not (not (not (not (not (not (not (not (not (not (not (not (not (not (*/ca,c,n)))))))))))))))\n', '<  Selector: selection "bb" defined with 39 atoms.\n', '< PyMOL>select bb = (all and all and all and (not (not all)) and (not none) and all and not (not (n;ca,c,n)))\n', '<  Selector: selection "bb" defined with 39 atoms.\n', '< PyMOL>select bb,(name ca or (n;c | (n. n) | (*/n)))\n', '<  Selector: selection "bb" defined with 39 atoms.\n', '< PyMOL>select bb, \\\n', '< PyMOL>name ca \\\n', '< PyMOL>or name c \\\n', '< PyMOL>or name n\n', '<  Selector: selection "bb" defined with 39 atoms.\n', '< PyMOL>select bb = bb\n', '<  Selector: selection "bb" defined with 39 atoms.\n', '< PyMOL>select bb = not not bb\n', '<  Selector: selection "bb" defined with 39 atoms.\n', '< PyMOL>select cc = not bb\n', '<  Selector: selection "cc" defined with 68 atoms.\n', '< PyMOL>select bb = not cc\n', '<  Selector: selection "bb" defined with 39 atoms.\n', '< PyMOL>enable\n', '< PyMOL>enable bb\n', '< PyMOL>enable cc\n', '< PyMOL>disable cc\n', '< PyMOL>hide lines,cc\n', '< PyMOL>hide lines,bb\n', '< PyMOL>show (bb)\n', '< PyMOL>set ray_default_renderer=2\n', '<  Setting: ray_default_renderer set to 2.\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 63 graphics primitives.\n', '< PyMOL>dele all\n', '< PyMOL>load dat/1tii.pdb\n', '< HEADER    ENTEROTOXIN                             20-MAR-96   1TII\n', '< TITLE     ESCHERICHIA COLI HEAT LABILE ENTEROTOXIN TYPE IIB\n', '< COMPND    MOL_ID: 1;\n', '< COMPND   2 MOLECULE: HEAT LABILE ENTEROTOXIN TYPE IIB;\n', '< COMPND   3 CHAIN: D, E, F, G, H, A, C;\n', '< COMPND   4 SYNONYM: LT-IIB;\n', '< COMPND   5 ENGINEERED: YES;\n', '< COMPND   6 OTHER_DETAILS: LATENT/INACTIVE FORM\n', '<  ObjectMolecule: Read secondary structure assignments.\n', '<  ObjectMolecule: Read crystal symmetry information.\n', '<  Symmetry: Found 6 symmetry operators.\n', '<  CmdLoad: "dat/1tii.pdb" loaded as "1tii".\n', '< PyMOL>count_atoms 1+2+3+4+5+6+7+8+9+10+11+12+13+14+15+16+17+18+19+20+21+22+23+24+25+26+27+28+29+30+31+32+33+34+35+36+37+38+39+40+41+42+43+44+45+46+47+48+49+50+51+52+53+54+55+56+57+58+59+60+61+62+63+64+65+66+67+68+69+70+71+72+73+74+75+76+77+78+79+80+81+82+83+84+85+86+87+88+89+90+91+92+93+94+95+96+97+98+99+100+101+102+103+104+105+106+107+108+109+110+111+112+113+114+115+116+117+118+119+120+121+122+123+124+125+126+127+128+129+130+131+132+133+134+135+136+137+138+139+140+141+142+143+144+145+146+147+148+149+150+151+152+153+154+155+156+157+158+159+160+161+162+163+164+165+166+167+168+169+170+171+172+173+174+175+176+177+178+179+180+181+182+183+184+185+186+187+195+196+197+198+199+200+201+202+203+204+205+206+207+208+209+210+211+212+213+214+215+216+217+218+219+220+221+222+223+224+225+226+227+228+229+230/\n', '<  count_atoms: 5655 atoms\n', '< PyMOL>print cmd.count_atoms("resi 1+2+3+4+5+6+7+8+9+10+11+12+13+14+15+16+17+18+19+20+21+22+23+24+25+26+27+28+29+30+31+32+33+34+35+36+37+38+39+40+41+42+43+44+45+46+47+48+49+50+51+52+53+54+55+56+57+58+59+60+61+62+63+64+65+66+67+68+69+70+71+72+73+74+75+76+77+78+79+80+81+82+83+84+85+86+87+88+89+90+91+92+93+94+95+96+97+98+99+100+101+102+103+104+105+106+107+108+109+110+111+112+113+114+115+116+117+118+119+120+121+122+123+124+125+126+127+128+129+130+131+132+133+134+135+136+137+138+139+140+141+142+143+144+145+146+147+148+149+150+151+152+153+154+155+156+157+158+159+160+161+162+163+164+165+166+167+168+169+170+171+172+173+174+175+176+177+178+179+180+181+182+183+184+185+186+187+195+196+197+198+199+200+201+202+203+204+205+206+207+208+209+210+211+212+213+214+215+216+217+218+219+220+221+222+223+224+225+226+227+228+229+230")\n', '< 5655\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>load dat/tiny.pdb, model\n', '<  Executive-Warning: name "model" collides with a selection language keyword.\n', '<  CmdLoad: "dat/tiny.pdb" loaded as "model".\n', '< PyMOL>load dat/small01.mol, test+me\n', '<  ExecutiveLoad: "dat/small01.mol" loaded as "test+me", through state 1.\n', '< PyMOL>load dat/small02.pdb, mymodel\n', '<  CmdLoad: "dat/small02.pdb" loaded as "mymodel".\n', '< PyMOL>load dat/small03.mol2, model2\n', '<  ObjectMoleculeReadStr: read through molecule 1.\n', '<  ObjectMoleculeReadStr: read through molecule 2.\n', '<  ObjectMoleculeReadStr: read through molecule 3.\n', '<  ObjectMoleculeReadStr: read through molecule 4.\n', '<  ObjectMoleculeReadStr: read through molecule 5.\n', '<  ObjectMoleculeReadStr: read through molecule 6.\n', '<  ObjectMoleculeReadStr: read through molecule 7.\n', '<  ObjectMoleculeReadStr: read through molecule 8.\n', '<  ObjectMoleculeReadStr: read through molecule 9.\n', '<  ObjectMoleculeReadStr: read through molecule 10.\n', '<  ExecutiveLoad: "dat/small03.mol2" loaded as "model2", through state 16.\n', '< PyMOL>count_atoms model\n', '< Selector-Error: Misplaced ).\n', '< Selector-Error: Malformed selection.\n', '< ( model )<--\n', '<  count_atoms: -1 atoms\n', '< PyMOL>count_atoms model model\n', '<  count_atoms: 37 atoms\n', '< PyMOL>count_atoms /model\n', '<  count_atoms: 37 atoms\n', '< PyMOL>count_atoms pept\n', '<  count_atoms: 107 atoms\n', '< PyMOL>count_atoms model model pept\n', '<  count_atoms: 144 atoms\n', '< PyMOL>count_atoms /model+pept\n', '<  count_atoms: 144 atoms\n', '< PyMOL>count_atoms /pept+model\n', '<  count_atoms: 144 atoms\n', '< PyMOL>count_atoms /test+\\me\n', '<  count_atoms: 36 atoms\n', '< PyMOL>count_atoms /pept+model+test\\+me\n', '<  count_atoms: 180 atoms\n', '< PyMOL>count_atoms test+me\n', '<  count_atoms: 36 atoms\n', '< PyMOL>count_atoms test+me model model\n', '<  count_atoms: 73 atoms\n', '< PyMOL>count_atoms mymodel\n', '<  count_atoms: 36 atoms\n', '< PyMOL>count_atoms model2\n', '<  count_atoms: 389 atoms\n']
 run_tests: C1035wildcards...
 run_tests: C1035wildcards.log DIFFERS over about 53 lines:
['1,106d0\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>count_atoms name C*\n', '<  count_atoms: 69 atoms\n', '< PyMOL>count_atoms */C*\n', '<  count_atoms: 69 atoms\n', '< PyMOL>count_atoms A*/\n', '<  count_atoms: 13 atoms\n', '< PyMOL>count_atoms A*/O*\n', '<  count_atoms: 4 atoms\n', "< PyMOL>alter all,segi='FOUR'\n", '<  Alter: modified 107 atoms.\n', "< PyMOL>alter 1-5/,segi='FIRE'\n", '<  Alter: modified 43 atoms.\n', "< PyMOL>alter 6-7/,segi='SORE'\n", '<  Alter: modified 12 atoms.\n', '< PyMOL>count_atoms F*///\n', '<  count_atoms: 95 atoms\n', '< PyMOL>count_atoms F*R*///\n', '<  count_atoms: 95 atoms\n', '< PyMOL>count_atoms F*R///\n', '<  count_atoms: 52 atoms\n', '< PyMOL>count_atoms *R*///\n', '<  count_atoms: 107 atoms\n', '< PyMOL>count_atoms *IRE///\n', '<  count_atoms: 43 atoms\n', '< PyMOL>count_atoms *RE///\n', '<  count_atoms: 55 atoms\n', '< PyMOL>count_atoms *E///\n', '<  count_atoms: 55 atoms\n', '< PyMOL>count_atoms *O*///\n', '<  count_atoms: 64 atoms\n', '< PyMOL>count_atoms chain E\n', '<  count_atoms: 107 atoms\n', "< PyMOL>alter 1-3/,chain='A'\n", '<  Alter: modified 19 atoms.\n', "< PyMOL>alter 6-9/,chain='B'\n", '<  Alter: modified 29 atoms.\n', "< PyMOL>alter 10-11/,chain='G'\n", '<  Alter: modified 21 atoms.\n', '< PyMOL>count_atoms chain A\n', '<  count_atoms: 19 atoms\n', '< PyMOL>count_atoms chain A:B\n', '<  count_atoms: 48 atoms\n', '< PyMOL>count_atoms chain B:F\n', '<  count_atoms: 67 atoms\n', '< PyMOL>count_atoms chain A:Z\n', '<  count_atoms: 107 atoms\n', '< PyMOL>count_atoms chain A+E\n', '<  count_atoms: 57 atoms\n', '< PyMOL>count_atoms chain A+F\n', '<  count_atoms: 19 atoms\n', '< PyMOL>count_atoms */*/*/*/*\n', '<  count_atoms: 107 atoms\n', '< PyMOL>count_atoms */*/*/*\n', '<  count_atoms: 107 atoms\n', '< PyMOL>count_atoms */*/*\n', '<  count_atoms: 107 atoms\n', '< PyMOL>count_atoms */*\n', '<  count_atoms: 107 atoms\n', '< PyMOL>count_atoms *\n', '<  count_atoms: 107 atoms\n', '< PyMOL>count_atoms /*/*/*/*/*\n', '<  count_atoms: 107 atoms\n', '< PyMOL>count_atoms /*/*/*/*\n', '<  count_atoms: 107 atoms\n', '< PyMOL>count_atoms /*/*/*\n', '<  count_atoms: 107 atoms\n', '< PyMOL>count_atoms /*/*\n', '<  count_atoms: 107 atoms\n', '< PyMOL>count_atoms /*\n', '<  count_atoms: 107 atoms\n', '< PyMOL>count_atom /*/*RE\n', '<  count_atoms: 55 atoms\n', '< PyMOL>count_atom /*////ca\n', '<  count_atoms: 13 atoms\n', '< PyMOL>count_atom *////ca\n', '<  count_atoms: 13 atoms\n', '< PyMOL>count_atom /////ca\n', '<  count_atoms: 13 atoms\n', '< PyMOL>create pap,pept and not elem o\n', '<  Selector: found 88 atoms.\n', '<  Executive: object "pap" created.\n', '< PyMOL>create abt,pept and not elem n\n', '<  Selector: found 90 atoms.\n', '<  Executive: object "abt" created.\n', '< PyMOL>count_atoms p*\n', '<  count_atoms: 195 atoms\n', '< PyMOL>count_atoms *t\n', '<  count_atoms: 197 atoms\n', '< PyMOL>count_atoms *pt\n', '<  count_atoms: 107 atoms\n', '< PyMOL>count_atoms p*p\n', '<  count_atoms: 88 atoms\n', '< PyMOL>count_atoms p*p*\n', '<  count_atoms: 195 atoms\n', '< PyMOL>count_atoms a*\n', '<  count_atoms: 90 atoms\n', '< PyMOL>count_atoms /p*/*RE\n', '<  count_atoms: 101 atoms\n', '< PyMOL>count_atoms /*t/*O*\n', '<  count_atoms: 119 atoms\n', '< PyMOL>count_atoms /*pt//A:E\n', '<  count_atoms: 86 atoms\n', '< PyMOL>count_atoms /p*/*RE/E/h*/c*\n', '<  count_atoms: 12 atoms\n']
 run_tests: C1040editing...
 run_tests: C1040editing.log DIFFERS over about 260 lines:
['1,519d0\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>alter (elem n,o),vdw=4.0\n', '<  Alter: modified 36 atoms.\n', '< PyMOL>show dots\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 2032 graphics primitives.\n', '< PyMOL>alter_state 1,(all),x=x+y\n', '<  AlterState: modified 107 atom coordinate states.\n', '< PyMOL>hide\n', '< PyMOL>show lines\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 166 graphics primitives.\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" appended into object "pept", state 2.\n', '< PyMOL>alter_state -1,(all),x=x+y\n', '<  AlterState: modified 107 atom coordinate states.\n', '< PyMOL>alter_state 0,(all), x=x+y\n', '<  AlterState: modified 214 atom coordinate states.\n', '< PyMOL>alter_state 1,(all), x=x+y\n', '<  AlterState: modified 107 atom coordinate states.\n', '< PyMOL>alter_state 2,(all), x=x+y\n', '<  AlterState: modified 107 atom coordinate states.\n', '< PyMOL>alter_state 3,(all), x=x+y\n', '<  AlterState: modified 0 atom coordinate states.\n', '< PyMOL>dele all\n', '< PyMOL>load dat/small01.mol\n', '<  ExecutiveLoad: "dat/small01.mol" loaded as "small01", through state 1.\n', '< PyMOL>remove hydro\n', '<  Remove: eliminated 20 atoms in model "small01".\n', '< PyMOL>h_add\n', '< PyMOL>count_atoms\n', '<  count_atoms: 36 atoms\n', '< PyMOL>dele all\n', '< PyMOL>load dat/small01.mol\n', '<  ExecutiveLoad: "dat/small01.mol" loaded as "small01", through state 1.\n', '< PyMOL>dele all\n', '< PyMOL>load dat/small01.mol\n', '<  ExecutiveLoad: "dat/small01.mol" loaded as "small01", through state 1.\n', '< PyMOL>remove id 17\n', '<  Remove: eliminated 1 atoms in model "small01".\n', '< PyMOL>count_atoms\n', '<  count_atoms: 35 atoms\n', '< PyMOL>edit id 3\n', '<  Selector: selection "pk1" defined with 1 atoms.\n', '< PyMOL>attach X,4,2\n', '< PyMOL>count_atoms\n', '<  count_atoms: 36 atoms\n', '< PyMOL>edit elem X\n', '<  Selector: selection "pk1" defined with 1 atoms.\n', '< PyMOL>remove_picked\n', '<  Remove: eliminated 1 atoms in model "small01".\n', '< PyMOL>unpick\n', '< PyMOL>print cmd.get_names()\n', "< ['small01']\n", '< PyMOL>count_atoms\n', '<  count_atoms: 35 atoms\n', '< PyMOL>h_add\n', '< PyMOL>count_atoms\n', '<  count_atoms: 36 atoms\n', '< PyMOL>dele all\n', '< PyMOL>load dat/small01.mol\n', '<  ExecutiveLoad: "dat/small01.mol" loaded as "small01", through state 1.\n', '< PyMOL>unbond id 1,id 2\n', '<  Unbond: 1 bonds removed from model "small01".\n', '< PyMOL>h_add\n', '< PyMOL>count_atoms\n', '<  count_atoms: 38 atoms\n', '< PyMOL>remove hydro\n', '<  Remove: eliminated 22 atoms in model "small01".\n', '< PyMOL>bond id 1,id 2\n', '<  Bond: 1 bonds added to model "small01".\n', '< PyMOL>h_add\n', '< PyMOL>count_atoms\n', '<  count_atoms: 36 atoms\n', '< PyMOL>dele all\n', '< PyMOL>load dat/small01.mol\n', '<  ExecutiveLoad: "dat/small01.mol" loaded as "small01", through state 1.\n', '< PyMOL>edit id 6,id 10\n', '<  Selector: selection "pk1" defined with 1 atoms.\n', '<  Selector: selection "pk2" defined with 1 atoms.\n', '< PyMOL>cycle_valence\n', '<  Remove: eliminated 2 atoms in model "small01".\n', '<  Remove: eliminated 2 atoms in model "small01".\n', '< PyMOL>count_atoms\n', '<  count_atoms: 34 atoms\n', '< PyMOL>cycle_valence\n', '<  Remove: eliminated 1 atoms in model "small01".\n', '<  Remove: eliminated 1 atoms in model "small01".\n', '< PyMOL>count_atoms\n', '<  count_atoms: 32 atoms\n', '< PyMOL>remove_picked\n', '< PyMOL>bond id 6,id 10,2\n', '<  Bond: 1 bonds added to model "small01".\n', '< PyMOL>h_add\n', '< PyMOL>set valence=0.05\n', '<  Setting: valence set to on.\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 59 graphics primitives.\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>get_extent\n', '<  cmd.extent: min: [  -5.188, -20.331,  13.157]\n', '<  cmd.extent: max: [   8.919,   0.863,  27.058]\n', '< PyMOL>protect resi 1-6\n', '<  Protect: 51 atoms protected from movement.\n', '< PyMOL>edit 2/sg,12/sg\n', '<  Selector: selection "pk1" defined with 1 atoms.\n', '<  Selector: selection "pk2" defined with 1 atoms.\n', '< PyMOL>torsion 90\n', '< PyMOL>get_extent\n', '<  cmd.extent: min: [ -10.445, -22.170,  11.965]\n', '<  cmd.extent: max: [   6.787,   0.863,  27.058]\n', '< PyMOL>undo\n', '< PyMOL>get_extent\n', '<  cmd.extent: min: [  -5.188, -20.331,  13.157]\n', '<  cmd.extent: max: [   8.919,   0.863,  27.058]\n', '< PyMOL>redo\n', '< PyMOL>get_extent\n', '<  cmd.extent: min: [ -10.445, -22.170,  11.965]\n', '<  cmd.extent: max: [   6.787,   0.863,  27.058]\n', '< PyMOL>undo\n', '< PyMOL>get_extent\n', '<  cmd.extent: min: [  -5.188, -20.331,  13.157]\n', '<  cmd.extent: max: [   8.919,   0.863,  27.058]\n', '< PyMOL>deprotect\n', '<  Protect: 107 atoms deprotected.\n', '< PyMOL>edit 2/sg,12/sg\n', '<  Selector: selection "pk1" defined with 1 atoms.\n', '<  Selector: selection "pk2" defined with 1 atoms.\n', '< PyMOL>torsion 90\n', '< PyMOL>get_extent\n', '<  cmd.extent: min: [ -15.562, -22.170,  11.965]\n', '<  cmd.extent: max: [   5.893,  -8.073,  25.808]\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>flag ignore,(!*/ca,c,n,o,cb)\n', '<  Flag: flag 25 is set in 43 of 107 atoms.\n', '< PyMOL>flag exfoliate,(*/cb)\n', '<  Flag: flag 24 is set in 12 of 107 atoms.\n', '< PyMOL>show surf\n', '< PyMOL>ray\n', '<  RepSurface: 921 surface points.\n', '<  RepSurface: 1838 triangles.\n', '<  RayRenderTest: obtained 1529 graphics primitives.\n', '< PyMOL>dele all\n', '< PyMOL>load dat/small01.mol,m1\n', '<  ExecutiveLoad: "dat/small01.mol" loaded as "m1", through state 1.\n', '< PyMOL>load dat/small01.mol,m2\n', '<  ExecutiveLoad: "dat/small01.mol" loaded as "m2", through state 1.\n', '< PyMOL>fuse m1 and id 31,m2 and id 31\n', '< PyMOL>dele m1\n', '< PyMOL>zoom\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 144 graphics primitives.\n', '< PyMOL>dele all\n', '< PyMOL>load dat/small01.mol,m1\n', '<  ExecutiveLoad: "dat/small01.mol" loaded as "m1", through state 1.\n', '< PyMOL>load dat/small01.mol,m2\n', '<  ExecutiveLoad: "dat/small01.mol" loaded as "m2", through state 1.\n', '< PyMOL>remove id 30\n', '<  Remove: eliminated 1 atoms in model "m1".\n', '<  Remove: eliminated 1 atoms in model "m2".\n', '< PyMOL>fuse m1 and id 12,m2 and id 12\n', '< PyMOL>dele m1\n', '< PyMOL>zoom\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 144 graphics primitives.\n', '< PyMOL>dele all\n', '< PyMOL>load dat/small01.mol\n', '<  ExecutiveLoad: "dat/small01.mol" loaded as "small01", through state 1.\n', '< PyMOL>edit id 2,id 6, id 5\n', '<  Selector: selection "pk1" defined with 1 atoms.\n', '<  Selector: selection "pk2" defined with 1 atoms.\n', '<  Selector: selection "pk3" defined with 1 atoms.\n', '< PyMOL>invert\n', '<  Editor: Inverted atom.\n', '< PyMOL>print "%8.3f"%cmd.dist("id 28","id 17")\n', '<    1.957\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>iterate (name n),print resi\n', '< 1\n', '< 2\n', '< 3\n', '< 4\n', '< 5\n', '< 6\n', '< 7\n', '< 8\n', '< 9\n', '< 10\n', '< 11\n', '< 12\n', '< 13\n', '<  Iterate: iterated over 13 atoms.\n', '< PyMOL>iterate_state 1,(name o),print "%8.3f %8.3f %8.3f"%(x,y,z)\n', '<    4.456  -15.889   23.517\n', '<    3.025  -12.039   25.188\n', '<    1.332   -9.867   21.362\n', '<    0.752   -5.592   23.297\n', '<   -2.092   -3.870   19.914\n', '<   -5.181   -3.100   20.933\n', '<   -5.188   -7.669   21.049\n', '<   -1.643   -7.529   19.691\n', '<   -0.699   -9.660   16.692\n', '<    2.708  -11.019   16.296\n', '<    3.449  -13.097   20.534\n', '<    5.278  -17.322   18.998\n', '<    5.962  -19.432   22.570\n', '<  IterateState: iterated over 13 atom coordinate states.\n', '< PyMOL>dele all\n', '< PyMOL>load dat/il2.pdb\n', '<  CmdLoad: "dat/il2.pdb" loaded as "il2".\n', '< PyMOL>stored.sum = 0\n', '< PyMOL>iterate_state 1,(il2),stored.sum=stored.sum+x\n', '<  IterateState: iterated over 2084 atom coordinate states.\n', '< PyMOL>print "%8.3f"%stored.sum\n', '< 20809.421\n', '< PyMOL>push_undo (il2)\n', '< PyMOL>alter_state 1,(il2),x=0.0\n', '<  AlterState: modified 2084 atom coordinate states.\n', '< PyMOL>rebuild\n', '< PyMOL>stored.sum = 0\n', '< PyMOL>iterate_state 1,(il2),stored.sum=stored.sum+x\n', '<  IterateState: iterated over 2084 atom coordinate states.\n', '< PyMOL>print "%8.3f"%stored.sum\n', '<    0.000\n', '< PyMOL>edit il2`1\n', '<  Selector: selection "pk1" defined with 1 atoms.\n', '< PyMOL>undo\n', '< PyMOL>stored.sum = 0\n', '< PyMOL>iterate_state 1,(il2),stored.sum=stored.sum+x\n', '<  IterateState: iterated over 2084 atom coordinate states.\n', '< PyMOL>print "%8.3f"%stored.sum\n', '< 20809.421\n', '< PyMOL>rebuild\n', '< PyMOL>show dots\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 111433 graphics primitives.\n', '< PyMOL>dele all\n', '< PyMOL>load dat/small01.mol\n', '<  ExecutiveLoad: "dat/small01.mol" loaded as "small01", through state 1.\n', '< PyMOL>iterate (all),print name\n', '< C\n', '< C\n', '< C\n', '< C\n', '< C\n', '< C\n', '< C\n', '< C\n', '< C\n', '< C\n', '< C\n', '< C\n', '< C\n', '< C\n', '< O\n', '< O\n', '< H\n', '< H\n', '< H\n', '< H\n', '< H\n', '< H\n', '< H\n', '< H\n', '< H\n', '< H\n', '< H\n', '< H\n', '< H\n', '< H\n', '< H\n', '< H\n', '< H\n', '< H\n', '< H\n', '< H\n', '<  Iterate: iterated over 36 atoms.\n', '< PyMOL>rename small01\n', '<  Rename: renamed 33 atoms.\n', '< PyMOL>iterate (all),print name\n', '< C01\n', '< C02\n', '< C03\n', '< C04\n', '< C05\n', '< C06\n', '< C07\n', '< C08\n', '< C09\n', '< C10\n', '< C11\n', '< C12\n', '< C13\n', '< C\n', '< O14\n', '< O\n', '< H15\n', '< H16\n', '< H17\n', '< H18\n', '< H19\n', '< H20\n', '< H21\n', '< H22\n', '< H23\n', '< H24\n', '< H25\n', '< H26\n', '< H27\n', '< H28\n', '< H29\n', '< H30\n', '< H31\n', '< H32\n', '< H33\n', '< H\n', '<  Iterate: iterated over 36 atoms.\n', '< PyMOL>dele all\n', '< PyMOL>load dat/small01.mol\n', '<  ExecutiveLoad: "dat/small01.mol" loaded as "small01", through state 1.\n', '< PyMOL>edit id 3\n', '<  Selector: selection "pk1" defined with 1 atoms.\n', '< PyMOL>replace N,3,3\n', '<  Remove: eliminated 1 atoms in model "small01".\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>get_extent\n', '<  cmd.extent: min: [  -5.188, -20.331,  13.157]\n', '<  cmd.extent: max: [   8.919,   0.863,  27.058]\n', '< PyMOL>origin pept,object=pept\n', '< PyMOL>rotate x,-45,object=pept\n', '< PyMOL>get_extent\n', '<  cmd.extent: min: [  -5.188, -18.391,  12.126]\n', '<  cmd.extent: max: [   8.919,  -1.236,  29.153]\n', '< PyMOL>reset\n', '< PyMOL>get_extent\n', '<  cmd.extent: min: [  -5.188, -18.391,  12.126]\n', '<  cmd.extent: max: [   8.919,  -1.236,  29.153]\n', '< PyMOL>rotate x,45,pept\n', '< PyMOL>get_extent\n', '<  cmd.extent: min: [  -5.188, -20.331,  13.157]\n', '<  cmd.extent: max: [   8.919,   0.863,  27.058]\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>get_dihedral 1/n,1/ca,1/c,1/o\n', '<  cmd.get_dihedral: -8.586 degrees.\n', '< PyMOL>get_extent\n', '<  cmd.extent: min: [  -5.188, -20.331,  13.157]\n', '<  cmd.extent: max: [   8.919,   0.863,  27.058]\n', '< PyMOL>set_dihedral 1/n,1/ca,1/c,1/o,180\n', '<  SetDihedral: adjusted to 180.000\n', '< PyMOL>get_dihedral 1/n,1/ca,1/c,1/o\n', '<  cmd.get_dihedral: 180.000 degrees.\n', '< PyMOL>get_extent\n', '<  cmd.extent: min: [  -1.282, -17.809,   6.314]\n', '<  cmd.extent: max: [  10.270,  -4.939,  29.070]\n', '< PyMOL>dele all\n', '< PyMOL>load dat/small01.mol\n', '<  ExecutiveLoad: "dat/small01.mol" loaded as "small01", through state 1.\n', '< PyMOL>remove not id 3\n', '<  Remove: eliminated 35 atoms in model "small01".\n', '< PyMOL>zoom\n', '< PyMOL>count_atoms\n', '<  count_atoms: 1 atoms\n', '< PyMOL>set_geometry (id 3),4,4\n', '< PyMOL>h_add\n', '< PyMOL>count_atoms\n', '<  count_atoms: 5 atoms\n', '< PyMOL>remove hydro\n', '<  Remove: eliminated 4 atoms in model "small01".\n', '< PyMOL>set_geometry (id 3),3,3\n', '< PyMOL>h_add\n', '< PyMOL>count_atoms\n', '<  count_atoms: 4 atoms\n', '< PyMOL>remove hydro\n', '<  Remove: eliminated 3 atoms in model "small01".\n', '< PyMOL>set_geometry (id 3),2,2\n', '< PyMOL>h_add\n', '< PyMOL>count_atoms\n', '<  count_atoms: 3 atoms\n', '< PyMOL>remove hydro\n', '<  Remove: eliminated 2 atoms in model "small01".\n', '< PyMOL>set_geometry (id 3),4,2\n', '< PyMOL>h_add\n', '< PyMOL>count_atoms\n', '<  count_atoms: 3 atoms\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>alter (all),resi = (999-int(resi)-ID/4)\n', '<  Alter: modified 107 atoms.\n', '< PyMOL>sort\n', '< PyMOL>show sph,(byres id 10)\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 210 graphics primitives.\n', '< PyMOL>dele all\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>get_extent\n', '<  cmd.extent: min: [  -5.188, -20.331,  13.157]\n', '<  cmd.extent: max: [   8.919,   0.863,  27.058]\n', '< PyMOL>cmd.edit("(pept`95)",pkresi=1)\n', '< PyMOL>cmd.push_undo("pept",1)\n', '< PyMOL>cmd.edit("(pept`10)",pkresi=1)\n', '< PyMOL>cmd.push_undo("pept",1)\n', '< PyMOL>get_extent\n', '<  cmd.extent: min: [  -5.124, -31.391,  12.760]\n', '<  cmd.extent: max: [   8.919, -12.759,  27.469]\n', '< PyMOL>dele all\n', '< PyMOL>load dat/small01.mol\n', '<  ExecutiveLoad: "dat/small01.mol" loaded as "small01", through state 1.\n', '< PyMOL>cmd.edit("(small01`3)",pkresi=1)\n', '< PyMOL>cmd.edit_mode()\n', '< PyMOL>cmd.push_undo("small01",1)\n', '< PyMOL>get_extent\n', '<  cmd.extent: min: [ -15.344,  -2.159,  -3.683]\n', '<  cmd.extent: max: [  -3.585,   2.683,   3.171]\n', '< PyMOL>undo\n', '< PyMOL>get_extent\n', '<  cmd.extent: min: [  -8.369,  -2.595,  -4.337]\n', '<  cmd.extent: max: [   2.256,   2.247,   2.517]\n', '< PyMOL>dele all\n', '< PyMOL>load dat/small01.mol\n', '<  ExecutiveLoad: "dat/small01.mol" loaded as "small01", through state 1.\n', '< PyMOL>get_extent\n', '<  cmd.extent: min: [  -8.369,  -2.595,  -4.337]\n', '<  cmd.extent: max: [   2.256,   2.247,   2.517]\n', "< PyMOL>cmd.set('valence','0.0500')\n", '< PyMOL>cmd.edit_mode()\n', '< PyMOL>cmd.push_undo("small01",1)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.020101367,   -0.020101367,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.040202733,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.020101367,   -0.040202733,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.040202733,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.060304098,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.020101367,   -0.020101367,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.020101367,   -0.040202733,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.020101367,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.020101367,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.020101367,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.020101367,   -0.040202733,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.020101367,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.040202733,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.040202733,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.020101367,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.020101367,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.020101367,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.020101367,   -0.020101367,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.160810933,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.040202733,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.160810933,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.040202733,   -0.120608196,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.040202755,   -0.160811022,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.060304098,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.040202733,   -0.120608196,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.040202755,   -0.160811022,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.160810933,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.040202733,   -0.160810933,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.060304098,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.160810933,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.060304098,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.040202733,   -0.160810933,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.060304098,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.040202733,   -0.120608196,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.040202733,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.060304098,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.020101367,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.020101367,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.020101367,   -0.020101367,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.040202733,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.060304098,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.060304098,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.040202733,   -0.160810933,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.160810933,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.040202733,   -0.160810933,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.040202733,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.000000000,   -0.040202733,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",   -0.020101367,    0.000000000,    0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`",    0.020101367,    0.000000000,    0.000000000,1,1,0)\n', '< PyMOL>get_extent\n', '<  cmd.extent: min: [  -8.369,  -3.896,  -4.337]\n', '<  cmd.extent: max: [   2.256,   2.247,   2.517]\n', '< PyMOL>undo\n', '< PyMOL>get_extent\n', '<  cmd.extent: min: [  -8.369,  -2.595,  -4.337]\n', '<  cmd.extent: max: [   2.256,   2.247,   2.517]\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>get_extent\n', '<  cmd.extent: min: [  -5.188, -20.331,  13.157]\n', '<  cmd.extent: max: [   8.919,   0.863,  27.058]\n', '< PyMOL>load dat/pept.pdb,sav\n', '<  CmdLoad: "dat/pept.pdb" loaded as "sav".\n', '< PyMOL>alter_state 1,(pept),x=1;y=2;z=3;\n', '<  AlterState: modified 107 atom coordinate states.\n', '< PyMOL>rebuild\n', '< PyMOL>get_extent pept\n', '<  cmd.extent: min: [   1.000,   2.000,   3.000]\n', '<  cmd.extent: max: [   1.000,   2.000,   3.000]\n', '< PyMOL>update pept,sav\n', '<  Update: coordinates updated for 107 atoms.\n', '< PyMOL>get_extent pept\n', '<  cmd.extent: min: [  -5.188, -20.331,  13.157]\n', '<  cmd.extent: max: [   8.919,   0.863,  27.058]\n']
 run_tests: C1050fitting...
 run_tests: C1050fitting.log DIFFERS over about 77 lines:
['1,153d0\n', '< the 1st random number should be    0.052\n', '< otherwise the rest of the test is meaningless...\n', '< \n', '<  Selector: found 107 atoms.\n', '<  Executive: object "trg" created.\n', '<  AlterState: modified 107 atom coordinate states.\n', '<  Selector: found 107 atoms.\n', '<  AlterState: modified 107 atom coordinate states.\n', '<  Selector: found 107 atoms.\n', '<  AlterState: modified 107 atom coordinate states.\n', '<  Selector: found 107 atoms.\n', '<  AlterState: modified 107 atom coordinate states.\n', '<  Selector: found 107 atoms.\n', '<  AlterState: modified 107 atom coordinate states.\n', '<  Selector: found 107 atoms.\n', '<  AlterState: modified 107 atom coordinate states.\n', '<  Selector: found 107 atoms.\n', '<  AlterState: modified 107 atom coordinate states.\n', '<  Selector: found 107 atoms.\n', '<  AlterState: modified 107 atom coordinate states.\n', '<  Selector: found 107 atoms.\n', '<  AlterState: modified 107 atom coordinate states.\n', '<  Selector: found 107 atoms.\n', '<  AlterState: modified 107 atom coordinate states.\n', '<    0.080\n', '< 1    0.073    0.080    0.198\n', '< 2    0.058    0.080    0.220\n', '< 3    0.053    0.080    0.320\n', '< 4    0.088    0.080    0.105\n', '< 5    0.052    0.080    0.138\n', '< 6    0.081    0.080    0.147\n', '< 7    0.035    0.080    1.396\n', '< 8    0.059    0.080    0.108\n', '< 9    0.098    0.080    0.113\n', '< 10    0.072    0.080    0.121\n', '< 11    0.056    0.080    0.119\n', '< 12    0.075    0.080    0.203\n', '< 13    0.078    0.080    0.341\n', '<    0.080\n', '< 1    0.073    0.080    0.198\n', '< 2    0.058    0.080    0.220\n', '< 3    0.053    0.080    0.320\n', '< 4    0.088    0.080    0.105\n', '< 5    0.052    0.080    0.138\n', '< 6    0.081    0.080    0.147\n', '< 7    0.035    0.080    1.396\n', '< 8    0.059    0.080    0.108\n', '< 9    0.098    0.080    0.113\n', '< 10    0.072    0.080    0.121\n', '< 11    0.056    0.080    0.119\n', '< 12    0.075    0.080    0.203\n', '< 13    0.078    0.080    0.341\n', '<    0.080\n', '<  -1.000   0.274   0.302   0.275   0.256   0.305   0.351   0.266   0.260\n', '<   0.329\n', '<  -1.000   0.372   0.356   0.340   0.338   0.346   0.346   0.355   0.354\n', '<   0.358\n', '<  -1.000   1.672   1.481   0.691   1.952   2.292   1.546   1.670   1.143\n', '<   1.372\n', '<   0.274  -1.000   0.305   0.308   0.227   0.329   0.320   0.309   0.269\n', '<   0.266\n', '<   0.372  -1.000   0.355   0.364   0.357   0.341   0.346   0.358   0.358\n', '<   0.357\n', '<   1.672  -1.000   0.740   1.325   0.924   0.842   1.237   0.692   0.872\n', '<   0.853\n', '<   0.302   0.305  -1.000   0.223   0.254   0.289   0.376   0.329   0.303\n', '<   0.355\n', '<   0.356   0.355  -1.000   0.363   0.338   0.343   0.331   0.362   0.343\n', '<   0.348\n', '<   1.481   0.740  -1.000   1.077   0.487   1.003   0.555   0.982   0.837\n', '<   0.963\n', '<   0.275   0.308   0.223  -1.000   0.211   0.325   0.358   0.303   0.271\n', '<   0.359\n', '<   0.340   0.364   0.363  -1.000   0.344   0.355   0.366   0.361   0.353\n', '<   0.356\n', '<   0.691   1.325   1.077  -1.000   1.309   1.795   0.834   1.378   0.874\n', '<   1.113\n', '<   0.256   0.227   0.254   0.211  -1.000   0.259   0.234   0.263   0.240\n', '<   0.300\n', '<   0.338   0.357   0.338   0.344  -1.000   0.346   0.334   0.344   0.338\n', '<   0.341\n', '<   1.952   0.924   0.487   1.309  -1.000   0.802   0.783   1.259   1.299\n', '<   1.292\n', '<   0.305   0.329   0.289   0.325   0.259  -1.000   0.280   0.359   0.292\n', '<   0.304\n', '<   0.346   0.341   0.343   0.355   0.346  -1.000   0.334   0.356   0.340\n', '<   0.346\n', '<   2.292   0.842   1.003   1.795   0.802  -1.000   1.352   1.063   1.420\n', '<   1.249\n', '<   0.351   0.320   0.376   0.358   0.234   0.280  -1.000   0.365   0.321\n', '<   0.301\n', '<   0.346   0.346   0.331   0.366   0.334   0.334  -1.000   0.352   0.357\n', '<   0.350\n', '<   1.546   1.237   0.555   0.834   0.783   1.352  -1.000   1.471   1.244\n', '<   1.364\n', '<   0.266   0.309   0.329   0.303   0.263   0.359   0.365  -1.000   0.262\n', '<   0.342\n', '<   0.355   0.358   0.362   0.361   0.344   0.356   0.352  -1.000   0.351\n', '<   0.350\n', '<   1.670   0.692   0.982   1.378   1.259   1.063   1.471  -1.000   0.748\n', '<   0.473\n', '<   0.260   0.269   0.303   0.271   0.240   0.292   0.321   0.262  -1.000\n', '<   0.354\n', '<   0.354   0.358   0.343   0.353   0.338   0.340   0.357   0.351  -1.000\n', '<   0.354\n', '<   1.143   0.872   0.837   0.874   1.299   1.420   1.244   0.748  -1.000\n', '<   0.526\n', '<   0.329   0.266   0.355   0.359   0.300   0.304   0.301   0.342   0.354\n', '<  -1.000\n', '<   0.358   0.357   0.348   0.356   0.341   0.346   0.350   0.350   0.354\n', '<  -1.000\n', '<   1.372   0.853   0.963   1.113   1.292   1.249   1.364   0.473   0.526\n', '<  -1.000\n', '< PyMOL>intra_fit (trg),10\n', '<  cmd.intra_fit: 0.358 in state 1 vs state 10\n', '<  cmd.intra_fit: 0.357 in state 2 vs state 10\n', '<  cmd.intra_fit: 0.348 in state 3 vs state 10\n', '<  cmd.intra_fit: 0.356 in state 4 vs state 10\n', '<  cmd.intra_fit: 0.341 in state 5 vs state 10\n', '<  cmd.intra_fit: 0.346 in state 6 vs state 10\n', '<  cmd.intra_fit: 0.350 in state 7 vs state 10\n', '<  cmd.intra_fit: 0.350 in state 8 vs state 10\n', '<  cmd.intra_fit: 0.354 in state 9 vs state 10\n', '< PyMOL>intra_fit (trg and resi 1),10\n', '<  cmd.intra_fit: 0.329 in state 1 vs state 10\n', '<  cmd.intra_fit: 0.266 in state 2 vs state 10\n', '<  cmd.intra_fit: 0.355 in state 3 vs state 10\n', '<  cmd.intra_fit: 0.359 in state 4 vs state 10\n', '<  cmd.intra_fit: 0.300 in state 5 vs state 10\n', '<  cmd.intra_fit: 0.304 in state 6 vs state 10\n', '<  cmd.intra_fit: 0.301 in state 7 vs state 10\n', '<  cmd.intra_fit: 0.342 in state 8 vs state 10\n', '<  cmd.intra_fit: 0.354 in state 9 vs state 10\n', '< PyMOL>intra_rms (trg),10\n', '<  cmd.intra_rms: 0.358 in state 1 vs state 10\n', '<  cmd.intra_rms: 0.357 in state 2 vs state 10\n', '<  cmd.intra_rms: 0.348 in state 3 vs state 10\n', '<  cmd.intra_rms: 0.356 in state 4 vs state 10\n', '<  cmd.intra_rms: 0.341 in state 5 vs state 10\n', '<  cmd.intra_rms: 0.346 in state 6 vs state 10\n', '<  cmd.intra_rms: 0.350 in state 7 vs state 10\n', '<  cmd.intra_rms: 0.350 in state 8 vs state 10\n', '<  cmd.intra_rms: 0.354 in state 9 vs state 10\n', '< PyMOL>intra_rms_cur (trg),10\n', '<  cmd.intra_rms_cur: 1.372 in state 1 vs state 10\n', '<  cmd.intra_rms_cur: 0.853 in state 2 vs state 10\n', '<  cmd.intra_rms_cur: 0.963 in state 3 vs state 10\n', '<  cmd.intra_rms_cur: 1.113 in state 4 vs state 10\n', '<  cmd.intra_rms_cur: 1.292 in state 5 vs state 10\n', '<  cmd.intra_rms_cur: 1.249 in state 6 vs state 10\n', '<  cmd.intra_rms_cur: 1.364 in state 7 vs state 10\n', '<  cmd.intra_rms_cur: 0.473 in state 8 vs state 10\n', '<  cmd.intra_rms_cur: 0.526 in state 9 vs state 10\n']
 run_tests: C1060controlling...
 run_tests: C1060controlling.log DIFFERS over about 7 lines:
['1,13d0\n', '< None\n', '< None\n', '< None\n', '< None\n', '< None\n', '< None\n', '< None\n', '< None\n', '< None\n', '< None\n', '< None\n', '< None\n', '< None\n']
 run_tests: C1070exporting...
 run_tests: C1070exporting.log DIFFERS over about 29 lines:
['1,58d0\n', '< PyMOL>load dat/small01.mol\n', '<  ExecutiveLoad: "dat/small01.mol" loaded as "small01", through state 1.\n', '< PyMOL>save tmp/small01.mol\n', '<  chempy: writing "tmp/small01.mol".\n', '<  Save: wrote "tmp/small01.mol".\n', '< PyMOL>save tmp/small01.pkl\n', '<  Save: wrote "tmp/small01.pkl".\n', '< PyMOL>save tmp/small02.pkl,format=pkla\n', '<  Save: wrote "tmp/small02.pkl".\n', '< PyMOL>save tmp/small01.mmod\n', '<  chempy: writing "tmp/small01.mmod".\n', '<  Save: wrote "tmp/small01.mmod".\n', '< PyMOL>save tmp/small01.mmd\n', '<  chempy: writing "tmp/small01.mmd".\n', '<  Save: wrote "tmp/small01.mmd".\n', '< PyMOL>save tmp/small01.pdb\n', '<  Save: wrote "tmp/small01.pdb".\n', '< PyMOL>multisave tmp/small01.pmo,small01\n', "<  Multisave: wrote 1 object(s) to 'tmp/small01.pmo'.\n", '< PyMOL>dele all\n', '< PyMOL>load tmp/small01.pmo\n', '<  CmdLoad: "tmp/small01.pmo" loaded as "small01".\n', '< PyMOL>dele all\n', '< PyMOL>load tmp/small01.pdb\n', '<  CmdLoad: "tmp/small01.pdb" loaded as "small01".\n', '< PyMOL>count_atoms\n', '<  count_atoms: 36 atoms\n', '< PyMOL>dele all\n', '< PyMOL>load tmp/small01.mmd\n', '<  CmdLoad: "tmp/small01.mmd" loaded as "small01".\n', '< PyMOL>count_atoms\n', '<  count_atoms: 36 atoms\n', '< PyMOL>dele all\n', '< PyMOL>load tmp/small01.mmod\n', '<  CmdLoad: "tmp/small01.mmod" loaded as "small01".\n', '< PyMOL>count_atoms\n', '<  count_atoms: 36 atoms\n', '< PyMOL>dele all\n', '< PyMOL>load tmp/small01.pkl\n', '<  Executive: object "small01" created.\n', '< PyMOL>count_atoms\n', '<  count_atoms: 36 atoms\n', '< PyMOL>dele all\n', '< PyMOL>load tmp/small02.pkl\n', '<  Executive: object "small02" created.\n', '< PyMOL>count_atoms\n', '<  count_atoms: 36 atoms\n', '< PyMOL>dele all\n', '< PyMOL>load tmp/small01.mol\n', '<  ExecutiveLoad: "tmp/small01.mol" loaded as "small01", through state 1.\n', '< PyMOL>count_atoms\n', '<  count_atoms: 36 atoms\n', '< PyMOL>feedback disable,ray,details\n', '< PyMOL>ray\n', '< PyMOL>png tmp/tmp.png\n', '<  ScenePNG: wrote 640x480 pixel image to file "tmp/tmp.png".\n', '< PyMOL>load_png tmp/tmp.png\n', "<  Scene: loaded image from 'tmp/tmp.png'.\n"]
 run_tests: C1080isomore...
 run_tests: C1080isomore.log DIFFERS over about 142 lines:
['1,283d0\n', '< PyMOL>load dat/pept.pdb,obj\n', '<  CmdLoad: "dat/pept.pdb" loaded as "obj".\n', '< PyMOL>load dat/il2.pdb,obj\n', '<  CmdLoad: "dat/il2.pdb" appended into object "obj", state 2.\n', '< PyMOL>load dat/3al1.pdb,obj,state=4\n', '< HEADER    STRUCTURAL PROTEIN                      26-OCT-98   3AL1\n', '< TITLE     DESIGNED PEPTIDE ALPHA-1, RACEMIC P1BAR FORM\n', '< COMPND    MOL_ID: 1;\n', '< COMPND   2 MOLECULE: D, L-ALPHA-1;\n', '< COMPND   3 CHAIN: A, B;\n', '< COMPND   4 ENGINEERED: YES;\n', '< COMPND   5 OTHER_DETAILS: N TERMINI ARE ACETYLATED\n', '<  ObjectMolecule: Read secondary structure assignments.\n', '<  ObjectMolecule: Read crystal symmetry information.\n', '<  Symmetry: Found 2 symmetry operators.\n', '<  CmdLoad: "dat/3al1.pdb" appended into object "obj", state 4.\n', '< PyMOL>map_new tst1,gaussian,1.0,state=-3\n', '<  ObjectMap: Map created.\n', '<  ObjectMap: Computing Gaussian map for 2870 atom positions.\n', '<  ObjectMap: Normalizing: mean = 0.049654 & stdev = 0.212673.\n', '<  Executive: object "tst1" created.\n', '< PyMOL>map_new tst2,gaussian,1.0,state=2\n', '<  ObjectMap: Map created.\n', '<  ObjectMap: Computing Gaussian map for 2084 atom positions.\n', '<  ObjectMap: Normalizing: mean = 0.074412 & stdev = 0.213934.\n', '<  Executive: object "tst2" created.\n', '< PyMOL>map_new tst2,gaussian,1.0,state=4\n', '<  ObjectMap: Map created.\n', '<  ObjectMap: Computing Gaussian map for 679 atom positions.\n', '<  ObjectMap: Normalizing: mean = 0.076772 & stdev = 0.351954.\n', '< PyMOL>map_new tst3,gaussian,1.0,state=-4\n', '<  ObjectMap: Map created.\n', '<  ObjectMap: Computing Gaussian map for 107 atom positions.\n', '<  ObjectMap: Normalizing: mean = 0.003829 & stdev = 0.054910.\n', '<  ObjectMap: Map created.\n', '<  ObjectMap: Computing Gaussian map for 2084 atom positions.\n', '<  ObjectMap: Normalizing: mean = 0.036107 & stdev = 0.153608.\n', '<  ObjectMap: Map created.\n', '<  ObjectMap: Computing Gaussian map for 0 atom positions.\n', '<  ObjectMap: Map created.\n', '<  ObjectMap: Computing Gaussian map for 679 atom positions.\n', '<  ObjectMap: Normalizing: mean = 0.009718 & stdev = 0.133319.\n', '<  Executive: object "tst3" created.\n', '< PyMOL>map_new tst4,gaussian,1.0,state=3\n', '<  Executive: object "tst4" created.\n', '< PyMOL>map_new tst5,gaussian,1.0,state=4\n', '<  ObjectMap: Map created.\n', '<  ObjectMap: Computing Gaussian map for 679 atom positions.\n', '<  ObjectMap: Normalizing: mean = 0.076772 & stdev = 0.351954.\n', '<  Executive: object "tst5" created.\n', '< PyMOL>map_new tst6,gaussian,1.0\n', '<  ObjectMap: Map created.\n', '<  ObjectMap: Computing Gaussian map for 107 atom positions.\n', '<  ObjectMap: Normalizing: mean = 0.079928 & stdev = 0.237612.\n', '<  Executive: object "tst6" created.\n', '<  ObjectMap: Map created.\n', '<  ObjectMap: Computing Gaussian map for 2084 atom positions.\n', '<  ObjectMap: Normalizing: mean = 0.074412 & stdev = 0.213934.\n', '<  ObjectMap: Map created.\n', '<  ObjectMap: Computing Gaussian map for 679 atom positions.\n', '<  ObjectMap: Normalizing: mean = 0.076772 & stdev = 0.351954.\n', '< PyMOL>frame 4\n', '< PyMOL>isomesh m8,tst2,state=-1\n', '<  Executive: object "m8" created.\n', '<  Isomesh: created "m8", setting level to 1.000\n', '< PyMOL>frame 3\n', '< PyMOL>isomesh m9,tst1,state=-1,source_state=1\n', '<  Executive: object "m9" created.\n', '<  Isomesh: created "m9", setting level to 1.000\n', '< PyMOL>isomesh m7,tst1,state=4,source_state=1\n', '<  Executive: object "m7" created.\n', '<  Isomesh: created "m7", setting level to 1.000\n', '< PyMOL>refresh\n', '<  ObjectMesh: updating "m8".\n', '<  IsosurfVolume: Surface generated using 6969 lines.\n', '<  ObjectMesh: updating "m9".\n', '<  IsosurfVolume: Surface generated using 37701 lines.\n', '<  ObjectMesh: updating "m7".\n', '<  IsosurfVolume: Surface generated using 37701 lines.\n', '< PyMOL>isomesh m7,tst6,state=3,source_state=1\n', '<  Isomesh: created "m7", setting level to 1.000\n', '< PyMOL>refresh\n', '<  ObjectMesh: updating "m7".\n', '<  IsosurfVolume: Surface generated using 2975 lines.\n', '< PyMOL>isomesh m7,tst5,state=2,source_state=4\n', '<  Isomesh: created "m7", setting level to 1.000\n', '< PyMOL>refresh\n', '<  ObjectMesh: updating "m7".\n', '<  IsosurfVolume: Surface generated using 6969 lines.\n', '< PyMOL>isomesh m7,tst2,state=1,source_state=2\n', '<  Isomesh: created "m7", setting level to 1.000\n', '< PyMOL>refresh\n', '<  ObjectMesh: updating "m7".\n', '<  IsosurfVolume: Surface generated using 29064 lines.\n', '< PyMOL>isomesh m1,tst1\n', '<  Executive: object "m1" created.\n', '<  Isomesh: created "m1", setting level to 1.000\n', '< PyMOL>refresh\n', '<  ObjectMesh: updating "m1".\n', '<  IsosurfVolume: Surface generated using 37701 lines.\n', '< PyMOL>isomesh m2,tst2\n', '<  Executive: object "m2" created.\n', '<  Isomesh: created "m2", setting level to 1.000\n', '<  Isomesh: created "m2", setting level to 1.000\n', '< PyMOL>refresh\n', '<  ObjectMesh: updating "m2".\n', '<  IsosurfVolume: Surface generated using 29064 lines.\n', '<  ObjectMesh: updating "m2".\n', '<  IsosurfVolume: Surface generated using 6969 lines.\n', '< PyMOL>isomesh m3,tst3\n', '<  Executive: object "m3" created.\n', '<  Isomesh: created "m3", setting level to 1.000\n', '<  Isomesh: created "m3", setting level to 1.000\n', '<  Isomesh: created "m3", setting level to 1.000\n', '< PyMOL>refresh\n', '<  ObjectMesh: updating "m3".\n', '<  IsosurfVolume: Surface generated using 3487 lines.\n', '<  ObjectMesh: updating "m3".\n', '<  IsosurfVolume: Surface generated using 29781 lines.\n', '<  ObjectMesh: updating "m3".\n', '<  IsosurfVolume: Surface generated using 9095 lines.\n', '< PyMOL>isomesh m4,tst4\n', '< PyMOL>refresh\n', '< PyMOL>isomesh m5a,tst5,source_state=1\n', '<  Isomesh-Warning: state 1 not present in map "tst5".\n', '< PyMOL>refresh\n', '< PyMOL>isomesh m5b,tst5\n', '<  Executive: object "m5b" created.\n', '<  Isomesh: created "m5b", setting level to 1.000\n', '< PyMOL>isomesh m6,tst6\n', '<  Executive: object "m6" created.\n', '<  Isomesh: created "m6", setting level to 1.000\n', '<  Isomesh: created "m6", setting level to 1.000\n', '<  Isomesh: created "m6", setting level to 1.000\n', '< PyMOL>isosurface s1,tst1\n', '<  Executive: object "s1" created.\n', '<  Isosurface: created "s1", setting level to 1.000\n', '< PyMOL>refresh\n', '<  ObjectMesh: updating "m5b".\n', '<  IsosurfVolume: Surface generated using 6969 lines.\n', '<  ObjectMesh: updating "m6".\n', '<  IsosurfVolume: Surface generated using 2975 lines.\n', '<  ObjectMesh: updating "m6".\n', '<  IsosurfVolume: Surface generated using 29064 lines.\n', '<  ObjectMesh: updating "m6".\n', '<  IsosurfVolume: Surface generated using 6969 lines.\n', '<  ObjectSurface: updating "s1".\n', '<  TetsurfVolume: Surface generated using 106172 triangles.\n', '< PyMOL>isosurface s2,tst2\n', '<  Executive: object "s2" created.\n', '<  Isosurface: created "s2", setting level to 1.000\n', '<  Isosurface: created "s2", setting level to 1.000\n', '< PyMOL>refresh\n', '<  ObjectSurface: updating "s2".\n', '<  TetsurfVolume: Surface generated using 82044 triangles.\n', '<  ObjectSurface: updating "s2".\n', '<  TetsurfVolume: Surface generated using 18780 triangles.\n', '< PyMOL>isosurface s3,tst3\n', '<  Executive: object "s3" created.\n', '<  Isosurface: created "s3", setting level to 1.000\n', '<  Isosurface: created "s3", setting level to 1.000\n', '<  Isosurface: created "s3", setting level to 1.000\n', '< PyMOL>refresh\n', '<  ObjectSurface: updating "s3".\n', '<  TetsurfVolume: Surface generated using 10220 triangles.\n', '<  ObjectSurface: updating "s3".\n', '<  TetsurfVolume: Surface generated using 84672 triangles.\n', '<  ObjectSurface: updating "s3".\n', '<  TetsurfVolume: Surface generated using 25480 triangles.\n', '< PyMOL>isosurface s4,tst4\n', '< PyMOL>refresh\n', '< PyMOL>isosurface s4,tst5\n', '<  Executive: object "s4" created.\n', '<  Isosurface: created "s4", setting level to 1.000\n', '< PyMOL>refresh\n', '<  ObjectSurface: updating "s4".\n', '<  TetsurfVolume: Surface generated using 18780 triangles.\n', '< PyMOL>isosurface s5a,tst5,source_state=1\n', '<  Isosurface-Warning: state 1 not present in map "tst5".\n', '< PyMOL>refresh\n', '< PyMOL>isosurface s5b,tst5\n', '<  Executive: object "s5b" created.\n', '<  Isosurface: created "s5b", setting level to 1.000\n', '< PyMOL>isosurface s6,tst6\n', '<  Executive: object "s6" created.\n', '<  Isosurface: created "s6", setting level to 1.000\n', '<  Isosurface: created "s6", setting level to 1.000\n', '<  Isosurface: created "s6", setting level to 1.000\n', '< PyMOL>isosurface s7,tst1,state=4,source_state=1\n', '<  Executive: object "s7" created.\n', '<  Isosurface: created "s7", setting level to 1.000\n', '< PyMOL>refresh\n', '<  ObjectSurface: updating "s5b".\n', '<  TetsurfVolume: Surface generated using 18780 triangles.\n', '<  ObjectSurface: updating "s6".\n', '<  TetsurfVolume: Surface generated using 8492 triangles.\n', '<  ObjectSurface: updating "s6".\n', '<  TetsurfVolume: Surface generated using 82044 triangles.\n', '<  ObjectSurface: updating "s6".\n', '<  TetsurfVolume: Surface generated using 18780 triangles.\n', '<  ObjectSurface: updating "s7".\n', '<  TetsurfVolume: Surface generated using 106172 triangles.\n', '< PyMOL>isosurface s7,tst6,state=3,source_state=1\n', '<  Isosurface: created "s7", setting level to 1.000\n', '< PyMOL>refresh\n', '<  ObjectSurface: updating "s7".\n', '<  TetsurfVolume: Surface generated using 8492 triangles.\n', '< PyMOL>isosurface s7,tst5,state=2,source_state=4\n', '<  Isosurface: created "s7", setting level to 1.000\n', '< PyMOL>refresh\n', '<  ObjectSurface: updating "s7".\n', '<  TetsurfVolume: Surface generated using 18780 triangles.\n', '< PyMOL>isosurface s7,tst2,state=1,source_state=2\n', '<  Isosurface: created "s7", setting level to 1.000\n', '< PyMOL>refresh\n', '<  ObjectSurface: updating "s7".\n', '<  TetsurfVolume: Surface generated using 82044 triangles.\n', '< PyMOL>frame 4\n', '< PyMOL>isosurface s8,tst2,state=-1\n', '<  Executive: object "s8" created.\n', '<  Isosurface: created "s8", setting level to 1.000\n', '< PyMOL>frame 3\n', '< PyMOL>isosurface s9,tst1,state=-1,source_state=1\n', '<  Executive: object "s9" created.\n', '<  Isosurface: created "s9", setting level to 1.000\n', '< PyMOL>reinit\n', '< PyMOL>load dat/pept.pdb,obj\n', '<  CmdLoad: "dat/pept.pdb" loaded as "obj".\n', '< PyMOL>alter all, b=10\n', '<  Alter: modified 107 atoms.\n', '< PyMOL>map_new m1, gaussian, 1.0, obj\n', '<  ObjectMap: Map created.\n', '<  ObjectMap: Computing Gaussian map for 107 atom positions.\n', '<  ObjectMap: Normalizing: mean = 0.079569 & stdev = 0.336150.\n', '<  Executive: object "m1" created.\n', '< PyMOL>map_new m2, gaussian, 1.0, obj, clamp=[-5, 5]\n', '<  ObjectMap: Map created.\n', '<  ObjectMap: Computing Gaussian map for 107 atom positions.\n', '<  ObjectMap: Normalizing: mean = 0.079569 & stdev = 0.336150.\n', '<  Executive: object "m2" created.\n', '< PyMOL>map_new m3, gaussian, 1.0, obj, clamp=[-3, 3]\n', '<  ObjectMap: Map created.\n', '<  ObjectMap: Computing Gaussian map for 107 atom positions.\n', '<  ObjectMap: Normalizing: mean = 0.079569 & stdev = 0.336150.\n', '<  Executive: object "m3" created.\n', '< PyMOL>map_new m4, gaussian, 1.0, obj, clamp=[-2, 2]\n', '<  ObjectMap: Map created.\n', '<  ObjectMap: Computing Gaussian map for 107 atom positions.\n', '<  ObjectMap: Normalizing: mean = 0.079569 & stdev = 0.336150.\n', '<  Executive: object "m4" created.\n', '< PyMOL>map_new m5, gaussian, 1.0, obj, clamp=[-0.9, 0.9]\n', '<  ObjectMap: Map created.\n', '<  ObjectMap: Computing Gaussian map for 107 atom positions.\n', '<  ObjectMap: Normalizing: mean = 0.079569 & stdev = 0.336150.\n', '<  Executive: object "m5" created.\n', '< PyMOL>isosurface s1, m1\n', '<  Executive: object "s1" created.\n', '<  Isosurface: created "s1", setting level to 1.000\n', '< PyMOL>isosurface s2, m2\n', '<  Executive: object "s2" created.\n', '<  Isosurface: created "s2", setting level to 1.000\n', '< PyMOL>isosurface s3, m3\n', '<  Executive: object "s3" created.\n', '<  Isosurface: created "s3", setting level to 1.000\n', '< PyMOL>isosurface s4, m4\n', '<  Executive: object "s4" created.\n', '<  Isosurface: created "s4", setting level to 1.000\n', '< PyMOL>isosurface s5, m5\n', '<  Executive: object "s5" created.\n', '<  Isosurface: created "s5", setting level to 1.000\n', '< PyMOL>ray renderer=2\n', '<  ObjectSurface: updating "s1".\n', '<  TetsurfVolume: Surface generated using 7120 triangles.\n', '<  ObjectSurface: updating "s2".\n', '<  TetsurfVolume: Surface generated using 7120 triangles.\n', '<  ObjectSurface: updating "s3".\n', '<  TetsurfVolume: Surface generated using 7120 triangles.\n', '<  ObjectSurface: updating "s4".\n', '<  TetsurfVolume: Surface generated using 7120 triangles.\n', '<  ObjectSurface: updating "s5".\n', '<  TetsurfVolume: Surface generated using 0 triangles.\n', '<  RayRenderTest: obtained 28646 graphics primitives.\n', '< PyMOL>print "END-LOG"\n']
 run_tests: C1090coulomb...
 run_tests: C1090coulomb.log DIFFERS over about 23 lines:
['1,45d0\n', '< PyMOL>set auto_zoom,0\n', '<  Setting: auto_zoom set to 0.\n', '< PyMOL>fragment phe\n', '<  Executive: object "phe" created.\n', '< PyMOL>map_new t1,coulomb,0.5,phe,5\n', '<  ObjectMap: Map created.\n', '<  SelectorMapCoulomb: Total charge is 0.000 for 20 points (20 atoms).\n', '<  SelectorMapCoulomb: Evaluating Coulomb potential for grid (no cutoff)...\n', '<  Executive: object "t1" created.\n', '< PyMOL>fragment phe,phe\n', '<  CmdLoad: ChemPy-model appended into object "phe", state 2.\n', '< PyMOL>map_new t2,coulomb,0.5,phe,5\n', '<  ObjectMap: Map created.\n', '<  SelectorMapCoulomb: Total charge is 0.000 for 20 points (20 atoms).\n', '<  SelectorMapCoulomb: Evaluating Coulomb potential for grid (no cutoff)...\n', '<  Executive: object "t2" created.\n', '<  ObjectMap: Map created.\n', '<  SelectorMapCoulomb: Total charge is 0.000 for 20 points (20 atoms).\n', '<  SelectorMapCoulomb: Evaluating Coulomb potential for grid (no cutoff)...\n', '< PyMOL>map_new t3,coulomb,0.5,phe,5,state=-3\n', '<  ObjectMap: Map created.\n', '<  SelectorMapCoulomb: Total charge is 0.000 for 40 points (40 atoms).\n', '<  SelectorMapCoulomb: Evaluating Coulomb potential for grid (no cutoff)...\n', '<  Executive: object "t3" created.\n', '< PyMOL>isomesh m1,t1,5\n', '<  Executive: object "m1" created.\n', '<  Isomesh: created "m1", setting level to 5.000\n', '< PyMOL>refresh\n', '<  ObjectMesh: updating "m1".\n', '<  IsosurfVolume: Surface generated using 3351 lines.\n', '< PyMOL>isomesh m2,t2,5\n', '<  Executive: object "m2" created.\n', '<  Isomesh: created "m2", setting level to 5.000\n', '<  Isomesh: created "m2", setting level to 5.000\n', '< PyMOL>refresh\n', '<  ObjectMesh: updating "m2".\n', '<  IsosurfVolume: Surface generated using 3351 lines.\n', '<  ObjectMesh: updating "m2".\n', '<  IsosurfVolume: Surface generated using 3351 lines.\n', '< PyMOL>isomesh m3,t3,5\n', '<  Executive: object "m3" created.\n', '<  Isomesh: created "m3", setting level to 5.000\n', '< PyMOL>refresh\n', '<  ObjectMesh: updating "m3".\n', '<  IsosurfVolume: Surface generated using 3351 lines.\n']
 run_tests: C1095slice...
 run_tests: C1095slice.log DIFFERS over about 33 lines:
['1,65d0\n', '< PyMOL>set auto_zoom,0\n', '<  Setting: auto_zoom set to 0.\n', '< PyMOL>fragment phe\n', '<  Executive: object "phe" created.\n', '< PyMOL>ray renderer=2\n', '<  RayRenderTest: obtained 31 graphics primitives.\n', '< PyMOL>map_new pot,coulomb,0.5,phe,5\n', '<  ObjectMap: Map created.\n', '<  SelectorMapCoulomb: Total charge is 0.000 for 20 points (20 atoms).\n', '<  SelectorMapCoulomb: Evaluating Coulomb potential for grid (no cutoff)...\n', '<  Executive: object "pot" created.\n', '< PyMOL>ray renderer=2\n', '<  RayRenderTest: obtained 31 graphics primitives.\n', '< PyMOL>ramp_new ramp, pot\n', '<  Executive: object "ramp" created.\n', '< PyMOL>ray renderer=2\n', '<  RayRenderTest: obtained 116 graphics primitives.\n', '< PyMOL>slice_new slice, pot\n', '<  Executive: object "slice" created.\n', '<  SliceMap: created "slice".\n', '< PyMOL>color ramp,slice\n', '<  Executive: Colored 1 object.\n', '< PyMOL>set ray_default_renderer,2\n', '<  Setting: ray_default_renderer set to 2.\n', '< PyMOL>refresh\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 5780 graphics primitives.\n', '< PyMOL>set slice_track_camera, on\n', '<  Setting: slice_track_camera set to on.\n', '< PyMOL>turn x,45\n', '< PyMOL>turn z,45\n', '< PyMOL>refresh\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 7337 graphics primitives.\n', '< PyMOL>set slice_track_camera,off\n', '<  Setting: slice_track_camera set to off.\n', '< PyMOL>refresh\n', '< PyMOL>reset\n', '< PyMOL>turn y,45\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 7337 graphics primitives.\n', '< PyMOL>set slice_height_map\n', '<  Setting: slice_height_map set to on.\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 7337 graphics primitives.\n', '< PyMOL>set slice_grid, 1\n', '<  Setting: slice_grid set to 1.00000.\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 716 graphics primitives.\n', '< PyMOL>set slice_grid, 0.2\n', '<  Setting: slice_grid set to 0.20000.\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 16622 graphics primitives.\n', '< PyMOL>ramp_new ramp, pot, color=sludge\n', '<  Executive: object "ramp" created.\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 16656 graphics primitives.\n', '< PyMOL>ramp_new ramp, pot, color=rainbow\n', '<  Executive: object "ramp" created.\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 16656 graphics primitives.\n', '< PyMOL>ramp_new ramp, pot, color=rainbow, selection=none\n', '<  Executive: object "ramp" created.\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 16642 graphics primitives.\n']
 run_tests: C1100do...
 run_tests: C1100do.log DIFFERS over about 40 lines:
['1,79d0\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>show sticks,pept\n', '< PyMOL>set ray_default_renderer=2\n', '<  Setting: ray_default_renderer set to 2.\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 166 graphics primitives.\n', '< PyMOL>dele all\n', '< PyMOL>load dat/il2.pdb\n', '<  CmdLoad: "dat/il2.pdb" loaded as "il2".\n', '< PyMOL>show dots,il2\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 111078 graphics primitives.\n', '< PyMOL>dele all\n', '< PyMOL>load dat/3al1.pdb\n', '< HEADER    STRUCTURAL PROTEIN                      26-OCT-98   3AL1\n', '< TITLE     DESIGNED PEPTIDE ALPHA-1, RACEMIC P1BAR FORM\n', '< COMPND    MOL_ID: 1;\n', '< COMPND   2 MOLECULE: D, L-ALPHA-1;\n', '< COMPND   3 CHAIN: A, B;\n', '< COMPND   4 ENGINEERED: YES;\n', '< COMPND   5 OTHER_DETAILS: N TERMINI ARE ACETYLATED\n', '<  ObjectMolecule: Read secondary structure assignments.\n', '<  ObjectMolecule: Read crystal symmetry information.\n', '<  Symmetry: Found 2 symmetry operators.\n', '<  CmdLoad: "dat/3al1.pdb" loaded as "3al1".\n', '< PyMOL>show sph,3al1\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 1945 graphics primitives.\n', '< PyMOL>dele all\n', '< PyMOL>fragment arg\n', '<  Executive: object "arg" created.\n', '< PyMOL>ray\n', '<  RayRenderTest: obtained 42 graphics primitives.\n', '< PyMOL>for a in range(1,10):\\\n', '< PyMOL>   print a\\\n', '< PyMOL>   print a+10\n', '< 1\n', '< 11\n', '< 2\n', '< 12\n', '< 3\n', '< 13\n', '< 4\n', '< 14\n', '< 5\n', '< 15\n', '< 6\n', '< 16\n', '< 7\n', '< 17\n', '< 8\n', '< 18\n', '< 9\n', '< 19\n', '< PyMOL>for a in range(11,21):\\\n', '< PyMOL>  print a\\\n', '< PyMOL>  print a+10\n', '< 11\n', '< 21\n', '< 12\n', '< 22\n', '< 13\n', '< 23\n', '< 14\n', '< 24\n', '< 15\n', '< 25\n', '< 16\n', '< 26\n', '< 17\n', '< 27\n', '< 18\n', '< 28\n', '< 19\n', '< 29\n', '< 20\n', '< 30\n', '< PyMOL>  \n']
 run_tests: C1110matrix_mode...
 run_tests: C1110matrix_mode.log DIFFERS over about 127 lines:
['1,253d0\n', '< PyMOL>reinit\n', '< PyMOL>set matrix_mode, 0\n', '<  Setting: matrix_mode set to 0.\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>remove not resi 5\n', '<  Remove: eliminated 97 atoms in model "pept".\n', '< PyMOL>iterate_state 1,all,print "%8.3f %8.3f %8.3f"%(x,y,z)\n', '<   -0.135   -5.634   21.235\n', '<   -0.006   -4.205   21.043\n', '<   -1.408   -3.636   20.918\n', '<   -2.092   -3.870   19.914\n', '<    0.791   -3.871   19.783\n', '<    0.939   -2.396   19.549\n', '<    0.582   -1.619   18.499\n', '<    1.470   -1.542   20.495\n', '<    1.431   -0.303   20.038\n', '<    0.896   -0.322   18.831\n', '<  IterateState: iterated over 10 atom coordinate states.\n', '< PyMOL>rotate x, 53, object=pept\n', '< PyMOL>rotate y, 27, object=pept\n', '< PyMOL>rotate z, 6, object=pept\n', '< PyMOL>translate [1,2,3], object=pept\n', '< PyMOL>save tmp/C1110a.pdb\n', '<  Save: wrote "tmp/C1110a.pdb".\n', '< PyMOL>for a in open("tmp/C1110a.pdb").readlines(): print a,\n', '< ATOM      1  N   HIS E   5       2.647  -5.977  27.838  1.00 32.18      E    N  \n', '< ATOM      2  CA  HIS E   5       3.119  -4.909  28.693  1.00 32.91      E    C  \n', '< ATOM      3  C   HIS E   5       2.002  -4.582  29.667  1.00 34.58      E    C  \n', '< ATOM      4  O   HIS E   5       0.969  -4.026  29.273  1.00 35.87      E    O  \n', '< ATOM      5  CB  HIS E   5       3.477  -3.657  27.893  1.00 33.02      E    C  \n', '< ATOM      6  CG  HIS E   5       3.964  -2.526  28.750  1.00 32.86      E    C  \n', '< ATOM      7  CD2 HIS E   5       3.506  -1.261  28.902  1.00 31.48      E    C  \n', '< ATOM      8  ND1 HIS E   5       5.025  -2.657  29.624  1.00 29.87      E    N  \n', '< ATOM      9  CE1 HIS E   5       5.197  -1.522  30.278  1.00 29.68      E    C  \n', '< ATOM     10  NE2 HIS E   5       4.288  -0.660  29.860  1.00 29.87      E    N  \n', '< END\n', '< PyMOL>save tmp/C1110b.pdb, ref=pept\n', '<  Save: wrote "tmp/C1110b.pdb".\n', '< PyMOL>for a in open("tmp/C1110b.pdb").readlines(): print a,\n', '< ATOM      1  N   HIS E   5      -0.135  -5.634  21.235  1.00 32.18      E    N  \n', '< ATOM      2  CA  HIS E   5      -0.006  -4.205  21.043  1.00 32.91      E    C  \n', '< ATOM      3  C   HIS E   5      -1.408  -3.636  20.918  1.00 34.58      E    C  \n', '< ATOM      4  O   HIS E   5      -2.092  -3.870  19.914  1.00 35.87      E    O  \n', '< ATOM      5  CB  HIS E   5       0.791  -3.871  19.783  1.00 33.02      E    C  \n', '< ATOM      6  CG  HIS E   5       0.939  -2.396  19.549  1.00 32.86      E    C  \n', '< ATOM      7  CD2 HIS E   5       0.582  -1.619  18.499  1.00 31.48      E    C  \n', '< ATOM      8  ND1 HIS E   5       1.470  -1.542  20.495  1.00 29.87      E    N  \n', '< ATOM      9  CE1 HIS E   5       1.431  -0.303  20.038  1.00 29.68      E    C  \n', '< ATOM     10  NE2 HIS E   5       0.896  -0.322  18.831  1.00 29.87      E    N  \n', '< END\n', '< PyMOL>load dat/pept.pdb, tmp\n', '<  CmdLoad: "dat/pept.pdb" loaded as "tmp".\n', '< PyMOL>remove tmp and not resi 5\n', '<  Remove: eliminated 97 atoms in model "tmp".\n', '< PyMOL>matrix_transfer pept, tmp\n', '< PyMOL>save tmp/C1110c.pdb, tmp,\n', '<  Save: wrote "tmp/C1110c.pdb".\n', '< PyMOL>for a in open("tmp/C1110c.pdb").readlines(): print a,\n', '< ATOM      1  N   HIS E   5       2.647  -5.977  27.838  1.00 32.18      E    N  \n', '< ATOM      2  CA  HIS E   5       3.119  -4.909  28.693  1.00 32.91      E    C  \n', '< ATOM      3  C   HIS E   5       2.002  -4.582  29.667  1.00 34.58      E    C  \n', '< ATOM      4  O   HIS E   5       0.969  -4.026  29.273  1.00 35.87      E    O  \n', '< ATOM      5  CB  HIS E   5       3.477  -3.657  27.893  1.00 33.02      E    C  \n', '< ATOM      6  CG  HIS E   5       3.964  -2.526  28.750  1.00 32.86      E    C  \n', '< ATOM      7  CD2 HIS E   5       3.506  -1.261  28.902  1.00 31.48      E    C  \n', '< ATOM      8  ND1 HIS E   5       5.025  -2.657  29.624  1.00 29.87      E    N  \n', '< ATOM      9  CE1 HIS E   5       5.197  -1.522  30.278  1.00 29.68      E    C  \n', '< ATOM     10  NE2 HIS E   5       4.288  -0.660  29.860  1.00 29.87      E    N  \n', '< END\n', '< PyMOL>save tmp/C1110d.pdb, tmp, ref=tmp\n', '<  Save: wrote "tmp/C1110d.pdb".\n', '< PyMOL>for a in open("tmp/C1110d.pdb").readlines(): print a,\n', '< ATOM      1  N   HIS E   5      -0.135  -5.634  21.235  1.00 32.18      E    N  \n', '< ATOM      2  CA  HIS E   5      -0.006  -4.205  21.043  1.00 32.91      E    C  \n', '< ATOM      3  C   HIS E   5      -1.408  -3.636  20.918  1.00 34.58      E    C  \n', '< ATOM      4  O   HIS E   5      -2.092  -3.870  19.914  1.00 35.87      E    O  \n', '< ATOM      5  CB  HIS E   5       0.791  -3.871  19.783  1.00 33.02      E    C  \n', '< ATOM      6  CG  HIS E   5       0.939  -2.396  19.549  1.00 32.86      E    C  \n', '< ATOM      7  CD2 HIS E   5       0.582  -1.619  18.499  1.00 31.48      E    C  \n', '< ATOM      8  ND1 HIS E   5       1.470  -1.542  20.495  1.00 29.87      E    N  \n', '< ATOM      9  CE1 HIS E   5       1.431  -0.303  20.038  1.00 29.68      E    C  \n', '< ATOM     10  NE2 HIS E   5       0.896  -0.322  18.831  1.00 29.87      E    N  \n', '< END\n', '< PyMOL>reinit\n', '< PyMOL>set matrix_mode, 1\n', '<  Setting: matrix_mode set to 1.\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>remove not resi 5\n', '<  Remove: eliminated 97 atoms in model "pept".\n', '< PyMOL>iterate_state 1,all,print "%8.3f %8.3f %8.3f"%(x,y,z)\n', '<   -0.135   -5.634   21.235\n', '<   -0.006   -4.205   21.043\n', '<   -1.408   -3.636   20.918\n', '<   -2.092   -3.870   19.914\n', '<    0.791   -3.871   19.783\n', '<    0.939   -2.396   19.549\n', '<    0.582   -1.619   18.499\n', '<    1.470   -1.542   20.495\n', '<    1.431   -0.303   20.038\n', '<    0.896   -0.322   18.831\n', '<  IterateState: iterated over 10 atom coordinate states.\n', '< PyMOL>rotate x, 53, object=pept\n', '< PyMOL>rotate y, 27, object=pept\n', '< PyMOL>rotate z, 6, object=pept\n', '< PyMOL>translate [1,2,3], object=pept\n', '< PyMOL>save tmp/C1110a.pdb\n', '<  Save: wrote "tmp/C1110a.pdb".\n', '< PyMOL>for a in open("tmp/C1110a.pdb").readlines(): print a,\n', '< ATOM      1  N   HIS E   5       2.647  -5.977  27.838  1.00 32.18      E    N  \n', '< ATOM      2  CA  HIS E   5       3.119  -4.909  28.693  1.00 32.91      E    C  \n', '< ATOM      3  C   HIS E   5       2.002  -4.582  29.667  1.00 34.58      E    C  \n', '< ATOM      4  O   HIS E   5       0.969  -4.026  29.273  1.00 35.87      E    O  \n', '< ATOM      5  CB  HIS E   5       3.477  -3.657  27.893  1.00 33.02      E    C  \n', '< ATOM      6  CG  HIS E   5       3.964  -2.526  28.750  1.00 32.86      E    C  \n', '< ATOM      7  CD2 HIS E   5       3.506  -1.261  28.902  1.00 31.48      E    C  \n', '< ATOM      8  ND1 HIS E   5       5.025  -2.657  29.624  1.00 29.87      E    N  \n', '< ATOM      9  CE1 HIS E   5       5.197  -1.522  30.278  1.00 29.68      E    C  \n', '< ATOM     10  NE2 HIS E   5       4.288  -0.660  29.860  1.00 29.87      E    N  \n', '< END\n', '< PyMOL>save tmp/C1110b.pdb, ref=pept\n', '<  Save: wrote "tmp/C1110b.pdb".\n', '< PyMOL>for a in open("tmp/C1110b.pdb").readlines(): print a,\n', '< ATOM      1  N   HIS E   5      -0.135  -5.634  21.235  1.00 32.18      E    N  \n', '< ATOM      2  CA  HIS E   5      -0.006  -4.205  21.043  1.00 32.91      E    C  \n', '< ATOM      3  C   HIS E   5      -1.408  -3.636  20.918  1.00 34.58      E    C  \n', '< ATOM      4  O   HIS E   5      -2.092  -3.870  19.914  1.00 35.87      E    O  \n', '< ATOM      5  CB  HIS E   5       0.791  -3.871  19.783  1.00 33.02      E    C  \n', '< ATOM      6  CG  HIS E   5       0.939  -2.396  19.549  1.00 32.86      E    C  \n', '< ATOM      7  CD2 HIS E   5       0.582  -1.619  18.499  1.00 31.48      E    C  \n', '< ATOM      8  ND1 HIS E   5       1.470  -1.542  20.495  1.00 29.87      E    N  \n', '< ATOM      9  CE1 HIS E   5       1.431  -0.303  20.038  1.00 29.68      E    C  \n', '< ATOM     10  NE2 HIS E   5       0.896  -0.322  18.831  1.00 29.87      E    N  \n', '< END\n', '< PyMOL>load dat/pept.pdb, tmp\n', '<  CmdLoad: "dat/pept.pdb" loaded as "tmp".\n', '< PyMOL>remove tmp and not resi 5\n', '<  Remove: eliminated 97 atoms in model "tmp".\n', '< PyMOL>matrix_transfer pept, tmp\n', '< PyMOL>save tmp/C1110c.pdb, tmp,\n', '<  Save: wrote "tmp/C1110c.pdb".\n', '< PyMOL>for a in open("tmp/C1110c.pdb").readlines(): print a,\n', '< ATOM      1  N   HIS E   5       2.647  -5.977  27.838  1.00 32.18      E    N  \n', '< ATOM      2  CA  HIS E   5       3.119  -4.909  28.693  1.00 32.91      E    C  \n', '< ATOM      3  C   HIS E   5       2.002  -4.582  29.667  1.00 34.58      E    C  \n', '< ATOM      4  O   HIS E   5       0.969  -4.026  29.273  1.00 35.87      E    O  \n', '< ATOM      5  CB  HIS E   5       3.477  -3.657  27.893  1.00 33.02      E    C  \n', '< ATOM      6  CG  HIS E   5       3.964  -2.526  28.750  1.00 32.86      E    C  \n', '< ATOM      7  CD2 HIS E   5       3.506  -1.261  28.902  1.00 31.48      E    C  \n', '< ATOM      8  ND1 HIS E   5       5.025  -2.657  29.624  1.00 29.87      E    N  \n', '< ATOM      9  CE1 HIS E   5       5.197  -1.522  30.278  1.00 29.68      E    C  \n', '< ATOM     10  NE2 HIS E   5       4.288  -0.660  29.860  1.00 29.87      E    N  \n', '< END\n', '< PyMOL>save tmp/C1110d.pdb, tmp, ref=tmp\n', '<  Save: wrote "tmp/C1110d.pdb".\n', '< PyMOL>for a in open("tmp/C1110d.pdb").readlines(): print a,\n', '< ATOM      1  N   HIS E   5      -0.135  -5.634  21.235  1.00 32.18      E    N  \n', '< ATOM      2  CA  HIS E   5      -0.006  -4.205  21.043  1.00 32.91      E    C  \n', '< ATOM      3  C   HIS E   5      -1.408  -3.636  20.918  1.00 34.58      E    C  \n', '< ATOM      4  O   HIS E   5      -2.092  -3.870  19.914  1.00 35.87      E    O  \n', '< ATOM      5  CB  HIS E   5       0.791  -3.871  19.783  1.00 33.02      E    C  \n', '< ATOM      6  CG  HIS E   5       0.939  -2.396  19.549  1.00 32.86      E    C  \n', '< ATOM      7  CD2 HIS E   5       0.582  -1.619  18.499  1.00 31.48      E    C  \n', '< ATOM      8  ND1 HIS E   5       1.470  -1.542  20.495  1.00 29.87      E    N  \n', '< ATOM      9  CE1 HIS E   5       1.431  -0.303  20.038  1.00 29.68      E    C  \n', '< ATOM     10  NE2 HIS E   5       0.896  -0.322  18.831  1.00 29.87      E    N  \n', '< END\n', '< PyMOL>reinit\n', '< PyMOL>set matrix_mode, 2\n', '<  Setting: matrix_mode set to 2.\n', '< PyMOL>load dat/pept.pdb\n', '<  CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>remove not resi 5\n', '<  Remove: eliminated 97 atoms in model "pept".\n', '< PyMOL>iterate_state 1,all,print "%8.3f %8.3f %8.3f"%(x,y,z)\n', '<   -0.135   -5.634   21.235\n', '<   -0.006   -4.205   21.043\n', '<   -1.408   -3.636   20.918\n', '<   -2.092   -3.870   19.914\n', '<    0.791   -3.871   19.783\n', '<    0.939   -2.396   19.549\n', '<    0.582   -1.619   18.499\n', '<    1.470   -1.542   20.495\n', '<    1.431   -0.303   20.038\n', '<    0.896   -0.322   18.831\n', '<  IterateState: iterated over 10 atom coordinate states.\n', '< PyMOL>rotate x, 53, object=pept, object_mode=1\n', '< PyMOL>rotate y, 27, object=pept, object_mode=1\n', '< PyMOL>rotate z, 6, object=pept, object_mode=1\n', '< PyMOL>translate [1,2,3], object=pept, object_mode=1\n', '< PyMOL>save tmp/C1110a.pdb\n', '<  Save: wrote "tmp/C1110a.pdb".\n', '< PyMOL>for a in open("tmp/C1110a.pdb").readlines(): print a,\n', '< ATOM      1  N   HIS E   5       2.647  -5.977  27.838  1.00 32.18      E    N  \n', '< ATOM      2  CA  HIS E   5       3.119  -4.909  28.693  1.00 32.91      E    C  \n', '< ATOM      3  C   HIS E   5       2.002  -4.582  29.667  1.00 34.58      E    C  \n', '< ATOM      4  O   HIS E   5       0.969  -4.026  29.273  1.00 35.87      E    O  \n', '< ATOM      5  CB  HIS E   5       3.477  -3.657  27.893  1.00 33.02      E    C  \n', '< ATOM      6  CG  HIS E   5       3.964  -2.526  28.750  1.00 32.86      E    C  \n', '< ATOM      7  CD2 HIS E   5       3.506  -1.261  28.902  1.00 31.48      E    C  \n', '< ATOM      8  ND1 HIS E   5       5.025  -2.657  29.624  1.00 29.87      E    N  \n', '< ATOM      9  CE1 HIS E   5       5.197  -1.522  30.278  1.00 29.68      E    C  \n', '< ATOM     10  NE2 HIS E   5       4.288  -0.660  29.860  1.00 29.87      E    N  \n', '< END\n', '< PyMOL>save tmp/C1110b.pdb, ref=pept\n', '<  Save: wrote "tmp/C1110b.pdb".\n', '< PyMOL>for a in open("tmp/C1110b.pdb").readlines(): print a,\n', '< ATOM      1  N   HIS E   5      -0.135  -5.634  21.235  1.00 32.18      E    N  \n', '< ATOM      2  CA  HIS E   5      -0.006  -4.205  21.043  1.00 32.91      E    C  \n', '< ATOM      3  C   HIS E   5      -1.408  -3.636  20.918  1.00 34.58      E    C  \n', '< ATOM      4  O   HIS E   5      -2.092  -3.870  19.914  1.00 35.87      E    O  \n', '< ATOM      5  CB  HIS E   5       0.791  -3.871  19.783  1.00 33.02      E    C  \n', '< ATOM      6  CG  HIS E   5       0.939  -2.396  19.549  1.00 32.86      E    C  \n', '< ATOM      7  CD2 HIS E   5       0.582  -1.619  18.499  1.00 31.48      E    C  \n', '< ATOM      8  ND1 HIS E   5       1.470  -1.542  20.495  1.00 29.87      E    N  \n', '< ATOM      9  CE1 HIS E   5       1.431  -0.303  20.038  1.00 29.68      E    C  \n', '< ATOM     10  NE2 HIS E   5       0.896  -0.322  18.831  1.00 29.87      E    N  \n', '< END\n', '< PyMOL>load dat/pept.pdb, tmp\n', '<  CmdLoad: "dat/pept.pdb" loaded as "tmp".\n', '< PyMOL>remove tmp and not resi 5\n', '<  Remove: eliminated 97 atoms in model "tmp".\n', '< PyMOL>matrix_transfer pept, tmp\n', '< PyMOL>save tmp/C1110c.pdb, tmp,\n', '<  Save: wrote "tmp/C1110c.pdb".\n', '< PyMOL>for a in open("tmp/C1110c.pdb").readlines(): print a,\n', '< ATOM      1  N   HIS E   5       2.647  -5.977  27.838  1.00 32.18      E    N  \n', '< ATOM      2  CA  HIS E   5       3.119  -4.909  28.693  1.00 32.91      E    C  \n', '< ATOM      3  C   HIS E   5       2.002  -4.582  29.667  1.00 34.58      E    C  \n', '< ATOM      4  O   HIS E   5       0.969  -4.026  29.273  1.00 35.87      E    O  \n', '< ATOM      5  CB  HIS E   5       3.477  -3.657  27.893  1.00 33.02      E    C  \n', '< ATOM      6  CG  HIS E   5       3.964  -2.526  28.750  1.00 32.86      E    C  \n', '< ATOM      7  CD2 HIS E   5       3.506  -1.261  28.902  1.00 31.48      E    C  \n', '< ATOM      8  ND1 HIS E   5       5.025  -2.657  29.624  1.00 29.87      E    N  \n', '< ATOM      9  CE1 HIS E   5       5.197  -1.522  30.278  1.00 29.68      E    C  \n', '< ATOM     10  NE2 HIS E   5       4.288  -0.660  29.860  1.00 29.87      E    N  \n', '< END\n', '< PyMOL>save tmp/C1110d.pdb, tmp, ref=tmp\n', '<  Save: wrote "tmp/C1110d.pdb".\n', '< PyMOL>for a in open("tmp/C1110d.pdb").readlines(): print a,\n', '< ATOM      1  N   HIS E   5      -0.135  -5.634  21.235  1.00 32.18      E    N  \n', '< ATOM      2  CA  HIS E   5      -0.006  -4.205  21.043  1.00 32.91      E    C  \n', '< ATOM      3  C   HIS E   5      -1.408  -3.636  20.918  1.00 34.58      E    C  \n', '< ATOM      4  O   HIS E   5      -2.092  -3.870  19.914  1.00 35.87      E    O  \n', '< ATOM      5  CB  HIS E   5       0.791  -3.871  19.783  1.00 33.02      E    C  \n', '< ATOM      6  CG  HIS E   5       0.939  -2.396  19.549  1.00 32.86      E    C  \n', '< ATOM      7  CD2 HIS E   5       0.582  -1.619  18.499  1.00 31.48      E    C  \n', '< ATOM      8  ND1 HIS E   5       1.470  -1.542  20.495  1.00 29.87      E    N  \n', '< ATOM      9  CE1 HIS E   5       1.431  -0.303  20.038  1.00 29.68      E    C  \n', '< ATOM     10  NE2 HIS E   5       0.896  -0.322  18.831  1.00 29.87      E    N  \n', '< END\n', '< PyMOL>print "END-LOG"\n']
 run_tests: C1200matrix_maps...
 run_tests: C1200matrix_maps.log DIFFERS over about 60 lines:
['1,119d0\n', '< PyMOL>load dat/pept.pdb,prot\n', '<  CmdLoad: "dat/pept.pdb" loaded as "prot".\n', '< PyMOL>map_new map1,gaussian,1.0,state=-3\n', '<  ObjectMap: Map created.\n', '<  ObjectMap: Computing Gaussian map for 107 atom positions.\n', '<  ObjectMap: Normalizing: mean = 0.079928 & stdev = 0.237612.\n', '<  Executive: object "map1" created.\n', '< PyMOL>translate [10,20,30], object=prot, object_mode=1\n', '< PyMOL>rotate x,30,prot,object=prot,object_mode=1\n', '< PyMOL>rotate y,30,prot,object=prot,object_mode=1\n', '< PyMOL>rotate z,30,prot,object=prot,object_mode=1\n', '< PyMOL>zoom prot\n', '< PyMOL>dump44(cmd.get_object_matrix("map1"))\n', '< [  1.00  0.00  0.00  0.00  \n', '<    0.00  1.00  0.00  0.00  \n', '<    0.00  0.00  1.00  0.00  \n', '<    0.00  0.00  0.00  1.00 ]\n', '< PyMOL>matrix_transfer prot, map1\n', '< PyMOL>dump44(cmd.get_object_matrix("map1"))\n', '< [  0.75 -0.22  0.62  7.79  \n', '<    0.43  0.88 -0.22 17.71  \n', '<   -0.50  0.43  0.75 36.18  \n', '<    0.00  0.00  0.00  1.00 ]\n', '< PyMOL>isomesh m1, map1, 1.0, 5/, carve=2.1\n', '<  Executive: object "m1" created.\n', '<  Isomesh: created "m1", setting level to 1.000\n', '< PyMOL>ray renderer=2\n', '<  ObjectMesh: updating "m1".\n', '<  RayRenderTest: obtained 464 graphics primitives.\n', '< PyMOL>isosurf s1, map1, 1.0, 5/, carve=2.1\n', '<  Executive: object "s1" created.\n', '<  Isosurface: created "s1", setting level to 1.000\n', '< PyMOL>ray renderer=2\n', '<  ObjectSurface: updating "s1".\n', '<  RayRenderTest: obtained 1284 graphics primitives.\n', '< PyMOL>translate [5,-10,2], object=prot, object_mode=1\n', '< PyMOL>rotate x,60,prot,object=prot,object_mode=1\n', '< PyMOL>rotate z,20,prot,object=prot,object_mode=1\n', '< PyMOL>rotate y,30,prot,object=prot,object_mode=1\n', '< PyMOL>matrix_transfer prot, map1\n', '< PyMOL>isomesh m1, map1, 1.0, 5/, carve=3\n', '<  Isomesh: created "m1", setting level to 1.000\n', '< PyMOL>ray renderer=2\n', '<  ObjectMesh: updating "m1".\n', '<  RayRenderTest: obtained 1404 graphics primitives.\n', '< PyMOL>disable\n', '< PyMOL>isosurf s1, map1, 1.0, 5/, carve=3\n', '<  Isosurface: created "s1", setting level to 1.000\n', '< PyMOL>ray renderer=2\n', '<  RayRenderTest: obtained 0 graphics primitives.\n', '< PyMOL>disable\n', '< PyMOL>isomesh m2, map1, 1.0, 5/, 3\n', '<  Executive: object "m2" created.\n', '<  Isomesh: created "m2", setting level to 1.000\n', '< PyMOL>ray renderer=2\n', '<  ObjectMesh: updating "m2".\n', '<  RayRenderTest: obtained 1468 graphics primitives.\n', '< PyMOL>disable\n', '< PyMOL>isosurf s2, map1, 1.0, 5/, 3\n', '<  Executive: object "s2" created.\n', '<  Isosurface: created "s2", setting level to 1.000\n', '< PyMOL>ray renderer=2\n', '<  ObjectSurface: updating "s2".\n', '<  RayRenderTest: obtained 4096 graphics primitives.\n', '< PyMOL>disable\n', '< PyMOL>isomesh m3, map1\n', '<  Executive: object "m3" created.\n', '<  Isomesh: created "m3", setting level to 1.000\n', '< PyMOL>ray renderer=2\n', '<  ObjectMesh: updating "m3".\n', '<  RayRenderTest: obtained 2908 graphics primitives.\n', '< PyMOL>disable\n', '< PyMOL>isosurf s3, map1\n', '<  Executive: object "s3" created.\n', '<  Isosurface: created "s3", setting level to 1.000\n', '< PyMOL>ray renderer=2\n', '<  ObjectSurface: updating "s3".\n', '<  RayRenderTest: obtained 8492 graphics primitives.\n', '< PyMOL>enable\n', '< PyMOL>ray renderer=2\n', '<  ObjectSurface: updating "s1".\n', '<  RayRenderTest: obtained 18753 graphics primitives.\n', '< PyMOL>save tmp/C1200.pse\n', '<  Save: wrote "tmp/C1200.pse".\n', '< PyMOL>reinit\n', '< PyMOL>load tmp/C1200.pse\n', '<  Executive: Loading version 1.20 session...\n', '< PyMOL>ray renderer=2\n', '<  ObjectMesh: updating "m1".\n', '<  ObjectSurface: updating "s1".\n', '<  ObjectMesh: updating "m2".\n', '<  ObjectSurface: updating "s2".\n', '<  ObjectMesh: updating "m3".\n', '<  ObjectSurface: updating "s3".\n', '<  RayRenderTest: obtained 18753 graphics primitives.\n', '< PyMOL>disable\n', '< PyMOL>isomesh m4, map1, 2.0, 2/, 4\n', '<  Executive: object "m4" created.\n', '<  Isomesh: created "m4", setting level to 2.000\n', '< PyMOL>isosurf s4, map1, 2.0, 2/, 4\n', '<  Executive: object "s4" created.\n', '<  Isosurface: created "s4", setting level to 2.000\n', '< PyMOL>ray renderer=2\n', '<  ObjectMesh: updating "m4".\n', '<  ObjectSurface: updating "s4".\n', '<  RayRenderTest: obtained 6533 graphics primitives.\n', '< PyMOL>disable\n', '< PyMOL>enable m1\n', '< PyMOL>isolevel m1, 3\n', '< PyMOL>ray renderer=2\n', '<  ObjectMesh: updating "m1".\n', '<  RayRenderTest: obtained 288 graphics primitives.\n', '< PyMOL>disable\n', '< PyMOL>enable s1\n', '< PyMOL>isolevel s1, 5\n', '< PyMOL>ray renderer=2\n', '<  ObjectSurface: updating "s1".\n', '<  RayRenderTest: obtained 168 graphics primitives.\n', '< PyMOL>print "END-LOG"\n']
 run_tests: C1300extras...
 run_tests: C1300extras.log DIFFERS over about 38 lines:
['1,76d0\n', '< PyMOL>delete all\n', '< PyMOL>fragment methane\n', '<  Executive: object "methane" created.\n', '< PyMOL>remove hydro and not first hydro\n', '<  Remove: eliminated 3 atoms in model "methane".\n', "< PyMOL>alter all,segi='METH'\n", '<  Alter: modified 2 atoms.\n', "< PyMOL>alter hydro, alt='A'\n", '<  Alter: modified 1 atoms.\n', "< PyMOL>alter hydro, text_type='Htype'\n", '<  Alter: modified 1 atoms.\n', "< PyMOL>alter all, ss='L'\n", '<  Alter: modified 2 atoms.\n', '< PyMOL>alter all, b=rank\n', '<  Alter: modified 2 atoms.\n', '< PyMOL>alter all, q=index\n', '<  Alter: modified 2 atoms.\n', '< PyMOL>alter all, elec_radius = vdw+1.0\n', '<  Alter: modified 2 atoms.\n', '< PyMOL>cmd.label2("all","\'some text\'")\n', '< PyMOL>cmd.iterate("all",r"print name +\' -> \' + \'\\\'\' + label + \'\\\'\'")\n', "< C01 -> 'some text'\n", "< H01 -> 'some text'\n", '< PyMOL>cmd.label2("all","\'some text \'+\'more text\'")\n', '< PyMOL>cmd.iterate("all",r"print name +\' -> \' + \'\\\'\' + label + \'\\\'\'")\n', "< C01 -> 'some text more text'\n", "< H01 -> 'some text more text'\n", '< PyMOL>cmd.label2("all"," \'some text \' + \'more text\' ")\n', '< PyMOL>cmd.iterate("all",r"print name +\' -> \' + \'\\\'\' + label + \'\\\'\'")\n', "< C01 -> 'some text more text'\n", "< H01 -> 'some text more text'\n", '< PyMOL>cmd.label2("all","model")\n', '< PyMOL>cmd.iterate("all",r"print name +\' -> \' + \'\\\'\' + label + \'\\\'\'")\n', "< C01 -> 'methane'\n", "< H01 -> 'methane'\n", '< PyMOL>cmd.label2("all","resv")\n', '< PyMOL>cmd.iterate("all",r"print name +\' -> \' + \'\\\'\' + label + \'\\\'\'")\n', "< C01 -> '9'\n", "< H01 -> '9'\n", '< PyMOL>cmd.label2("all","model+\' index:\'+index+ \' type:\' +type")\n', '< PyMOL>cmd.iterate("all",r"print name +\' -> \' + \'\\\'\' + label + \'\\\'\'")\n', "< C01 -> 'methane index:1 type:ATOM'\n", "< H01 -> 'methane index:2 type:ATOM'\n", '< PyMOL>cmd.label2("all","segi+\' \'+chain+\' \'+resi+\'`\'+resn+\' \'+str(resv)+name+\'`\'+alt")\n', '< PyMOL>cmd.iterate("all",r"print name +\' -> \' + \'\\\'\' + label + \'\\\'\'")\n', "< C01 -> 'METH E 9`LEU 9C01`'\n", "< H01 -> 'METH E 9`LEU 9H01`A'\n", '< PyMOL>cmd.label2("all","str(index)+\' \'+str(rank)+\' \'+str(ID)")\n', '< PyMOL>cmd.iterate("all",r"print name +\' -> \' + \'\\\'\' + label + \'\\\'\'")\n', "< C01 -> '1 0 0'\n", "< H01 -> '2 1 1'\n", '< PyMOL>cmd.label2("all","flags")\n', '< PyMOL>cmd.iterate("all",r"print name +\' -> \' + \'\\\'\' + label + \'\\\'\'")\n', "< C01 -> '8000000'\n", "< H01 -> '8000000'\n", '< PyMOL>cmd.label2("all","str(numeric_type)+text_type")\n', '< PyMOL>cmd.iterate("all",r"print name +\' -> \' + \'\\\'\' + label + \'\\\'\'")\n', "< C01 -> '0'\n", "< H01 -> '0Htype'\n", '< PyMOL>cmd.label2("all","str(formal_charge) + \' \' + str(partial_charge)")\n', '< PyMOL>cmd.iterate("all",r"print name +\' -> \' + \'\\\'\' + label + \'\\\'\'")\n', "< C01 -> '0 0.000'\n", "< H01 -> '0 0.000'\n", '< PyMOL>cmd.label2("all","ss + str(cartoon) + str(color)")\n', '< PyMOL>cmd.iterate("all",r"print name +\' -> \' + \'\\\'\' + label + \'\\\'\'")\n', "< C01 -> 'L026'\n", "< H01 -> 'L029'\n", '< PyMOL>cmd.label2("all",\'str(valence) + " " + str(geom)\')\n', '< PyMOL>cmd.iterate("all",r"print name +\' -> \' + \'\\\'\' + label + \'\\\'\'")\n', "< C01 -> '4 4'\n", "< H01 -> '1 1'\n", '< PyMOL>cmd.label2("all",\'str(elec_radius)+" "+str(vdw)+" "+b+" "+q+" "+elem\')\n', '< PyMOL>cmd.iterate("all",r"print name +\' -> \' + \'\\\'\' + label + \'\\\'\'")\n', "< C01 -> '2.80 1.80 0.00 1.00 C'\n", "< H01 -> '2.10 1.10 1.00 2.00 H'\n", '< PyMOL>print "END-LOG"\n']
 run_tests: C2000returns...
 run_tests: C2000returns.log DIFFERS over about 121 lines:
['1,242d0\n', '< cmd.load("dat/pept.pdb")\n', '< None\n', '< cmd.load("dat/nonexistent.pdb")\n', "< ExecutiveProcessPDBFile-Error: Unable to open file 'dat/nonexistent.pdb'.\n", '< -1\n', "< ExecutiveProcessPDBFile-Error: Unable to open file 'dat/nonexistent.pdb'.\n", '< CmdException raised.\n', '< cmd.load("dat/small01.mol")\n', '< None\n', '< cmd.load("dat/nonexistent.mol")\n', "< ExecutiveLoad-Error: Unable to open file 'dat/nonexistent.mol'.\n", '< -1\n', "< ExecutiveLoad-Error: Unable to open file 'dat/nonexistent.mol'.\n", '< CmdException raised.\n', '< cmd.load("dat/ligs3d.sdf")\n', '< None\n', '< cmd.load("dat/nonexistent.sdf")\n', "< ExecutiveLoad-Error: Unable to open file 'dat/nonexistent.sdf'.\n", '< -1\n', "< ExecutiveLoad-Error: Unable to open file 'dat/nonexistent.sdf'.\n", '< CmdException raised.\n', '< cmd.load("dat/small03.mol2")\n', '< None\n', '< cmd.load("dat/nonexistent.mol2")\n', "< ExecutiveLoad-Error: Unable to open file 'dat/nonexistent.mol2'.\n", '< -1\n', "< ExecutiveLoad-Error: Unable to open file 'dat/nonexistent.mol2'.\n", '< CmdException raised.\n', '< cmd.load("dat/pept.r3d")\n', '< None\n', '< cmd.load("dat/nonexistent.r3d")\n', "< Load-Error: Unable to open file 'dat/nonexistent.r3d'.\n", '< -1\n', "< Load-Error: Unable to open file 'dat/nonexistent.r3d'.\n", '< CmdException raised.\n', '< cmd.load("dat/pept.pkl")\n', '< None\n', '< cmd.load("dat/nonexistent.pkl")\n', "< Load-Error: Unable to load file 'dat/nonexistent.pkl'.\n", '< -1\n', "< Load-Error: Unable to load file 'dat/nonexistent.pkl'.\n", '< CmdException raised.\n', '< cmd.get_names()\n', "< ['small01', 'ligs3d', 'small03', 'pept']\n", '< cmd.delete("all")\n', '< None\n', '< cmd.get_names()\n', '< []\n', '< cmd.get_model("nonexistent")\n', '< Selector-Error: Invalid selection name "nonexistent".\n', '< ( nonexistent )<--\n', '< -1\n', '< Selector-Error: Invalid selection name "nonexistent".\n', '< ( nonexistent )<--\n', '< CmdException raised.\n', '< cmd.space("cmyk")\n', "<  Color: loaded table '/Users/delwarl/pymol/data/pymol/cmyk.png'.\n", '< None\n', '< cmd.space("unknown")\n', "< Error: unknown color space 'unknown'.\n", '< -1\n', "< Error: unknown color space 'unknown'.\n", '< CmdException raised.\n', '< cmd.space("rgb")\n', '<  Color: purged table; restoring RGB colors.\n', '< None\n', '< cmd.space()\n', '< None\n', '< chempy.models.Indexed\n', '< 107\n', '< chempy.models.Indexed\n', '< 0\n', '< cmd.get_model("nonexistent")\n', '< Selector-Error: Invalid selection name "nonexistent".\n', '< ( nonexistent )<--\n', '< -1\n', '< Selector-Error: Invalid selection name "nonexistent".\n', '< ( nonexistent )<--\n', '< CmdException raised.\n', '< cmd.create("test","none",quiet=0)\n', '<  Selector: found 0 atoms.\n', '<  Executive: object "test" created.\n', '< None\n', '< cmd.create("test2","nonexistent")\n', '< Selector-Error: Invalid selection name "nonexistent".\n', '< ( nonexistent )<--\n', '< -1\n', '< Selector-Error: Invalid selection name "nonexistent".\n', '< ( nonexistent )<--\n', '< CmdException raised.\n', '< cmd.create("test3","?allowed",quiet=0)\n', '<  Selector: found 0 atoms.\n', '<  Executive: object "test3" created.\n', '< None\n', '< cmd.fragment("arg")\n', '< None\n', '< cmd.fragment("nonexistent")\n', "< Error: unable to load fragment 'nonexistent'.\n", '< -1\n', "< Error: unable to load fragment 'nonexistent'.\n", '< CmdException raised.\n', '< cmd.distance("none","none","none")\n', '< -1.0\n', '< cmd.distance("none","invalid1","none")\n', '< Selector-Error: Invalid selection name "invalid1".\n', '< ( invalid1 )<--\n', '< -1\n', '< Selector-Error: Invalid selection name "invalid1".\n', '< ( invalid1 )<--\n', '< CmdException raised.\n', '< cmd.distance("none","none","invalid2")\n', '< Selector-Error: Invalid selection name "invalid2".\n', '< ( invalid2 )<--\n', '< -1\n', '< Selector-Error: Invalid selection name "invalid2".\n', '< ( invalid2 )<--\n', '< CmdException raised.\n', '< cmd.distance("none","invalid1","invalid2")\n', '< Selector-Error: Invalid selection name "invalid1".\n', '< ( invalid1 )<--\n', '< Selector-Error: Invalid selection name "invalid2".\n', '< ( invalid2 )<--\n', '< -1\n', '< Selector-Error: Invalid selection name "invalid1".\n', '< ( invalid1 )<--\n', '< Selector-Error: Invalid selection name "invalid2".\n', '< ( invalid2 )<--\n', '< CmdException raised.\n', '< cmd.index("none")\n', '< []\n', '< cmd.index("first pept")\n', "< [('pept', 1)]\n", '< cmd.index("invalid")\n', '< Selector-Error: Invalid selection name "invalid".\n', '< ( invalid )<--\n', '< -1\n', '< Selector-Error: Invalid selection name "invalid".\n', '< ( invalid )<--\n', '< CmdException raised.\n', '< cmd.identify("none")\n', '< []\n', '< cmd.identify("first pept")\n', '< [1]\n', '< cmd.identify("invalid")\n', '< Selector-Error: Invalid selection name "invalid".\n', '< ( invalid )<--\n', '< -1\n', '< Selector-Error: Invalid selection name "invalid".\n', '< ( invalid )<--\n', '< CmdException raised.\n', '< cmd.identify("none",mode=1)\n', '< []\n', '< cmd.identify("first pept",mode=1)\n', "< [('pept', 1)]\n", '< cmd.identify("invalid",mode=1)\n', '< Selector-Error: Invalid selection name "invalid".\n', '< ( invalid )<--\n', '< -1\n', '< Selector-Error: Invalid selection name "invalid".\n', '< ( invalid )<--\n', '< CmdException raised.\n', '< cmd.count_atoms("none")\n', '< 0\n', '< cmd.count_atoms()\n', '< 107\n', '< cmd.count_atoms("pept")\n', '< 107\n', '< cmd.count_atoms("invalid")\n', '< Selector-Error: Invalid selection name "invalid".\n', '< ( invalid )<--\n', '< -1\n', '< Selector-Error: Invalid selection name "invalid".\n', '< ( invalid )<--\n', '< CmdException raised.\n', '< cmd.count_frames()\n', '< 1\n', '< cmd.count_states()\n', '< 1\n', '< cmd.count_states("all")\n', '< 1\n', '< cmd.count_states("none")\n', '< 0\n', '< cmd.count_states("invalid")\n', '< Selector-Error: Invalid selection name "invalid".\n', '< invalid<--\n', '< -1\n', '< Selector-Error: Invalid selection name "invalid".\n', '< invalid<--\n', '< CmdException raised.\n', '< cmd.get_area()\n', '< 1381.18615723\n', '< cmd.get_area("resi 1")\n', '< 107.905807495\n', '< cmd.get_area("none")\n', '< 0.0\n', '< cmd.get_area("invalid")\n', '< Selector-Error: Invalid selection name "invalid".\n', '< ( invalid )<--\n', '< -1.0\n', '< cmd.get_chains()\n', "< ['E']\n", '< cmd.get_chains("pept")\n', "< ['E']\n", '< cmd.get_chains("resi 1")\n', "< ['E']\n", '< cmd.get_chains("none")\n', '< []\n', '< cmd.get_chains("invalid")\n', '< Selector-Error: Invalid selection name "invalid".\n', '< ( invalid )<--\n', '< -1\n', '< Selector-Error: Invalid selection name "invalid".\n', '< ( invalid )<--\n', '< CmdException raised.\n', '< cmd.zoom()\n', '< None\n', '< cmd.zoom("pept")\n', '< None\n', '< cmd.zoom("none")\n', "< ExecutiveWindowZoom-Warning: selection doesn't specify any coordinates.\n", '< None\n', '< cmd.zoom("invalid")\n', '< Selector-Error: Invalid selection name "invalid".\n', '< invalid<--\n', '< -1\n', '< Selector-Error: Invalid selection name "invalid".\n', '< invalid<--\n', '< QuietException raised.\n', '< cmd.center()\n', '< None\n', '< cmd.center("pept")\n', '< None\n', '< cmd.center("none")\n', "< ExecutiveCenter-Warning: selection doesn't specify any coordinates.\n", '< None\n', '< cmd.center("invalid")\n', '< Selector-Error: Invalid selection name "invalid".\n', '< invalid<--\n', '< -1\n', '< Selector-Error: Invalid selection name "invalid".\n', '< invalid<--\n', '< QuietException raised.\n']
make[1]: Leaving directory '/«PKGBUILDDIR»'
 fakeroot debian/rules binary-arch
dh binary-arch --with python2 --parallel
   dh_testroot -a -O--parallel
   dh_prep -a -O--parallel
   dh_installdirs -a -O--parallel
   dh_auto_install -a -O--parallel
	python setup.py install --force --root=/«PKGBUILDDIR»/debian/pymol --no-compile -O0 --install-layout=deb
running install
running build
running build_py
running build_ext
running install_lib
creating /«PKGBUILDDIR»/debian/pymol/usr/lib
creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7
creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages
creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/embed
creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/embed/epymol
copying build/lib.linux-armv7l-2.7/pymol/embed/epymol/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/embed/epymol
copying build/lib.linux-armv7l-2.7/pymol/embed/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/embed
creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/embed/wxpymol
copying build/lib.linux-armv7l-2.7/pymol/embed/wxpymol/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/embed/wxpymol
creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/opengl
creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/opengl/glu
copying build/lib.linux-armv7l-2.7/pymol/opengl/glu/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/opengl/glu
creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/opengl/glut
copying build/lib.linux-armv7l-2.7/pymol/opengl/glut/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/opengl/glut
creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/opengl/gl
copying build/lib.linux-armv7l-2.7/pymol/opengl/gl/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/opengl/gl
copying build/lib.linux-armv7l-2.7/pymol/opengl/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/opengl
creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/contrib
copying build/lib.linux-armv7l-2.7/pymol/contrib/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/contrib
creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard
copying build/lib.linux-armv7l-2.7/pymol/wizard/security.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard
copying build/lib.linux-armv7l-2.7/pymol/wizard/box.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard
copying build/lib.linux-armv7l-2.7/pymol/wizard/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard
copying build/lib.linux-armv7l-2.7/pymol/wizard/distance.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard
copying build/lib.linux-armv7l-2.7/pymol/wizard/pair_fit.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard
copying build/lib.linux-armv7l-2.7/pymol/wizard/charge.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard
copying build/lib.linux-armv7l-2.7/pymol/wizard/message.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard
copying build/lib.linux-armv7l-2.7/pymol/wizard/density.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard
copying build/lib.linux-armv7l-2.7/pymol/wizard/pseudoatom.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard
copying build/lib.linux-armv7l-2.7/pymol/wizard/mutagenesis.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard
copying build/lib.linux-armv7l-2.7/pymol/wizard/appearance.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard
copying build/lib.linux-armv7l-2.7/pymol/wizard/filter.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard
copying build/lib.linux-armv7l-2.7/pymol/wizard/fedora.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard
copying build/lib.linux-armv7l-2.7/pymol/wizard/benchmark.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard
copying build/lib.linux-armv7l-2.7/pymol/wizard/stereodemo.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard
copying build/lib.linux-armv7l-2.7/pymol/wizard/label.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard
copying build/lib.linux-armv7l-2.7/pymol/wizard/annotation.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard
copying build/lib.linux-armv7l-2.7/pymol/wizard/sculpting.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard
copying build/lib.linux-armv7l-2.7/pymol/wizard/cleanup.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard
copying build/lib.linux-armv7l-2.7/pymol/wizard/demo.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard
copying build/lib.linux-armv7l-2.7/pymol/wizard/dragging.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard
copying build/lib.linux-armv7l-2.7/pymol/wizard/measurement.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard
copying build/lib.linux-armv7l-2.7/pymol/wizard/renaming.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard
copying build/lib.linux-armv7l-2.7/pymol/wizard/toggle.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard
copying build/lib.linux-armv7l-2.7/pymol/setting.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/editor.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/internal.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/keywords.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/constants_palette.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/querying.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/moving.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/importing.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/cmd.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/gui.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/parsing.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/m4x.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/menu.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/colorramping.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/fitting.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/editing.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/parser.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/shortcut.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/controlling.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/constants.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/preset.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/xray.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/invocation.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/checking.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/viewing.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/computing.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/experimenting.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/externing.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/selecting.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/selector.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/xwin.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/headering.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/helping.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/keyboard.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/movie.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/callback.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/completing.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/rpc.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/creating.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/feedingback.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/wizarding.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/cgo.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/exporting.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/monitoring.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/api.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/vfont.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/locking.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/util.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/povray.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
copying build/lib.linux-armv7l-2.7/pymol/commanding.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/plugins
copying build/lib.linux-armv7l-2.7/pymol/plugins/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/plugins
copying build/lib.linux-armv7l-2.7/pymol/plugins/repository.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/plugins
copying build/lib.linux-armv7l-2.7/pymol/plugins/managergui.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/plugins
copying build/lib.linux-armv7l-2.7/pymol/plugins/installation.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/plugins
copying build/lib.linux-armv7l-2.7/pymol/plugins/legacysupport.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/plugins
copying build/lib.linux-armv7l-2.7/pymol/_cmd.so -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol
creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy
creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/tinker
copying build/lib.linux-armv7l-2.7/chempy/tinker/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/tinker
copying build/lib.linux-armv7l-2.7/chempy/tinker/amber.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/tinker
copying build/lib.linux-armv7l-2.7/chempy/tinker/keyword.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/tinker
copying build/lib.linux-armv7l-2.7/chempy/tinker/realtime.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/tinker
copying build/lib.linux-armv7l-2.7/chempy/tinker/state.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/tinker
creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/fast
copying build/lib.linux-armv7l-2.7/chempy/fast/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/fast
creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/fragments
copying build/lib.linux-armv7l-2.7/chempy/fragments/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/fragments
creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/champ
copying build/lib.linux-armv7l-2.7/chempy/champ/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/champ
copying build/lib.linux-armv7l-2.7/chempy/champ/assign.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/champ
copying build/lib.linux-armv7l-2.7/chempy/champ/formal_charges.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/champ
copying build/lib.linux-armv7l-2.7/chempy/champ/amber99.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/champ
copying build/lib.linux-armv7l-2.7/chempy/champ/_champ.so -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/champ
creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/bmin
copying build/lib.linux-armv7l-2.7/chempy/bmin/commands.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/bmin
copying build/lib.linux-armv7l-2.7/chempy/bmin/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/bmin
copying build/lib.linux-armv7l-2.7/chempy/bmin/realtime.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/bmin
copying build/lib.linux-armv7l-2.7/chempy/bmin/state.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/bmin
copying build/lib.linux-armv7l-2.7/chempy/bmin/util.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/bmin
copying build/lib.linux-armv7l-2.7/chempy/neighbor.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy
copying build/lib.linux-armv7l-2.7/chempy/cex.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy
copying build/lib.linux-armv7l-2.7/chempy/arc.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy
copying build/lib.linux-armv7l-2.7/chempy/protein_amber99.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy
copying build/lib.linux-armv7l-2.7/chempy/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy
copying build/lib.linux-armv7l-2.7/chempy/dictdb.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy
copying build/lib.linux-armv7l-2.7/chempy/lst.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy
copying build/lib.linux-armv7l-2.7/chempy/brick.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy
copying build/lib.linux-armv7l-2.7/chempy/cif.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy
copying build/lib.linux-armv7l-2.7/chempy/place.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy
copying build/lib.linux-armv7l-2.7/chempy/charge.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy
copying build/lib.linux-armv7l-2.7/chempy/io.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy
copying build/lib.linux-armv7l-2.7/chempy/pdb.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy
copying build/lib.linux-armv7l-2.7/chempy/bond_amber.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy
copying build/lib.linux-armv7l-2.7/chempy/cc1.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy
copying build/lib.linux-armv7l-2.7/chempy/water_amber.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy
copying build/lib.linux-armv7l-2.7/chempy/mol.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy
copying build/lib.linux-armv7l-2.7/chempy/gms.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy
copying build/lib.linux-armv7l-2.7/chempy/hetatm.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy
copying build/lib.linux-armv7l-2.7/chempy/mae.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy
copying build/lib.linux-armv7l-2.7/chempy/protein.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy
copying build/lib.linux-armv7l-2.7/chempy/mmd.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy
copying build/lib.linux-armv7l-2.7/chempy/pkl.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy
copying build/lib.linux-armv7l-2.7/chempy/water_residues.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy
copying build/lib.linux-armv7l-2.7/chempy/bond_mmff.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy
copying build/lib.linux-armv7l-2.7/chempy/protein_amber.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy
copying build/lib.linux-armv7l-2.7/chempy/protein_mmff.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy
copying build/lib.linux-armv7l-2.7/chempy/models.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy
copying build/lib.linux-armv7l-2.7/chempy/xyz.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy
copying build/lib.linux-armv7l-2.7/chempy/mass.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy
copying build/lib.linux-armv7l-2.7/chempy/protein_residues.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy
copying build/lib.linux-armv7l-2.7/chempy/bonds.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy
copying build/lib.linux-armv7l-2.7/chempy/gamess1.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy
copying build/lib.linux-armv7l-2.7/chempy/map.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy
copying build/lib.linux-armv7l-2.7/chempy/cpv.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy
copying build/lib.linux-armv7l-2.7/chempy/solvate.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy
copying build/lib.linux-armv7l-2.7/chempy/sdf.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy
copying build/lib.linux-armv7l-2.7/chempy/mol2.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy
creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk
creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk/skins
creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk/skins/demo
copying build/lib.linux-armv7l-2.7/pmg_tk/skins/demo/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk/skins/demo
copying build/lib.linux-armv7l-2.7/pmg_tk/skins/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk/skins
creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk/skins/normal
copying build/lib.linux-armv7l-2.7/pmg_tk/skins/normal/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk/skins/normal
copying build/lib.linux-armv7l-2.7/pmg_tk/skins/normal/builder.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk/skins/normal
copying build/lib.linux-armv7l-2.7/pmg_tk/skins/normal/ModalWindow.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk/skins/normal
creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk/startup
copying build/lib.linux-armv7l-2.7/pmg_tk/startup/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk/startup
copying build/lib.linux-armv7l-2.7/pmg_tk/startup/remote_pdb_load.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk/startup
copying build/lib.linux-armv7l-2.7/pmg_tk/startup/apbs_tools.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk/startup
copying build/lib.linux-armv7l-2.7/pmg_tk/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk
copying build/lib.linux-armv7l-2.7/pmg_tk/PyMOLMapLoad.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk
copying build/lib.linux-armv7l-2.7/pmg_tk/Demo.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk
copying build/lib.linux-armv7l-2.7/pmg_tk/Setting.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk
copying build/lib.linux-armv7l-2.7/pmg_tk/volume.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk
copying build/lib.linux-armv7l-2.7/pmg_tk/SetEditor.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk
copying build/lib.linux-armv7l-2.7/pmg_tk/ColorEditor.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk
copying build/lib.linux-armv7l-2.7/pmg_tk/TextEditor.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk
copying build/lib.linux-armv7l-2.7/pmg_tk/PMGApp.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk
creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_wx
copying build/lib.linux-armv7l-2.7/pmg_wx/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_wx
creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/web
copying build/lib.linux-armv7l-2.7/web/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/web
copying build/lib.linux-armv7l-2.7/web/pymolhttpd.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/web
creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/web/examples
copying build/lib.linux-armv7l-2.7/web/examples/justhttpd.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/web/examples
copying build/lib.linux-armv7l-2.7/web/examples/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/web/examples
creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol2
copying build/lib.linux-armv7l-2.7/pymol2/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol2
copying build/lib.linux-armv7l-2.7/pymol2/cmd2.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol2
copying build/lib.linux-armv7l-2.7/pymol2/make_cmd2.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol2
running install_egg_info
Writing /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol-1.7.2.1.egg-info
copying pymol -> /«PKGBUILDDIR»/debian/pymol/usr/bin
   debian/rules override_dh_install
make[1]: Entering directory '/«PKGBUILDDIR»'
pdflatex -output-directory debian -jobname pymol-ref-card debian/pymolRef.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.15 (TeX Live 2015/dev/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./debian/pymolRef.tex
LaTeX2e <2014/05/01>
Babel <3.9l> and hyphenation patterns for 2 languages loaded.
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2014/09/29 v1.4h Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))
(/usr/share/texlive/texmf-dist/tex/latex/tools/multicol.sty)
No file pymol-ref-card.aux.

Underfull \hbox (badness 10000) in paragraph at lines 78--79

[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}]
(/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [2]
(debian/pymol-ref-card.aux) )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fo
nts/type1/public/amsfonts/cm/cmitt10.pfb></usr/share/texlive/texmf-dist/fonts/t
ype1/public/amsfonts/cm/cmmi9.pfb></usr/share/texlive/texmf-dist/fonts/type1/pu
blic/amsfonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/am
sfonts/cm/cmr12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmr9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy9
.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti9.pfb></
usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt9.pfb>
Output written on debian/pymol-ref-card.pdf (2 pages, 108281 bytes).
Transcript written on debian/pymol-ref-card.log.
sed -e s/@PYTHON_VERSION@/2.7/g < debian/pymol.launch.in > debian/pymol.launch
dh_numpy
dh_install data/shaders usr/lib/python2.7/dist-packages/pymol/data/
install -m 755 debian/pymol.launch debian/pymol/usr/bin/pymol
make[1]: Leaving directory '/«PKGBUILDDIR»'
   dh_installdocs -a -O--parallel
   dh_installchangelogs -a -O--parallel
   dh_installexamples -a -O--parallel
   dh_installman -a -O--parallel
   dh_python2 -a -O--parallel
W: dh_python2:479: Please add dh-python package to Build-Depends
   dh_installmenu -a -O--parallel
   dh_installmime -a -O--parallel
   dh_perl -a -O--parallel
   dh_link -a -O--parallel
   debian/rules override_dh_compress
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_compress -Xpdb
make[1]: Leaving directory '/«PKGBUILDDIR»'
   dh_fixperms -a -O--parallel
   dh_strip -a -O--parallel
   dh_makeshlibs -a -O--parallel
   dh_shlibdeps -a -O--parallel
   dh_installdeb -a -O--parallel
   dh_gencontrol -a -O--parallel
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
   dh_md5sums -a -O--parallel
   dh_builddeb -a -O--parallel
dpkg-deb: building package `pymol' in `../pymol_1.7.2.1-2_armhf.deb'.
 dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../pymol_1.7.2.1-2_armhf.changes
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
 dpkg-source --after-build pymol-1.7.2.1
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20150621-1044

Finished
────────

I: Built successfully

┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build Chroot                                                            │
└──────────────────────────────────────────────────────────────────────────────┘


┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes                                                                      │
└──────────────────────────────────────────────────────────────────────────────┘


pymol_1.7.2.1-2_armhf.changes:
──────────────────────────────

Format: 1.8
Date: Sat, 13 Jun 2015 15:38:14 +0200
Source: pymol
Binary: pymol
Architecture: armhf
Version: 1.7.2.1-2
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Michael Banck <mbanck@debian.org>
Description:
 pymol      - Molecular Graphics System
Changes:
 pymol (1.7.2.1-2) unstable; urgency=medium
 .
   * debian/patches/21_fix_png_batch_mode.patch: Removed, broke functionality.
Checksums-Sha1:
 c09f247ff93f2e3cf9f9ed282411c3cadad9dbf4 4496722 pymol_1.7.2.1-2_armhf.deb
Checksums-Sha256:
 a7ae83aeac123cbdc5e1a2e12704c44fe5105bb3d0c6ca89242cf1e2e5fc36e3 4496722 pymol_1.7.2.1-2_armhf.deb
Files:
 967c0113bb06b25657ec2c21182f3f25 4496722 science optional pymol_1.7.2.1-2_armhf.deb

┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents                                                             │
└──────────────────────────────────────────────────────────────────────────────┘


pymol_1.7.2.1-2_armhf.deb
─────────────────────────

 new debian package, version 2.0.
 size 4496722 bytes: control archive=13833 bytes.
    1186 bytes,    25 lines      control              
   36855 bytes,   438 lines      md5sums              
     412 bytes,    18 lines   *  postinst             #!/bin/sh
     160 bytes,     5 lines   *  postrm               #!/bin/sh
     247 bytes,    14 lines   *  prerm                #!/bin/sh
 Package: pymol
 Version: 1.7.2.1-2
 Architecture: armhf
 Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
 Installed-Size: 16540
 Depends: python-numpy (>= 1:1.8.0), python-pmw, python-tk, python-numpy-abi9, python (>= 2.7), python (<< 2.8), python2.7:any, freeglut3, libc6 (>= 2.15), libfreetype6 (>= 2.2.1), libgcc1 (>= 1:4.4.0), libgl1-mesa-glx | libgl1, libglew1.10 (>= 1.10.0), libglu1-mesa | libglu1, libpng12-0 (>= 1.2.13-4), libstdc++6 (>= 4.9)
 Recommends: apbs
 Section: science
 Priority: optional
 Homepage: http://www.pymol.org
 Description: Molecular Graphics System
  PyMOL is a molecular graphics system targeted at medium to large
  biomolecules like proteins. It can generate high-quality publication-ready
  molecular graphics images and animations.
  .
  Features include:
   * Visualization of molecules, molecular trajectories and surfaces
     of crystallography data or orbitals
   * Molecular builder and sculptor
   * Internal raytracer and movie generator
   * Fully extensible and scriptable via a Python interface
  .
  File formats PyMOL can read include PDB, XYZ, CIF, MDL Molfile, ChemDraw,
  CCP4 maps, XPLOR maps and Gaussian cube maps.
 Python-Version: 2.7

drwxr-xr-x root/root         0 2015-06-21 10:43 ./
drwxr-xr-x root/root         0 2015-06-21 10:43 ./usr/
drwxr-xr-x root/root         0 2015-06-21 10:43 ./usr/bin/
-rwxr-xr-x root/root       469 2015-06-21 10:43 ./usr/bin/pymol
drwxr-xr-x root/root         0 2015-06-21 10:43 ./usr/lib/
drwxr-xr-x root/root         0 2015-06-21 10:43 ./usr/lib/mime/
drwxr-xr-x root/root         0 2015-06-21 10:43 ./usr/lib/mime/packages/
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drwxr-xr-x root/root         0 2014-08-26 17:41 ./usr/share/pymol/data/pmg_tk/bitmaps/
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drwxr-xr-x root/root         0 2014-08-26 17:41 ./usr/share/pymol/data/xray/
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-rwxr-xr-x root/root    107405 2014-08-26 17:41 ./usr/share/pymol/data/xray/spgbase.dat
drwxr-xr-x root/root         0 2015-06-21 10:43 ./usr/share/pymol/demo/
drwxr-xr-x root/root         0 2015-06-21 10:43 ./usr/share/pymol/pmg_tk/
drwxr-xr-x root/root         0 2015-06-21 10:43 ./usr/share/pymol/pmg_tk/bitmaps/
drwxr-xr-x root/root         0 2015-06-21 10:43 ./usr/share/pymol/pmg_tk/bitmaps/builder/
drwxr-xr-x root/root         0 2014-08-26 17:41 ./usr/share/pymol/scripts/
drwxr-xr-x root/root         0 2014-08-26 17:41 ./usr/share/pymol/scripts/metaphorics/
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-rw-r--r-- root/root      1356 2014-08-26 17:41 ./usr/share/pymol/scripts/metaphorics/fedora.pml
drwxr-xr-x root/root         0 2015-06-21 10:43 ./usr/share/python/
drwxr-xr-x root/root         0 2015-06-21 10:43 ./usr/share/python/runtime.d/
-rwxr-xr-x root/root       128 2015-06-21 10:43 ./usr/share/python/runtime.d/pymol.rtupdate


┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build                                                                   │
└──────────────────────────────────────────────────────────────────────────────┘


┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup                                                                      │
└──────────────────────────────────────────────────────────────────────────────┘

Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use

┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary                                                                      │
└──────────────────────────────────────────────────────────────────────────────┘

Build Architecture: armhf
Build-Space: 113916
Build-Time: 759
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 771
Job: pymol_1.7.2.1-2
Machine Architecture: armhf
Package: pymol
Package-Time: 1606
Source-Version: 1.7.2.1-2
Space: 113916
Status: successful
Version: 1.7.2.1-2
────────────────────────────────────────────────────────────────────────────────
Finished at 20150621-1044
Build needed 00:26:46, 113916k disc space

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