clustalo →
1.2.1-1 →
armhf → 2014-04-19 08:19:54
sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on bm-wb-04
╔══════════════════════════════════════════════════════════════════════════════╗
║ clustalo 1.2.1-1 (armhf) 19 Apr 2014 08:03 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: clustalo
Version: 1.2.1-1
Source Version: 1.2.1-1
Distribution: jessie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/clustalo-T8foBG/clustalo-1.2.1' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/clustalo-T8foBG' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/jessie-staging-armhf-sbuild-85031316-4ad1-4d3f-9636-4a03d5e777f0' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
Get:1 http://172.17.0.1 jessie-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1 jessie-staging/main Sources [7367 kB]
Get:3 http://172.17.0.1 jessie-staging/main armhf Packages [8537 kB]
Ign http://172.17.0.1 jessie-staging/main Translation-en
Fetched 15.9 MB in 37s (425 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
└──────────────────────────────────────────────────────────────────────────────┘
Check APT
─────────
Checking available source versions...
Download source files with APT
──────────────────────────────
Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'clustalo' packaging is maintained in the 'Svn' version control system at:
svn://anonscm.debian.org/debian-med/trunk/packages/clustalo/trunk/
Need to get 1170 kB of source archives.
Get:1 http://172.17.0.1/private/ jessie-staging/main clustalo 1.2.1-1 (dsc) [2128 B]
Get:2 http://172.17.0.1/private/ jessie-staging/main clustalo 1.2.1-1 (tar) [1164 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main clustalo 1.2.1-1 (diff) [3744 B]
Fetched 1170 kB in 0s (3969 kB/s)
Download complete and in download only mode
Check arch
──────────
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-nspjYV/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install core build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 1 newly installed, 0 to remove and 40 not upgraded.
Need to get 0 B/818 B of archives.
After this operation, 0 B of additional disk space will be used.
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 11599 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), dh-autoreconf, libargtable2-dev, doxygen, graphviz
Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), dh-autoreconf, libargtable2-dev, doxygen, graphviz
dpkg-deb: building package `sbuild-build-depends-clustalo-dummy' in `/«BUILDDIR»/resolver-0D6HeH/apt_archive/sbuild-build-depends-clustalo-dummy.deb'.
OK
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install clustalo build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf doxygen file fontconfig fontconfig-config fonts-dejavu-core
gettext gettext-base graphviz groff-base intltool-debian libargtable2-0
libargtable2-dev libargtable2-docs libasprintf0c2 libcairo2 libcdt4
libcgraph5 libcroco3 libdatrie1 libdrm2 libexpat1 libffi6 libfontconfig1
libfreetype6 libgd3 libgl1-mesa-glx libglapi-mesa libglib2.0-0 libgraph4
libgraphite2-3 libgvc5 libgvpr1 libharfbuzz0b libice6 libjbig0 libjpeg8
libltdl7 libmagic1 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0
libpathplan4 libpipeline1 libpixman-1-0 libpng12-0 libsigsegv2 libsm6
libthai-data libthai0 libtiff4 libtool libunistring0 libvpx1 libx11-6
libx11-data libx11-xcb1 libxau6 libxaw7 libxcb-dri2-0 libxcb-dri3-0
libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb1
libxdamage1 libxdmcp6 libxdot4 libxext6 libxfixes3 libxml2 libxmu6 libxpm4
libxrender1 libxshmfence1 libxt6 libxxf86vm1 m4 man-db po-debconf ucf
x11-common
Suggested packages:
autoconf2.13 autoconf-archive gnu-standards autoconf-doc wamerican wordlist
whois vacation dh-make doxygen-latex doxygen-doc doxygen-gui gettext-doc
gsfonts graphviz-doc groff libgd-tools ttf-baekmuk ttf-arphic-gbsn00lp
ttf-arphic-bsmi00lp ttf-arphic-gkai00mp ttf-arphic-bkai00mp libtool-doc
automaken gfortran fortran95-compiler gcj-jdk less www-browser
libmail-box-perl
Recommended packages:
curl wget lynx-cur libasprintf-dev libgettextpo-dev ttf-liberation
libgl1-mesa-dri libglib2.0-data shared-mime-info libltdl-dev xml-core
libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf doxygen file fontconfig fontconfig-config fonts-dejavu-core
gettext gettext-base graphviz groff-base intltool-debian libargtable2-0
libargtable2-dev libargtable2-docs libasprintf0c2 libcairo2 libcdt4
libcgraph5 libcroco3 libdatrie1 libdrm2 libexpat1 libffi6 libfontconfig1
libfreetype6 libgd3 libgl1-mesa-glx libglapi-mesa libglib2.0-0 libgraph4
libgraphite2-3 libgvc5 libgvpr1 libharfbuzz0b libice6 libjbig0 libjpeg8
libltdl7 libmagic1 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0
libpathplan4 libpipeline1 libpixman-1-0 libpng12-0 libsigsegv2 libsm6
libthai-data libthai0 libtiff4 libtool libunistring0 libvpx1 libx11-6
libx11-data libx11-xcb1 libxau6 libxaw7 libxcb-dri2-0 libxcb-dri3-0
libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb1
libxdamage1 libxdmcp6 libxdot4 libxext6 libxfixes3 libxml2 libxmu6 libxpm4
libxrender1 libxshmfence1 libxt6 libxxf86vm1 m4 man-db po-debconf
sbuild-build-depends-clustalo-dummy ucf x11-common
0 upgraded, 91 newly installed, 0 to remove and 40 not upgraded.
Need to get 26.2 MB/26.2 MB of archives.
After this operation, 62.6 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ jessie-staging/main libpipeline1 armhf 1.3.0-1 [21.1 kB]
Get:2 http://172.17.0.1/private/ jessie-staging/main groff-base armhf 1.22.2-5 [962 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main bsdmainutils armhf 9.0.5 [206 kB]
Get:4 http://172.17.0.1/private/ jessie-staging/main man-db armhf 2.6.7.1-1 [964 kB]
Get:5 http://172.17.0.1/private/ jessie-staging/main libasprintf0c2 armhf 0.18.3.2-1 [29.0 kB]
Get:6 http://172.17.0.1/private/ jessie-staging/main libmagic1 armhf 1:5.17-1 [225 kB]
Get:7 http://172.17.0.1/private/ jessie-staging/main libxml2 armhf 2.9.1+dfsg1-3 [836 kB]
Get:8 http://172.17.0.1/private/ jessie-staging/main libexpat1 armhf 2.1.0-4 [117 kB]
Get:9 http://172.17.0.1/private/ jessie-staging/main libpng12-0 armhf 1.2.50-1 [180 kB]
Get:10 http://172.17.0.1/private/ jessie-staging/main libfreetype6 armhf 2.5.2-1 [397 kB]
Get:11 http://172.17.0.1/private/ jessie-staging/main ucf all 3.0027+nmu1 [70.6 kB]
Get:12 http://172.17.0.1/private/ jessie-staging/main fonts-dejavu-core all 2.34-1 [1047 kB]
Get:13 http://172.17.0.1/private/ jessie-staging/main fontconfig-config all 2.11.0-2 [270 kB]
Get:14 http://172.17.0.1/private/ jessie-staging/main libfontconfig1 armhf 2.11.0-2 [329 kB]
Get:15 http://172.17.0.1/private/ jessie-staging/main libdrm2 armhf 2.4.52-1 [25.5 kB]
Get:16 http://172.17.0.1/private/ jessie-staging/main libglapi-mesa armhf 10.1.0-5 [63.4 kB]
Get:17 http://172.17.0.1/private/ jessie-staging/main libxau6 armhf 1:1.0.8-1 [19.9 kB]
Get:18 http://172.17.0.1/private/ jessie-staging/main libxdmcp6 armhf 1:1.1.1-1 [24.6 kB]
Get:19 http://172.17.0.1/private/ jessie-staging/main libxcb1 armhf 1.10-2 [36.9 kB]
Get:20 http://172.17.0.1/private/ jessie-staging/main libx11-data all 2:1.6.2-1 [125 kB]
Get:21 http://172.17.0.1/private/ jessie-staging/main libx11-6 armhf 2:1.6.2-1 [867 kB]
Get:22 http://172.17.0.1/private/ jessie-staging/main libx11-xcb1 armhf 2:1.6.2-1 [163 kB]
Get:23 http://172.17.0.1/private/ jessie-staging/main libxcb-dri2-0 armhf 1.10-2 [11.8 kB]
Get:24 http://172.17.0.1/private/ jessie-staging/main libxcb-dri3-0 armhf 1.10-2 [10.3 kB]
Get:25 http://172.17.0.1/private/ jessie-staging/main libxcb-glx0 armhf 1.10-2 [23.2 kB]
Get:26 http://172.17.0.1/private/ jessie-staging/main libxcb-present0 armhf 1.10-2 [10.4 kB]
Get:27 http://172.17.0.1/private/ jessie-staging/main libxcb-sync1 armhf 1.10-2 [12.9 kB]
Get:28 http://172.17.0.1/private/ jessie-staging/main libxfixes3 armhf 1:5.0.1-1 [21.0 kB]
Get:29 http://172.17.0.1/private/ jessie-staging/main libxdamage1 armhf 1:1.1.4-1 [14.6 kB]
Get:30 http://172.17.0.1/private/ jessie-staging/main libxext6 armhf 2:1.3.2-1 [51.1 kB]
Get:31 http://172.17.0.1/private/ jessie-staging/main libxshmfence1 armhf 1.1-2 [6736 B]
Get:32 http://172.17.0.1/private/ jessie-staging/main libxxf86vm1 armhf 1:1.1.3-1 [20.0 kB]
Get:33 http://172.17.0.1/private/ jessie-staging/main libgl1-mesa-glx armhf 10.1.0-5 [134 kB]
Get:34 http://172.17.0.1/private/ jessie-staging/main libpixman-1-0 armhf 0.32.4-1 [476 kB]
Get:35 http://172.17.0.1/private/ jessie-staging/main libxcb-render0 armhf 1.10-2 [15.7 kB]
Get:36 http://172.17.0.1/private/ jessie-staging/main libxcb-shm0 armhf 1.10-2 [10.8 kB]
Get:37 http://172.17.0.1/private/ jessie-staging/main libxrender1 armhf 1:0.9.8-1 [30.4 kB]
Get:38 http://172.17.0.1/private/ jessie-staging/main libcairo2 armhf 1.12.16-2+rpi1 [894 kB]
Get:39 http://172.17.0.1/private/ jessie-staging/main libffi6 armhf 3.1~rc1+r3.0.13-12 [17.6 kB]
Get:40 http://172.17.0.1/private/ jessie-staging/main libglib2.0-0 armhf 2.40.0-2+rpi1 [2249 kB]
Get:41 http://172.17.0.1/private/ jessie-staging/main libcroco3 armhf 0.6.8-2 [119 kB]
Get:42 http://172.17.0.1/private/ jessie-staging/main libdatrie1 armhf 0.2.8-1 [29.1 kB]
Get:43 http://172.17.0.1/private/ jessie-staging/main libjpeg8 armhf 8d-2 [133 kB]
Get:44 http://172.17.0.1/private/ jessie-staging/main libjbig0 armhf 2.0-2 [31.5 kB]
Get:45 http://172.17.0.1/private/ jessie-staging/main libtiff4 armhf 3.9.7-3 [190 kB]
Get:46 http://172.17.0.1/private/ jessie-staging/main libvpx1 armhf 1.3.0-2+rpi1 [363 kB]
Get:47 http://172.17.0.1/private/ jessie-staging/main libxpm4 armhf 1:3.5.10-1 [44.9 kB]
Get:48 http://172.17.0.1/private/ jessie-staging/main libgd3 armhf 2.1.0-3 [156 kB]
Get:49 http://172.17.0.1/private/ jessie-staging/main libgraphite2-3 armhf 1.2.4-2 [48.0 kB]
Get:50 http://172.17.0.1/private/ jessie-staging/main libharfbuzz0b armhf 0.9.27-1 [430 kB]
Get:51 http://172.17.0.1/private/ jessie-staging/main x11-common all 1:7.7+7 [287 kB]
Get:52 http://172.17.0.1/private/ jessie-staging/main libice6 armhf 2:1.0.8-2 [56.2 kB]
Get:53 http://172.17.0.1/private/ jessie-staging/main libltdl7 armhf 2.4.2-1.7 [349 kB]
Get:54 http://172.17.0.1/private/ jessie-staging/main libthai-data all 0.1.20-3 [157 kB]
Get:55 http://172.17.0.1/private/ jessie-staging/main libthai0 armhf 0.1.20-3 [41.6 kB]
Get:56 http://172.17.0.1/private/ jessie-staging/main fontconfig armhf 2.11.0-2 [407 kB]
Get:57 http://172.17.0.1/private/ jessie-staging/main libpango-1.0-0 armhf 1.36.3-1 [265 kB]
Get:58 http://172.17.0.1/private/ jessie-staging/main libpangoft2-1.0-0 armhf 1.36.3-1 [199 kB]
Get:59 http://172.17.0.1/private/ jessie-staging/main libpangocairo-1.0-0 armhf 1.36.3-1 [189 kB]
Get:60 http://172.17.0.1/private/ jessie-staging/main libsigsegv2 armhf 2.10-2 [29.2 kB]
Get:61 http://172.17.0.1/private/ jessie-staging/main libsm6 armhf 2:1.2.1-2 [32.5 kB]
Get:62 http://172.17.0.1/private/ jessie-staging/main libunistring0 armhf 0.9.3-5 [408 kB]
Get:63 http://172.17.0.1/private/ jessie-staging/main libxt6 armhf 1:1.1.4-1 [183 kB]
Get:64 http://172.17.0.1/private/ jessie-staging/main libxmu6 armhf 2:1.1.1-1 [59.1 kB]
Get:65 http://172.17.0.1/private/ jessie-staging/main libxaw7 armhf 2:1.0.12-1 [158 kB]
Get:66 http://172.17.0.1/private/ jessie-staging/main file armhf 1:5.17-1 [55.3 kB]
Get:67 http://172.17.0.1/private/ jessie-staging/main gettext-base armhf 0.18.3.2-1 [112 kB]
Get:68 http://172.17.0.1/private/ jessie-staging/main m4 armhf 1.4.17-3 [238 kB]
Get:69 http://172.17.0.1/private/ jessie-staging/main autoconf all 2.69-6 [340 kB]
Get:70 http://172.17.0.1/private/ jessie-staging/main autotools-dev all 20130810.1 [69.6 kB]
Get:71 http://172.17.0.1/private/ jessie-staging/main automake all 1:1.14.1-3 [725 kB]
Get:72 http://172.17.0.1/private/ jessie-staging/main autopoint all 0.18.3.2-1 [393 kB]
Get:73 http://172.17.0.1/private/ jessie-staging/main gettext armhf 0.18.3.2-1 [1137 kB]
Get:74 http://172.17.0.1/private/ jessie-staging/main intltool-debian all 0.35.0+20060710.1 [29.8 kB]
Get:75 http://172.17.0.1/private/ jessie-staging/main po-debconf all 1.0.16+nmu2 [223 kB]
Get:76 http://172.17.0.1/private/ jessie-staging/main debhelper all 9.20140228 [691 kB]
Get:77 http://172.17.0.1/private/ jessie-staging/main libtool armhf 2.4.2-1.7 [505 kB]
Get:78 http://172.17.0.1/private/ jessie-staging/main dh-autoreconf all 9 [15.5 kB]
Get:79 http://172.17.0.1/private/ jessie-staging/main doxygen armhf 1.8.6-2 [2148 kB]
Get:80 http://172.17.0.1/private/ jessie-staging/main libcdt4 armhf 2.26.3-16.2 [55.4 kB]
Get:81 http://172.17.0.1/private/ jessie-staging/main libcgraph5 armhf 2.26.3-16.2 [73.2 kB]
Get:82 http://172.17.0.1/private/ jessie-staging/main libgraph4 armhf 2.26.3-16.2 [64.7 kB]
Get:83 http://172.17.0.1/private/ jessie-staging/main libpathplan4 armhf 2.26.3-16.2 [59.4 kB]
Get:84 http://172.17.0.1/private/ jessie-staging/main libxdot4 armhf 2.26.3-16.2 [51.9 kB]
Get:85 http://172.17.0.1/private/ jessie-staging/main libgvc5 armhf 2.26.3-16.2 [366 kB]
Get:86 http://172.17.0.1/private/ jessie-staging/main libgvpr1 armhf 2.26.3-16.2 [186 kB]
Get:87 http://172.17.0.1/private/ jessie-staging/main graphviz armhf 2.26.3-16.2 [284 kB]
Get:88 http://172.17.0.1/private/ jessie-staging/main libargtable2-0 armhf 12-1 [17.0 kB]
Get:89 http://172.17.0.1/private/ jessie-staging/main libargtable2-docs all 12-1 [2958 kB]
Get:90 http://172.17.0.1/private/ jessie-staging/main libargtable2-dev armhf 12-1 [57.9 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libpipeline1:armhf (1.3.0-1) ...
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Setting up bsdmainutils (9.0.5) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
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Setting up libxau6:armhf (1:1.0.8-1) ...
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Setting up libgl1-mesa-glx:armhf (10.1.0-5) ...
Setting up libpixman-1-0:armhf (0.32.4-1) ...
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Setting up libcairo2:armhf (1.12.16-2+rpi1) ...
Setting up libffi6:armhf (3.1~rc1+r3.0.13-12) ...
Setting up libglib2.0-0:armhf (2.40.0-2+rpi1) ...
No schema files found: doing nothing.
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Setting up libdatrie1:armhf (0.2.8-1) ...
Setting up libjpeg8:armhf (8d-2) ...
Setting up libjbig0:armhf (2.0-2) ...
Setting up libtiff4:armhf (3.9.7-3) ...
Setting up libvpx1:armhf (1.3.0-2+rpi1) ...
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Setting up libgd3:armhf (2.1.0-3) ...
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Setting up libharfbuzz0b:armhf (0.9.27-1) ...
Setting up x11-common (1:7.7+7) ...
update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
All runlevel operations denied by policy
invoke-rc.d: policy-rc.d denied execution of start.
Setting up libice6:armhf (2:1.0.8-2) ...
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Setting up fontconfig (2.11.0-2) ...
Regenerating fonts cache... done.
Setting up libpango-1.0-0:armhf (1.36.3-1) ...
Setting up libpangoft2-1.0-0:armhf (1.36.3-1) ...
Setting up libpangocairo-1.0-0:armhf (1.36.3-1) ...
Setting up libsigsegv2:armhf (2.10-2) ...
Setting up libsm6:armhf (2:1.2.1-2) ...
Setting up libunistring0:armhf (0.9.3-5) ...
Setting up libxt6:armhf (1:1.1.4-1) ...
Setting up libxmu6:armhf (2:1.1.1-1) ...
Setting up libxaw7:armhf (2:1.0.12-1) ...
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Setting up automake (1:1.14.1-3) ...
update-alternatives: using /usr/bin/automake-1.14 to provide /usr/bin/automake (automake) in auto mode
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Setting up dh-autoreconf (9) ...
Setting up doxygen (1.8.6-2) ...
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Setting up libcgraph5 (2.26.3-16.2) ...
Setting up libgraph4 (2.26.3-16.2) ...
Setting up libpathplan4 (2.26.3-16.2) ...
Setting up libxdot4 (2.26.3-16.2) ...
Setting up libgvc5 (2.26.3-16.2) ...
Setting up libgvpr1 (2.26.3-16.2) ...
Setting up graphviz (2.26.3-16.2) ...
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Processing triggers for libc-bin (2.18-4) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.13-1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.24-3 dpkg-dev_1.17.6+rpi1 g++-4.8_4.8.2-16 gcc-4.8_4.8.2-16 libc6-dev_2.18-4 libstdc++-4.8-dev_4.8.2-16 libstdc++6_4.8.2-16 linux-libc-dev_3.12.6-2+rpi1
Package versions: apt_0.9.15.4 autoconf_2.69-6 automake_1:1.14.1-3 autopoint_0.18.3.2-1 autotools-dev_20130810.1 base-files_7.2+rpi1 base-passwd_3.5.28 bash_4.2+dfsg-1 binutils_2.24-3 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.6 build-essential_11.6 bzip2_1.0.6-5 coreutils_8.21-1 cpio_2.11+dfsg-1 cpp_4:4.8.2-2 cpp-4.8_4.8.2-16 dash_0.5.7-4 debconf_1.5.52 debconf-i18n_1.5.52 debfoster_2.7-1.2 debhelper_9.20140228 debianutils_4.4 dh-autoreconf_9 diffutils_1:3.3-1 doxygen_1.8.6-2 dpkg_1.17.6+rpi1 dpkg-dev_1.17.6+rpi1 e2fslibs_1.42.9-3 e2fsprogs_1.42.9-3 fakeroot_1.18.4-2 file_1:5.17-1 findutils_4.4.2-7 fontconfig_2.11.0-2 fontconfig-config_2.11.0-2 fonts-dejavu-core_2.34-1 g++_4:4.8.2-2 g++-4.8_4.8.2-16 gcc_4:4.8.2-2 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-10+rpi1 gcc-4.8_4.8.2-16 gcc-4.8-base_4.8.2-16 gettext_0.18.3.2-1 gettext-base_0.18.3.2-1 gnupg_1.4.16-1.1 gpgv_1.4.16-1.1 graphviz_2.26.3-16.2 grep_2.16-1 groff-base_1.22.2-5 gzip_1.6-3 hostname_3.15 initramfs-tools_0.115 initscripts_2.88dsf-51 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 klibc-utils_2.0.2-1+rpi1 kmod_16-2 libacl1_2.2.52-1 libapt-pkg4.12_0.9.15.4 libargtable2-0_12-1 libargtable2-dev_12-1 libargtable2-docs_12-1 libasan0_4.8.2-16 libasprintf0c2_0.18.3.2-1 libatomic1_4.8.2-16 libattr1_1:2.4.47-1 libaudit-common_1:2.3.3-4 libaudit1_1:2.3.3-4 libblkid1_2.20.1-5.6 libbz2-1.0_1.0.6-5 libc-bin_2.18-4 libc-dev-bin_2.18-4 libc6_2.18-4 libc6-dev_2.18-4 libcairo2_1.12.16-2+rpi1 libcap2_1:2.22-1.2 libcdt4_2.26.3-16.2 libcgraph5_2.26.3-16.2 libcloog-isl4_0.18.2-1 libcomerr2_1.42.9-3 libcroco3_0.6.8-2 libdatrie1_0.2.8-1 libdb5.1_5.1.29-6 libdb5.3_5.3.28-3 libdbus-1-3_1.8.0-1 libdpkg-perl_1.17.6+rpi1 libdrm2_2.4.52-1 libexpat1_2.1.0-4 libffi6_3.1~rc1+r3.0.13-12 libfontconfig1_2.11.0-2 libfreetype6_2.5.2-1 libgc1c2_1:7.2d-6 libgcc-4.8-dev_4.8.2-16 libgcc1_1:4.8.2-16 libgd3_2.1.0-3 libgdbm3_1.8.3-12 libgl1-mesa-glx_10.1.0-5 libglapi-mesa_10.1.0-5 libglib2.0-0_2.40.0-2+rpi1 libgmp10_2:5.1.3+dfsg-1 libgomp1_4.8.2-16 libgraph4_2.26.3-16.2 libgraphite2-3_1.2.4-2 libgvc5_2.26.3-16.2 libgvpr1_2.26.3-16.2 libharfbuzz0b_0.9.27-1 libice6_2:1.0.8-2 libisl10_0.12.2-1 libjbig0_2.0-2 libjpeg8_8d-2 libklibc_2.0.2-1+rpi1 libkmod2_16-2 liblocale-gettext-perl_1.05-7+b3 libltdl7_2.4.2-1.7 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.17-1 libmount1_2.20.1-5.6 libmpc3_1.0.1-1 libmpfr4_3.1.2-1 libncurses5_5.9+20140118-1 libncursesw5_5.9+20140118-1 libpam-modules_1.1.8-2 libpam-modules-bin_1.1.8-2 libpam-runtime_1.1.8-2 libpam0g_1.1.8-2 libpango-1.0-0_1.36.3-1 libpangocairo-1.0-0_1.36.3-1 libpangoft2-1.0-0_1.36.3-1 libpathplan4_2.26.3-16.2 libpcre3_1:8.31-2 libpipeline1_1.3.0-1 libpixman-1-0_0.32.4-1 libpng12-0_1.2.50-1 libprocps0_1:3.3.4-2 libprocps3_1:3.3.9-2 libreadline6_6.2+dfsg-0.1 libselinux1_2.2.2-1 libsemanage-common_2.2-1 libsemanage1_2.2-1 libsepol1_2.2-1 libsigsegv2_2.10-2 libslang2_2.2.4-16 libsm6_2:1.2.1-2 libss2_1.42.9-3 libstdc++-4.8-dev_4.8.2-16 libstdc++6_4.8.2-16 libtext-charwidth-perl_0.04-7+b3 libtext-iconv-perl_1.7-5+b3 libtext-wrapi18n-perl_0.06-7 libthai-data_0.1.20-3 libthai0_0.1.20-3 libtiff4_3.9.7-3 libtimedate-perl_2.3000-1 libtinfo5_5.9+20140118-1 libtool_2.4.2-1.7 libudev1_204-7 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23.3 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.6 libvpx1_1.3.0-2+rpi1 libx11-6_2:1.6.2-1 libx11-data_2:1.6.2-1 libx11-xcb1_2:1.6.2-1 libxau6_1:1.0.8-1 libxaw7_2:1.0.12-1 libxcb-dri2-0_1.10-2 libxcb-dri3-0_1.10-2 libxcb-glx0_1.10-2 libxcb-present0_1.10-2 libxcb-render0_1.10-2 libxcb-shm0_1.10-2 libxcb-sync1_1.10-2 libxcb1_1.10-2 libxdamage1_1:1.1.4-1 libxdmcp6_1:1.1.1-1 libxdot4_2.26.3-16.2 libxext6_2:1.3.2-1 libxfixes3_1:5.0.1-1 libxml2_2.9.1+dfsg1-3 libxmu6_2:1.1.1-1 libxpm4_1:3.5.10-1 libxrender1_1:0.9.8-1 libxshmfence1_1.1-2 libxt6_1:1.1.4-1 libxxf86vm1_1:1.1.3-1 linux-libc-dev_3.12.6-2+rpi1 login_1:4.1.5.1-1 lsb-base_4.1+Debian12+rpi1 m4_1.4.17-3 make_3.81-8.3 makedev_2.3.1-93 man-db_2.6.7.1-1 mawk_1.3.3-17 mount_2.20.1-5.6 multiarch-support_2.18-4 nano_2.2.6-1 ncurses-base_5.9+20140118-1 ncurses-bin_5.9+20140118-1 passwd_1:4.1.5.1-1 patch_2.7.1-4 perl_5.18.2-2 perl-base_5.18.2-2 perl-modules_5.18.2-2 plymouth_0.8.8-6+deb8u3 po-debconf_1.0.16+nmu2 procps_1:3.3.9-2 raspbian-archive-keyring_20120528.2 readline-common_6.2+dfsg-0.1 sbuild-build-depends-clustalo-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.2.2-4 sensible-utils_0.0.9 sysv-rc_2.88dsf-51 sysvinit_2.88dsf-51 sysvinit-core_2.88dsf-51 sysvinit-utils_2.88dsf-51 tar_1.27.1-1 tzdata_2013i-1 ucf_3.0027+nmu1 udev_204-7 util-linux_2.20.1-5.6 x11-common_1:7.7+7 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.8.dfsg-1
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Sun Apr 13 19:21:39 2014 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./clustalo_1.2.1-1.dsc
dpkg-source: info: extracting clustalo in clustalo-1.2.1
dpkg-source: info: unpacking clustalo_1.2.1.orig.tar.gz
dpkg-source: info: unpacking clustalo_1.2.1-1.debian.tar.xz
Check disc space
────────────────
Sufficient free space for build
User Environment
────────────────
APT_CONFIG=/var/lib/sbuild/apt.conf
COLUMNS=80
CONSOLE=/dev/console
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INIT_VERSION=sysvinit-2.88
LC_ALL=POSIX
LINES=24
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PREVLEVEL=N
PWD=/
RUNLEVEL=2
SCHROOT_ALIAS_NAME=jessie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=jessie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=jessie-staging-armhf-sbuild-85031316-4ad1-4d3f-9636-4a03d5e777f0
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
init=/sbin/init
previous=N
rootmnt=/root
runlevel=2
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package clustalo
dpkg-buildpackage: source version 1.2.1-1
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build clustalo-1.2.1
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
dh clean --with autoreconf
dh_testdir
dh_auto_clean
dh_autoreconf_clean
debian/rules override_dh_clean
make[1]: Entering directory `/«PKGBUILDDIR»'
dh_clean
rm -f _configs.sed
rm -rf doc
make[1]: Leaving directory `/«PKGBUILDDIR»'
debian/rules build-arch
dh build-arch --with autoreconf
dh_testdir -a
dh_autoreconf -a
configure.ac:141: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2661: _AC_LINK_IFELSE is expanded from...
../../lib/autoconf/general.m4:2678: AC_LINK_IFELSE is expanded from...
m4/libtool.m4:1022: _LT_SYS_MODULE_PATH_AIX is expanded from...
m4/libtool.m4:4170: _LT_LINKER_SHLIBS is expanded from...
m4/libtool.m4:5249: _LT_LANG_C_CONFIG is expanded from...
m4/libtool.m4:138: _LT_SETUP is expanded from...
m4/libtool.m4:67: LT_INIT is expanded from...
configure.ac:141: the top level
configure.ac:141: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2661: _AC_LINK_IFELSE is expanded from...
../../lib/autoconf/general.m4:2678: AC_LINK_IFELSE is expanded from...
m4/libtool.m4:4170: _LT_LINKER_SHLIBS is expanded from...
m4/libtool.m4:5249: _LT_LANG_C_CONFIG is expanded from...
m4/libtool.m4:138: _LT_SETUP is expanded from...
m4/libtool.m4:67: LT_INIT is expanded from...
configure.ac:141: the top level
configure.ac:163: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2661: _AC_LINK_IFELSE is expanded from...
../../lib/autoconf/general.m4:2678: AC_LINK_IFELSE is expanded from...
m4/libtool.m4:1022: _LT_SYS_MODULE_PATH_AIX is expanded from...
m4/libtool.m4:5356: _LT_LANG_CXX_CONFIG is expanded from...
m4/libtool.m4:785: _LT_LANG is expanded from...
m4/libtool.m4:768: LT_LANG is expanded from...
configure.ac:163: the top level
configure.ac:141: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2661: _AC_LINK_IFELSE is expanded from...
../../lib/autoconf/general.m4:2678: AC_LINK_IFELSE is expanded from...
m4/libtool.m4:1022: _LT_SYS_MODULE_PATH_AIX is expanded from...
m4/libtool.m4:4170: _LT_LINKER_SHLIBS is expanded from...
m4/libtool.m4:5249: _LT_LANG_C_CONFIG is expanded from...
m4/libtool.m4:138: _LT_SETUP is expanded from...
m4/libtool.m4:67: LT_INIT is expanded from...
configure.ac:141: the top level
configure.ac:141: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2661: _AC_LINK_IFELSE is expanded from...
../../lib/autoconf/general.m4:2678: AC_LINK_IFELSE is expanded from...
m4/libtool.m4:4170: _LT_LINKER_SHLIBS is expanded from...
m4/libtool.m4:5249: _LT_LANG_C_CONFIG is expanded from...
m4/libtool.m4:138: _LT_SETUP is expanded from...
m4/libtool.m4:67: LT_INIT is expanded from...
configure.ac:141: the top level
configure.ac:163: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2661: _AC_LINK_IFELSE is expanded from...
../../lib/autoconf/general.m4:2678: AC_LINK_IFELSE is expanded from...
m4/libtool.m4:1022: _LT_SYS_MODULE_PATH_AIX is expanded from...
m4/libtool.m4:5356: _LT_LANG_CXX_CONFIG is expanded from...
m4/libtool.m4:785: _LT_LANG is expanded from...
m4/libtool.m4:768: LT_LANG is expanded from...
configure.ac:163: the top level
configure.ac:141: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2661: _AC_LINK_IFELSE is expanded from...
../../lib/autoconf/general.m4:2678: AC_LINK_IFELSE is expanded from...
m4/libtool.m4:1022: _LT_SYS_MODULE_PATH_AIX is expanded from...
m4/libtool.m4:4170: _LT_LINKER_SHLIBS is expanded from...
m4/libtool.m4:5249: _LT_LANG_C_CONFIG is expanded from...
m4/libtool.m4:138: _LT_SETUP is expanded from...
m4/libtool.m4:67: LT_INIT is expanded from...
configure.ac:141: the top level
configure.ac:141: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2661: _AC_LINK_IFELSE is expanded from...
../../lib/autoconf/general.m4:2678: AC_LINK_IFELSE is expanded from...
m4/libtool.m4:4170: _LT_LINKER_SHLIBS is expanded from...
m4/libtool.m4:5249: _LT_LANG_C_CONFIG is expanded from...
m4/libtool.m4:138: _LT_SETUP is expanded from...
m4/libtool.m4:67: LT_INIT is expanded from...
configure.ac:141: the top level
configure.ac:163: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
../../lib/autoconf/general.m4:2661: _AC_LINK_IFELSE is expanded from...
../../lib/autoconf/general.m4:2678: AC_LINK_IFELSE is expanded from...
m4/libtool.m4:1022: _LT_SYS_MODULE_PATH_AIX is expanded from...
m4/libtool.m4:5356: _LT_LANG_CXX_CONFIG is expanded from...
m4/libtool.m4:785: _LT_LANG is expanded from...
m4/libtool.m4:768: LT_LANG is expanded from...
configure.ac:163: the top level
libtoolize: putting auxiliary files in `.'.
libtoolize: copying file `./ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIR, `m4'.
libtoolize: copying file `m4/libtool.m4'
libtoolize: copying file `m4/ltoptions.m4'
libtoolize: copying file `m4/ltsugar.m4'
libtoolize: copying file `m4/ltversion.m4'
libtoolize: copying file `m4/lt~obsolete.m4'
configure.ac:124: installing './compile'
dh_auto_configure -a
configure: WARNING: unrecognized options: --disable-maintainer-mode
configure:
Welcome to Clustal Omega - version 1.2.1 (AndreaGiacomo)
+NMMMMMMMMMS=
MMMMM? :MMMMM8
IMMMMS MMMMM,
~MMMMN ,MMMMM
=MMMMM MMMMM
?MMMMM +MMMMM
MMMMMS MMMMM
MMMMM MMMMM:
MMMMM MMMMM+
MMMMM MMMMM~
MMMMM MMMMM
MMMMMZ MMMMM
MMMMM ,MMMMZ
MMMM8 MMMM+
MMMMS MMMM,
MMMMO MMMM
,N SMMM MMM8 +8
,M7 M+ M+ :M8
,MMMMMMMMMMMMI MMMMMMMMMMMM8
,MMMMMMMMMMMM8 MMMMMMMMMMMM8
,MMMMMMMMMMMMN MMMMMMMMMMMM8
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for style of include used by make... GNU
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking build system type... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
checking whether make sets $(MAKE)... (cached) yes
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 805306365
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert arm-unknown-linux-gnueabihf file names to arm-unknown-linux-gnueabihf format... func_convert_file_noop
checking how to convert arm-unknown-linux-gnueabihf file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
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checking if mt is a manifest tool... no
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checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
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checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
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checking whether to build static libraries... yes
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking whether gcc understands -c and -o together... (cached) yes
checking dependency style of gcc... (cached) none
checking how to run the C preprocessor... gcc -E
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... none
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking how to run the C++ preprocessor... g++ -E
checking for ANSI C header files... (cached) yes
checking assert.h usability... yes
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checking time.h usability... yes
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checking for an ANSI C-conforming const... yes
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checking for inline... inline
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checking for ntons... no
checking for ntonl... no
checking size of unsigned short... 2
checking size of unsigned int... 4
checking size of unsigned long... 4
checking size of unsigned long long... 8
checking for stroul... no
checking for strtoull... yes
checking for ftello... yes
checking for fseeko... yes
checking for ftello64... yes
checking for fseeko64... yes
checking for ftell64... no
checking for fseek64... no
checking for off_t... yes
checking size of fpos_t... 12
checking if malloc debugging is wanted... no
checking whether to build with debug information... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating clustalo.pc
config.status: creating Doxyfile
config.status: creating src/clustal/Makefile
config.status: creating src/hhalign/Makefile
config.status: creating src/kmpp/Makefile
config.status: creating src/squid/Makefile
config.status: creating src/config.h
config.status: executing src/clustal-omega-config.h commands
config.status: creating src/clustal-omega-config.h - prefix CLUSTAL_OMEGA for src/config.h defines
config.status: executing depfiles commands
config.status: executing libtool commands
configure: WARNING: unrecognized options: --disable-maintainer-mode
dh_auto_build -a
make[1]: Entering directory `/«PKGBUILDDIR»'
Making all in src
make[2]: Entering directory `/«PKGBUILDDIR»/src'
make all-recursive
make[3]: Entering directory `/«PKGBUILDDIR»/src'
Making all in hhalign
make[4]: Entering directory `/«PKGBUILDDIR»/src/hhalign'
/bin/bash ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o hhalign.lo hhalign.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c hhalign.cpp -fPIC -DPIC -o .libs/hhalign.o
In file included from hhalign.cpp:62:0:
hhutil-C.h: In function 'void ReadDefaultsFile(int&, char**)':
hhutil-C.h:516:53: warning: ISO C++ does not support variable-length array types [-Wvla]
argv_conf[argc_conf]=new(char[strlen(c_first)+1]);
^
hhutil-C.h:521:56: warning: ISO C++ does not support variable-length array types [-Wvla]
argv_conf[argc_conf]=new(char[strlen(c_first)+1]);
^
In file included from hhalign.cpp:70:0:
hhhmm-C.h: In member function 'HMM& HMM::operator=(HMM&)':
hhhmm-C.h:188:44: warning: ISO C++ does not support variable-length array types [-Wvla]
sname[k]=new(char[strlen(q.sname[k])+1]);
^
hhhmm-C.h:193:40: warning: ISO C++ does not support variable-length array types [-Wvla]
seq[k]=new(char[strlen(q.seq[k])+1]);
^
hhhmm-C.h: In member function 'int HMM::Read(FILE*, char*)':
hhhmm-C.h:329:48: warning: ISO C++ does not support variable-length array types [-Wvla]
char *cur_seq = new(char[par.maxColCnt]); //Sequence currently read in
^
hhhmm-C.h:360:43: warning: ISO C++ does not support variable-length array types [-Wvla]
seq[k-1]=new(char[strlen(cur_seq)+1]);
^
hhhmm-C.h:367:43: warning: ISO C++ does not support variable-length array types [-Wvla]
sname[k] = new (char[strlen(line+1)+1]); //+1 for terminating '\0'
^
hhhmm-C.h:463:40: warning: ISO C++ does not support variable-length array types [-Wvla]
seq[k]=new(char[strlen(cur_seq)+1]);
^
hhhmm-C.h: In member function 'int HMM::ReadHMMer(FILE*, char*)':
hhhmm-C.h:735:59: warning: ISO C++ does not support variable-length array types [-Wvla]
seq[nsa_dssp] = new(char[/*MAXRES*/par.maxResLen+2]);
^
hhhmm-C.h:756:59: warning: ISO C++ does not support variable-length array types [-Wvla]
seq[nss_pred] = new(char[/*MAXRES*/par.maxResLen+2]);
^
hhhmm-C.h:777:59: warning: ISO C++ does not support variable-length array types [-Wvla]
seq[nss_conf] = new(char[/*MAXRES*/par.maxResLen+2]);
^
hhhmm-C.h:859:55: warning: ISO C++ does not support variable-length array types [-Wvla]
seq[nss_dssp] = new(char[/*MAXRES*/par.maxResLen+2]);
^
hhhmm-C.h:1035:46: warning: ISO C++ does not support variable-length array types [-Wvla]
sname[k+1]=new(char[strlen(longname)+1]);
^
hhhmm-C.h:1037:27: warning: ISO C++ does not support variable-length array types [-Wvla]
seq[k]=new(char[L+2]);
^
hhhmm-C.h:1040:29: warning: ISO C++ does not support variable-length array types [-Wvla]
seq[k+1]=new(char[L+2]);
^
hhhmm-C.h:1058:44: warning: ISO C++ does not support variable-length array types [-Wvla]
sname[k]=new(char[strlen(longname)+1]);
^
hhhmm-C.h:1062:27: warning: ISO C++ does not support variable-length array types [-Wvla]
seq[k]=new(char[L+2]);
^
hhhmm-C.h: In member function 'int HMM::ReadHMMer3(FILE*, char*)':
hhhmm-C.h:1237:77: warning: ISO C++ does not support variable-length array types [-Wvla]
seq[nsa_dssp] = new(char[/*MAXRES*/par.maxResLen+2]);
^
hhhmm-C.h:1258:77: warning: ISO C++ does not support variable-length array types [-Wvla]
seq[nss_pred] = new(char[/*MAXRES*/par.maxResLen+2]);
^
hhhmm-C.h:1279:77: warning: ISO C++ does not support variable-length array types [-Wvla]
seq[nss_conf] = new(char[/*MAXRES*/par.maxResLen+2]);
^
hhhmm-C.h:1349:69: warning: ISO C++ does not support variable-length array types [-Wvla]
seq[nss_dssp] = new(char[/*MAXRES*/par.maxResLen+2]);
^
hhhmm-C.h:1529:49: warning: ISO C++ does not support variable-length array types [-Wvla]
sname[k+1]=new(char[strlen(longname)+1]);
^
hhhmm-C.h:1531:30: warning: ISO C++ does not support variable-length array types [-Wvla]
seq[k]=new(char[L+2]);
^
hhhmm-C.h:1534:32: warning: ISO C++ does not support variable-length array types [-Wvla]
seq[k+1]=new(char[L+2]);
^
hhhmm-C.h:1552:47: warning: ISO C++ does not support variable-length array types [-Wvla]
sname[k]=new(char[strlen(longname)+1]);
^
hhhmm-C.h:1554:30: warning: ISO C++ does not support variable-length array types [-Wvla]
seq[k]=new(char[L+2]);
^
hhhmm-C.h: In member function 'void HMM::InsertCalibration(char*)':
hhhmm-C.h:2109:39: warning: ISO C++ does not support variable-length array types [-Wvla]
char** lines = new(char*[3*L+100000]);
^
hhhmm-C.h:2138:44: warning: ISO C++ does not support variable-length array types [-Wvla]
lines[nline]=new(char[strlen(line)+1]);
^
In file included from hhalign.cpp:71:0:
hhalignment-C.h: In constructor 'Alignment::Alignment(int, int)':
hhalignment-C.h:80:30: warning: ISO C++ does not support variable-length array types [-Wvla]
sname = new(char*[maxseq+2]); /* MR1 */
^
hhalignment-C.h:81:28: warning: ISO C++ does not support variable-length array types [-Wvla]
seq = new(char*[maxseq+2]); /* MR1 */
^
hhalignment-C.h:82:22: warning: ISO C++ does not support variable-length array types [-Wvla]
l = new(int[maxres]);
^
hhalignment-C.h:83:26: warning: ISO C++ does not support variable-length array types [-Wvla]
X = new(char*[maxseq+2]); /* MR1 */
^
hhalignment-C.h:84:40: warning: ISO C++ does not support variable-length array types [-Wvla]
I = new(short unsigned int*[maxseq+2]); /* MR1 */
^
hhalignment-C.h:85:28: warning: ISO C++ does not support variable-length array types [-Wvla]
keep = new(char[maxseq+2]); /* MR1 */
^
hhalignment-C.h:86:31: warning: ISO C++ does not support variable-length array types [-Wvla]
display = new(char[maxseq+2]); /* MR1 */
^
hhalignment-C.h:87:27: warning: ISO C++ does not support variable-length array types [-Wvla]
wg = new(float[maxseq+2]); /* MR1 */
^
hhalignment-C.h:88:28: warning: ISO C++ does not support variable-length array types [-Wvla]
nseqs = new(int[maxres+2]); /* MR1 */
^
hhalignment-C.h: In member function 'void Alignment::Read(FILE*, char*, char*)':
hhalignment-C.h:141:40: warning: ISO C++ does not support variable-length array types [-Wvla]
char *cur_seq=new(char[par.maxColCnt]);
^
hhalignment-C.h:183:61: warning: ISO C++ does not support variable-length array types [-Wvla]
seq[k]=new(char[strlen(cur_seq)+2]);
^
hhalignment-C.h:185:59: warning: ISO C++ does not support variable-length array types [-Wvla]
X[k]=new(char[strlen(cur_seq)+2]);
^
hhalignment-C.h:187:73: warning: ISO C++ does not support variable-length array types [-Wvla]
I[k]=new(short unsigned int[strlen(cur_seq)+2]);
^
In file included from hhalign.cpp:71:0:
hhalignment-C.h:236:58: warning: ISO C++ does not support variable-length array types [-Wvla]
sname[k] = new(char[strlen(cur_name)+1]);
^
hhalignment-C.h:351:45: warning: ISO C++ does not support variable-length array types [-Wvla]
seq[k]=new(char[strlen(cur_seq)+2]);
^
hhalignment-C.h:353:43: warning: ISO C++ does not support variable-length array types [-Wvla]
X[k]=new(char[strlen(cur_seq)+2]);
^
hhalignment-C.h:355:57: warning: ISO C++ does not support variable-length array types [-Wvla]
I[k]=new(short unsigned int[strlen(cur_seq)+2]);
^
hhalignment-C.h: In member function 'void Alignment::Compress(const char*)':
hhalignment-C.h:423:43: warning: ISO C++ does not support variable-length array types [-Wvla]
h = new(/*short*/ unsigned int[N_in+2]); /* short -> overflow, FS, r235 -> r236 */
^
hhalignment-C.h:555:52: warning: ISO C++ does not support variable-length array types [-Wvla]
percent_gaps = new(float[par.maxColCnt]);
^
hhalignment-C.h:561:47: warning: ISO C++ does not support variable-length array types [-Wvla]
if (nres==NULL) nres=new(int[N_in]);
^
hhalignment-C.h:783:50: warning: ISO C++ does not support variable-length array types [-Wvla]
match_state = new(char[par.maxColCnt]);
^
hhalignment-C.h: In member function 'int Alignment::FilterForDisplay(int, int, int, float, int)':
hhalignment-C.h:945:35: warning: ISO C++ does not support variable-length array types [-Wvla]
char *dummy = new(char[N_in+1]);
^
hhalignment-C.h: In member function 'int Alignment::Filter2(char*, int, int, float, int, int, int)':
hhalignment-C.h:1008:30: warning: ISO C++ does not support variable-length array types [-Wvla]
char* in=new(char[N_in+1]); // in[k]=1: seq k has been accepted; in[k]=0: seq k has not yet been accepted at current seqid
^
hhalignment-C.h:1009:32: warning: ISO C++ does not support variable-length array types [-Wvla]
char* inkk=new(char[N_in+1]); // inkk[k]=1 iff in[ksort[k]]=1 else 0;
^
hhalignment-C.h:1010:27: warning: ISO C++ does not support variable-length array types [-Wvla]
int* Nmax=new(int[L+2]); // position-dependent maximum-sequence-identity threshold for filtering /* MR1, used to be called idmax*/
^
hhalignment-C.h:1011:31: warning: ISO C++ does not support variable-length array types [-Wvla]
int* idmaxwin=new(int[L+2]); // minimum value of idmax[i-WFIL,i+WFIL]
^
hhalignment-C.h:1012:36: warning: ISO C++ does not support variable-length array types [-Wvla]
int* seqid_prev=new(int[N_in+1]); // maximum-sequence-identity threshold used in previous round of filtering (with lower seqid)
^
hhalignment-C.h:1013:24: warning: ISO C++ does not support variable-length array types [-Wvla]
int* N=new(int[L+2]); // N[i] number of already accepted sequences at position i
^
hhalignment-C.h:1042:32: warning: ISO C++ does not support variable-length array types [-Wvla]
first=new(int[N_in]);// first non-gap position in sequence k
^
hhalignment-C.h:1043:32: warning: ISO C++ does not support variable-length array types [-Wvla]
last =new(int[N_in]);// last non-gap position in sequence k
^
hhalignment-C.h:1056:31: warning: ISO C++ does not support variable-length array types [-Wvla]
nres=new(int[N_in]);
^
hhalignment-C.h:1070:32: warning: ISO C++ does not support variable-length array types [-Wvla]
ksort=new(int[N_in]); // never reuse alignment object for new alignment with more sequences
^
hhalignment-C.h: In member function 'int Alignment::HomologyFilter(int, float, float)':
hhalignment-C.h:1313:33: warning: ISO C++ does not support variable-length array types [-Wvla]
char* coreseq=new(char[N_in]); // coreseq[k]=1 if sequence belongs to core of alignment (i.e. it is very similar to query)
^
hhalignment-C.h: In member function 'int Alignment::FilterWithCoreHMM(char*, float, HMM&)':
hhalignment-C.h:1364:36: warning: ISO C++ does not support variable-length array types [-Wvla]
float** logodds=new(float*[L+1]); // log-odds ratios for HMM qcore
^
hhalignment-C.h:1373:32: warning: ISO C++ does not support variable-length array types [-Wvla]
first=new(int[N_in]);// first non-gap position in sequence k
^
hhalignment-C.h:1374:32: warning: ISO C++ does not support variable-length array types [-Wvla]
last =new(int[N_in]);// last non-gap position in sequence k
^
hhalignment-C.h:1387:31: warning: ISO C++ does not support variable-length array types [-Wvla]
nres=new(int[N_in]);
^
hhalignment-C.h: In member function 'void Alignment::FrequenciesAndTransitions(HMM&, char*)':
hhalignment-C.h:1669:49: warning: ISO C++ does not support variable-length array types [-Wvla]
q.seq[q.ncons]=new(char[L+2]);
^
hhalignment-C.h:1676:64: warning: ISO C++ does not support variable-length array types [-Wvla]
q.sname[q.nfirst]=new(char[strlen(name)+11]);
^
hhalignment-C.h:1680:50: warning: ISO C++ does not support variable-length array types [-Wvla]
q.seq[q.nfirst]=new(char[L+2]);
^
hhalignment-C.h:1738:61: warning: ISO C++ does not support variable-length array types [-Wvla]
q.sname[nn]=new(char[strlen(sname[k])+1]);
^
hhalignment-C.h:1741:57: warning: ISO C++ does not support variable-length array types [-Wvla]
q.seq[nn]=new(char[strlen(seq[k])+1]);
^
hhalignment-C.h: In member function 'void Alignment::Amino_acid_frequencies_and_transitions_from_M_state(HMM&, char*)':
hhalignment-C.h:1828:41: warning: ISO C++ does not support variable-length array types [-Wvla]
float *Neff = new(float[par.maxResLen]); // diversity of subalignment i
^
hhalignment-C.h:1835:25: warning: ISO C++ does not support variable-length array types [-Wvla]
wi = new(float[N_in+2]);
^
hhalignment-C.h:1844:20: warning: ISO C++ does not support variable-length array types [-Wvla]
n = new(int*[L+2]);
^
hhalignment-C.h: In member function 'void Alignment::Transitions_from_I_state(HMM&, char*)':
hhalignment-C.h:2054:43: warning: ISO C++ does not support variable-length array types [-Wvla]
float *Neff = new(float[par.maxResLen]); // diversity of subalignment i
^
hhalignment-C.h:2062:27: warning: ISO C++ does not support variable-length array types [-Wvla]
wi = new(float[N_in+2]);
^
hhalignment-C.h:2073:22: warning: ISO C++ does not support variable-length array types [-Wvla]
n = new(int*[L+2]);
^
hhalignment-C.h: In member function 'void Alignment::Transitions_from_D_state(HMM&, char*)':
hhalignment-C.h:2256:43: warning: ISO C++ does not support variable-length array types [-Wvla]
float *Neff = new(float[par.maxResLen]); // diversity of subalignment i
^
hhalignment-C.h:2265:27: warning: ISO C++ does not support variable-length array types [-Wvla]
wi = new(float[N_in+2]); /* FIXME: FS */
^
hhalignment-C.h:2275:22: warning: ISO C++ does not support variable-length array types [-Wvla]
n = new(int*[L+2]);
^
hhalignment-C.h: In member function 'void Alignment::MergeMasterSlave(Hit&, char*)':
hhalignment-C.h:2546:31: warning: ISO C++ does not support variable-length array types [-Wvla]
int* imatch=new(int[hit.j2+1]);
^
hhalignment-C.h:2678:34: warning: ISO C++ does not support variable-length array types [-Wvla]
char* new_seq=new(char[2*maxcol]);
^
hhalignment-C.h:2691:23: warning: ISO C++ does not support variable-length array types [-Wvla]
seq[N_in]=new(char[h]);
^
hhalignment-C.h:2694:21: warning: ISO C++ does not support variable-length array types [-Wvla]
X[N_in]=new(char[h]);
^
hhalignment-C.h:2696:35: warning: ISO C++ does not support variable-length array types [-Wvla]
I[N_in]=new(short unsigned int[h]);
^
hhalignment-C.h:2698:47: warning: ISO C++ does not support variable-length array types [-Wvla]
sname[N_in]=new(char[strlen(Tali.sname[k])+1]);
^
hhalignment-C.h: In member function 'void Alignment::AddSequence(char*, int*)':
hhalignment-C.h:2729:23: warning: ISO C++ does not support variable-length array types [-Wvla]
X[N_in]=new(char[L+2]);
^
hhalignment-C.h: In member function 'void Alignment::GetPositionSpecificWeights(float**)':
hhalignment-C.h:2779:19: warning: ISO C++ does not support variable-length array types [-Wvla]
n = new(int*[L+2]);
^
hhalignment-C.h: In member function 'void Alignment::Transfer(char**, int)':
hhalignment-C.h:2896:59: warning: ISO C++ does not support variable-length array types [-Wvla]
I[k] = new(short unsigned int[iLen+2+GOOD_MEASURE]);
^
hhalignment-C.h:2897:45: warning: ISO C++ does not support variable-length array types [-Wvla]
X[k] = new(char[iLen+2+GOOD_MEASURE]);
^
hhalignment-C.h:2898:47: warning: ISO C++ does not support variable-length array types [-Wvla]
seq[k] = new(char[iLen+2+GOOD_MEASURE]);
^
In file included from hhalign.cpp:72:0:
hhhit-C.h: In member function 'void Hit::AllocateBacktraceMatrix(int, int)':
hhhit-C.h:179:20: warning: ISO C++ does not support variable-length array types [-Wvla]
bMM=new(char*[Nq]);
^
hhhit-C.h:180:20: warning: ISO C++ does not support variable-length array types [-Wvla]
bMI=new(char*[Nq]);
^
hhhit-C.h:181:20: warning: ISO C++ does not support variable-length array types [-Wvla]
bIM=new(char*[Nq]);
^
hhhit-C.h:182:20: warning: ISO C++ does not support variable-length array types [-Wvla]
bDG=new(char*[Nq]);
^
hhhit-C.h:183:20: warning: ISO C++ does not support variable-length array types [-Wvla]
bGD=new(char*[Nq]);
^
hhhit-C.h:184:25: warning: ISO C++ does not support variable-length array types [-Wvla]
cell_off=new(char*[Nq]);
^
hhhit-C.h:187:26: warning: ISO C++ does not support variable-length array types [-Wvla]
bMM[i]=new(char[Nt]);
^
hhhit-C.h:188:26: warning: ISO C++ does not support variable-length array types [-Wvla]
bMI[i]=new(char[Nt]);
^
hhhit-C.h:189:26: warning: ISO C++ does not support variable-length array types [-Wvla]
bIM[i]=new(char[Nt]);
^
hhhit-C.h:190:26: warning: ISO C++ does not support variable-length array types [-Wvla]
bGD[i]=new(char[Nt]);
^
hhhit-C.h:191:26: warning: ISO C++ does not support variable-length array types [-Wvla]
bDG[i]=new(char[Nt]);
^
hhhit-C.h:192:31: warning: ISO C++ does not support variable-length array types [-Wvla]
cell_off[i]=new(char[Nt]);
^
hhhit-C.h: In member function 'void Hit::AllocateForwardMatrix(int, int)':
hhhit-C.h:239:23: warning: ISO C++ does not support variable-length array types [-Wvla]
F_MM=new(double*[Nq]);
^
hhhit-C.h:240:23: warning: ISO C++ does not support variable-length array types [-Wvla]
F_MI=new(double*[Nq]);
^
hhhit-C.h:241:23: warning: ISO C++ does not support variable-length array types [-Wvla]
F_DG=new(double*[Nq]);
^
hhhit-C.h:242:23: warning: ISO C++ does not support variable-length array types [-Wvla]
F_IM=new(double*[Nq]);
^
hhhit-C.h:243:23: warning: ISO C++ does not support variable-length array types [-Wvla]
F_GD=new(double*[Nq]);
^
hhhit-C.h:244:25: warning: ISO C++ does not support variable-length array types [-Wvla]
scale=new(double[Nq+1]); // need Nq+3?
^
hhhit-C.h:247:31: warning: ISO C++ does not support variable-length array types [-Wvla]
F_MM[i] = new(double[Nt]);
^
hhhit-C.h:248:31: warning: ISO C++ does not support variable-length array types [-Wvla]
F_MI[i] = new(double[Nt]);
^
hhhit-C.h:249:31: warning: ISO C++ does not support variable-length array types [-Wvla]
F_DG[i] = new(double[Nt]);
^
hhhit-C.h:250:31: warning: ISO C++ does not support variable-length array types [-Wvla]
F_IM[i] = new(double[Nt]);
^
hhhit-C.h:251:31: warning: ISO C++ does not support variable-length array types [-Wvla]
F_GD[i] = new(double[Nt]);
^
hhhit-C.h: In member function 'void Hit::AllocateBackwardMatrix(int, int)':
hhhit-C.h:296:23: warning: ISO C++ does not support variable-length array types [-Wvla]
B_MM=new(double*[Nq]);
^
hhhit-C.h:303:31: warning: ISO C++ does not support variable-length array types [-Wvla]
B_MM[i] = new(double[Nt]);
^
hhhit-C.h: In member function 'void Hit::Viterbi(HMM&, HMM&, float**)':
hhhit-C.h:376:42: warning: ISO C++ does not support variable-length array types [-Wvla]
float *sMM = new(float[par.maxResLen]); // sMM[i][j] = score of best alignment up to indices (i,j) ending in (Match,Match)
^
hhhit-C.h:377:42: warning: ISO C++ does not support variable-length array types [-Wvla]
float *sGD = new(float[par.maxResLen]); // sGD[i][j] = score of best alignment up to indices (i,j) ending in (Gap,Delete)
^
hhhit-C.h:378:42: warning: ISO C++ does not support variable-length array types [-Wvla]
float *sDG = new(float[par.maxResLen]); // sDG[i][j] = score of best alignment up to indices (i,j) ending in (Delete,Gap)
^
hhhit-C.h:379:42: warning: ISO C++ does not support variable-length array types [-Wvla]
float *sIM = new(float[par.maxResLen]); // sIM[i][j] = score of best alignment up to indices (i,j) ending in (Ins,Match)
^
hhhit-C.h:380:42: warning: ISO C++ does not support variable-length array types [-Wvla]
float *sMI = new(float[par.maxResLen]); // sMI[i][j] = score of best alignment up to indices (i,j) ending in (Match,Ins)
^
hhhit-C.h: In member function 'void Hit::Backtrace(HMM&, HMM&)':
hhhit-C.h:1126:40: warning: ISO C++ does not support variable-length array types [-Wvla]
if (t.Xcons) Xcons = new( char[q.L+2]); // for template consensus sequence aligned to query
^
hhhit-C.h:1127:30: warning: ISO C++ does not support variable-length array types [-Wvla]
S = new( float[nsteps+1]);
^
hhhit-C.h:1128:30: warning: ISO C++ does not support variable-length array types [-Wvla]
S_ss = new( float[nsteps+1]);
^
hhhit-C.h: In member function 'void Hit::StochasticBacktrace(HMM&, HMM&, char)':
hhhit-C.h:1228:40: warning: ISO C++ does not support variable-length array types [-Wvla]
double* scale_cum = new(double[q.L+2]);
^
hhhit-C.h:1247:39: warning: ISO C++ does not support variable-length array types [-Wvla]
double* sumF=new(double[q.L+t.L]);
^
hhhit-C.h:1371:40: warning: ISO C++ does not support variable-length array types [-Wvla]
if (t.Xcons) Xcons = new( char[q.L+2]); // for template consensus sequence aligned to query
^
hhhit-C.h:1372:30: warning: ISO C++ does not support variable-length array types [-Wvla]
S = new( float[nsteps+1]);
^
hhhit-C.h:1373:30: warning: ISO C++ does not support variable-length array types [-Wvla]
S_ss = new( float[nsteps+1]);
^
hhhit-C.h: In member function 'void Hit::BacktraceMAC(HMM&, HMM&)':
hhhit-C.h:1475:40: warning: ISO C++ does not support variable-length array types [-Wvla]
if (t.Xcons) Xcons = new( char[q.L+2]); // for template consensus sequence aligned to query
^
hhhit-C.h:1476:30: warning: ISO C++ does not support variable-length array types [-Wvla]
S = new( float[nsteps+1]);
^
hhhit-C.h:1477:30: warning: ISO C++ does not support variable-length array types [-Wvla]
S_ss = new( float[nsteps+1]);
^
hhhit-C.h:1478:37: warning: ISO C++ does not support variable-length array types [-Wvla]
P_posterior = new( float[nsteps+1]);
^
hhhit-C.h: In member function 'void Hit::InitializeBacktrace(HMM&, HMM&)':
hhhit-C.h:1683:54: warning: ISO C++ does not support variable-length array types [-Wvla]
longname=new(char[strlen(t.longname)+1])();
^
hhhit-C.h:1684:50: warning: ISO C++ does not support variable-length array types [-Wvla]
name =new(char[strlen(t.name)+1])();
^
hhhit-C.h:1685:50: warning: ISO C++ does not support variable-length array types [-Wvla]
file =new(char[strlen(t.file)+1])();
^
hhhit-C.h:1696:43: warning: ISO C++ does not support variable-length array types [-Wvla]
sname=new(char*[t.n_display])(); // Call Compare only once with irep=1
^
hhhit-C.h:1697:43: warning: ISO C++ does not support variable-length array types [-Wvla]
seq =new(char*[t.n_display])(); // Call Compare only once with irep=1
^
hhhit-C.h:1730:34: warning: ISO C++ does not support variable-length array types [-Wvla]
this->i = new( int[i2+j2+2])();
^
hhhit-C.h:1731:34: warning: ISO C++ does not support variable-length array types [-Wvla]
this->j = new( int[i2+j2+2])();
^
hhhit-C.h:1732:35: warning: ISO C++ does not support variable-length array types [-Wvla]
states = new( char[i2+j2+2])();
^
In file included from hhalign.cpp:73:0:
hhhalfalignment-C.h: In constructor 'HalfAlignment::HalfAlignment(int)':
hhhalfalignment-C.h:66:25: warning: ISO C++ does not support variable-length array types [-Wvla]
h = new(int[maxseqdis]); //h[k] = next position of sequence k to be written
^
hhhalfalignment-C.h:67:27: warning: ISO C++ does not support variable-length array types [-Wvla]
s = new(char*[maxseqdis]); //s[k][h] = character in column h, sequence k of output alignment
^
hhhalfalignment-C.h:68:26: warning: ISO C++ does not support variable-length array types [-Wvla]
l = new(int*[maxseqdis]); //counts non-gap residues: l[k][i] = index of last residue AT OR BEFORE match state i in seq k
^
hhhalfalignment-C.h:69:26: warning: ISO C++ does not support variable-length array types [-Wvla]
m = new(int*[maxseqdis]); //counts positions: m[k][i] = position of match state i in string seq[k]
^
In file included from hhalign.cpp:74:0:
hhfullalignment-C.h: In member function 'void FullAlignment::PrintHHR(FILE*, Hit&)':
hhfullalignment-C.h:359:39: warning: ISO C++ does not support variable-length array types [-Wvla]
lq = new(short unsigned int[qa->n+2]);
^
hhfullalignment-C.h:360:39: warning: ISO C++ does not support variable-length array types [-Wvla]
lt = new(short unsigned int[ta->n+2]);
^
In file included from hhalign.cpp:75:0:
hhhitlist-C.h: In member function 'void HitList::TransitiveScoring()':
hhhitlist-C.h:1285:20: warning: ISO C++ does not support variable-length array types [-Wvla]
Z = new(float*[N]);
^
hhhitlist-C.h:1288:26: warning: ISO C++ does not support variable-length array types [-Wvla]
Z[k] = new(float[N]);
^
hhhitlist-C.h:1293:20: warning: ISO C++ does not support variable-length array types [-Wvla]
C = new(float*[N]);
^
hhhitlist-C.h:1296:26: warning: ISO C++ does not support variable-length array types [-Wvla]
C[k] = new(float[N]);
^
hhhitlist-C.h:1303:20: warning: ISO C++ does not support variable-length array types [-Wvla]
Zq = new(float[N]);
^
hhhitlist-C.h:1304:21: warning: ISO C++ does not support variable-length array types [-Wvla]
Ztq = new(float[N]);
^
hhhitlist-C.h:1305:21: warning: ISO C++ does not support variable-length array types [-Wvla]
Zrq = new(float[N]);
^
hhhitlist-C.h:1306:22: warning: ISO C++ does not support variable-length array types [-Wvla]
fold = new(char*[N]);
^
hhhitlist-C.h:1307:21: warning: ISO C++ does not support variable-length array types [-Wvla]
fam = new(char*[N]);
^
hhhitlist-C.h:1308:22: warning: ISO C++ does not support variable-length array types [-Wvla]
Prob = new(float[N]);
^
hhhitlist-C.h:1309:18: warning: ISO C++ does not support variable-length array types [-Wvla]
ll = new(int[N]);
^
hhhitlist-C.h:1310:19: warning: ISO C++ does not support variable-length array types [-Wvla]
w = new(float[N]);
^
hhhitlist-C.h:1373:37: warning: ISO C++ does not support variable-length array types [-Wvla]
double** Csub = new(double*[M]);
^
hhhitlist-C.h:1374:37: warning: ISO C++ does not support variable-length array types [-Wvla]
double** Cinv = new(double*[M]);
^
hhhitlist-C.h:1377:27: warning: ISO C++ does not support variable-length array types [-Wvla]
Csub[m] = new(double[M]);
^
hhhitlist-C.h:1378:27: warning: ISO C++ does not support variable-length array types [-Wvla]
Cinv[m] = new(double[M]);
^
hhhitlist-C.h:1453:34: warning: ISO C++ does not support variable-length array types [-Wvla]
double** Csub = new(double*[M]);
^
hhhitlist-C.h:1456:31: warning: ISO C++ does not support variable-length array types [-Wvla]
Csub[m] = new(double[M]);
^
hhhitlist-C.h:1470:38: warning: ISO C++ does not support variable-length array types [-Wvla]
double** Cinv = new(double*[M]);
^
hhhitlist-C.h:1471:51: warning: ISO C++ does not support variable-length array types [-Wvla]
for (m=0; m<M; m++) Cinv[m] = new(double[M]);
^
hhhitlist-C.h: In member function 'void HitList::TransitiveScoring2()':
hhhitlist-C.h:1650:20: warning: ISO C++ does not support variable-length array types [-Wvla]
Z = new(float*[N]);
^
hhhitlist-C.h:1653:26: warning: ISO C++ does not support variable-length array types [-Wvla]
Z[k] = new(float[N]);
^
hhhitlist-C.h:1658:20: warning: ISO C++ does not support variable-length array types [-Wvla]
C = new(float*[N]);
^
hhhitlist-C.h:1661:26: warning: ISO C++ does not support variable-length array types [-Wvla]
C[k] = new(float[N]);
^
hhhitlist-C.h:1668:20: warning: ISO C++ does not support variable-length array types [-Wvla]
Zq = new(float[N]);
^
hhhitlist-C.h:1669:21: warning: ISO C++ does not support variable-length array types [-Wvla]
Ztq = new(float[N]);
^
hhhitlist-C.h:1670:21: warning: ISO C++ does not support variable-length array types [-Wvla]
Zrq = new(float[N]);
^
hhhitlist-C.h:1671:22: warning: ISO C++ does not support variable-length array types [-Wvla]
fold = new(char*[N]);
^
hhhitlist-C.h:1672:21: warning: ISO C++ does not support variable-length array types [-Wvla]
fam = new(char*[N]);
^
hhhitlist-C.h:1673:22: warning: ISO C++ does not support variable-length array types [-Wvla]
Prob = new(float[N]);
^
hhhitlist-C.h:1674:18: warning: ISO C++ does not support variable-length array types [-Wvla]
ll = new(int[N]);
^
hhhitlist-C.h:1675:19: warning: ISO C++ does not support variable-length array types [-Wvla]
w = new(float[N]);
^
hhhitlist-C.h:1739:37: warning: ISO C++ does not support variable-length array types [-Wvla]
double** Csub = new(double*[M]);
^
hhhitlist-C.h:1740:37: warning: ISO C++ does not support variable-length array types [-Wvla]
double** Cinv = new(double*[M]);
^
hhhitlist-C.h:1743:27: warning: ISO C++ does not support variable-length array types [-Wvla]
Csub[m] = new(double[M]);
^
hhhitlist-C.h:1744:27: warning: ISO C++ does not support variable-length array types [-Wvla]
Cinv[m] = new(double[M]);
^
hhhitlist-C.h:1821:34: warning: ISO C++ does not support variable-length array types [-Wvla]
double** Csub = new(double*[M]);
^
hhhitlist-C.h:1824:31: warning: ISO C++ does not support variable-length array types [-Wvla]
Csub[m] = new(double[M]);
^
hhhitlist-C.h:1838:38: warning: ISO C++ does not support variable-length array types [-Wvla]
double** Cinv = new(double*[M]);
^
hhhitlist-C.h:1839:51: warning: ISO C++ does not support variable-length array types [-Wvla]
for (m=0; m<M; m++) Cinv[m] = new(double[M]);
^
hhhitlist-C.h: In member function 'void HitList::TransitiveScoring3()':
hhhitlist-C.h:2020:20: warning: ISO C++ does not support variable-length array types [-Wvla]
Z = new(float*[N]);
^
hhhitlist-C.h:2023:26: warning: ISO C++ does not support variable-length array types [-Wvla]
Z[k] = new(float[N]);
^
hhhitlist-C.h:2028:20: warning: ISO C++ does not support variable-length array types [-Wvla]
C = new(float*[N]);
^
hhhitlist-C.h:2031:26: warning: ISO C++ does not support variable-length array types [-Wvla]
C[k] = new(float[N]);
^
hhhitlist-C.h:2038:20: warning: ISO C++ does not support variable-length array types [-Wvla]
Zq = new(float[N]);
^
hhhitlist-C.h:2039:21: warning: ISO C++ does not support variable-length array types [-Wvla]
Ztq = new(float[N]);
^
hhhitlist-C.h:2040:21: warning: ISO C++ does not support variable-length array types [-Wvla]
Zrq = new(float[N]);
^
hhhitlist-C.h:2041:22: warning: ISO C++ does not support variable-length array types [-Wvla]
fold = new(char*[N]);
^
hhhitlist-C.h:2042:21: warning: ISO C++ does not support variable-length array types [-Wvla]
fam = new(char*[N]);
^
hhhitlist-C.h:2043:22: warning: ISO C++ does not support variable-length array types [-Wvla]
Prob = new(float[N]);
^
hhhitlist-C.h:2044:18: warning: ISO C++ does not support variable-length array types [-Wvla]
ll = new(int[N]);
^
hhhitlist-C.h:2045:19: warning: ISO C++ does not support variable-length array types [-Wvla]
w = new(float[N]);
^
hhhitlist-C.h:2114:34: warning: ISO C++ does not support variable-length array types [-Wvla]
double** Csub = new(double*[M]);
^
hhhitlist-C.h:2115:34: warning: ISO C++ does not support variable-length array types [-Wvla]
double** Cinv = new(double*[M]);
^
hhhitlist-C.h:2118:31: warning: ISO C++ does not support variable-length array types [-Wvla]
Csub[m] = new(double[M]);
^
hhhitlist-C.h:2119:31: warning: ISO C++ does not support variable-length array types [-Wvla]
Cinv[m] = new(double[M]);
^
hhhitlist-C.h:2186:34: warning: ISO C++ does not support variable-length array types [-Wvla]
double** Csub = new(double*[M]);
^
hhhitlist-C.h:2189:31: warning: ISO C++ does not support variable-length array types [-Wvla]
Csub[m] = new(double[M]);
^
hhhitlist-C.h:2203:38: warning: ISO C++ does not support variable-length array types [-Wvla]
double** Cinv = new(double*[M]);
^
hhhitlist-C.h:2204:51: warning: ISO C++ does not support variable-length array types [-Wvla]
for (m=0; m<M; m++) Cinv[m] = new(double[M]);
^
hhhitlist-C.h: In member function 'void HitList::TransitiveScoring4()':
hhhitlist-C.h:2385:20: warning: ISO C++ does not support variable-length array types [-Wvla]
Z = new(float*[N]);
^
hhhitlist-C.h:2388:26: warning: ISO C++ does not support variable-length array types [-Wvla]
Z[k] = new(float[N]);
^
hhhitlist-C.h:2393:20: warning: ISO C++ does not support variable-length array types [-Wvla]
C = new(float*[N]);
^
hhhitlist-C.h:2396:26: warning: ISO C++ does not support variable-length array types [-Wvla]
C[k] = new(float[N]);
^
hhhitlist-C.h:2403:20: warning: ISO C++ does not support variable-length array types [-Wvla]
Zq = new(float[N]);
^
hhhitlist-C.h:2404:21: warning: ISO C++ does not support variable-length array types [-Wvla]
Ztq = new(float[N]);
^
hhhitlist-C.h:2405:21: warning: ISO C++ does not support variable-length array types [-Wvla]
Zrq = new(float[N]);
^
hhhitlist-C.h:2406:22: warning: ISO C++ does not support variable-length array types [-Wvla]
fold = new(char*[N]);
^
hhhitlist-C.h:2407:21: warning: ISO C++ does not support variable-length array types [-Wvla]
fam = new(char*[N]);
^
hhhitlist-C.h:2408:22: warning: ISO C++ does not support variable-length array types [-Wvla]
Prob = new(float[N]);
^
hhhitlist-C.h:2409:18: warning: ISO C++ does not support variable-length array types [-Wvla]
ll = new(int[N]);
^
hhhitlist-C.h:2410:19: warning: ISO C++ does not support variable-length array types [-Wvla]
w = new(float[N]);
^
hhhitlist-C.h:2472:37: warning: ISO C++ does not support variable-length array types [-Wvla]
double** Csub = new(double*[M]);
^
hhhitlist-C.h:2475:27: warning: ISO C++ does not support variable-length array types [-Wvla]
Csub[m] = new(double[M]);
^
hhhitlist-C.h:2538:34: warning: ISO C++ does not support variable-length array types [-Wvla]
double** Csub = new(double*[M]);
^
hhhitlist-C.h:2541:31: warning: ISO C++ does not support variable-length array types [-Wvla]
Csub[m] = new(double[M]);
^
hhhitlist-C.h: In member function 'void HitList::InvertMatrix(double**, double**, int)':
hhhitlist-C.h:2840:30: warning: ISO C++ does not support variable-length array types [-Wvla]
double** V = new(double*[N]);
^
hhhitlist-C.h:2841:29: warning: ISO C++ does not support variable-length array types [-Wvla]
double* s = new(double[N]);
^
hhhitlist-C.h:2842:43: warning: ISO C++ does not support variable-length array types [-Wvla]
for (k=0; k<N; k++) V[k] = new(double[N]);
^
hhhitlist-C.h: In member function 'void HitList::SVD(double**, int, double*, double**)':
hhhitlist-C.h:2925:20: warning: ISO C++ does not support variable-length array types [-Wvla]
rv1=new(double[n]);
^
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c hhalign.cpp -o hhalign.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CXX --mode=link g++ -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro -o libhhalign.la hhalign.lo -largtable2 -lm
libtool: link: ar cru .libs/libhhalign.a .libs/hhalign.o
libtool: link: ranlib .libs/libhhalign.a
libtool: link: ( cd ".libs" && rm -f "libhhalign.la" && ln -s "../libhhalign.la" "libhhalign.la" )
make[4]: Leaving directory `/«PKGBUILDDIR»/src/hhalign'
Making all in squid
make[4]: Entering directory `/«PKGBUILDDIR»/src/squid'
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o a2m.lo a2m.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c a2m.c -fPIC -DPIC -o .libs/a2m.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c a2m.c -o a2m.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o aligneval.lo aligneval.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c aligneval.c -fPIC -DPIC -o .libs/aligneval.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c aligneval.c -o aligneval.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o alignio.lo alignio.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c alignio.c -fPIC -DPIC -o .libs/alignio.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c alignio.c -o alignio.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o clustal.lo clustal.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c clustal.c -fPIC -DPIC -o .libs/clustal.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c clustal.c -o clustal.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o cluster.lo cluster.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c cluster.c -fPIC -DPIC -o .libs/cluster.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c cluster.c -o cluster.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o dayhoff.lo dayhoff.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c dayhoff.c -fPIC -DPIC -o .libs/dayhoff.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c dayhoff.c -o dayhoff.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o eps.lo eps.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c eps.c -fPIC -DPIC -o .libs/eps.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c eps.c -o eps.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o file.lo file.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c file.c -fPIC -DPIC -o .libs/file.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c file.c -o file.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o getopt.lo getopt.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c getopt.c -fPIC -DPIC -o .libs/getopt.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c getopt.c -o getopt.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gki.lo gki.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c gki.c -fPIC -DPIC -o .libs/gki.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c gki.c -o gki.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsi.lo gsi.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c gsi.c -fPIC -DPIC -o .libs/gsi.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c gsi.c -o gsi.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o gsi64.lo gsi64.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c gsi64.c -fPIC -DPIC -o .libs/gsi64.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c gsi64.c -o gsi64.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o hsregex.lo hsregex.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c hsregex.c -fPIC -DPIC -o .libs/hsregex.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c hsregex.c -o hsregex.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o iupac.lo iupac.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c iupac.c -fPIC -DPIC -o .libs/iupac.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c iupac.c -o iupac.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o msa.lo msa.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c msa.c -fPIC -DPIC -o .libs/msa.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c msa.c -o msa.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o msf.lo msf.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c msf.c -fPIC -DPIC -o .libs/msf.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c msf.c -o msf.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o phylip.lo phylip.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c phylip.c -fPIC -DPIC -o .libs/phylip.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c phylip.c -o phylip.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o revcomp.lo revcomp.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c revcomp.c -fPIC -DPIC -o .libs/revcomp.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c revcomp.c -o revcomp.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o rk.lo rk.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c rk.c -fPIC -DPIC -o .libs/rk.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c rk.c -o rk.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o selex.lo selex.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c selex.c -fPIC -DPIC -o .libs/selex.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c selex.c -o selex.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o seqencode.lo seqencode.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c seqencode.c -fPIC -DPIC -o .libs/seqencode.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c seqencode.c -o seqencode.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o shuffle.lo shuffle.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c shuffle.c -fPIC -DPIC -o .libs/shuffle.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c shuffle.c -o shuffle.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o sqerror.lo sqerror.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c sqerror.c -fPIC -DPIC -o .libs/sqerror.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c sqerror.c -o sqerror.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o sqio.lo sqio.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c sqio.c -fPIC -DPIC -o .libs/sqio.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c sqio.c -o sqio.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o squidcore.lo squidcore.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c squidcore.c -fPIC -DPIC -o .libs/squidcore.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c squidcore.c -o squidcore.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o sre_ctype.lo sre_ctype.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c sre_ctype.c -fPIC -DPIC -o .libs/sre_ctype.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c sre_ctype.c -o sre_ctype.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o sre_math.lo sre_math.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c sre_math.c -fPIC -DPIC -o .libs/sre_math.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c sre_math.c -o sre_math.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o sre_random.lo sre_random.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c sre_random.c -fPIC -DPIC -o .libs/sre_random.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c sre_random.c -o sre_random.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o sre_string.lo sre_string.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c sre_string.c -fPIC -DPIC -o .libs/sre_string.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c sre_string.c -o sre_string.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o ssi.lo ssi.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c ssi.c -fPIC -DPIC -o .libs/ssi.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c ssi.c -o ssi.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o stack.lo stack.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c stack.c -fPIC -DPIC -o .libs/stack.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c stack.c -o stack.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o stockholm.lo stockholm.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c stockholm.c -fPIC -DPIC -o .libs/stockholm.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c stockholm.c -o stockholm.o >/dev/null 2>&1
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c stopwatch.c -fPIC -DPIC -o .libs/stopwatch.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c stopwatch.c -o stopwatch.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o translate.lo translate.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c translate.c -fPIC -DPIC -o .libs/translate.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c translate.c -o translate.o >/dev/null 2>&1
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c types.c -fPIC -DPIC -o .libs/types.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c types.c -o types.o >/dev/null 2>&1
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c vectorops.c -fPIC -DPIC -o .libs/vectorops.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c vectorops.c -o vectorops.o >/dev/null 2>&1
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c weight.c -fPIC -DPIC -o .libs/weight.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c weight.c -o weight.o >/dev/null 2>&1
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libtool: link: ranlib .libs/libsquid.a
libtool: link: ( cd ".libs" && rm -f "libsquid.la" && ln -s "../libsquid.la" "libsquid.la" )
make[4]: Leaving directory `/«PKGBUILDDIR»/src/squid'
Making all in kmpp
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libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c KmTree.cpp -o KmTree.o >/dev/null 2>&1
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libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c KmUtils.cpp -fPIC -DPIC -o .libs/KmUtils.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c KmUtils.cpp -o KmUtils.o >/dev/null 2>&1
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libtool: link: ar cru .libs/libkmpp.a .libs/KMeans.o .libs/KmTree.o .libs/KmUtils.o
libtool: link: ranlib .libs/libkmpp.a
libtool: link: ( cd ".libs" && rm -f "libkmpp.la" && ln -s "../libkmpp.la" "libkmpp.la" )
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Making all in clustal
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c hhalign_wrapper.c -o hhalign_wrapper.o >/dev/null 2>&1
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c ktuple_pair.c -fPIC -DPIC -o .libs/ktuple_pair.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c ktuple_pair.c -o ktuple_pair.o >/dev/null 2>&1
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c list.c -fPIC -DPIC -o .libs/list.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c list.c -o list.o >/dev/null 2>&1
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c log.c -fPIC -DPIC -o .libs/log.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c log.c -o log.o >/dev/null 2>&1
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c muscle_upgma.c -o muscle_upgma.o >/dev/null 2>&1
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c muscle_tree.c -fPIC -DPIC -o .libs/muscle_tree.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c muscle_tree.c -o muscle_tree.o >/dev/null 2>&1
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c mbed.c -fPIC -DPIC -o .libs/mbed.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c mbed.c -o mbed.o >/dev/null 2>&1
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c symmatrix.c -o symmatrix.o >/dev/null 2>&1
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c weights.c -fPIC -DPIC -o .libs/weights.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c weights.c -o weights.o >/dev/null 2>&1
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libtool: link: ranlib .libs/libclustal.a
libtool: link: ( cd ".libs" && rm -f "libclustal.la" && ln -s "../libclustal.la" "libclustal.la" )
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libtool: link: (cd .libs/libclustalo.lax/libhhalign.a && ar x "/«PKGBUILDDIR»/src/hhalign/.libs/libhhalign.a")
libtool: link: (cd .libs/libclustalo.lax/libsquid.a && ar x "/«PKGBUILDDIR»/src/squid/.libs/libsquid.a")
libtool: link: (cd .libs/libclustalo.lax/libkmpp.a && ar x "/«PKGBUILDDIR»/src/kmpp/.libs/libkmpp.a")
libtool: link: ar cru .libs/libclustalo.a clustal-omega.o .libs/libclustalo.lax/libclustal.a/hhalign_wrapper.o .libs/libclustalo.lax/libclustal.a/ktuple_pair.o .libs/libclustalo.lax/libclustal.a/list.o .libs/libclustalo.lax/libclustal.a/log.o .libs/libclustalo.lax/libclustal.a/mbed.o .libs/libclustalo.lax/libclustal.a/muscle_tree.o .libs/libclustalo.lax/libclustal.a/muscle_upgma.o .libs/libclustalo.lax/libclustal.a/pair_dist.o .libs/libclustalo.lax/libclustal.a/progress.o .libs/libclustalo.lax/libclustal.a/seq.o .libs/libclustalo.lax/libclustal.a/symmatrix.o .libs/libclustalo.lax/libclustal.a/tree.o .libs/libclustalo.lax/libclustal.a/util.o .libs/libclustalo.lax/libclustal.a/weights.o .libs/libclustalo.lax/libhhalign.a/hhalign.o .libs/libclustalo.lax/libsquid.a/a2m.o .libs/libclustalo.lax/libsquid.a/aligneval.o .libs/libclustalo.lax/libsquid.a/alignio.o .libs/libclustalo.lax/libsquid.a/clustal.o .libs/libclustalo.lax/libsquid.a/cluster.o .libs/libclustalo.lax/libsquid.a/dayhoff.o .libs/libclustalo.lax/libsquid.a/eps.o .libs/libclustalo.lax/libsquid.a/file.o .libs/libclustalo.lax/libsquid.a/getopt.o .libs/libclustalo.lax/libsquid.a/gki.o .libs/libclustalo.lax/libsquid.a/gsi.o .libs/libclustalo.lax/libsquid.a/gsi64.o .libs/libclustalo.lax/libsquid.a/hsregex.o .libs/libclustalo.lax/libsquid.a/iupac.o .libs/libclustalo.lax/libsquid.a/msa.o .libs/libclustalo.lax/libsquid.a/msf.o .libs/libclustalo.lax/libsquid.a/phylip.o .libs/libclustalo.lax/libsquid.a/revcomp.o .libs/libclustalo.lax/libsquid.a/rk.o .libs/libclustalo.lax/libsquid.a/selex.o .libs/libclustalo.lax/libsquid.a/seqencode.o .libs/libclustalo.lax/libsquid.a/shuffle.o .libs/libclustalo.lax/libsquid.a/sqerror.o .libs/libclustalo.lax/libsquid.a/sqio.o .libs/libclustalo.lax/libsquid.a/squidcore.o .libs/libclustalo.lax/libsquid.a/sre_ctype.o .libs/libclustalo.lax/libsquid.a/sre_math.o .libs/libclustalo.lax/libsquid.a/sre_random.o .libs/libclustalo.lax/libsquid.a/sre_string.o .libs/libclustalo.lax/libsquid.a/ssi.o .libs/libclustalo.lax/libsquid.a/stack.o .libs/libclustalo.lax/libsquid.a/stockholm.o .libs/libclustalo.lax/libsquid.a/stopwatch.o .libs/libclustalo.lax/libsquid.a/translate.o .libs/libclustalo.lax/libsquid.a/types.o .libs/libclustalo.lax/libsquid.a/vectorops.o .libs/libclustalo.lax/libsquid.a/weight.o .libs/libclustalo.lax/libkmpp.a/KMeans.o .libs/libclustalo.lax/libkmpp.a/KmTree.o .libs/libclustalo.lax/libkmpp.a/KmUtils.o
libtool: link: ranlib .libs/libclustalo.a
libtool: link: rm -fr .libs/libclustalo.lax
libtool: link: ( cd ".libs" && rm -f "libclustalo.la" && ln -s "../libclustalo.la" "libclustalo.la" )
g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o main.o main.cpp
gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o mymain.o mymain.c
/bin/bash ../libtool --tag=CXX --mode=link g++ -O3 -fopenmp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z,relro -o clustalo main.o mymain.o libclustalo.la -largtable2 -lm
libtool: link: g++ -O3 -fopenmp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wl,-z -Wl,relro -o clustalo main.o mymain.o ./.libs/libclustalo.a /usr/lib/libargtable2.so -lm -fopenmp
./.libs/libclustalo.a(clustal-omega.o): In function `AlnToHHMFile':
/«PKGBUILDDIR»/src/clustal-omega.c:392: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp'
make[4]: Leaving directory `/«PKGBUILDDIR»/src'
make[3]: Leaving directory `/«PKGBUILDDIR»/src'
make[2]: Leaving directory `/«PKGBUILDDIR»/src'
make[2]: Entering directory `/«PKGBUILDDIR»'
make[2]: Nothing to be done for `all-am'.
make[2]: Leaving directory `/«PKGBUILDDIR»'
make[1]: Leaving directory `/«PKGBUILDDIR»'
dh_auto_test -a
make[1]: Entering directory `/«PKGBUILDDIR»'
Making check in src
make[2]: Entering directory `/«PKGBUILDDIR»/src'
Making check in hhalign
make[3]: Entering directory `/«PKGBUILDDIR»/src/hhalign'
make[3]: Nothing to be done for `check'.
make[3]: Leaving directory `/«PKGBUILDDIR»/src/hhalign'
Making check in squid
make[3]: Entering directory `/«PKGBUILDDIR»/src/squid'
make[3]: Nothing to be done for `check'.
make[3]: Leaving directory `/«PKGBUILDDIR»/src/squid'
Making check in kmpp
make[3]: Entering directory `/«PKGBUILDDIR»/src/kmpp'
make[3]: Nothing to be done for `check'.
make[3]: Leaving directory `/«PKGBUILDDIR»/src/kmpp'
Making check in clustal
make[3]: Entering directory `/«PKGBUILDDIR»/src/clustal'
make[3]: Nothing to be done for `check'.
make[3]: Leaving directory `/«PKGBUILDDIR»/src/clustal'
make[3]: Entering directory `/«PKGBUILDDIR»/src'
make[3]: Leaving directory `/«PKGBUILDDIR»/src'
make[2]: Leaving directory `/«PKGBUILDDIR»/src'
make[2]: Entering directory `/«PKGBUILDDIR»'
make[2]: Nothing to be done for `check-am'.
make[2]: Leaving directory `/«PKGBUILDDIR»'
make[1]: Leaving directory `/«PKGBUILDDIR»'
fakeroot debian/rules binary-arch
dh binary-arch --with autoreconf
dh_testroot -a
dh_prep -a
dh_installdirs -a
dh_auto_install -a
make[1]: Entering directory `/«PKGBUILDDIR»'
Making install in src
make[2]: Entering directory `/«PKGBUILDDIR»/src'
Making install in hhalign
make[3]: Entering directory `/«PKGBUILDDIR»/src/hhalign'
make[4]: Entering directory `/«PKGBUILDDIR»/src/hhalign'
make[4]: Nothing to be done for `install-exec-am'.
/bin/mkdir -p '/«PKGBUILDDIR»/debian/tmp/usr/include/clustalo/hhalign'
/usr/bin/install -c -m 644 general.h hhfunc.h '/«PKGBUILDDIR»/debian/tmp/usr/include/clustalo/hhalign'
make[4]: Leaving directory `/«PKGBUILDDIR»/src/hhalign'
make[3]: Leaving directory `/«PKGBUILDDIR»/src/hhalign'
Making install in squid
make[3]: Entering directory `/«PKGBUILDDIR»/src/squid'
make[4]: Entering directory `/«PKGBUILDDIR»/src/squid'
make[4]: Nothing to be done for `install-exec-am'.
/bin/mkdir -p '/«PKGBUILDDIR»/debian/tmp/usr/include/clustalo/squid'
/usr/bin/install -c -m 644 gki.h gsi64.h msa.h rk.h squid.h stopwatch.h sqfuncs.h sre_random.h ssi.h stockholm.h vectorops.h version.h '/«PKGBUILDDIR»/debian/tmp/usr/include/clustalo/squid'
make[4]: Leaving directory `/«PKGBUILDDIR»/src/squid'
make[3]: Leaving directory `/«PKGBUILDDIR»/src/squid'
Making install in kmpp
make[3]: Entering directory `/«PKGBUILDDIR»/src/kmpp'
make[4]: Entering directory `/«PKGBUILDDIR»/src/kmpp'
make[4]: Nothing to be done for `install-exec-am'.
make[4]: Nothing to be done for `install-data-am'.
make[4]: Leaving directory `/«PKGBUILDDIR»/src/kmpp'
make[3]: Leaving directory `/«PKGBUILDDIR»/src/kmpp'
Making install in clustal
make[3]: Entering directory `/«PKGBUILDDIR»/src/clustal'
make[4]: Entering directory `/«PKGBUILDDIR»/src/clustal'
make[4]: Nothing to be done for `install-exec-am'.
/bin/mkdir -p '/«PKGBUILDDIR»/debian/tmp/usr/include/clustalo/clustal'
/usr/bin/install -c -m 644 hhalign_wrapper.h ktuple_pair.h log.h mbed.h muscle_tree.h pair_dist.h progress.h seq.h symmatrix.h tree.h util.h weights.h '/«PKGBUILDDIR»/debian/tmp/usr/include/clustalo/clustal'
make[4]: Leaving directory `/«PKGBUILDDIR»/src/clustal'
make[3]: Leaving directory `/«PKGBUILDDIR»/src/clustal'
make[3]: Entering directory `/«PKGBUILDDIR»/src'
make[4]: Entering directory `/«PKGBUILDDIR»/src'
/bin/mkdir -p '/«PKGBUILDDIR»/debian/tmp/usr/lib/arm-linux-gnueabihf'
/bin/bash ../libtool --mode=install /usr/bin/install -c libclustalo.la '/«PKGBUILDDIR»/debian/tmp/usr/lib/arm-linux-gnueabihf'
libtool: install: /usr/bin/install -c .libs/libclustalo.lai /«PKGBUILDDIR»/debian/tmp/usr/lib/arm-linux-gnueabihf/libclustalo.la
libtool: install: /usr/bin/install -c .libs/libclustalo.a /«PKGBUILDDIR»/debian/tmp/usr/lib/arm-linux-gnueabihf/libclustalo.a
libtool: install: chmod 644 /«PKGBUILDDIR»/debian/tmp/usr/lib/arm-linux-gnueabihf/libclustalo.a
libtool: install: ranlib /«PKGBUILDDIR»/debian/tmp/usr/lib/arm-linux-gnueabihf/libclustalo.a
libtool: install: warning: remember to run `libtool --finish /usr/lib/arm-linux-gnueabihf'
/bin/mkdir -p '/«PKGBUILDDIR»/debian/tmp/usr/bin'
/bin/bash ../libtool --mode=install /usr/bin/install -c clustalo '/«PKGBUILDDIR»/debian/tmp/usr/bin'
libtool: install: /usr/bin/install -c clustalo /«PKGBUILDDIR»/debian/tmp/usr/bin/clustalo
/bin/mkdir -p '/«PKGBUILDDIR»/debian/tmp/usr/include/clustalo/'
/usr/bin/install -c -m 644 clustal-omega-config.h clustal-omega.h '/«PKGBUILDDIR»/debian/tmp/usr/include/clustalo/'
make[4]: Leaving directory `/«PKGBUILDDIR»/src'
make[3]: Leaving directory `/«PKGBUILDDIR»/src'
make[2]: Leaving directory `/«PKGBUILDDIR»/src'
make[2]: Entering directory `/«PKGBUILDDIR»'
make[3]: Entering directory `/«PKGBUILDDIR»'
make[3]: Nothing to be done for `install-exec-am'.
/bin/mkdir -p '/«PKGBUILDDIR»/debian/tmp/usr/share/doc/clustal-omega'
/usr/bin/install -c -m 644 README '/«PKGBUILDDIR»/debian/tmp/usr/share/doc/clustal-omega'
/bin/mkdir -p '/«PKGBUILDDIR»/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig'
/usr/bin/install -c -m 644 clustalo.pc '/«PKGBUILDDIR»/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig'
make[3]: Leaving directory `/«PKGBUILDDIR»'
make[2]: Leaving directory `/«PKGBUILDDIR»'
make[1]: Leaving directory `/«PKGBUILDDIR»'
debian/rules override_dh_install
make[1]: Entering directory `/«PKGBUILDDIR»'
# Generate doxygen doc
mkdir -p doc
doxygen Doxyfile
Warning: Tag `SYMBOL_CACHE_SIZE' at line 289 of file Doxyfile has become obsolete.
To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
Warning: Tag `SHOW_DIRECTORIES' at line 473 of file Doxyfile has become obsolete.
To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
Warning: Tag `HTML_ALIGN_MEMBERS' at line 799 of file Doxyfile has become obsolete.
To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
Warning: doxygen no longer ships with the FreeSans font.
You may want to clear or change DOT_FONTNAME.
Otherwise you run the risk that the wrong font is being used for dot generated graphs.
/«PKGBUILDDIR»/src/clustal-omega.c:718: warning: The following parameters of AlignmentOrder(int **piOrderLR_p, double **pdSeqWeights_p, mseq_t *prMSeq, int iPairDistType, char *pcDistmatInfile, char *pcDistmatOutfile, int iClusteringType, int iClustersizes, char *pcGuidetreeInfile, char *pcGuidetreeOutfile, char *pcClusterFile, bool bUseMbed, bool bPercID) are not documented:
parameter 'iClustersizes'
parameter 'pcClusterFile'
parameter 'bPercID'
/«PKGBUILDDIR»/src/clustal-omega.c:718: warning: The following parameters of AlignmentOrder(int **piOrderLR_p, double **pdSeqWeights_p, mseq_t *prMSeq, int iPairDistType, char *pcDistmatInfile, char *pcDistmatOutfile, int iClusteringType, int iClustersizes, char *pcGuidetreeInfile, char *pcGuidetreeOutfile, char *pcClusterFile, bool bUseMbed, bool bPercID) are not documented:
parameter 'iClustersizes'
parameter 'pcClusterFile'
parameter 'bPercID'
/«PKGBUILDDIR»/src/clustal/mbed.c:640: warning: The following parameters of BisectingKmeans(bisecting_kmeans_result_t **prKMeansResult_p, const int iNObjs, const int iDim, double **ppdVectors, const int iMinRequiredObjsPerCluster, const int iMaxAllowedObjsPerCluster, char ***ppcClusterSplits_p) are not documented:
parameter 'ppcClusterSplits_p'
/«PKGBUILDDIR»/src/clustal/mbed.c:1127: warning: The following parameters of Mbed(tree_t **prMbedTree_p, mseq_t *prMSeq, const int iPairDistType, const char *pcGuidetreeOut, int iClustersizes, const char *pcClusterFile) are not documented:
parameter 'iClustersizes'
parameter 'pcClusterFile'
/«PKGBUILDDIR»/src/clustal/mbed.c:1127: warning: The following parameters of Mbed(tree_t **prMbedTree_p, mseq_t *prMSeq, const int iPairDistType, const char *pcGuidetreeOut, int iClustersizes, const char *pcClusterFile) are not documented:
parameter 'iClustersizes'
parameter 'pcClusterFile'
/«PKGBUILDDIR»/src/clustal/pair_dist.c:246: warning: Unsupported xml/html tag <j> found
/«PKGBUILDDIR»/src/clustal/pair_dist.c:252: warning: Unsupported xml/html tag <j> found
/«PKGBUILDDIR»/src/clustal/pair_dist.c:244: warning: The following parameters of PairDistances(symmatrix_t **distmat, mseq_t *mseq, int pairdist_type, bool bPercID, int istart, int iend, int jstart, int jend, char *fdist_in, char *fdist_out) are not documented:
parameter 'bPercID'
/«PKGBUILDDIR»/src/clustal/pair_dist.c:259: warning: Unsupported xml/html tag <j> found
/«PKGBUILDDIR»/src/clustal/pair_dist.c:265: warning: Unsupported xml/html tag <j> found
/«PKGBUILDDIR»/src/clustal/pair_dist.c:244: warning: The following parameters of PairDistances(symmatrix_t **distmat, mseq_t *mseq, int pairdist_type, bool bPercID, int istart, int iend, int jstart, int jend, char *fdist_in, char *fdist_out) are not documented:
parameter 'bPercID'
/«PKGBUILDDIR»/src/clustal/seq.c:397: warning: The following parameters of ReadSequences(mseq_t *prMSeq, char *seqfile, int iSeqType, int iSeqFmt, bool bIsProfile, bool bDealignInputSeqs, int iMaxNumSeq, int iMaxSeqLen) are not documented:
parameter 'iSeqFmt'
parameter 'bIsProfile'
parameter 'bDealignInputSeqs'
/«PKGBUILDDIR»/src/clustal/seq.c:1012: warning: The following parameters of SeqsAreAligned(mseq_t *prMSeq, bool bIsProfile, bool bDealignInputSeqs) are not documented:
parameter 'bIsProfile'
parameter 'bDealignInputSeqs'
/«PKGBUILDDIR»/src/clustal/seq.c:777: warning: The following parameters of WriteAlignment(mseq_t *mseq, const char *pcAlnOutfile, int outfmt, int iWrap, bool bResno) are not documented:
parameter 'bResno'
/«PKGBUILDDIR»/src/clustal/seq.c:397: warning: The following parameters of ReadSequences(mseq_t *prMSeq, char *seqfile, int iSeqType, int iSeqFmt, bool bIsProfile, bool bDealignInputSeqs, int iMaxNumSeq, int iMaxSeqLen) are not documented:
parameter 'iSeqFmt'
parameter 'bIsProfile'
parameter 'bDealignInputSeqs'
/«PKGBUILDDIR»/src/clustal/seq.c:1012: warning: The following parameters of SeqsAreAligned(mseq_t *prMSeq, bool bIsProfile, bool bDealignInputSeqs) are not documented:
parameter 'bIsProfile'
parameter 'bDealignInputSeqs'
/«PKGBUILDDIR»/src/clustal/seq.c:777: warning: The following parameters of WriteAlignment(mseq_t *mseq, const char *pcAlnOutfile, int outfmt, int iWrap, bool bResno) are not documented:
parameter 'bResno'
/«PKGBUILDDIR»/src/clustal/symmatrix.c:262: warning: The following parameters of SymMatrixPrint(symmatrix_t *symmat, char **labels, const char *path, bool bPercID) are not documented:
parameter 'bPercID'
/«PKGBUILDDIR»/src/clustal/symmatrix.c:262: warning: The following parameters of SymMatrixPrint(symmatrix_t *symmat, char **labels, const char *path, bool bPercID) are not documented:
parameter 'bPercID'
dh_install
rm -rf debian/tmp/usr/lib/pkgconfig
rm -f debian/tmp/usr/lib/*/libclustalo.la
mv debian/tmp/usr/include debian/libclustalo-dev/usr
mv debian/tmp/usr/lib debian/libclustalo-dev/usr
mv debian/tmp/usr/bin debian/clustalo/usr
make[1]: Leaving directory `/«PKGBUILDDIR»'
dh_installdocs -a
dh_installchangelogs -a
dh_installman -a
dh_perl -a
dh_link -a
dh_compress -a
dh_fixperms -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: Depends field of package libclustalo-dev: unknown substitution variable ${shlibs:Depends}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package `clustalo' in `../clustalo_1.2.1-1_armhf.deb'.
dpkg-deb: building package `libclustalo-dev' in `../libclustalo-dev_1.2.1-1_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../clustalo_1.2.1-1_armhf.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
dpkg-source --after-build clustalo-1.2.1
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20140419-0819
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
clustalo_1.2.1-1_armhf.changes:
───────────────────────────────
Format: 1.8
Date: Sun, 13 Apr 2014 21:09:34 +0200
Source: clustalo
Binary: clustalo libclustalo-dev libclustalo-doc
Architecture: armhf
Version: 1.2.1-1
Distribution: jessie-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
clustalo - General purpose multiple sequence alignment program for proteins
libclustalo-dev - library to embed Clustal Omega
libclustalo-doc - API documentation
Closes: 744421
Changes:
clustalo (1.2.1-1) unstable; urgency=medium
.
* New upstream version
* Moved debian/upstream to debian/upstream/metadata
* cme fix dpkg-control
* cme fix dpkg-copyright
* use dh-autoreconf
Closes: #744421
Checksums-Sha1:
39ae853f66a78a7d1cf4138c41394cac982cc724 223526 clustalo_1.2.1-1_armhf.deb
cddff411b50401877fc56b2eecc4e1055cc7657b 276490 libclustalo-dev_1.2.1-1_armhf.deb
Checksums-Sha256:
cbd3e8eb90d5342973047596547021d8a91ffa81d2010f8dac1044f9605ea704 223526 clustalo_1.2.1-1_armhf.deb
c2fc6a53fb2371b1569fcf33a659a358c574d197ac3245df8dbdf0b8ce36aaec 276490 libclustalo-dev_1.2.1-1_armhf.deb
Files:
0adb4af75f8bd040e542d9827d64348e 223526 science optional clustalo_1.2.1-1_armhf.deb
9904b25b499fcfe581dba3d74ba4599e 276490 libdevel optional libclustalo-dev_1.2.1-1_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
clustalo_1.2.1-1_armhf.deb
──────────────────────────
new debian package, version 2.0.
size 223526 bytes: control archive=822 bytes.
655 bytes, 14 lines control
399 bytes, 6 lines md5sums
Package: clustalo
Version: 1.2.1-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 534
Depends: libargtable2-0 (>= 7), libc6 (>= 2.4), libgcc1 (>= 1:4.4.0), libgomp1 (>= 4.2.1), libstdc++6 (>= 4.4.0)
Section: science
Priority: optional
Homepage: http://www.clustal.org/omega/
Description: General purpose multiple sequence alignment program for proteins
Clustal-Omega is a general purpose multiple sequence alignment (MSA)
program for dna/rna/proteins. It produces high quality MSAs and is capable of
handling data-sets of hundreds of thousands of sequences in reasonable
time.
drwxr-xr-x root/root 0 2014-04-19 08:19 ./
drwxr-xr-x root/root 0 2014-04-19 08:19 ./usr/
drwxr-xr-x root/root 0 2014-04-19 08:19 ./usr/bin/
-rwxr-xr-x root/root 532040 2014-04-19 08:19 ./usr/bin/clustalo
drwxr-xr-x root/root 0 2014-04-19 08:19 ./usr/share/
drwxr-xr-x root/root 0 2014-04-19 08:19 ./usr/share/doc/
drwxr-xr-x root/root 0 2014-04-19 08:19 ./usr/share/doc/clustalo/
-rw-r--r-- root/root 1174 2014-04-13 19:13 ./usr/share/doc/clustalo/copyright
-rw-r--r-- root/root 10994 2013-08-27 12:07 ./usr/share/doc/clustalo/README.gz
-rw-r--r-- root/root 465 2014-04-13 19:16 ./usr/share/doc/clustalo/changelog.Debian.gz
-rw-r--r-- root/root 744 2012-06-27 14:48 ./usr/share/doc/clustalo/changelog.gz
drwxr-xr-x root/root 0 2014-04-19 08:19 ./usr/share/man/
drwxr-xr-x root/root 0 2014-04-19 08:19 ./usr/share/man/man1/
-rw-r--r-- root/root 1083 2014-04-19 08:19 ./usr/share/man/man1/clustalo.1.gz
libclustalo-dev_1.2.1-1_armhf.deb
─────────────────────────────────
new debian package, version 2.0.
size 276490 bytes: control archive=1554 bytes.
504 bytes, 15 lines control
2409 bytes, 33 lines md5sums
Package: libclustalo-dev
Source: clustalo
Version: 1.2.1-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 895
Depends: libargtable2-dev, clustalo (= 1.2.1-1)
Suggests: libclustalo-doc
Section: libdevel
Priority: optional
Homepage: http://www.clustal.org/omega/
Description: library to embed Clustal Omega
This package contains headers and libraries to include
Clustal Omega in a program. It provides clustal usage
with an API.
drwxr-xr-x root/root 0 2014-04-19 08:19 ./
drwxr-xr-x root/root 0 2014-04-19 08:19 ./usr/
drwxr-xr-x root/root 0 2014-04-19 08:18 ./usr/include/
drwxr-xr-x root/root 0 2014-04-19 08:18 ./usr/include/clustalo/
drwxr-xr-x root/root 0 2014-04-19 08:18 ./usr/include/clustalo/hhalign/
-rw-r--r-- root/root 2961 2014-04-19 08:18 ./usr/include/clustalo/hhalign/general.h
-rw-r--r-- root/root 859 2014-04-19 08:18 ./usr/include/clustalo/hhalign/hhfunc.h
drwxr-xr-x root/root 0 2014-04-19 08:18 ./usr/include/clustalo/squid/
-rw-r--r-- root/root 1381 2014-04-19 08:18 ./usr/include/clustalo/squid/gki.h
-rw-r--r-- root/root 3473 2014-04-19 08:18 ./usr/include/clustalo/squid/gsi64.h
-rw-r--r-- root/root 13096 2014-04-19 08:18 ./usr/include/clustalo/squid/msa.h
-rw-r--r-- root/root 1264 2014-04-19 08:18 ./usr/include/clustalo/squid/rk.h
-rw-r--r-- root/root 19433 2014-04-19 08:18 ./usr/include/clustalo/squid/squid.h
-rw-r--r-- root/root 1937 2014-04-19 08:18 ./usr/include/clustalo/squid/stopwatch.h
-rw-r--r-- root/root 10390 2014-04-19 08:18 ./usr/include/clustalo/squid/sqfuncs.h
-rw-r--r-- root/root 489 2014-04-19 08:18 ./usr/include/clustalo/squid/sre_random.h
-rw-r--r-- root/root 7610 2014-04-19 08:18 ./usr/include/clustalo/squid/ssi.h
-rw-r--r-- root/root 1868 2014-04-19 08:18 ./usr/include/clustalo/squid/stockholm.h
-rw-r--r-- root/root 1434 2014-04-19 08:18 ./usr/include/clustalo/squid/vectorops.h
-rw-r--r-- root/root 333 2014-04-19 08:18 ./usr/include/clustalo/squid/version.h
drwxr-xr-x root/root 0 2014-04-19 08:18 ./usr/include/clustalo/clustal/
-rw-r--r-- root/root 1159 2014-04-19 08:18 ./usr/include/clustalo/clustal/hhalign_wrapper.h
-rw-r--r-- root/root 1251 2014-04-19 08:18 ./usr/include/clustalo/clustal/ktuple_pair.h
-rw-r--r-- root/root 1787 2014-04-19 08:18 ./usr/include/clustalo/clustal/log.h
-rw-r--r-- root/root 866 2014-04-19 08:18 ./usr/include/clustalo/clustal/mbed.h
-rw-r--r-- root/root 4112 2014-04-19 08:18 ./usr/include/clustalo/clustal/muscle_tree.h
-rw-r--r-- root/root 1275 2014-04-19 08:18 ./usr/include/clustalo/clustal/pair_dist.h
-rw-r--r-- root/root 1257 2014-04-19 08:18 ./usr/include/clustalo/clustal/progress.h
-rw-r--r-- root/root 3936 2014-04-19 08:18 ./usr/include/clustalo/clustal/seq.h
-rw-r--r-- root/root 2310 2014-04-19 08:18 ./usr/include/clustalo/clustal/symmatrix.h
-rw-r--r-- root/root 1066 2014-04-19 08:18 ./usr/include/clustalo/clustal/tree.h
-rw-r--r-- root/root 2308 2014-04-19 08:18 ./usr/include/clustalo/clustal/util.h
-rw-r--r-- root/root 741 2014-04-19 08:18 ./usr/include/clustalo/clustal/weights.h
-rw-r--r-- root/root 9529 2014-04-19 08:18 ./usr/include/clustalo/clustal-omega-config.h
-rw-r--r-- root/root 4640 2014-04-19 08:18 ./usr/include/clustalo/clustal-omega.h
drwxr-xr-x root/root 0 2014-04-19 08:18 ./usr/lib/
drwxr-xr-x root/root 0 2014-04-19 08:19 ./usr/lib/arm-linux-gnueabihf/
drwxr-xr-x root/root 0 2014-04-19 08:18 ./usr/lib/arm-linux-gnueabihf/pkgconfig/
-rw-r--r-- root/root 250 2014-04-19 08:18 ./usr/lib/arm-linux-gnueabihf/pkgconfig/clustalo.pc
-rw-r--r-- root/root 809234 2014-04-19 08:19 ./usr/lib/arm-linux-gnueabihf/libclustalo.a
drwxr-xr-x root/root 0 2014-04-19 08:19 ./usr/share/
drwxr-xr-x root/root 0 2014-04-19 08:19 ./usr/share/doc/
drwxr-xr-x root/root 0 2014-04-19 08:19 ./usr/share/doc/libclustalo-dev/
-rw-r--r-- root/root 1174 2014-04-13 19:13 ./usr/share/doc/libclustalo-dev/copyright
-rw-r--r-- root/root 465 2014-04-13 19:16 ./usr/share/doc/libclustalo-dev/changelog.Debian.gz
-rw-r--r-- root/root 744 2012-06-27 14:48 ./usr/share/doc/libclustalo-dev/changelog.gz
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 29256
Build-Time: 564
Distribution: jessie-staging
Host Architecture: armhf
Install-Time: 345
Job: clustalo_1.2.1-1
Machine Architecture: armhf
Package: clustalo
Package-Time: 968
Source-Version: 1.2.1-1
Space: 29256
Status: successful
Version: 1.2.1-1
────────────────────────────────────────────────────────────────────────────────
Finished at 20140419-0819
Build needed 00:16:08, 29256k disc space