pdb2pqr →
2.1.1+dfsg-4 →
armhf → 2018-07-20 05:33:22
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-04
+==============================================================================+
| pdb2pqr 2.1.1+dfsg-4 (armhf) Fri, 20 Jul 2018 05:17:25 +0000 |
+==============================================================================+
Package: pdb2pqr
Version: 2.1.1+dfsg-4
Source Version: 2.1.1+dfsg-4
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-0ee9aae0-c026-47b4-8d33-38dcd0c14d07' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [10.9 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.7 MB]
Fetched 23.6 MB in 26s (904 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'pdb2pqr' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/pdb2pqr.git
Please use:
git clone https://salsa.debian.org/med-team/pdb2pqr.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 5207 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main pdb2pqr 2.1.1+dfsg-4 (dsc) [2266 B]
Get:2 http://172.17.0.1/private buster-staging/main pdb2pqr 2.1.1+dfsg-4 (tar) [5191 kB]
Get:3 http://172.17.0.1/private buster-staging/main pdb2pqr 2.1.1+dfsg-4 (diff) [13.5 kB]
Fetched 5207 kB in 1s (8876 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/pdb2pqr-rDBOj4/pdb2pqr-2.1.1+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/pdb2pqr-rDBOj4' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-c9UIax/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-c9UIax/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-c9UIax/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-c9UIax/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-c9UIax/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-c9UIax/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-c9UIax/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-c9UIax/apt_archive ./ Packages [431 B]
Fetched 2107 B in 1s (3000 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session libexpat1 libnss-systemd
libpam-systemd libssl1.1 openssl systemd-sysv
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 47 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-c9UIax/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 13980 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 11~), gfortran, swig, xmlto, openbabel, python-dev, python-numpy, scons, dos2unix
Filtered Build-Depends: debhelper (>= 11~), gfortran, swig, xmlto, openbabel, python-dev, python-numpy, scons, dos2unix
dpkg-deb: building package 'sbuild-build-depends-pdb2pqr-dummy' in '/<<BUILDDIR>>/resolver-c9UIax/apt_archive/sbuild-build-depends-pdb2pqr-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-pdb2pqr-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-c9UIax/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-c9UIax/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-c9UIax/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-c9UIax/apt_archive ./ Sources [541 B]
Get:5 copy:/<<BUILDDIR>>/resolver-c9UIax/apt_archive ./ Packages [623 B]
Fetched 2497 B in 1s (3820 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install pdb2pqr build dependencies (apt-based resolver)
-------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session libnss-systemd libpam-systemd openssl
systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism docbook-xml docbook-xsl dos2unix dwz
file fontconfig-config fonts-dejavu-core gettext gettext-base gfortran
gfortran-7 groff-base intltool-debian libarchive-zip-perl libblas3 libbsd0
libcairo2 libcroco3 libelf1 libexpat1-dev libfile-stripnondeterminism-perl
libfontconfig1 libfreetype6 libgfortran-7-dev libgfortran4 libglib2.0-0
libgraphite2-3 libharfbuzz0b libicu-le-hb0 libicu60 liblapack3 libmagic-mgc
libmagic1 libopenbabel5 libpipeline1 libpixman-1-0 libpython-dev
libpython-stdlib libpython2-dev libpython2-stdlib libpython2.7
libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libsigsegv2
libtimedate-perl libtool libx11-6 libx11-data libxau6 libxcb-render0
libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxml2 libxml2-utils libxrender1
libxslt1.1 m4 man-db mime-support openbabel po-debconf python python-dev
python-minimal python-numpy python2 python2-dev python2-minimal python2.7
python2.7-dev python2.7-minimal scons sgml-base sgml-data swig swig3.0 ucf
xml-core xmlto xsltproc
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make docbook docbook-dsssl docbook-defguide dbtoepub
docbook-xsl-doc-html | docbook-xsl-doc-pdf | docbook-xsl-doc-text
| docbook-xsl-doc docbook-xsl-saxon fop libsaxon-java libxalan2-java
libxslthl-java xalan gettext-doc libasprintf-dev libgettextpo-dev
gfortran-doc gfortran-7-doc libgfortran4-dbg libcoarrays-dev groff
libtool-doc gcj-jdk m4-doc apparmor less www-browser libmail-box-perl
python-doc python-tk python-nose python-numpy-dbg python-numpy-doc
python2-doc python2.7-doc binfmt-support sgml-base-doc perlsgml w3-recs
opensp swig-doc swig-examples swig3.0-examples swig3.0-doc w3m | lynx-cur
| links texlive-htmlxml
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libltdl-dev libmail-sendmail-perl dblatex | fop libpaper-utils
zip
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism docbook-xml docbook-xsl dos2unix dwz
file fontconfig-config fonts-dejavu-core gettext gettext-base gfortran
gfortran-7 groff-base intltool-debian libarchive-zip-perl libblas3 libbsd0
libcairo2 libcroco3 libelf1 libexpat1-dev libfile-stripnondeterminism-perl
libfontconfig1 libfreetype6 libgfortran-7-dev libgfortran4 libglib2.0-0
libgraphite2-3 libharfbuzz0b libicu-le-hb0 libicu60 liblapack3 libmagic-mgc
libmagic1 libopenbabel5 libpipeline1 libpixman-1-0 libpython-dev
libpython-stdlib libpython2-dev libpython2-stdlib libpython2.7
libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libsigsegv2
libtimedate-perl libtool libx11-6 libx11-data libxau6 libxcb-render0
libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxml2 libxml2-utils libxrender1
libxslt1.1 m4 man-db mime-support openbabel po-debconf python python-dev
python-minimal python-numpy python2 python2-dev python2-minimal python2.7
python2.7-dev python2.7-minimal sbuild-build-depends-pdb2pqr-dummy scons
sgml-base sgml-data swig swig3.0 ucf xml-core xmlto xsltproc
0 upgraded, 92 newly installed, 0 to remove and 47 not upgraded.
Need to get 71.5 MB/74.2 MB of archives.
After this operation, 212 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-c9UIax/apt_archive ./ sbuild-build-depends-pdb2pqr-dummy 0.invalid.0 [904 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.3-2 [1146 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libpython2.7-minimal armhf 2.7.15-1 [393 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf python2.7-minimal armhf 2.7.15-1 [1077 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf python2-minimal armhf 2.7.15-3 [41.3 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf python-minimal armhf 2.7.15-3 [20.9 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf mime-support all 3.61 [37.1 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libpython2.7-stdlib armhf 2.7.15-1 [1841 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf python2.7 armhf 2.7.15-1 [298 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf libpython2-stdlib armhf 2.7.15-3 [20.7 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf libpython-stdlib armhf 2.7.15-3 [20.7 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf python2 armhf 2.7.15-3 [41.5 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf python armhf 2.7.15-3 [22.7 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf sgml-base all 1.29 [14.8 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.33-3 [234 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.33-3 [106 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.33-3 [64.7 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-6 [117 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3.1 [736 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-6 [434 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2.1 [547 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.60-1 [95.6 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.042-1 [20.1 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.042-1 [12.1 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.170-0.5 [160 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-2 [67.4 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.56.1-2 [2754 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libharfbuzz0b armhf 1.8.2-2 [832 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libicu-le-hb0 armhf 1.0.3+git161113-5 [12.8 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libicu60 armhf 60.2-6 [7789 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7 [602 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-6 [1218 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.3.5 [981 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf xml-core all 0.18 [23.4 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf sgml-data all 2.0.10 [181 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf docbook-xml all 4.5-8 [84.7 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf docbook-xsl all 1.79.1+dfsg-2 [1249 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf dos2unix armhf 7.4.0-1 [386 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf fontconfig-config all 2.13.0-5 [280 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libgfortran4 armhf 7.3.0-19 [191 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libgfortran-7-dev armhf 7.3.0-19 [232 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf gfortran-7 armhf 7.3.0-19 [5459 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf gfortran armhf 4:7.3.0-3+rpi1 [1436 B]
Get:56 http://172.17.0.1/private buster-staging/main armhf libblas3 armhf 3.8.0-1 [103 kB]
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Get:58 http://172.17.0.1/private buster-staging/main armhf libx11-data all 2:1.6.5-1 [292 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf libx11-6 armhf 2:1.6.5-1 [683 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf libcairo2 armhf 1.15.10-3 [575 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf liblapack3 armhf 3.8.0-1 [1518 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf libopenbabel5 armhf 2.4.1+dfsg-2 [2554 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf libpython2.7 armhf 2.7.15-1 [886 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf libpython2.7-dev armhf 2.7.15-1 [27.6 MB]
Get:65 http://172.17.0.1/private buster-staging/main armhf libpython2-dev armhf 2.7.15-3 [20.8 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf libpython-dev armhf 2.7.15-3 [20.8 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf libxml2-utils armhf 2.9.4+dfsg1-7 [95.9 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf libxslt1.1 armhf 1.1.32-2 [215 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf openbabel armhf 2.4.1+dfsg-2 [118 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf python2.7-dev armhf 2.7.15-1 [289 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf python2-dev armhf 2.7.15-3 [1216 B]
Get:72 http://172.17.0.1/private buster-staging/main armhf python-dev armhf 2.7.15-3 [1192 B]
Get:73 http://172.17.0.1/private buster-staging/main armhf python-numpy armhf 1:1.14.5-1 [1782 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf scons all 3.0.1-1 [538 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf swig3.0 armhf 3.0.12-1.1 [1225 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf swig armhf 3.0.12-1.1 [310 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf xsltproc armhf 1.1.32-2 [121 kB]
Get:78 http://172.17.0.1/private buster-staging/main armhf xmlto armhf 0.0.28-2 [32.1 kB]
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W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.4-armmp armhf (armv7l)
Toolchain package versions: binutils_2.30-21+rpi1 dpkg-dev_1.19.0.5 g++-7_7.3.0-19 gcc-7_7.3.0-19 libc6-dev_2.27-3+rpi1 libstdc++-7-dev_7.3.0-19 libstdc++6_8.1.0-8+rpi1 linux-libc-dev_4.16.12-1+rpi1
Package versions: adduser_3.117 apt_1.6.1 autoconf_2.69-11 automake_1:1.15.1-3.1 autopoint_0.19.8.1-6 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-3 binutils_2.30-21+rpi1 binutils-arm-linux-gnueabihf_2.30-21+rpi1 binutils-common_2.30-21+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.32-0.1 build-essential_12.5 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.28-1 cpio_2.12+dfsg-6 cpp_4:7.3.0-3+rpi1 cpp-7_7.3.0-19 dash_0.5.8-2.10 dbus_1.12.8-3 dbus-user-session_1.12.8-3 debconf_1.5.67 debhelper_11.3.5 debianutils_4.8.6 dh-autoreconf_19 dh-strip-nondeterminism_0.042-1 diffutils_1:3.6-1 dirmngr_2.2.8-1 dmsetup_2:1.02.145-4.1+b4 docbook-xml_4.5-8 docbook-xsl_1.79.1+dfsg-2 dos2unix_7.4.0-1 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 dwz_0.12-2 e2fslibs_1.44.2-1 e2fsprogs_1.44.2-1 fakeroot_1.22-2 fdisk_2.32-0.1 file_1:5.33-3 findutils_4.6.0+git+20171230-2 fontconfig-config_2.13.0-5 fonts-dejavu-core_2.37-1 g++_4:7.3.0-3+rpi1 g++-7_7.3.0-19 gcc_4:7.3.0-3+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.4-2+rpi1+b7 gcc-5-base_5.5.0-8 gcc-6-base_6.4.0-18+rpi1 gcc-7_7.3.0-19 gcc-7-base_7.3.0-19 gcc-8-base_8.1.0-8+rpi1 gettext_0.19.8.1-6 gettext-base_0.19.8.1-6 gfortran_4:7.3.0-3+rpi1 gfortran-7_7.3.0-19 gnupg_2.2.8-1 gnupg-l10n_2.2.8-1 gnupg-utils_2.2.8-1 gpg_2.2.8-1 gpg-agent_2.2.8-1 gpg-wks-client_2.2.8-1 gpg-wks-server_2.2.8-1 gpgconf_2.2.8-1 gpgsm_2.2.8-1 gpgv_2.2.8-1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5 hostname_3.20 inetutils-ping_2:1.9.4-3 init-system-helpers_1.51 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-11+rpi1 kmod_25-1 libacl1_2.2.52-3 libapparmor1_2.12-4 libapt-pkg5.0_1.6.1 libarchive-zip-perl_1.60-1 libargon2-0_0~20161029-2 libasan4_7.3.0-19 libassuan0_2.5.1-2 libatomic1_8.1.0-8+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.3-1 libaudit1_1:2.8.3-1 libbinutils_2.30-21+rpi1 libblas3_3.8.0-1 libblkid1_2.32-0.1 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.27-3+rpi1 libc-dev-bin_2.27-3+rpi1 libc6_2.27-3+rpi1 libc6-dev_2.27-3+rpi1 libcairo2_1.15.10-3 libcap-ng0_0.7.9-1 libcap2_1:2.25-1.2 libcc1-0_8.1.0-8+rpi1 libcilkrts5_7.3.0-19 libcom-err2_1.44.2-1 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.2-1 libcryptsetup4_2:1.7.5-1 libdb5.3_5.3.28-13.1 libdbus-1-3_1.12.8-3 libdebconfclient0_0.243 libdevmapper1.02.1_2:1.02.145-4.1+b4 libdpkg-perl_1.19.0.5 libdrm-common_2.4.92-1+rpi1 libdrm2_2.4.92-1+rpi1 libelf1_0.170-0.5 libexpat1_2.2.5-3 libexpat1-dev_2.2.5-3 libext2fs2_1.44.2-1 libfakeroot_1.22-2 libfdisk1_2.32-0.1 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.042-1 libfontconfig1_2.13.0-5 libfreetype6_2.8.1-2 libgcc-7-dev_7.3.0-19 libgcc1_1:8.1.0-8+rpi1 libgcrypt20_1.8.3-1 libgdbm-compat4_1.14.1-6 libgdbm3_1.8.3-14 libgdbm5_1.14.1-6 libgfortran-7-dev_7.3.0-19 libgfortran4_7.3.0-19 libglib2.0-0_2.56.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.18-1 libgomp1_8.1.0-8+rpi1 libgpg-error0_1.31-1 libgraphite2-3_1.3.11-2 libharfbuzz0b_1.8.2-2 libhogweed4_3.4-1 libicu-le-hb0_1.0.3+git161113-5 libicu60_60.2-6 libidn11_1.33-2.2 libidn2-0_2.0.4-1.1 libip4tc0_1.6.2-1 libisl19_0.19-1 libjson-c3_0.12.1-1.3 libklibc_2.0.4-11+rpi1 libkmod2_25-1 libksba8_1.3.5-2 liblapack3_3.8.0-1 libldap-2.4-2_2.4.46+dfsg-5+rpi1 libldap-common_2.4.46+dfsg-5+rpi1 liblocale-gettext-perl_1.07-3+b2 liblz4-1_1.8.2-1+rpi1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.33-3 libmagic1_1:5.33-3 libmount1_2.32-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libncurses5_6.1+20180210-4 libncurses6_6.1+20180210-4 libncursesw5_6.1+20180210-4 libncursesw6_6.1+20180210-4 libnettle6_3.4-1 libnpth0_1.5-4 libnss-systemd_238-4 libopenbabel5_2.4.1+dfsg-2 libp11-kit0_0.23.12-2 libpam-modules_1.1.8-3.7 libpam-modules-bin_1.1.8-3.7 libpam-runtime_1.1.8-3.7 libpam-systemd_238-4 libpam0g_1.1.8-3.7 libpcre3_2:8.39-9 libperl5.26_5.26.2-6 libpipeline1_1.5.0-1 libpixman-1-0_0.34.0-2 libplymouth4_0.9.3-3 libpng16-16_1.6.34-1 libprocps7_2:3.3.15-2 libpython-dev_2.7.15-3 libpython-stdlib_2.7.15-3 libpython2-dev_2.7.15-3 libpython2-stdlib_2.7.15-3 libpython2.7_2.7.15-1 libpython2.7-dev_2.7.15-1 libpython2.7-minimal_2.7.15-1 libpython2.7-stdlib_2.7.15-1 libreadline7_7.0-5 libsasl2-2_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3.1 libseccomp2_2.3.3-2 libselinux1_2.8-1 libsemanage-common_2.8-1 libsemanage1_2.8-1 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.32-0.1 libsqlite3-0_3.24.0-1 libss2_1.44.2-1 libssl1.1_1.1.0h-4 libstdc++-7-dev_7.3.0-19 libstdc++6_8.1.0-8+rpi1 libsystemd0_238-4 libtasn1-6_4.13-3 libtext-charwidth-perl_0.04-7.1 libtext-iconv-perl_1.7-5+b9 libtext-wrapi18n-perl_0.06-7.1 libtimedate-perl_2.3000-2 libtinfo5_6.1+20180210-4 libtinfo6_6.1+20180210-4 libtool_2.4.6-2.1 libubsan0_7.3.0-19 libudev1_238-4 libunistring2_0.9.8-1 libuuid1_2.32-0.1 libx11-6_2:1.6.5-1 libx11-data_2:1.6.5-1 libxau6_1:1.0.8-1+b2 libxcb-render0_1.13-1 libxcb-shm0_1.13-1 libxcb1_1.13-1 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1+b2 libxml2_2.9.4+dfsg1-7 libxml2-utils_2.9.4+dfsg1-7 libxrender1_1:0.9.10-1 libxslt1.1_1.1.32-2 libzstd1_1.3.4+dfsg-3+rpi1 linux-base_4.5 linux-libc-dev_4.16.12-1+rpi1 login_1:4.5-1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.8.3-2 mawk_1.3.3-17 mime-support_3.61 mount_2.32-0.1 multiarch-support_2.27-3+rpi1 nano_2.9.8-1 ncurses-base_6.1+20180210-4 ncurses-bin_6.1+20180210-4 netbase_5.4 openbabel_2.4.1+dfsg-2 openssl_1.1.0h-4 passwd_1:4.5-1 patch_2.7.6-2 perl_5.26.2-6 perl-base_5.26.2-6 perl-modules-5.26_5.26.2-6 pinentry-curses_1.1.0-1 plymouth_0.9.3-3 po-debconf_1.0.20 procps_2:3.3.15-2 python_2.7.15-3 python-dev_2.7.15-3 python-minimal_2.7.15-3 python-numpy_1:1.14.5-1 python2_2.7.15-3 python2-dev_2.7.15-3 python2-minimal_2.7.15-3 python2.7_2.7.15-1 python2.7-dev_2.7.15-1 python2.7-minimal_2.7.15-1 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-pdb2pqr-dummy_0.invalid.0 scons_3.0.1-1 sed_4.4-2 sensible-utils_0.0.12 sgml-base_1.29 sgml-data_2.0.10 swig_3.0.12-1.1 swig3.0_3.0.12-1.1 systemd_238-4 systemd-sysv_238-4 sysvinit-utils_2.88dsf-59.10 tar_1.30+dfsg-2 tzdata_2018e-1 ucf_3.0038 udev_238-4 util-linux_2.32-0.1 xml-core_0.18 xmlto_0.0.28-2 xsltproc_1.1.32-2 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Sat Jul 14 14:12:32 2018 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./pdb2pqr_2.1.1+dfsg-4.dsc
dpkg-source: info: extracting pdb2pqr in /<<BUILDDIR>>/pdb2pqr-2.1.1+dfsg
dpkg-source: info: unpacking pdb2pqr_2.1.1+dfsg.orig.tar.xz
dpkg-source: info: unpacking pdb2pqr_2.1.1+dfsg-4.debian.tar.xz
dpkg-source: info: applying fix-hashbangs.patch
dpkg-source: info: applying no_privacy_breach_logo.patch
dpkg-source: info: applying do_not_try_to_build_removed_js_target.patch
dpkg-source: info: applying fix_hardening_no_relro
dpkg-source: info: applying fix_no_debug_symbols_warning
dpkg-source: info: applying spelling.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-0ee9aae0-c026-47b4-8d33-38dcd0c14d07
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package pdb2pqr
dpkg-buildpackage: info: source version 2.1.1+dfsg-4
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build pdb2pqr-2.1.1+dfsg
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --with python2
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/pdb2pqr-2.1.1+dfsg'
( cd pdb2pka && \
if [ -e pMC_mult_wrap.cpp.saved ]; then mv pMC_mult_wrap.cpp.saved pMC_mult_wrap.cpp; fi && \
if [ -e pMC_mult.py.saved ]; then mv pMC_mult.py.saved pMC_mult.py; fi )
find . -name *.pyc -delete
find . -name *.so -delete
find . -name *.os -delete
rm -f *.cgi .sconsign.dblite .variables.cache pdb2pqr.py html/server.html src/aconf.py
dh_auto_clean
make[1]: Leaving directory '/<<BUILDDIR>>/pdb2pqr-2.1.1+dfsg'
dh_clean
debian/rules build-arch
dh build-arch --with python2
dh_update_autotools_config -a
dh_autoreconf -a
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<BUILDDIR>>/pdb2pqr-2.1.1+dfsg'
dh_auto_configure
( cd pdb2pka && \
cp -a pMC_mult_wrap.cpp pMC_mult_wrap.cpp.saved && \
cp -a pMC_mult.py pMC_mult.py.saved && \
swig -c++ -python -o pMC_mult_wrap.cpp pMC_mult.i )
python scons/scons.py \
URL="http://localhost/pdb2pqr/" \
PREFIX="/usr/share/pdb2pqr"
scons: Reading SConscript files ...
not using opal
scons: done reading SConscript files.
scons: Building targets ...
CopySubAction("pdb2pqr.py", "pdb2pqr.py.in")
Chmod("pdb2pqr.py", 0755)
CopySubAction("apbs_cgi.cgi", "apbs_cgi.py")
Chmod("apbs_cgi.cgi", 0755)
CopySubAction("visualize.cgi", "visualize.py")
Chmod("visualize.cgi", 0755)
CopySubAction("querystatus.cgi", "querystatus.py")
Chmod("querystatus.cgi", 0755)
CopySubAction("src/aconf.py", "src/aconf.py.in")
CopySubAction("html/server.html", "html/server.html.in")
Copy("pdb2pqr.cgi", "pdb2pqr.py")
g++ -o pdb2pka/substruct/Algorithms.os -c -g -fPIC -I/usr/include/python2.7 -I/usr/lib/python2.7/dist-packages/numpy/core/include pdb2pka/substruct/Algorithms.cpp
In file included from /usr/include/python2.7/numpy/ndarraytypes.h:1816:0,
from /usr/include/python2.7/numpy/ndarrayobject.h:18,
from /usr/include/python2.7/numpy/arrayobject.h:4,
from pdb2pka/substruct/Algorithms.cpp:43:
/usr/include/python2.7/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 " \
^~~~~~~
g++ -o pdb2pka/substruct/Algorithms.so -Wl,-z,relro -Wl,-z,now -shared pdb2pka/substruct/Algorithms.os -L/usr/lib -lpython2.7
g++ -o pdb2pka/pMC_mult.os -c -g -fPIC -I/usr/include/python2.7 -I/usr/lib/python2.7/dist-packages/numpy/core/include pdb2pka/pMC_mult.cpp
In file included from /usr/include/c++/7/vector:64:0,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/7/bits/stl_vector.h: In copy constructor 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/stl_vector.h:331:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
std::__uninitialized_copy_a(__x.begin(), __x.end(),
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
this->_M_impl._M_start,
~~~~~~~~~~~~~~~~~~~~~~~
_M_get_Tp_allocator());
~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:63:0,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/7/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >; _ForwardIterator = double*; _Tp = double]':
/usr/include/c++/7/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
__uninitialized_copy_a(_InputIterator __first, _InputIterator __last,
^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_uninitialized.h:289:63: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
{ return std::uninitialized_copy(__first, __last, __result); }
^
In file included from /usr/include/c++/7/vector:69:0,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:63:0,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/7/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >; _ForwardIterator = double*]':
/usr/include/c++/7/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
uninitialized_copy(_InputIterator __first, _InputIterator __last,
^~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_uninitialized.h:134:41: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
__uninit_copy(__first, __last, __result);
^
/usr/include/c++/7/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = double*; _ForwardIterator = double*; _Allocator = std::allocator<double>]':
/usr/include/c++/7/bits/stl_uninitialized.h:312:69: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc);
^
In file included from /usr/include/c++/7/vector:69:0,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:63:0,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/7/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<true>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >; _ForwardIterator = double*]':
/usr/include/c++/7/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
__uninit_copy(_InputIterator __first, _InputIterator __last,
^~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_uninitialized.h:101:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
{ return std::copy(__first, __last, __result); }
^
/usr/include/c++/7/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator<double*>; _ForwardIterator = double*; _Tp = double]':
/usr/include/c++/7/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
__uninitialized_copy_a(_InputIterator __first, _InputIterator __last,
^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
/usr/include/c++/7/bits/stl_uninitialized.h:289:63: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
{ return std::uninitialized_copy(__first, __last, __result); }
^
In file included from /usr/include/c++/7/bits/char_traits.h:39:0,
from /usr/include/c++/7/string:40,
from pdb2pka/pMC_mult.h:9,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/7/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >; _OI = double*]':
/usr/include/c++/7/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
copy(_II __first, _II __last, _OI __result)
^~~~
/usr/include/c++/7/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algobase.h:456:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
__result));
^
In file included from /usr/include/c++/7/vector:63:0,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/7/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<double*>; _ForwardIterator = double*]':
/usr/include/c++/7/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
uninitialized_copy(_InputIterator __first, _InputIterator __last,
^~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
/usr/include/c++/7/bits/stl_uninitialized.h:134:41: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
__uninit_copy(__first, __last, __result);
^
In file included from /usr/include/c++/7/bits/stl_algobase.h:61:0,
from /usr/include/c++/7/bits/char_traits.h:39,
from /usr/include/c++/7/string:40,
from pdb2pka/pMC_mult.h:9,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/7/bits/cpp_type_traits.h: In function '_Iterator std::__miter_base(_Iterator) [with _Iterator = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >]':
/usr/include/c++/7/bits/cpp_type_traits.h:408:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
__miter_base(_Iterator __it)
^~~~~~~~~~~~
In file included from /usr/include/c++/7/bits/char_traits.h:39:0,
from /usr/include/c++/7/string:40,
from pdb2pka/pMC_mult.h:9,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/7/bits/stl_algobase.h: In function '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >; _OI = double*]':
/usr/include/c++/7/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
__copy_move_a2(_II __first, _II __last, _OI __result)
^~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/7/vector:63:0,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/7/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<true>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<double*>; _ForwardIterator = double*]':
/usr/include/c++/7/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
__uninit_copy(_InputIterator __first, _InputIterator __last,
^~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
/usr/include/c++/7/bits/stl_uninitialized.h:101:53: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
{ return std::copy(__first, __last, __result); }
^
In file included from /usr/include/c++/7/bits/stl_algobase.h:67:0,
from /usr/include/c++/7/bits/char_traits.h:39,
from /usr/include/c++/7/string:40,
from pdb2pka/pMC_mult.h:9,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/7/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = const double*; _Container = std::vector<double>]':
/usr/include/c++/7/bits/stl_iterator.h:983:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container> __it)
^~~~~~~~~~~~
In file included from /usr/include/c++/7/bits/char_traits.h:39:0,
from /usr/include/c++/7/string:40,
from pdb2pka/pMC_mult.h:9,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/7/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = std::move_iterator<double*>; _OI = double*]':
/usr/include/c++/7/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
copy(_II __first, _II __last, _OI __result)
^~~~
/usr/include/c++/7/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
In file included from /usr/include/c++/7/bits/stl_algobase.h:67:0,
from /usr/include/c++/7/bits/char_traits.h:39,
from /usr/include/c++/7/string:40,
from pdb2pka/pMC_mult.h:9,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/7/bits/stl_iterator.h: In function 'decltype (std::__miter_base(__it.base())) std::__miter_base(std::move_iterator<_IteratorL>) [with _Iterator = double*]':
/usr/include/c++/7/bits/stl_iterator.h:1241:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
__miter_base(move_iterator<_Iterator> __it)
^~~~~~~~~~~~
g++ -o pdb2pka/pMC_mult_wrap.os -c -g -fPIC -I/usr/include/python2.7 -I/usr/lib/python2.7/dist-packages/numpy/core/include pdb2pka/pMC_mult_wrap.cpp
pdb2pka/pMC_mult_wrap.cpp: In function 'std::vector<double>::iterator std_vector_Sl_double_Sg__erase__SWIG_0(std::vector<double>*, std::vector<double>::iterator)':
pdb2pka/pMC_mult_wrap.cpp:5076:44: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
SWIGINTERN std::vector< double >::iterator std_vector_Sl_double_Sg__erase__SWIG_0(std::vector< double > *self,std::vector< double >::iterator pos){ return self->erase(pos); }
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pdb2pka/pMC_mult_wrap.cpp:5076:171: note: parameter passing for argument of type 'std::vector<double>::const_iterator {aka __gnu_cxx::__normal_iterator<const double*, std::vector<double> >}' changed in GCC 7.1
SWIGINTERN std::vector< double >::iterator std_vector_Sl_double_Sg__erase__SWIG_0(std::vector< double > *self,std::vector< double >::iterator pos){ return self->erase(pos); }
^
pdb2pka/pMC_mult_wrap.cpp: In function 'std::vector<double>::iterator std_vector_Sl_double_Sg__erase__SWIG_1(std::vector<double>*, std::vector<double>::iterator, std::vector<double>::iterator)':
pdb2pka/pMC_mult_wrap.cpp:5077:44: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
SWIGINTERN std::vector< double >::iterator std_vector_Sl_double_Sg__erase__SWIG_1(std::vector< double > *self,std::vector< double >::iterator first,std::vector< double >::iterator last){ return self->erase(first, last); }
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pdb2pka/pMC_mult_wrap.cpp:5077:44: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
pdb2pka/pMC_mult_wrap.cpp:5077:218: note: parameter passing for argument of type 'std::vector<double>::const_iterator {aka __gnu_cxx::__normal_iterator<const double*, std::vector<double> >}' changed in GCC 7.1
SWIGINTERN std::vector< double >::iterator std_vector_Sl_double_Sg__erase__SWIG_1(std::vector< double > *self,std::vector< double >::iterator first,std::vector< double >::iterator last){ return self->erase(first, last); }
^
pdb2pka/pMC_mult_wrap.cpp: In function 'std::vector<double>::iterator std_vector_Sl_double_Sg__insert__SWIG_0(std::vector<double>*, std::vector<double>::iterator, const value_type&)':
pdb2pka/pMC_mult_wrap.cpp:5078:44: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
SWIGINTERN std::vector< double >::iterator std_vector_Sl_double_Sg__insert__SWIG_0(std::vector< double > *self,std::vector< double >::iterator pos,std::vector< double >::value_type const &x){ return self->insert(pos, x); }
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pdb2pka/pMC_mult_wrap.cpp:5078:219: note: parameter passing for argument of type 'std::vector<double>::const_iterator {aka __gnu_cxx::__normal_iterator<const double*, std::vector<double> >}' changed in GCC 7.1
SWIGINTERN std::vector< double >::iterator std_vector_Sl_double_Sg__insert__SWIG_0(std::vector< double > *self,std::vector< double >::iterator pos,std::vector< double >::value_type const &x){ return self->insert(pos, x); }
^
pdb2pka/pMC_mult_wrap.cpp: In function 'void std_vector_Sl_double_Sg__insert__SWIG_1(std::vector<double>*, std::vector<double>::iterator, std::vector<double>::size_type, const value_type&)':
pdb2pka/pMC_mult_wrap.cpp:5079:17: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
SWIGINTERN void std_vector_Sl_double_Sg__insert__SWIG_1(std::vector< double > *self,std::vector< double >::iterator pos,std::vector< double >::size_type n,std::vector< double >::value_type const &x){ self->insert(pos, n, x); }
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pdb2pka/pMC_mult_wrap.cpp:5079:213: note: parameter passing for argument of type 'std::vector<double>::const_iterator {aka __gnu_cxx::__normal_iterator<const double*, std::vector<double> >}' changed in GCC 7.1
SWIGINTERN void std_vector_Sl_double_Sg__insert__SWIG_1(std::vector< double > *self,std::vector< double >::iterator pos,std::vector< double >::size_type n,std::vector< double >::value_type const &x){ self->insert(pos, n, x); }
~~~~~~~~~~~~^~~~~~~~~~~
pdb2pka/pMC_mult_wrap.cpp: In function 'PyObject* _wrap_DoubleVector_erase__SWIG_0(PyObject*, PyObject*)':
pdb2pka/pMC_mult_wrap.cpp:9277:10: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
result = std_vector_Sl_double_Sg__erase__SWIG_0(arg1,arg2);
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pdb2pka/pMC_mult_wrap.cpp: In function 'PyObject* _wrap_DoubleVector_erase__SWIG_1(PyObject*, PyObject*)':
pdb2pka/pMC_mult_wrap.cpp:9330:10: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
result = std_vector_Sl_double_Sg__erase__SWIG_1(arg1,arg2,arg3);
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pdb2pka/pMC_mult_wrap.cpp: In function 'PyObject* _wrap_DoubleVector_insert__SWIG_0(PyObject*, PyObject*)':
pdb2pka/pMC_mult_wrap.cpp:9740:10: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
result = std_vector_Sl_double_Sg__insert__SWIG_0(arg1,arg2,(double const &)*arg3);
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pdb2pka/pMC_mult_wrap.cpp: In function 'PyObject* _wrap_DoubleVector_insert__SWIG_1(PyObject*, PyObject*)':
pdb2pka/pMC_mult_wrap.cpp:9797:42: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
std_vector_Sl_double_Sg__insert__SWIG_1(arg1,arg2,arg3,(double const &)*arg4);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3130:
/usr/include/c++/7/bits/stl_vector.h: In copy constructor 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/stl_vector.h:331:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
std::__uninitialized_copy_a(__x.begin(), __x.end(),
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
this->_M_impl._M_start,
~~~~~~~~~~~~~~~~~~~~~~~
_M_get_Tp_allocator());
~~~~~~~~~~~~~~~~~~~~~~
pdb2pka/pMC_mult_wrap.cpp: In function 'swig::SwigPyIterator* swig::make_output_iterator(const OutIter&, const OutIter&, const OutIter&, PyObject*) [with OutIter = __gnu_cxx::__normal_iterator<double*, std::vector<double> >]':
pdb2pka/pMC_mult_wrap.cpp:4428:12: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
return new SwigPyIteratorClosed_T<OutIter>(current, begin, end, seq);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pdb2pka/pMC_mult_wrap.cpp:4428:12: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
pdb2pka/pMC_mult_wrap.cpp: In function 'Sequence* swig::getslice(const Sequence*, Difference, Difference, Py_ssize_t) [with Sequence = std::vector<double>; Difference = int]':
pdb2pka/pMC_mult_wrap.cpp:4093:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
return new Sequence(sb, se);
^~~~~~~~~~~~~~~~~~~~
pdb2pka/pMC_mult_wrap.cpp: In function 'void swig::setslice(Sequence*, Difference, Difference, Py_ssize_t, const InputSeq&) [with Sequence = std::vector<double>; Difference = int; InputSeq = std::vector<double>]':
pdb2pka/pMC_mult_wrap.cpp:4139:33: note: parameter passing for argument of type 'std::vector<double>::const_iterator {aka __gnu_cxx::__normal_iterator<const double*, std::vector<double> >}' changed in GCC 7.1
self->insert(std::copy(is.begin(), isit, sb), isit, is.end());
~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
pdb2pka/pMC_mult_wrap.cpp:4139:11: note: parameter passing for argument of type 'std::vector<double>::const_iterator {aka __gnu_cxx::__normal_iterator<const double*, std::vector<double> >}' changed in GCC 7.1
self->insert(std::copy(is.begin(), isit, sb), isit, is.end());
^~~~
pdb2pka/pMC_mult_wrap.cpp:4139:11: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
pdb2pka/pMC_mult_wrap.cpp:4146:11: note: parameter passing for argument of type 'std::vector<double>::const_iterator {aka __gnu_cxx::__normal_iterator<const double*, std::vector<double> >}' changed in GCC 7.1
self->erase(sb,se);
^~~~
pdb2pka/pMC_mult_wrap.cpp:4149:11: note: parameter passing for argument of type 'std::vector<double>::const_iterator {aka __gnu_cxx::__normal_iterator<const double*, std::vector<double> >}' changed in GCC 7.1
self->insert(sb, is.begin(), is.end());
^~~~
pdb2pka/pMC_mult_wrap.cpp:4149:11: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
pdb2pka/pMC_mult_wrap.cpp: In function 'void swig::delslice(Sequence*, Difference, Difference, Py_ssize_t) [with Sequence = std::vector<double>; Difference = int]':
pdb2pka/pMC_mult_wrap.cpp:4198:9: note: parameter passing for argument of type 'std::vector<double>::const_iterator {aka __gnu_cxx::__normal_iterator<const double*, std::vector<double> >}' changed in GCC 7.1
self->erase(sb,se);
^~~~
pdb2pka/pMC_mult_wrap.cpp:4203:11: note: parameter passing for argument of type 'std::vector<double>::const_iterator {aka __gnu_cxx::__normal_iterator<const double*, std::vector<double> >}' changed in GCC 7.1
it = self->erase(it);
^~
pdb2pka/pMC_mult_wrap.cpp:4215:9: note: parameter passing for argument of type 'std::vector<double>::const_iterator {aka __gnu_cxx::__normal_iterator<const double*, std::vector<double> >}' changed in GCC 7.1
it = typename Sequence::reverse_iterator(self->erase((++it).base()));
^~
pdb2pka/pMC_mult_wrap.cpp:4215:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
pdb2pka/pMC_mult_wrap.cpp: In function 'void swig::erase(Sequence*, const typename Sequence::iterator&) [with Sequence = std::vector<double>]':
pdb2pka/pMC_mult_wrap.cpp:4069:5: note: parameter passing for argument of type 'std::vector<double>::const_iterator {aka __gnu_cxx::__normal_iterator<const double*, std::vector<double> >}' changed in GCC 7.1
seq->erase(position);
^~~
In file included from /usr/include/c++/7/vector:64:0,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3130:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(std::vector<_Tp, _Alloc>::const_iterator) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/stl_vector.h:1179:7: note: parameter passing for argument of type 'std::vector<double>::const_iterator {aka __gnu_cxx::__normal_iterator<const double*, std::vector<double> >}' changed in GCC 7.1
erase(const_iterator __position)
^~~~~
/usr/include/c++/7/bits/stl_vector.h:1180:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
{ return _M_erase(begin() + (__position - cbegin())); }
^
/usr/include/c++/7/bits/stl_vector.h: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(std::vector<_Tp, _Alloc>::const_iterator, std::vector<_Tp, _Alloc>::const_iterator) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/stl_vector.h:1206:7: note: parameter passing for argument of type 'std::vector<double>::const_iterator {aka __gnu_cxx::__normal_iterator<const double*, std::vector<double> >}' changed in GCC 7.1
erase(const_iterator __first, const_iterator __last)
^~~~~
/usr/include/c++/7/bits/stl_vector.h:1206:7: note: parameter passing for argument of type 'std::vector<double>::const_iterator {aka __gnu_cxx::__normal_iterator<const double*, std::vector<double> >}' changed in GCC 7.1
/usr/include/c++/7/bits/stl_vector.h:1210:71: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg));
^
In file included from /usr/include/c++/7/vector:69:0,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3130:
/usr/include/c++/7/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(std::vector<_Tp, _Alloc>::const_iterator, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:114:5: note: parameter passing for argument of type 'std::vector<double>::const_iterator {aka __gnu_cxx::__normal_iterator<const double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc:136:19: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_insert_aux(__pos, std::move(__x_copy._M_val()));
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc:143:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(begin() + (__position - cbegin()), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3130:
/usr/include/c++/7/bits/stl_vector.h: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(std::vector<_Tp, _Alloc>::const_iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/stl_vector.h:1084:7: note: parameter passing for argument of type 'std::vector<double>::const_iterator {aka __gnu_cxx::__normal_iterator<const double*, std::vector<double> >}' changed in GCC 7.1
insert(const_iterator __position, size_type __n, const value_type& __x)
^~~~~~
/usr/include/c++/7/bits/stl_vector.h:1087:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pdb2pka/pMC_mult_wrap.cpp: In function 'swig::SwigPyIterator* swig::make_output_iterator(const OutIter&, PyObject*) [with OutIter = __gnu_cxx::__normal_iterator<double*, std::vector<double> >]':
pdb2pka/pMC_mult_wrap.cpp:4435:12: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
return new SwigPyIteratorOpen_T<OutIter>(current, seq);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3130:
/usr/include/c++/7/bits/stl_vector.h: In member function 'std::vector<_Tp, _Alloc>::reverse_iterator std::vector<_Tp, _Alloc>::rbegin() [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/stl_vector.h:600:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
{ return reverse_iterator(end()); }
^
/usr/include/c++/7/bits/stl_vector.h: In member function 'std::vector<_Tp, _Alloc>::reverse_iterator std::vector<_Tp, _Alloc>::rend() [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/stl_vector.h:618:40: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
{ return reverse_iterator(begin()); }
^
/usr/include/c++/7/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::resize(std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/stl_vector.h:712:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3130:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::reserve(std::vector<_Tp, _Alloc>::size_type) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:73:12: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
pointer __tmp = _M_allocate_and_copy(__n,
^~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:206:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
pointer __tmp = _M_allocate_and_copy(__xlen, __x.begin(),
^~~~~
/usr/include/c++/7/bits/vector.tcc:218:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
std::_Destroy(std::copy(__x.begin(), __x.end(), begin()),
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
end(), _M_get_Tp_allocator());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc:218:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/7/vector:63:0,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3130:
/usr/include/c++/7/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >; _ForwardIterator = double*; _Tp = double]':
/usr/include/c++/7/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
__uninitialized_copy_a(_InputIterator __first, _InputIterator __last,
^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_uninitialized.h:289:63: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
{ return std::uninitialized_copy(__first, __last, __result); }
^
pdb2pka/pMC_mult_wrap.cpp: In constructor 'swig::SwigPyIteratorClosed_T<OutIterator, ValueType, FromOper>::SwigPyIteratorClosed_T(swig::SwigPyIteratorClosed_T<OutIterator, ValueType, FromOper>::out_iterator, swig::SwigPyIteratorClosed_T<OutIterator, ValueType, FromOper>::out_iterator, swig::SwigPyIteratorClosed_T<OutIterator, ValueType, FromOper>::out_iterator, PyObject*) [with OutIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; ValueType = double; FromOper = swig::from_oper<double>]':
pdb2pka/pMC_mult_wrap.cpp:4377:5: note: parameter passing for argument of type 'swig::SwigPyIteratorClosed_T<__gnu_cxx::__normal_iterator<double*, std::vector<double> >, double, swig::from_oper<double> >::out_iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
SwigPyIteratorClosed_T(out_iterator curr, out_iterator first, out_iterator last, PyObject *seq)
^~~~~~~~~~~~~~~~~~~~~~
pdb2pka/pMC_mult_wrap.cpp:4377:5: note: parameter passing for argument of type 'swig::SwigPyIteratorClosed_T<__gnu_cxx::__normal_iterator<double*, std::vector<double> >, double, swig::from_oper<double> >::out_iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
pdb2pka/pMC_mult_wrap.cpp:4377:5: note: parameter passing for argument of type 'swig::SwigPyIteratorClosed_T<__gnu_cxx::__normal_iterator<double*, std::vector<double> >, double, swig::from_oper<double> >::out_iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
pdb2pka/pMC_mult_wrap.cpp:4378:73: note: parameter passing for argument of type 'swig::SwigPyIteratorClosed_T<__gnu_cxx::__normal_iterator<double*, std::vector<double> >, double, swig::from_oper<double> >::out_iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
: SwigPyIterator_T<OutIterator>(curr, seq), begin(first), end(last)
^
In file included from /usr/include/c++/7/vector:64:0,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3130:
/usr/include/c++/7/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(_InputIterator, _InputIterator, const allocator_type&) [with _InputIterator = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >; <template-parameter-2-2> = void; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/stl_vector.h:411:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
vector(_InputIterator __first, _InputIterator __last,
^~~~~~
/usr/include/c++/7/bits/stl_vector.h:411:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_vector.h:414:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
{ _M_initialize_dispatch(__first, __last, __false_type()); }
~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In member function 'std::vector<_Tp, _Alloc>::const_reverse_iterator std::vector<_Tp, _Alloc>::rbegin() const [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/stl_vector.h:609:44: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
{ return const_reverse_iterator(end()); }
^
In file included from /usr/include/c++/7/bits/char_traits.h:39:0,
from /usr/include/c++/7/string:40,
from /usr/include/c++/7/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:3057:
/usr/include/c++/7/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >; _OI = __gnu_cxx::__normal_iterator<double*, std::vector<double> >]':
/usr/include/c++/7/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
copy(_II __first, _II __last, _OI __result)
^~~~
/usr/include/c++/7/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algobase.h:456:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
__result));
^
In file included from /usr/include/c++/7/vector:64:0,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3130:
/usr/include/c++/7/bits/stl_vector.h: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(std::vector<_Tp, _Alloc>::const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >; <template-parameter-2-2> = void; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/stl_vector.h:1128:2: note: parameter passing for argument of type 'std::vector<double>::const_iterator {aka __gnu_cxx::__normal_iterator<const double*, std::vector<double> >}' changed in GCC 7.1
insert(const_iterator __position, _InputIterator __first,
^~~~~~
/usr/include/c++/7/bits/stl_vector.h:1128:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_vector.h:1128:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_vector.h:1132:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_insert_dispatch(begin() + __offset,
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
__first, __last, __false_type());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:1132:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/7/bits/stl_algobase.h:67:0,
from /usr/include/c++/7/bits/char_traits.h:39,
from /usr/include/c++/7/string:40,
from /usr/include/c++/7/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:3057:
/usr/include/c++/7/bits/stl_iterator.h: In constructor 'std::reverse_iterator<_Iterator>::reverse_iterator(std::reverse_iterator<_Iterator>::iterator_type) [with _Iterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >]':
/usr/include/c++/7/bits/stl_iterator.h:132:7: note: parameter passing for argument of type 'std::reverse_iterator<__gnu_cxx::__normal_iterator<double*, std::vector<double> > >::iterator_type {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
reverse_iterator(iterator_type __x) : current(__x) { }
^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3130:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:153:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/bits/char_traits.h:39:0,
from /usr/include/c++/7/string:40,
from /usr/include/c++/7/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:3057:
/usr/include/c++/7/bits/vector.tcc:157:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_GLIBCXX_MOVE3(__position + 1, end(), __position);
^
In file included from /usr/include/c++/7/vector:69:0,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3130:
/usr/include/c++/7/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::iterator) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:165:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc:165:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
In file included from /usr/include/c++/7/bits/char_traits.h:39:0,
from /usr/include/c++/7/string:40,
from /usr/include/c++/7/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:3057:
/usr/include/c++/7/bits/vector.tcc:171:6: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_GLIBCXX_MOVE3(__last, end(), __first);
^
In file included from /usr/include/c++/7/vector:69:0,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3130:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_insert_aux(std::vector<_Tp, _Alloc>::iterator, _Arg&&) [with _Arg = double; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:364:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:458:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
pdb2pka/pMC_mult_wrap.cpp: In constructor 'swig::SwigPyIteratorOpen_T<OutIterator, ValueType, FromOper>::SwigPyIteratorOpen_T(swig::SwigPyIteratorOpen_T<OutIterator, ValueType, FromOper>::out_iterator, PyObject*) [with OutIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; ValueType = double; FromOper = swig::from_oper<double>]':
pdb2pka/pMC_mult_wrap.cpp:4334:5: note: parameter passing for argument of type 'swig::SwigPyIteratorOpen_T<__gnu_cxx::__normal_iterator<double*, std::vector<double> >, double, swig::from_oper<double> >::out_iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
SwigPyIteratorOpen_T(out_iterator curr, PyObject *seq)
^~~~~~~~~~~~~~~~~~~~
pdb2pka/pMC_mult_wrap.cpp:4335:48: note: parameter passing for argument of type 'swig::SwigPyIteratorOpen_T<__gnu_cxx::__normal_iterator<double*, std::vector<double> >, double, swig::from_oper<double> >::out_iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
: SwigPyIterator_T<OutIterator>(curr, seq)
^
In file included from /usr/include/c++/7/vector:69:0,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3130:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_assign(std::size_t, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:247:13: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::fill(begin(), end(), __val);
~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3130:
/usr/include/c++/7/bits/stl_vector.h: In member function 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(std::vector<_Tp, _Alloc>::size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = std::move_iterator<double*>; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/stl_vector.h:1257:2: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
_M_allocate_and_copy(size_type __n,
^~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:1257:2: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
/usr/include/c++/7/bits/stl_vector.h:1263:35: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
std::__uninitialized_copy_a(__first, __last, __result,
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
_M_get_Tp_allocator());
~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In member function 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(std::vector<_Tp, _Alloc>::size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/stl_vector.h:1257:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
_M_allocate_and_copy(size_type __n,
^~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:1257:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_vector.h:1263:35: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
std::__uninitialized_copy_a(__first, __last, __result,
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
_M_get_Tp_allocator());
~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:62:0,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3130:
/usr/include/c++/7/bits/stl_construct.h: In function 'void std::_Destroy(_ForwardIterator, _ForwardIterator, std::allocator<_T2>&) [with _ForwardIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Tp = double]':
/usr/include/c++/7/bits/stl_construct.h:203:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_Destroy(_ForwardIterator __first, _ForwardIterator __last,
^~~~~~~~
/usr/include/c++/7/bits/stl_construct.h:203:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_construct.h:206:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_Destroy(__first, __last);
~~~~~~~~^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:63:0,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3130:
/usr/include/c++/7/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >; _ForwardIterator = double*]':
/usr/include/c++/7/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
uninitialized_copy(_InputIterator __first, _InputIterator __last,
^~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_uninitialized.h:134:41: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
__uninit_copy(__first, __last, __result);
^
pdb2pka/pMC_mult_wrap.cpp: In constructor 'swig::SwigPyIterator_T<OutIterator>::SwigPyIterator_T(swig::SwigPyIterator_T<OutIterator>::out_iterator, PyObject*) [with OutIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >]':
pdb2pka/pMC_mult_wrap.cpp:4276:5: note: parameter passing for argument of type 'swig::SwigPyIterator_T<__gnu_cxx::__normal_iterator<double*, std::vector<double> > >::out_iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
SwigPyIterator_T(out_iterator curr, PyObject *seq)
^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3130:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::_M_initialize_dispatch(_InputIterator, _InputIterator, std::__false_type) [with _InputIterator = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/stl_vector.h:1294:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
_M_initialize_dispatch(_InputIterator __first, _InputIterator __last,
^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:1294:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_vector.h:1299:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
_M_range_initialize(__first, __last, _IterCategory());
~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/bits/stl_algobase.h:67:0,
from /usr/include/c++/7/bits/char_traits.h:39,
from /usr/include/c++/7/string:40,
from /usr/include/c++/7/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:3057:
/usr/include/c++/7/bits/stl_iterator.h: In constructor 'std::reverse_iterator<_Iterator>::reverse_iterator(std::reverse_iterator<_Iterator>::iterator_type) [with _Iterator = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >]':
/usr/include/c++/7/bits/stl_iterator.h:132:7: note: parameter passing for argument of type 'std::reverse_iterator<__gnu_cxx::__normal_iterator<const double*, std::vector<double> > >::iterator_type {aka __gnu_cxx::__normal_iterator<const double*, std::vector<double> >}' changed in GCC 7.1
reverse_iterator(iterator_type __x) : current(__x) { }
^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/cmath:42:0,
from /usr/include/c++/7/math.h:36,
from /usr/include/python2.7/pyport.h:325,
from /usr/include/python2.7/Python.h:61,
from pdb2pka/pMC_mult_wrap.cpp:173:
/usr/include/c++/7/bits/cpp_type_traits.h: In function '_Iterator std::__miter_base(_Iterator) [with _Iterator = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >]':
/usr/include/c++/7/bits/cpp_type_traits.h:408:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
__miter_base(_Iterator __it)
^~~~~~~~~~~~
In file included from /usr/include/c++/7/bits/char_traits.h:39:0,
from /usr/include/c++/7/string:40,
from /usr/include/c++/7/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:3057:
/usr/include/c++/7/bits/stl_algobase.h: In function '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >; _OI = __gnu_cxx::__normal_iterator<double*, std::vector<double> >]':
/usr/include/c++/7/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
__copy_move_a2(_II __first, _II __last, _OI __result)
^~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/7/vector:64:0,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3130:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::_M_insert_dispatch(std::vector<_Tp, _Alloc>::iterator, _InputIterator, _InputIterator, std::__false_type) [with _InputIterator = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/stl_vector.h:1403:2: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
_M_insert_dispatch(iterator __pos, _InputIterator __first,
^~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:1403:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_vector.h:1403:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_vector.h:1406:19: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
_M_range_insert(__pos, __first, __last,
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
std::__iterator_category(__first));
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:1406:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/7/vector:63:0,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3130:
/usr/include/c++/7/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = double*; _ForwardIterator = double*; _Allocator = std::allocator<double>]':
/usr/include/c++/7/bits/stl_uninitialized.h:312:69: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc);
^
In file included from /usr/include/c++/7/bits/char_traits.h:39:0,
from /usr/include/c++/7/string:40,
from /usr/include/c++/7/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:3057:
/usr/include/c++/7/bits/stl_algobase.h: In function '_OI std::move(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _OI = __gnu_cxx::__normal_iterator<double*, std::vector<double> >]':
/usr/include/c++/7/bits/stl_algobase.h:479:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
move(_II __first, _II __last, _OI __result)
^~~~
/usr/include/c++/7/bits/stl_algobase.h:479:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algobase.h:479:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algobase.h:488:47: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__miter_base(__last), __result);
^
In file included from /usr/include/c++/7/vector:63:0,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3130:
/usr/include/c++/7/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = double*; _ForwardIterator = double*; _Allocator = std::allocator<double>]':
/usr/include/c++/7/bits/stl_uninitialized.h:299:24: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
__result, __alloc);
^
In file included from /usr/include/c++/7/bits/char_traits.h:39:0,
from /usr/include/c++/7/string:40,
from /usr/include/c++/7/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:3057:
/usr/include/c++/7/bits/stl_algobase.h: In function 'void std::fill(_ForwardIterator, _ForwardIterator, const _Tp&) [with _ForwardIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Tp = double]':
/usr/include/c++/7/bits/stl_algobase.h:724:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
fill(_ForwardIterator __first, _ForwardIterator __last, const _Tp& __value)
^~~~
/usr/include/c++/7/bits/stl_algobase.h:724:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/7/vector:63:0,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3130:
/usr/include/c++/7/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator<double*>; _ForwardIterator = double*; _Tp = double]':
/usr/include/c++/7/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
__uninitialized_copy_a(_InputIterator __first, _InputIterator __last,
^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
/usr/include/c++/7/bits/stl_uninitialized.h:289:63: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
{ return std::uninitialized_copy(__first, __last, __result); }
^
In file included from /usr/include/c++/7/vector:62:0,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3130:
/usr/include/c++/7/bits/stl_construct.h: In function 'void std::_Destroy(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >]':
/usr/include/c++/7/bits/stl_construct.h:127:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_Destroy(_ForwardIterator __first, _ForwardIterator __last)
^~~~~~~~
/usr/include/c++/7/bits/stl_construct.h:127:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_construct.h:137:11: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::_Destroy_aux<__has_trivial_destructor(_Value_type)>::
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__destroy(__first, __last);
~~~~~~~~~^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:63:0,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3130:
/usr/include/c++/7/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<true>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >; _ForwardIterator = double*]':
/usr/include/c++/7/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
__uninit_copy(_InputIterator __first, _InputIterator __last,
^~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_uninitialized.h:101:53: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
{ return std::copy(__first, __last, __result); }
^
In file included from /usr/include/c++/7/vector:64:0,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3130:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::_M_range_initialize(_ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/stl_vector.h:1319:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
_M_range_initialize(_ForwardIterator __first,
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:1319:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_vector.h:1322:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
const size_type __n = std::distance(__first, __last);
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:1326:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
std::__uninitialized_copy_a(__first, __last,
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
this->_M_impl._M_start,
~~~~~~~~~~~~~~~~~~~~~~~
_M_get_Tp_allocator());
~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/bits/stl_algobase.h:67:0,
from /usr/include/c++/7/bits/char_traits.h:39,
from /usr/include/c++/7/string:40,
from /usr/include/c++/7/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:3057:
/usr/include/c++/7/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = const double*; _Container = std::vector<double>]':
/usr/include/c++/7/bits/stl_iterator.h:983:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container> __it)
^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = double*; _Container = std::vector<double>]':
/usr/include/c++/7/bits/stl_iterator.h:983:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/7/vector:69:0,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3130:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:630:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc:630:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/vector.tcc:630:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/vector.tcc:636:41: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
const size_type __n = std::distance(__first, __last);
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc:651:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
std::copy(__first, __last, __position);
~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc:657:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
std::__uninitialized_copy_a(__mid, __last,
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
this->_M_impl._M_finish,
~~~~~~~~~~~~~~~~~~~~~~~~
_M_get_Tp_allocator());
~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc:666:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
std::copy(__first, __mid, __position);
~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc:681:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
__new_finish
^~~~~~~~~~~~
In file included from /usr/include/c++/7/cmath:42:0,
from /usr/include/c++/7/math.h:36,
from /usr/include/python2.7/pyport.h:325,
from /usr/include/python2.7/Python.h:61,
from pdb2pka/pMC_mult_wrap.cpp:173:
/usr/include/c++/7/bits/cpp_type_traits.h: In function '_Iterator std::__miter_base(_Iterator) [with _Iterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >]':
/usr/include/c++/7/bits/cpp_type_traits.h:408:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__miter_base(_Iterator __it)
^~~~~~~~~~~~
In file included from /usr/include/c++/7/bits/char_traits.h:39:0,
from /usr/include/c++/7/string:40,
from /usr/include/c++/7/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:3057:
/usr/include/c++/7/bits/stl_algobase.h: In function '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = true; _II = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _OI = __gnu_cxx::__normal_iterator<double*, std::vector<double> >]':
/usr/include/c++/7/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__copy_move_a2(_II __first, _II __last, _OI __result)
^~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
pdb2pka/pMC_mult_wrap.cpp: In function 'void swig::assign(const SwigPySeq&, Seq*) [with SwigPySeq = swig::SwigPySequence_Cont<double>; Seq = std::vector<double>]':
pdb2pka/pMC_mult_wrap.cpp:4726:7: note: parameter passing for argument of type 'std::vector<double>::const_iterator {aka __gnu_cxx::__normal_iterator<const double*, std::vector<double> >}' changed in GCC 7.1
seq->insert(seq->end(),(value_type)(*it));
^~~
In file included from /usr/include/c++/7/vector:63:0,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3130:
/usr/include/c++/7/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<double*>; _ForwardIterator = double*]':
/usr/include/c++/7/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
uninitialized_copy(_InputIterator __first, _InputIterator __last,
^~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
/usr/include/c++/7/bits/stl_uninitialized.h:134:41: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
__uninit_copy(__first, __last, __result);
^
In file included from /usr/include/c++/7/vector:62:0,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3130:
/usr/include/c++/7/bits/stl_construct.h: In static member function 'static void std::_Destroy_aux<true>::__destroy(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >]':
/usr/include/c++/7/bits/stl_construct.h:117:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__destroy(_ForwardIterator, _ForwardIterator) { }
^~~~~~~~~
/usr/include/c++/7/bits/stl_construct.h:117:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/7/bits/char_traits.h:39:0,
from /usr/include/c++/7/string:40,
from /usr/include/c++/7/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:3057:
/usr/include/c++/7/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >; _OI = double*]':
/usr/include/c++/7/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
copy(_II __first, _II __last, _OI __result)
^~~~
/usr/include/c++/7/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algobase.h:456:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
__result));
^
In file included from /usr/include/c++/7/bits/stl_algobase.h:66:0,
from /usr/include/c++/7/bits/char_traits.h:39,
from /usr/include/c++/7/string:40,
from /usr/include/c++/7/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:3057:
/usr/include/c++/7/bits/stl_iterator_base_funcs.h: In function 'typename std::iterator_traits<_Iterator>::difference_type std::distance(_InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >]':
/usr/include/c++/7/bits/stl_iterator_base_funcs.h:138:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
distance(_InputIterator __first, _InputIterator __last)
^~~~~~~~
/usr/include/c++/7/bits/stl_iterator_base_funcs.h:138:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_iterator_base_funcs.h:142:42: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
std::__iterator_category(__first));
^
In file included from /usr/include/c++/7/vector:64:0,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3130:
/usr/include/c++/7/bits/stl_vector.h: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(std::vector<_Tp, _Alloc>::const_iterator, std::vector<_Tp, _Alloc>::value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/stl_vector.h:1042:7: note: parameter passing for argument of type 'std::vector<double>::const_iterator {aka __gnu_cxx::__normal_iterator<const double*, std::vector<double> >}' changed in GCC 7.1
insert(const_iterator __position, value_type&& __x)
^~~~~~
/usr/include/c++/7/bits/stl_vector.h:1043:57: note: parameter passing for argument of type 'std::vector<double>::const_iterator {aka __gnu_cxx::__normal_iterator<const double*, std::vector<double> >}' changed in GCC 7.1
{ return _M_insert_rval(__position, std::move(__x)); }
^
In file included from /usr/include/c++/7/vector:63:0,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3130:
/usr/include/c++/7/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<true>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<double*>; _ForwardIterator = double*]':
/usr/include/c++/7/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
__uninit_copy(_InputIterator __first, _InputIterator __last,
^~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
/usr/include/c++/7/bits/stl_uninitialized.h:101:53: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
{ return std::copy(__first, __last, __result); }
^
In file included from /usr/include/c++/7/bits/char_traits.h:39:0,
from /usr/include/c++/7/string:40,
from /usr/include/c++/7/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:3057:
/usr/include/c++/7/bits/stl_algobase.h: In function '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >; _OI = double*]':
/usr/include/c++/7/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
__copy_move_a2(_II __first, _II __last, _OI __result)
^~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/7/bits/stl_algobase.h:66:0,
from /usr/include/c++/7/bits/char_traits.h:39,
from /usr/include/c++/7/string:40,
from /usr/include/c++/7/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:3057:
/usr/include/c++/7/bits/stl_iterator_base_funcs.h: In function 'constexpr typename std::iterator_traits<_Iterator>::difference_type std::__distance(_RandomAccessIterator, _RandomAccessIterator, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >]':
/usr/include/c++/7/bits/stl_iterator_base_funcs.h:98:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
__distance(_RandomAccessIterator __first, _RandomAccessIterator __last,
^~~~~~~~~~
/usr/include/c++/7/bits/stl_iterator_base_funcs.h:98:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/7/vector:69:0,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3130:
/usr/include/c++/7/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_insert_rval(std::vector<_Tp, _Alloc>::const_iterator, std::vector<_Tp, _Alloc>::value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:313:5: note: parameter passing for argument of type 'std::vector<double>::const_iterator {aka __gnu_cxx::__normal_iterator<const double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc:325:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_insert_aux(begin() + __n, std::move(__v));
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc:327:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(begin() + __n, std::move(__v));
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/bits/char_traits.h:39:0,
from /usr/include/c++/7/string:40,
from /usr/include/c++/7/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:3057:
/usr/include/c++/7/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = std::move_iterator<double*>; _OI = double*]':
/usr/include/c++/7/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
copy(_II __first, _II __last, _OI __result)
^~~~
/usr/include/c++/7/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
In file included from /usr/include/c++/7/vector:69:0,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3130:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/bits/stl_algobase.h:67:0,
from /usr/include/c++/7/bits/char_traits.h:39,
from /usr/include/c++/7/string:40,
from /usr/include/c++/7/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:3057:
/usr/include/c++/7/bits/stl_iterator.h: In function 'decltype (std::__miter_base(__it.base())) std::__miter_base(std::move_iterator<_IteratorL>) [with _Iterator = double*]':
/usr/include/c++/7/bits/stl_iterator.h:1241:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
__miter_base(move_iterator<_Iterator> __it)
^~~~~~~~~~~~
pdb2pka/pMC_mult_wrap.cpp: In member function 'ptrdiff_t swig::SwigPyIterator_T<OutIterator>::distance(const swig::SwigPyIterator&) const [with OutIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >]':
pdb2pka/pMC_mult_wrap.cpp:4301:52: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
return std::distance(current, iters->get_current());
^
In file included from /usr/include/c++/7/bits/stl_algobase.h:66:0,
from /usr/include/c++/7/bits/char_traits.h:39,
from /usr/include/c++/7/string:40,
from /usr/include/c++/7/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:3057:
/usr/include/c++/7/bits/stl_iterator_base_funcs.h: In function 'typename std::iterator_traits<_Iterator>::difference_type std::distance(_InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >]':
/usr/include/c++/7/bits/stl_iterator_base_funcs.h:138:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
distance(_InputIterator __first, _InputIterator __last)
^~~~~~~~
/usr/include/c++/7/bits/stl_iterator_base_funcs.h:138:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_iterator_base_funcs.h:142:42: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__iterator_category(__first));
^
/usr/include/c++/7/bits/stl_iterator_base_funcs.h: In function 'constexpr typename std::iterator_traits<_Iterator>::difference_type std::__distance(_RandomAccessIterator, _RandomAccessIterator, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >]':
/usr/include/c++/7/bits/stl_iterator_base_funcs.h:98:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__distance(_RandomAccessIterator __first, _RandomAccessIterator __last,
^~~~~~~~~~
/usr/include/c++/7/bits/stl_iterator_base_funcs.h:98:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
g++ -o pdb2pka/_pMC_mult.so -Wl,-z,relro -Wl,-z,now -shared pdb2pka/pMC_mult.os pdb2pka/pMC_mult_wrap.os -L/usr/lib -lpython2.7
scons: done building targets.
TARGETS: ['pdb2pqr.py', 'apbs_cgi.cgi', 'visualize.cgi', 'querystatus.cgi', 'src/aconf.py', 'html/server.html', 'pdb2pqr.cgi', 'pdb2pka/substruct/Algorithms.so', 'pdb2pka/_pMC_mult.so']
========================
Configuration Parameters
========================
Version: 2.1.1
Install directory: /usr/share/pdb2pqr/
pdb2pka and ligand support: True
Path to the website directory: http://localhost/pdb2pqr/
PDB2PQR jobs run via the web interface will be forked on the server.
The preferred way to configure the build is by editing the file build_config.py
Run scons with the python that you intend to use with pdb2pqr.
For example: "/opt/bin/python scons/scons.py" will setup pdb2pqr to be run with /opt/bin/python
Run "python scons/scons.py install" to install pdb2pqr in /usr/share/pdb2pqr/
Run "python scons/scons.py basic-test" for a basic functionality test
Run "python scons/scons.py advanced-test" for a single test of ligand and PROPKA support. Requires numpy and PDB2PKA support compiled.
Run "python scons/scons.py complete-test" for a complete test of all functionality EXCEPT PDB2PKA. Requires numpy and PDB2PKA support compiled.
Run "python scons/scons.py pdb2pka-test" for a test of PDB2PKA functionality.
Requires numpy, PDB2PKA support compiled AND the APBS python libraries compiled and installed in the pdb2pka directory.
To setup a web service create a symbolic link to /usr/share/pdb2pqr/ that enables you to view http://localhost/pdb2pqr/ after running "scons/scons.py install"
Run "python scons/scons.py msvs" to build Visual Studio projects for the Algorithms and pMC_mult modules.
VS project generation is not well supported in scons. Resulting projects should build using NMAKE but cannot be used for debugging.
The resulting projects will need to modified to use VS natively to compile the code or debug.
Build succeeded.
make[1]: Leaving directory '/<<BUILDDIR>>/pdb2pqr-2.1.1+dfsg'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch --with python2
dh_testroot -a
dh_prep -a
dh_installdirs -a
debian/rules override_dh_install-arch
make[1]: Entering directory '/<<BUILDDIR>>/pdb2pqr-2.1.1+dfsg'
dh_install -a
dos2unix debian/pdb2pqr/usr/share/pdb2pqr/propka30/propka.py
dos2unix: converting file debian/pdb2pqr/usr/share/pdb2pqr/propka30/propka.py to Unix format...
dos2unix debian/pdb2pqr/usr/share/pdb2pqr/src/psize.py
dos2unix: converting file debian/pdb2pqr/usr/share/pdb2pqr/src/psize.py to Unix format...
make[1]: Leaving directory '/<<BUILDDIR>>/pdb2pqr-2.1.1+dfsg'
dh_installdocs -a
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/<<BUILDDIR>>/pdb2pqr-2.1.1+dfsg'
dh_installchangelogs ChangeLog.md
make[1]: Leaving directory '/<<BUILDDIR>>/pdb2pqr-2.1.1+dfsg'
dh_installexamples -a
debian/rules override_dh_installman-arch
make[1]: Entering directory '/<<BUILDDIR>>/pdb2pqr-2.1.1+dfsg'
dh_installman -a
xmlto -o debian/pdb2pqr/usr/share/man/man1/ man debian/pdb2pqr.1.xml
Note: Writing pdb2pqr.1
xmlto -o debian/pdb2pqr/usr/share/man/man1/ man debian/psize.1.xml
Note: Writing psize.1
xmlto -o debian/pdb2pqr/usr/share/man/man1/ man debian/propka.1.xml
Note: Writing propka.1
make[1]: Leaving directory '/<<BUILDDIR>>/pdb2pqr-2.1.1+dfsg'
dh_python2 -a
W: dh_python2:479: Please add dh-python package to Build-Depends
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
debian/rules override_dh_fixperms-arch
make[1]: Entering directory '/<<BUILDDIR>>/pdb2pqr-2.1.1+dfsg'
dh_fixperms -a
chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/main.py
chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/main_cgi.py
chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/pdb2pka/ligandclean/__init__.py
chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/pdb2pka/pka_routines.py
chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/pdb2pka/pKaIO_compat.py
chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/pdb2pka/pKa_utility_functions_compat.py
chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/src/errors.py
chmod +x debian/pdb2pqr/usr/share/pdb2pqr/propka30/propka.py
chmod +x debian/pdb2pqr/usr/share/pdb2pqr/src/psize.py
make[1]: Leaving directory '/<<BUILDDIR>>/pdb2pqr-2.1.1+dfsg'
dh_missing -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'pdb2pqr-dbgsym' in '../pdb2pqr-dbgsym_2.1.1+dfsg-4_armhf.deb'.
dpkg-deb: building package 'pdb2pqr' in '../pdb2pqr_2.1.1+dfsg-4_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../pdb2pqr_2.1.1+dfsg-4_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build pdb2pqr-2.1.1+dfsg
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-07-20T05:33:04Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
pdb2pqr_2.1.1+dfsg-4_armhf.changes:
-----------------------------------
Format: 1.8
Date: Sat, 14 Jul 2018 16:09:27 +0200
Source: pdb2pqr
Binary: pdb2pqr pdb2pqr-doc
Architecture: armhf
Version: 2.1.1+dfsg-4
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
pdb2pqr - Preparation of protein structures for electrostatics calculations
pdb2pqr-doc - example files accompanying pdb2pqr
Closes: 903759
Changes:
pdb2pqr (2.1.1+dfsg-4) unstable; urgency=medium
.
* Adapt test to new location of examples
Closes: #903759
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Files:
1355fc97912a41ef29619d02811c1a88 297212 debug optional pdb2pqr-dbgsym_2.1.1+dfsg-4_armhf.deb
870b0f5533e8f797f0d41e2b3d8700d2 6310 science optional pdb2pqr_2.1.1+dfsg-4_armhf.buildinfo
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+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
pdb2pqr-dbgsym_2.1.1+dfsg-4_armhf.deb
-------------------------------------
new Debian package, version 2.0.
size 297212 bytes: control archive=604 bytes.
421 bytes, 12 lines control
212 bytes, 2 lines md5sums
Package: pdb2pqr-dbgsym
Source: pdb2pqr
Version: 2.1.1+dfsg-4
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 503
Depends: pdb2pqr (= 2.1.1+dfsg-4)
Section: debug
Priority: optional
Description: debug symbols for pdb2pqr
Build-Ids: eb9e73bed90e24da7e7ac2d10bd67b317a2a99e7 f2d0eb4c12bbce1a94a249d153937f65e10067d0
drwxr-xr-x root/root 0 2018-07-14 14:09 ./
drwxr-xr-x root/root 0 2018-07-14 14:09 ./usr/
drwxr-xr-x root/root 0 2018-07-14 14:09 ./usr/lib/
drwxr-xr-x root/root 0 2018-07-14 14:09 ./usr/lib/debug/
drwxr-xr-x root/root 0 2018-07-14 14:09 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2018-07-14 14:09 ./usr/lib/debug/.build-id/eb/
-rw-r--r-- root/root 29868 2018-07-14 14:09 ./usr/lib/debug/.build-id/eb/9e73bed90e24da7e7ac2d10bd67b317a2a99e7.debug
drwxr-xr-x root/root 0 2018-07-14 14:09 ./usr/lib/debug/.build-id/f2/
-rw-r--r-- root/root 472472 2018-07-14 14:09 ./usr/lib/debug/.build-id/f2/d0eb4c12bbce1a94a249d153937f65e10067d0.debug
drwxr-xr-x root/root 0 2018-07-14 14:09 ./usr/share/
drwxr-xr-x root/root 0 2018-07-14 14:09 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-07-14 14:09 ./usr/share/doc/pdb2pqr-dbgsym -> pdb2pqr
pdb2pqr_2.1.1+dfsg-4_armhf.deb
------------------------------
new Debian package, version 2.0.
size 366768 bytes: control archive=4680 bytes.
1405 bytes, 28 lines control
9624 bytes, 130 lines md5sums
175 bytes, 9 lines * postinst #!/bin/sh
253 bytes, 14 lines * prerm #!/bin/sh
Package: pdb2pqr
Version: 2.1.1+dfsg-4
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2816
Depends: libc6 (>= 2.4), libgcc1 (>= 1:3.5), libpython2.7 (>= 2.7), libstdc++6 (>= 5.2), python:any (>= 2.6.6-7~), python-numpy, python-networkx
Suggests: apbs
Enhances: autodocktools
Replaces: propka
Provides: propka
Section: science
Priority: optional
Homepage: https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html
Description: Preparation of protein structures for electrostatics calculations
PDB2PQR is a Python software package that automates many of the common
tasks of preparing structures for continuum electrostatics calculations.
It thus provides a platform-independent utility for converting protein files
in PDB format to PQR format. These tasks include:
* Adding a limited number of missing heavy atoms to biomolecular structures
* Determining side-chain pKas
* Placing missing hydrogens
* Optimizing the protein for favorable hydrogen bonding
* Assigning charge and radius parameters from a variety of force fields
.
This package also includes PropKa, a tool to modify the protonation state of
protein structures in the Protein Data Bank (PDB) format to match a given pKa
value. It can also be used to refine NMR structures, which often yield
inaccurate pKa values for some residues.
drwxr-xr-x root/root 0 2018-07-14 14:09 ./
drwxr-xr-x root/root 0 2018-07-14 14:09 ./usr/
drwxr-xr-x root/root 0 2018-07-14 14:09 ./usr/bin/
lrwxrwxrwx root/root 0 2018-07-14 14:09 ./usr/bin/pdb2pqr -> ../share/pdb2pqr/pdb2pqr.py
lrwxrwxrwx root/root 0 2018-07-14 14:09 ./usr/bin/propka -> ../share/pdb2pqr/propka30/propka.py
lrwxrwxrwx root/root 0 2018-07-14 14:09 ./usr/bin/psize -> ../share/pdb2pqr/src/psize.py
drwxr-xr-x root/root 0 2018-07-14 14:09 ./usr/lib/
drwxr-xr-x root/root 0 2018-07-14 14:09 ./usr/lib/pdb2pqr/
drwxr-xr-x root/root 0 2018-07-14 14:09 ./usr/lib/pdb2pqr/pdb2pka/
-rw-r--r-- root/root 553904 2018-07-14 14:09 ./usr/lib/pdb2pqr/pdb2pka/_pMC_mult.so
drwxr-xr-x root/root 0 2018-07-14 14:09 ./usr/lib/pdb2pqr/pdb2pka/substruct/
-rw-r--r-- root/root 14436 2018-07-14 14:09 ./usr/lib/pdb2pqr/pdb2pka/substruct/Algorithms.so
drwxr-xr-x root/root 0 2018-07-14 14:09 ./usr/share/
drwxr-xr-x root/root 0 2018-07-14 14:09 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-07-14 14:09 ./usr/share/doc/pdb2pqr/
-rw-r--r-- root/root 31 2016-02-18 19:56 ./usr/share/doc/pdb2pqr/AUTHORS
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| Summary |
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Build Architecture: armhf
Build-Space: 53712
Build-Time: 110
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 775
Job: pdb2pqr_2.1.1+dfsg-4
Machine Architecture: armhf
Package: pdb2pqr
Package-Time: 939
Source-Version: 2.1.1+dfsg-4
Space: 53712
Status: successful
Version: 2.1.1+dfsg-4
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Finished at 2018-07-20T05:33:04Z
Build needed 00:15:39, 53712k disc space