clustalo →
1.2.1-2 →
armhf → 2015-11-30 08:58:44
sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on bm-wb-02
╔══════════════════════════════════════════════════════════════════════════════╗
║ clustalo 1.2.1-2 (armhf) 30 Nov 2015 08:38 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: clustalo
Version: 1.2.1-2
Source Version: 1.2.1-2
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/clustalo-Yfj6Es/clustalo-1.2.1' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/clustalo-Yfj6Es' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-cfc88a5d-6644-48ff-85d1-08277d353cde' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
Get:1 http://172.17.0.1 stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1 stretch-staging/main Sources [8497 kB]
Get:3 http://172.17.0.1 stretch-staging/main armhf Packages [10.5 MB]
Ign http://172.17.0.1 stretch-staging/main Translation-en
Fetched 19.0 MB in 34s (544 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 1171 kB of source archives.
Get:1 http://172.17.0.1/private/ stretch-staging/main clustalo 1.2.1-2 (dsc) [2186 B]
Get:2 http://172.17.0.1/private/ stretch-staging/main clustalo 1.2.1-2 (tar) [1164 kB]
Get:3 http://172.17.0.1/private/ stretch-staging/main clustalo 1.2.1-2 (diff) [4304 B]
Fetched 1171 kB in 0s (3775 kB/s)
Download complete and in download only mode
Check architectures
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Check dependencies
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Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-kaCOsY/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Ign file: ./ InRelease
Get:1 file: ./ Release.gpg [299 B]
Get:2 file: ./ Release [2119 B]
Ign file: ./ Translation-en
Reading package lists...
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install core build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
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 22 not upgraded.
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(Reading database ... 12877 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
Merged Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), dh-autoreconf, dh-linktree, libargtable2-dev, doxygen, graphviz, sphinx-common
Filtered Build-Depends: libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), dh-autoreconf, dh-linktree, libargtable2-dev, doxygen, graphviz, sphinx-common
dpkg-deb: building package 'sbuild-build-depends-clustalo-dummy' in '/«BUILDDIR»/resolver-IjkEXe/apt_archive/sbuild-build-depends-clustalo-dummy.deb'.
OK
Ign file: ./ InRelease
Get:1 file: ./ Release.gpg [299 B]
Get:2 file: ./ Release [2119 B]
Ign file: ./ Translation-en
Reading package lists...
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install clustalo build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
libisl13
Use 'apt-get autoremove' to remove it.
The following extra packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils cpp-5 debhelper
dh-autoreconf dh-linktree dh-strip-nondeterminism doxygen file fontconfig
fontconfig-config fonts-dejavu-core g++-5 gcc-5 gcc-5-base gettext
gettext-base graphviz groff-base intltool-debian libarchive-zip-perl
libargtable2-0 libargtable2-dev libargtable2-docs libasan2 libatomic1
libbsd0 libcairo2 libcc1-0 libcdt5 libcgraph6 libclang1-3.5 libcroco3
libdatrie1 libedit2 libexpat1 libffi6 libfile-stripnondeterminism-perl
libfontconfig1 libfreetype6 libgcc-5-dev libgcc1 libgd3 libglib2.0-0
libgomp1 libgraphite2-3 libgvc6 libgvpr2 libharfbuzz0b libice6 libicu55
libisl15 libjbig0 libjpeg62-turbo libjs-jquery libjs-sphinxdoc
libjs-underscore libllvm3.5v5 libltdl7 libmagic1 libobjc-5-dev libobjc4
libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpathplan4
libpipeline1 libpixman-1-0 libsigsegv2 libsm6 libstdc++-5-dev libstdc++6
libthai-data libthai0 libtiff5 libtool libubsan0 libunistring0 libvpx2
libx11-6 libx11-data libxapian22v5 libxau6 libxaw7 libxcb-render0
libxcb-shm0 libxcb1 libxdmcp6 libxdot4 libxext6 libxml2 libxmu6 libxpm4
libxrender1 libxt6 m4 man-db po-debconf sphinx-common ucf x11-common
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican wordlist whois
vacation gcc-5-locales dh-make doxygen-latex doxygen-doc doxygen-gui
gcc-5-doc libstdc++6-5-dbg libgcc1-dbg libgomp1-dbg libitm1-dbg
libatomic1-dbg libasan2-dbg liblsan0-dbg libtsan0-dbg libubsan0-dbg
libcilkrts5-dbg libmpx0-dbg libquadmath-dbg gettext-doc libasprintf-dev
libgettextpo-dev gsfonts graphviz-doc groff libgd-tools libstdc++-5-doc
libtool-doc automaken gfortran fortran95-compiler gcj-jdk xapian-tools less
www-browser libmail-box-perl
Recommended packages:
curl wget lynx-cur fonts-liberation libglib2.0-data shared-mime-info
xdg-user-dirs javascript-common libltdl-dev xml-core libmail-sendmail-perl
python-sphinx python3-sphinx
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-linktree dh-strip-nondeterminism doxygen file fontconfig
fontconfig-config fonts-dejavu-core gettext gettext-base graphviz groff-base
intltool-debian libarchive-zip-perl libargtable2-0 libargtable2-dev
libargtable2-docs libbsd0 libcairo2 libcdt5 libcgraph6 libclang1-3.5
libcroco3 libdatrie1 libedit2 libexpat1 libffi6
libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgd3
libglib2.0-0 libgraphite2-3 libgvc6 libgvpr2 libharfbuzz0b libice6 libicu55
libisl15 libjbig0 libjpeg62-turbo libjs-jquery libjs-sphinxdoc
libjs-underscore libllvm3.5v5 libltdl7 libmagic1 libobjc-5-dev libobjc4
libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpathplan4
libpipeline1 libpixman-1-0 libsigsegv2 libsm6 libthai-data libthai0 libtiff5
libtool libunistring0 libvpx2 libx11-6 libx11-data libxapian22v5 libxau6
libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxdot4 libxext6
libxml2 libxmu6 libxpm4 libxrender1 libxt6 m4 man-db po-debconf
sbuild-build-depends-clustalo-dummy sphinx-common ucf x11-common
The following packages will be upgraded:
cpp-5 g++-5 gcc-5 gcc-5-base libasan2 libatomic1 libcc1-0 libgcc-5-dev
libgcc1 libgomp1 libstdc++-5-dev libstdc++6 libubsan0
13 upgraded, 92 newly installed, 0 to remove and 9 not upgraded.
Need to get 126 MB/126 MB of archives.
After this operation, 151 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ stretch-staging/main libgomp1 armhf 5.2.1-23+rpi1+b1 [47.4 kB]
Get:2 http://172.17.0.1/private/ stretch-staging/main libatomic1 armhf 5.2.1-23+rpi1+b1 [6606 B]
Get:3 http://172.17.0.1/private/ stretch-staging/main gcc-5-base armhf 5.2.1-23+rpi1+b1 [167 kB]
Get:4 http://172.17.0.1/private/ stretch-staging/main libgcc1 armhf 1:5.2.1-23+rpi1+b1 [38.5 kB]
Get:5 http://172.17.0.1/private/ stretch-staging/main libasan2 armhf 5.2.1-23+rpi1+b1 [227 kB]
Get:6 http://172.17.0.1/private/ stretch-staging/main libubsan0 armhf 5.2.1-23+rpi1+b1 [84.3 kB]
Get:7 http://172.17.0.1/private/ stretch-staging/main libisl15 armhf 0.15-3 [397 kB]
Get:8 http://172.17.0.1/private/ stretch-staging/main cpp-5 armhf 5.2.1-23+rpi1+b1 [22.9 MB]
Get:9 http://172.17.0.1/private/ stretch-staging/main libcc1-0 armhf 5.2.1-23+rpi1+b1 [24.7 kB]
Get:10 http://172.17.0.1/private/ stretch-staging/main g++-5 armhf 5.2.1-23+rpi1+b1 [32.0 MB]
Get:11 http://172.17.0.1/private/ stretch-staging/main gcc-5 armhf 5.2.1-23+rpi1+b1 [22.9 MB]
Get:12 http://172.17.0.1/private/ stretch-staging/main libgcc-5-dev armhf 5.2.1-23+rpi1+b1 [449 kB]
Get:13 http://172.17.0.1/private/ stretch-staging/main libstdc++-5-dev armhf 5.2.1-23+rpi1+b1 [1428 kB]
Get:14 http://172.17.0.1/private/ stretch-staging/main libstdc++6 armhf 5.2.1-23+rpi1+b1 [327 kB]
Get:15 http://172.17.0.1/private/ stretch-staging/main groff-base armhf 1.22.3-4 [1084 kB]
Get:16 http://172.17.0.1/private/ stretch-staging/main bsdmainutils armhf 9.0.6 [177 kB]
Get:17 http://172.17.0.1/private/ stretch-staging/main libpipeline1 armhf 1.4.1-1 [23.9 kB]
Get:18 http://172.17.0.1/private/ stretch-staging/main man-db armhf 2.7.5-1 [975 kB]
Get:19 http://172.17.0.1/private/ stretch-staging/main libbsd0 armhf 0.7.0-2 [63.7 kB]
Get:20 http://172.17.0.1/private/ stretch-staging/main libedit2 armhf 3.1-20150325-1 [70.7 kB]
Get:21 http://172.17.0.1/private/ stretch-staging/main libexpat1 armhf 2.1.0-7 [59.8 kB]
Get:22 http://172.17.0.1/private/ stretch-staging/main libfreetype6 armhf 2.6.1-0.1 [411 kB]
Get:23 http://172.17.0.1/private/ stretch-staging/main ucf all 3.0031 [68.9 kB]
Get:24 http://172.17.0.1/private/ stretch-staging/main fonts-dejavu-core all 2.35-1 [1064 kB]
Get:25 http://172.17.0.1/private/ stretch-staging/main fontconfig-config all 2.11.0-6.3 [273 kB]
Get:26 http://172.17.0.1/private/ stretch-staging/main libfontconfig1 armhf 2.11.0-6.3 [311 kB]
Get:27 http://172.17.0.1/private/ stretch-staging/main fontconfig armhf 2.11.0-6.3 [402 kB]
Get:28 http://172.17.0.1/private/ stretch-staging/main libffi6 armhf 3.2.1-3 [18.5 kB]
Get:29 http://172.17.0.1/private/ stretch-staging/main libjbig0 armhf 2.1-3.1 [27.5 kB]
Get:30 http://172.17.0.1/private/ stretch-staging/main libltdl7 armhf 2.4.2-1.11 [42.5 kB]
Get:31 http://172.17.0.1/private/ stretch-staging/main libsigsegv2 armhf 2.10-4 [28.2 kB]
Get:32 http://172.17.0.1/private/ stretch-staging/main libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:33 http://172.17.0.1/private/ stretch-staging/main libxau6 armhf 1:1.0.8-1 [19.9 kB]
Get:34 http://172.17.0.1/private/ stretch-staging/main libxdmcp6 armhf 1:1.1.2-1 [25.0 kB]
Get:35 http://172.17.0.1/private/ stretch-staging/main libxcb1 armhf 1.10-3+b1 [40.6 kB]
Get:36 http://172.17.0.1/private/ stretch-staging/main libx11-data all 2:1.6.3-1 [128 kB]
Get:37 http://172.17.0.1/private/ stretch-staging/main libx11-6 armhf 2:1.6.3-1 [678 kB]
Get:38 http://172.17.0.1/private/ stretch-staging/main libxext6 armhf 2:1.3.3-1 [48.1 kB]
Get:39 http://172.17.0.1/private/ stretch-staging/main libxapian22v5 armhf 1.2.21-1.2 [857 kB]
Get:40 http://172.17.0.1/private/ stretch-staging/main libmagic1 armhf 1:5.25-2 [250 kB]
Get:41 http://172.17.0.1/private/ stretch-staging/main file armhf 1:5.25-2 [61.2 kB]
Get:42 http://172.17.0.1/private/ stretch-staging/main gettext-base armhf 0.19.6-1 [119 kB]
Get:43 http://172.17.0.1/private/ stretch-staging/main libicu55 armhf 55.1-6 [7379 kB]
Get:44 http://172.17.0.1/private/ stretch-staging/main libxml2 armhf 2.9.2+zdfsg1-4 [797 kB]
Get:45 http://172.17.0.1/private/ stretch-staging/main m4 armhf 1.4.17-4 [238 kB]
Get:46 http://172.17.0.1/private/ stretch-staging/main autoconf all 2.69-9 [338 kB]
Get:47 http://172.17.0.1/private/ stretch-staging/main autotools-dev all 20150820.1 [71.7 kB]
Get:48 http://172.17.0.1/private/ stretch-staging/main automake all 1:1.15-3 [735 kB]
Get:49 http://172.17.0.1/private/ stretch-staging/main autopoint all 0.19.6-1 [429 kB]
Get:50 http://172.17.0.1/private/ stretch-staging/main libglib2.0-0 armhf 2.46.2-1 [2482 kB]
Get:51 http://172.17.0.1/private/ stretch-staging/main libcroco3 armhf 0.6.9-1 [129 kB]
Get:52 http://172.17.0.1/private/ stretch-staging/main gettext armhf 0.19.6-1 [1393 kB]
Get:53 http://172.17.0.1/private/ stretch-staging/main intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:54 http://172.17.0.1/private/ stretch-staging/main po-debconf all 1.0.18 [248 kB]
Get:55 http://172.17.0.1/private/ stretch-staging/main libarchive-zip-perl all 1.53-1 [97.3 kB]
Get:56 http://172.17.0.1/private/ stretch-staging/main libfile-stripnondeterminism-perl all 0.014-1 [10.6 kB]
Get:57 http://172.17.0.1/private/ stretch-staging/main dh-strip-nondeterminism all 0.014-1 [7472 B]
Get:58 http://172.17.0.1/private/ stretch-staging/main debhelper all 9.20151005 [817 kB]
Get:59 http://172.17.0.1/private/ stretch-staging/main libtool all 2.4.2-1.11 [190 kB]
Get:60 http://172.17.0.1/private/ stretch-staging/main dh-autoreconf all 10 [15.2 kB]
Get:61 http://172.17.0.1/private/ stretch-staging/main dh-linktree all 0.4 [10.3 kB]
Get:62 http://172.17.0.1/private/ stretch-staging/main libllvm3.5v5 armhf 1:3.5.2-3 [6503 kB]
Get:63 http://172.17.0.1/private/ stretch-staging/main libobjc4 armhf 5.2.1-23+rpi1+b1 [91.0 kB]
Get:64 http://172.17.0.1/private/ stretch-staging/main libobjc-5-dev armhf 5.2.1-23+rpi1+b1 [335 kB]
Get:65 http://172.17.0.1/private/ stretch-staging/main libclang1-3.5 armhf 1:3.5.2-3 [2822 kB]
Get:66 http://172.17.0.1/private/ stretch-staging/main doxygen armhf 1.8.9.1-5 [2582 kB]
Get:67 http://172.17.0.1/private/ stretch-staging/main libcdt5 armhf 2.38.0-12 [60.2 kB]
Get:68 http://172.17.0.1/private/ stretch-staging/main libcgraph6 armhf 2.38.0-12 [78.9 kB]
Get:69 http://172.17.0.1/private/ stretch-staging/main libjpeg62-turbo armhf 1:1.4.1-2 [103 kB]
Get:70 http://172.17.0.1/private/ stretch-staging/main libtiff5 armhf 4.0.5-1 [200 kB]
Get:71 http://172.17.0.1/private/ stretch-staging/main libvpx2 armhf 1.4.0-4+rpi1 [409 kB]
Get:72 http://172.17.0.1/private/ stretch-staging/main libxpm4 armhf 1:3.5.11-1+b1 [42.4 kB]
Get:73 http://172.17.0.1/private/ stretch-staging/main libgd3 armhf 2.1.1-4 [125 kB]
Get:74 http://172.17.0.1/private/ stretch-staging/main libpixman-1-0 armhf 0.33.4-1 [453 kB]
Get:75 http://172.17.0.1/private/ stretch-staging/main libxcb-render0 armhf 1.10-3+b1 [16.9 kB]
Get:76 http://172.17.0.1/private/ stretch-staging/main libxcb-shm0 armhf 1.10-3+b1 [11.4 kB]
Get:77 http://172.17.0.1/private/ stretch-staging/main libxrender1 armhf 1:0.9.9-2 [28.9 kB]
Get:78 http://172.17.0.1/private/ stretch-staging/main libcairo2 armhf 1.14.4-1 [687 kB]
Get:79 http://172.17.0.1/private/ stretch-staging/main libthai-data all 0.1.24-1 [163 kB]
Get:80 http://172.17.0.1/private/ stretch-staging/main libdatrie1 armhf 0.2.10-1 [32.2 kB]
Get:81 http://172.17.0.1/private/ stretch-staging/main libthai0 armhf 0.1.24-1 [46.2 kB]
Get:82 http://172.17.0.1/private/ stretch-staging/main libpango-1.0-0 armhf 1.38.1-1 [292 kB]
Get:83 http://172.17.0.1/private/ stretch-staging/main libgraphite2-3 armhf 1.3.3-1 [61.1 kB]
Get:84 http://172.17.0.1/private/ stretch-staging/main libharfbuzz0b armhf 1.0.1-1+b1 [501 kB]
Get:85 http://172.17.0.1/private/ stretch-staging/main libpangoft2-1.0-0 armhf 1.38.1-1 [229 kB]
Get:86 http://172.17.0.1/private/ stretch-staging/main libpangocairo-1.0-0 armhf 1.38.1-1 [218 kB]
Get:87 http://172.17.0.1/private/ stretch-staging/main libpathplan4 armhf 2.38.0-12 [63.6 kB]
Get:88 http://172.17.0.1/private/ stretch-staging/main libxdot4 armhf 2.38.0-12 [57.7 kB]
Get:89 http://172.17.0.1/private/ stretch-staging/main libgvc6 armhf 2.38.0-12 [533 kB]
Get:90 http://172.17.0.1/private/ stretch-staging/main libgvpr2 armhf 2.38.0-12 [190 kB]
Get:91 http://172.17.0.1/private/ stretch-staging/main x11-common all 1:7.7+12 [251 kB]
Get:92 http://172.17.0.1/private/ stretch-staging/main libice6 armhf 2:1.0.9-1+b1 [51.9 kB]
Get:93 http://172.17.0.1/private/ stretch-staging/main libsm6 armhf 2:1.2.2-1+b1 [31.2 kB]
Get:94 http://172.17.0.1/private/ stretch-staging/main libxt6 armhf 1:1.1.5-1 [155 kB]
Get:95 http://172.17.0.1/private/ stretch-staging/main libxmu6 armhf 2:1.1.2-2 [52.0 kB]
Get:96 http://172.17.0.1/private/ stretch-staging/main libxaw7 armhf 2:1.0.13-1 [164 kB]
Get:97 http://172.17.0.1/private/ stretch-staging/main graphviz armhf 2.38.0-12 [648 kB]
Get:98 http://172.17.0.1/private/ stretch-staging/main libargtable2-0 armhf 12-1.1 [15.3 kB]
Get:99 http://172.17.0.1/private/ stretch-staging/main libargtable2-docs all 12-1.1 [2621 kB]
Get:100 http://172.17.0.1/private/ stretch-staging/main libargtable2-dev armhf 12-1.1 [54.1 kB]
Get:101 http://172.17.0.1/private/ stretch-staging/main libjs-jquery all 1.11.3+dfsg-4 [163 kB]
Get:102 http://172.17.0.1/private/ stretch-staging/main libjs-underscore all 1.7.0~dfsg-1 [49.9 kB]
Get:103 http://172.17.0.1/private/ stretch-staging/main libjs-sphinxdoc all 1.3.1-8 [53.1 kB]
Get:104 http://172.17.0.1/private/ stretch-staging/main sphinx-common all 1.3.1-8 [320 kB]
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Setting up fontconfig (2.11.0-6.3) ...
Regenerating fonts cache... done.
Setting up libffi6:armhf (3.2.1-3) ...
Setting up libjbig0:armhf (2.1-3.1) ...
Setting up libltdl7:armhf (2.4.2-1.11) ...
Setting up libsigsegv2:armhf (2.10-4) ...
Setting up libunistring0:armhf (0.9.3-5.2) ...
Setting up libxau6:armhf (1:1.0.8-1) ...
Setting up libxdmcp6:armhf (1:1.1.2-1) ...
Setting up libxcb1:armhf (1.10-3+b1) ...
Setting up libx11-data (2:1.6.3-1) ...
Setting up libx11-6:armhf (2:1.6.3-1) ...
Setting up libxext6:armhf (2:1.3.3-1) ...
Setting up libxapian22v5 (1.2.21-1.2) ...
Setting up libmagic1:armhf (1:5.25-2) ...
Setting up file (1:5.25-2) ...
Setting up gettext-base (0.19.6-1) ...
Setting up libicu55:armhf (55.1-6) ...
Setting up libxml2:armhf (2.9.2+zdfsg1-4) ...
Setting up m4 (1.4.17-4) ...
Setting up autoconf (2.69-9) ...
Setting up autotools-dev (20150820.1) ...
Setting up automake (1:1.15-3) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up autopoint (0.19.6-1) ...
Setting up libglib2.0-0:armhf (2.46.2-1) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.9-1) ...
Setting up gettext (0.19.6-1) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up po-debconf (1.0.18) ...
Setting up libarchive-zip-perl (1.53-1) ...
Setting up libfile-stripnondeterminism-perl (0.014-1) ...
Setting up libtool (2.4.2-1.11) ...
Setting up libllvm3.5v5:armhf (1:3.5.2-3) ...
Setting up libobjc4:armhf (5.2.1-23+rpi1+b1) ...
Setting up libobjc-5-dev:armhf (5.2.1-23+rpi1+b1) ...
Setting up libclang1-3.5:armhf (1:3.5.2-3) ...
Setting up doxygen (1.8.9.1-5) ...
Setting up libcdt5 (2.38.0-12) ...
Setting up libcgraph6 (2.38.0-12) ...
Setting up libjpeg62-turbo:armhf (1:1.4.1-2) ...
Setting up libtiff5:armhf (4.0.5-1) ...
Setting up libvpx2:armhf (1.4.0-4+rpi1) ...
Setting up libxpm4:armhf (1:3.5.11-1+b1) ...
Setting up libgd3:armhf (2.1.1-4) ...
Setting up libpixman-1-0:armhf (0.33.4-1) ...
Setting up libxcb-render0:armhf (1.10-3+b1) ...
Setting up libxcb-shm0:armhf (1.10-3+b1) ...
Setting up libxrender1:armhf (1:0.9.9-2) ...
Setting up libcairo2:armhf (1.14.4-1) ...
Setting up libthai-data (0.1.24-1) ...
Setting up libdatrie1:armhf (0.2.10-1) ...
Setting up libthai0:armhf (0.1.24-1) ...
Setting up libpango-1.0-0:armhf (1.38.1-1) ...
Setting up libgraphite2-3:armhf (1.3.3-1) ...
Setting up libharfbuzz0b:armhf (1.0.1-1+b1) ...
Setting up libpangoft2-1.0-0:armhf (1.38.1-1) ...
Setting up libpangocairo-1.0-0:armhf (1.38.1-1) ...
Setting up libpathplan4 (2.38.0-12) ...
Setting up libxdot4 (2.38.0-12) ...
Setting up libgvc6 (2.38.0-12) ...
Setting up libgvpr2 (2.38.0-12) ...
Setting up x11-common (1:7.7+12) ...
update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
Running in chroot, ignoring request.
All runlevel operations denied by policy
invoke-rc.d: policy-rc.d denied execution of start.
Setting up libice6:armhf (2:1.0.9-1+b1) ...
Setting up libsm6:armhf (2:1.2.2-1+b1) ...
Setting up libxt6:armhf (1:1.1.5-1) ...
Setting up libxmu6:armhf (2:1.1.2-2) ...
Setting up libxaw7:armhf (2:1.0.13-1) ...
Setting up graphviz (2.38.0-12) ...
Setting up libargtable2-0 (12-1.1) ...
Setting up libargtable2-docs (12-1.1) ...
Setting up libargtable2-dev (12-1.1) ...
Setting up libjs-jquery (1.11.3+dfsg-4) ...
Setting up libjs-underscore (1.7.0~dfsg-1) ...
Setting up libjs-sphinxdoc (1.3.1-8) ...
Setting up sphinx-common (1.3.1-8) ...
Setting up debhelper (9.20151005) ...
Setting up dh-autoreconf (10) ...
Setting up dh-linktree (0.4) ...
Setting up sbuild-build-depends-clustalo-dummy (0.invalid.0) ...
Setting up dh-strip-nondeterminism (0.014-1) ...
Processing triggers for libc-bin (2.19-22) ...
Processing triggers for systemd (228-2) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.25.1-7 dpkg-dev_1.18.3 g++-5_5.2.1-23+rpi1+b1 gcc-5_5.2.1-23+rpi1+b1 libc6-dev_2.19-22 libstdc++-4.9-dev_4.9.3-5 libstdc++-5-dev_5.2.1-23+rpi1+b1 libstdc++6_5.2.1-23+rpi1+b1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: acl_2.2.52-2 adduser_3.113+nmu3 apt_1.0.10.2 autoconf_2.69-9 automake_1:1.15-3 autopoint_0.19.6-1 autotools-dev_20150820.1 base-files_9.4+rpi1 base-passwd_3.5.38 bash_4.3-14 binutils_2.25.1-7 bsdmainutils_9.0.6 bsdutils_1:2.27.1-1 build-essential_11.7 bzip2_1.0.6-8 coreutils_8.23-4 cpio_2.11+dfsg-4.1 cpp_4:5.2.1-4+rpi2 cpp-5_5.2.1-23+rpi1+b1 dash_0.5.7-4 debconf_1.5.58 debfoster_2.7-2 debhelper_9.20151005 debianutils_4.5.1 dh-autoreconf_10 dh-linktree_0.4 dh-strip-nondeterminism_0.014-1 diffutils_1:3.3-2 dmsetup_2:1.02.110-1+rpi1 doxygen_1.8.9.1-5 dpkg_1.18.3 dpkg-dev_1.18.3 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 fakeroot_1.20.2-1 file_1:5.25-2 findutils_4.4.2-10 fontconfig_2.11.0-6.3 fontconfig-config_2.11.0-6.3 fonts-dejavu-core_2.35-1 g++_4:5.2.1-4+rpi2 g++-5_5.2.1-23+rpi1+b1 gcc_4:5.2.1-4+rpi2 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-1 gcc-4.9-base_4.9.3-5 gcc-5_5.2.1-23+rpi1+b1 gcc-5-base_5.2.1-23+rpi1+b1 gettext_0.19.6-1 gettext-base_0.19.6-1 gnupg_1.4.19-6 gpgv_1.4.19-6 graphviz_2.38.0-12 grep_2.22-1 groff-base_1.22.3-4 gzip_1.6-4 hostname_3.16 init_1.24 init-system-helpers_1.24 initramfs-tools_0.120 initscripts_2.88dsf-59.2 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-2+rpi1 kmod_21-1 libacl1_2.2.52-2 libapparmor1_2.10-2+b2 libapt-pkg4.12_1.0.9.10 libapt-pkg4.16_1.0.10.2 libarchive-zip-perl_1.53-1 libargtable2-0_12-1.1 libargtable2-dev_12-1.1 libargtable2-docs_12-1.1 libasan1_4.9.3-5 libasan2_5.2.1-23+rpi1+b1 libatomic1_5.2.1-23+rpi1+b1 libattr1_1:2.4.47-2 libaudit-common_1:2.4.4-4 libaudit1_1:2.4.4-4 libblkid1_2.27.1-1 libbsd0_0.7.0-2 libbz2-1.0_1.0.6-8 libc-bin_2.19-22 libc-dev-bin_2.19-22 libc6_2.19-22 libc6-dev_2.19-22 libcairo2_1.14.4-1 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_5.2.1-23+rpi1+b1 libcdt5_2.38.0-12 libcgraph6_2.38.0-12 libclang1-3.5_1:3.5.2-3 libcomerr2_1.42.13-1 libcroco3_0.6.9-1 libcryptsetup4_2:1.6.6-5 libdatrie1_0.2.10-1 libdb5.3_5.3.28-11 libdbus-1-3_1.10.4-1 libdebconfclient0_0.197 libdevmapper1.02.1_2:1.02.110-1+rpi1 libdpkg-perl_1.18.3 libdrm2_2.4.65-3 libedit2_3.1-20150325-1 libexpat1_2.1.0-7 libfakeroot_1.20.2-1 libfdisk1_2.27.1-1 libffi6_3.2.1-3 libfile-stripnondeterminism-perl_0.014-1 libfontconfig1_2.11.0-6.3 libfreetype6_2.6.1-0.1 libgc1c2_1:7.4.2-7 libgcc-4.9-dev_4.9.3-5 libgcc-5-dev_5.2.1-23+rpi1+b1 libgcc1_1:5.2.1-23+rpi1+b1 libgcrypt20_1.6.4-3 libgd3_2.1.1-4 libgdbm3_1.8.3-13.1 libglib2.0-0_2.46.2-1 libgmp10_2:6.1.0+dfsg-2 libgomp1_5.2.1-23+rpi1+b1 libgpg-error0_1.20-1 libgraphite2-3_1.3.3-1 libgvc6_2.38.0-12 libgvpr2_2.38.0-12 libharfbuzz0b_1.0.1-1+b1 libice6_2:1.0.9-1+b1 libicu55_55.1-6 libisl13_0.14-2 libisl15_0.15-3 libjbig0_2.1-3.1 libjpeg62-turbo_1:1.4.1-2 libjs-jquery_1.11.3+dfsg-4 libjs-sphinxdoc_1.3.1-8 libjs-underscore_1.7.0~dfsg-1 libklibc_2.0.4-2+rpi1 libkmod2_21-1 libllvm3.5v5_1:3.5.2-3 liblocale-gettext-perl_1.07-1 libltdl7_2.4.2-1.11 liblzma5_5.1.1alpha+20120614-2.1 libmagic1_1:5.25-2 libmount1_2.27.1-1 libmpc3_1.0.3-1 libmpfr4_3.1.3-1 libncurses5_6.0+20151024-2 libncursesw5_6.0+20151024-2 libnih-dbus1_1.0.3-4.3 libnih1_1.0.3-4.3 libobjc-5-dev_5.2.1-23+rpi1+b1 libobjc4_5.2.1-23+rpi1+b1 libpam-modules_1.1.8-3.1 libpam-modules-bin_1.1.8-3.1 libpam-runtime_1.1.8-3.1 libpam0g_1.1.8-3.1 libpango-1.0-0_1.38.1-1 libpangocairo-1.0-0_1.38.1-1 libpangoft2-1.0-0_1.38.1-1 libpathplan4_2.38.0-12 libpcre3_2:8.35-7.4 libpipeline1_1.4.1-1 libpixman-1-0_0.33.4-1 libpng12-0_1.2.54-1 libprocps3_2:3.3.9-9 libprocps4_2:3.3.10-2 libreadline6_6.3-8+b3 libseccomp2_2.2.3-2 libselinux1_2.4-3 libsemanage-common_2.4-3 libsemanage1_2.4-3 libsepol1_2.4-2 libsigsegv2_2.10-4 libslang2_2.3.0-2+b1 libsm6_2:1.2.2-1+b1 libsmartcols1_2.27.1-1 libss2_1.42.13-1 libstdc++-4.9-dev_4.9.3-5 libstdc++-5-dev_5.2.1-23+rpi1+b1 libstdc++6_5.2.1-23+rpi1+b1 libsystemd0_228-2 libtext-charwidth-perl_0.04-7+b4 libtext-iconv-perl_1.7-5+b5 libtext-wrapi18n-perl_0.06-7.1 libthai-data_0.1.24-1 libthai0_0.1.24-1 libtiff5_4.0.5-1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20151024-2 libtool_2.4.2-1.11 libubsan0_5.2.1-23+rpi1+b1 libudev1_228-2 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-27 libustr-1.0-1_1.0.4-5 libuuid1_2.27.1-1 libvpx2_1.4.0-4+rpi1 libx11-6_2:1.6.3-1 libx11-data_2:1.6.3-1 libxapian22v5_1.2.21-1.2 libxau6_1:1.0.8-1 libxaw7_2:1.0.13-1 libxcb-render0_1.10-3+b1 libxcb-shm0_1.10-3+b1 libxcb1_1.10-3+b1 libxdmcp6_1:1.1.2-1 libxdot4_2.38.0-12 libxext6_2:1.3.3-1 libxml2_2.9.2+zdfsg1-4 libxmu6_2:1.1.2-2 libxpm4_1:3.5.11-1+b1 libxrender1_1:0.9.9-2 libxt6_1:1.1.5-1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.1 lsb-base_4.1+Debian13+rpi1+nmu1 m4_1.4.17-4 make_4.0-8.2 makedev_2.3.1-93 man-db_2.7.5-1 mawk_1.3.3-17 mount_2.27.1-1 multiarch-support_2.19-22 nano_2.4.2-1 ncurses-base_6.0+20151024-2 ncurses-bin_6.0+20151024-2 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.20.2-6 perl-base_5.20.2-6 perl-modules_5.20.2-6 po-debconf_1.0.18 procps_2:3.3.10-2 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 sbuild-build-depends-clustalo-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.2.2-6.1 sensible-utils_0.0.9 sphinx-common_1.3.1-8 startpar_0.59-3 systemd_228-2 systemd-sysv_228-2 sysv-rc_2.88dsf-59.2 sysvinit-utils_2.88dsf-59.2 tar_1.28-2.1 tzdata_2015g-1 ucf_3.0031 udev_228-2 util-linux_2.27.1-1 x11-common_1:7.7+12 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Tue Nov 24 17:17:38 2015 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./clustalo_1.2.1-2.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_1.2.1-2.debian.tar.xz
Check disc space
────────────────
Sufficient free space for build
User Environment
────────────────
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-cfc88a5d-6644-48ff-85d1-08277d353cde
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package clustalo
dpkg-buildpackage: source version 1.2.1-2
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 --with linktree
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 --with linktree
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.m4:2672: _AC_LINK_IFELSE is expanded from...
../../lib/autoconf/general.m4:2689: 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.m4:2672: _AC_LINK_IFELSE is expanded from...
../../lib/autoconf/general.m4:2689: 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.m4:2672: _AC_LINK_IFELSE is expanded from...
../../lib/autoconf/general.m4:2689: 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.m4:2672: _AC_LINK_IFELSE is expanded from...
../../lib/autoconf/general.m4:2689: 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.m4:2672: _AC_LINK_IFELSE is expanded from...
../../lib/autoconf/general.m4:2689: 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.m4:2672: _AC_LINK_IFELSE is expanded from...
../../lib/autoconf/general.m4:2689: 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.m4:2672: _AC_LINK_IFELSE is expanded from...
../../lib/autoconf/general.m4:2689: 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.m4:2672: _AC_LINK_IFELSE is expanded from...
../../lib/autoconf/general.m4:2689: 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.m4:2672: _AC_LINK_IFELSE is expanded from...
../../lib/autoconf/general.m4:2689: 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 --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --libexecdir=\${prefix}/lib/arm-linux-gnueabihf --disable-maintainer-mode --disable-dependency-tracking
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
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checking whether make sets $(MAKE)... yes
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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
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checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
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checking whether we are using the GNU C++ compiler... yes
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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 -j1
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-strong -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-strong -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: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
argv_conf[argc_conf]=new(char[strlen(c_first)+1]);
^
hhutil-C.h:521:56: warning: non-constant array new length must be specified without parentheses around the type-id [-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: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
sname[k]=new(char[strlen(q.sname[k])+1]);
^
hhhmm-C.h:193:40: warning: non-constant array new length must be specified without parentheses around the type-id [-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: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
char *cur_seq = new(char[par.maxColCnt]); //Sequence currently read in
^
hhhmm-C.h:360:43: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq[k-1]=new(char[strlen(cur_seq)+1]);
^
hhhmm-C.h:367:43: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
sname[k] = new (char[strlen(line+1)+1]); //+1 for terminating '\0'
^
hhhmm-C.h:463:40: warning: non-constant array new length must be specified without parentheses around the type-id [-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: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq[nsa_dssp] = new(char[/*MAXRES*/par.maxResLen+2]);
^
hhhmm-C.h:756:59: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq[nss_pred] = new(char[/*MAXRES*/par.maxResLen+2]);
^
hhhmm-C.h:777:59: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq[nss_conf] = new(char[/*MAXRES*/par.maxResLen+2]);
^
hhhmm-C.h:859:55: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq[nss_dssp] = new(char[/*MAXRES*/par.maxResLen+2]);
^
hhhmm-C.h:1035:46: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
sname[k+1]=new(char[strlen(longname)+1]);
^
hhhmm-C.h:1037:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq[k]=new(char[L+2]);
^
hhhmm-C.h:1040:29: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq[k+1]=new(char[L+2]);
^
hhhmm-C.h:1058:44: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
sname[k]=new(char[strlen(longname)+1]);
^
hhhmm-C.h:1062:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq[k]=new(char[L+2]);
^
hhhmm-C.h: In member function 'int HMM::ReadHMMer3(FILE*, char*)':
hhhmm-C.h:1237:77: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq[nsa_dssp] = new(char[/*MAXRES*/par.maxResLen+2]);
^
hhhmm-C.h:1258:77: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq[nss_pred] = new(char[/*MAXRES*/par.maxResLen+2]);
^
hhhmm-C.h:1279:77: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq[nss_conf] = new(char[/*MAXRES*/par.maxResLen+2]);
^
hhhmm-C.h:1349:69: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq[nss_dssp] = new(char[/*MAXRES*/par.maxResLen+2]);
^
hhhmm-C.h:1529:49: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
sname[k+1]=new(char[strlen(longname)+1]);
^
hhhmm-C.h:1531:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq[k]=new(char[L+2]);
^
hhhmm-C.h:1534:32: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq[k+1]=new(char[L+2]);
^
hhhmm-C.h:1552:47: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
sname[k]=new(char[strlen(longname)+1]);
^
hhhmm-C.h:1554:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq[k]=new(char[L+2]);
^
hhhmm-C.h: In member function 'void HMM::InsertCalibration(char*)':
hhhmm-C.h:2109:39: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
char** lines = new(char*[3*L+100000]);
^
hhhmm-C.h:2138:44: warning: non-constant array new length must be specified without parentheses around the type-id [-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: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
sname = new(char*[maxseq+2]); /* MR1 */
^
hhalignment-C.h:81:28: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq = new(char*[maxseq+2]); /* MR1 */
^
hhalignment-C.h:82:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
l = new(int[maxres]);
^
hhalignment-C.h:83:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
X = new(char*[maxseq+2]); /* MR1 */
^
hhalignment-C.h:84:40: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
I = new(short unsigned int*[maxseq+2]); /* MR1 */
^
hhalignment-C.h:85:28: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
keep = new(char[maxseq+2]); /* MR1 */
^
hhalignment-C.h:86:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
display = new(char[maxseq+2]); /* MR1 */
^
hhalignment-C.h:87:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
wg = new(float[maxseq+2]); /* MR1 */
^
hhalignment-C.h:88:28: warning: non-constant array new length must be specified without parentheses around the type-id [-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: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
char *cur_seq=new(char[par.maxColCnt]);
^
hhalignment-C.h:183:61: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq[k]=new(char[strlen(cur_seq)+2]);
^
hhalignment-C.h:185:59: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
X[k]=new(char[strlen(cur_seq)+2]);
^
hhalignment-C.h:187:73: warning: non-constant array new length must be specified without parentheses around the type-id [-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: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
sname[k] = new(char[strlen(cur_name)+1]);
^
hhalignment-C.h:351:45: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq[k]=new(char[strlen(cur_seq)+2]);
^
hhalignment-C.h:353:43: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
X[k]=new(char[strlen(cur_seq)+2]);
^
hhalignment-C.h:355:57: warning: non-constant array new length must be specified without parentheses around the type-id [-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: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
h = new(/*short*/ unsigned int[N_in+2]); /* short -> overflow, FS, r235 -> r236 */
^
hhalignment-C.h:555:52: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
percent_gaps = new(float[par.maxColCnt]);
^
hhalignment-C.h:561:47: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
if (nres==NULL) nres=new(int[N_in]);
^
hhalignment-C.h:783:50: warning: non-constant array new length must be specified without parentheses around the type-id [-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: non-constant array new length must be specified without parentheses around the type-id [-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: non-constant array new length must be specified without parentheses around the type-id [-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: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
char* inkk=new(char[N_in+1]); // inkk[k]=1 iff in[ksort[k]]=1 else 0;
^
hhalignment-C.h:1010:27: warning: non-constant array new length must be specified without parentheses around the type-id [-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: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
int* idmaxwin=new(int[L+2]); // minimum value of idmax[i-WFIL,i+WFIL]
^
hhalignment-C.h:1012:36: warning: non-constant array new length must be specified without parentheses around the type-id [-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: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
int* N=new(int[L+2]); // N[i] number of already accepted sequences at position i
^
hhalignment-C.h:1042:32: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
first=new(int[N_in]);// first non-gap position in sequence k
^
hhalignment-C.h:1043:32: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
last =new(int[N_in]);// last non-gap position in sequence k
^
hhalignment-C.h:1056:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
nres=new(int[N_in]);
^
hhalignment-C.h:1070:32: warning: non-constant array new length must be specified without parentheses around the type-id [-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: non-constant array new length must be specified without parentheses around the type-id [-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: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
float** logodds=new(float*[L+1]); // log-odds ratios for HMM qcore
^
hhalignment-C.h:1373:32: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
first=new(int[N_in]);// first non-gap position in sequence k
^
hhalignment-C.h:1374:32: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
last =new(int[N_in]);// last non-gap position in sequence k
^
hhalignment-C.h:1387:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
nres=new(int[N_in]);
^
hhalignment-C.h: In member function 'void Alignment::FrequenciesAndTransitions(HMM&, char*)':
hhalignment-C.h:1669:49: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
q.seq[q.ncons]=new(char[L+2]);
^
hhalignment-C.h:1676:64: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
q.sname[q.nfirst]=new(char[strlen(name)+11]);
^
hhalignment-C.h:1680:50: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
q.seq[q.nfirst]=new(char[L+2]);
^
hhalignment-C.h:1738:61: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
q.sname[nn]=new(char[strlen(sname[k])+1]);
^
hhalignment-C.h:1741:57: warning: non-constant array new length must be specified without parentheses around the type-id [-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: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
float *Neff = new(float[par.maxResLen]); // diversity of subalignment i
^
hhalignment-C.h:1835:25: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
wi = new(float[N_in+2]);
^
hhalignment-C.h:1844:20: warning: non-constant array new length must be specified without parentheses around the type-id [-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: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
float *Neff = new(float[par.maxResLen]); // diversity of subalignment i
^
hhalignment-C.h:2062:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
wi = new(float[N_in+2]);
^
hhalignment-C.h:2073:22: warning: non-constant array new length must be specified without parentheses around the type-id [-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: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
float *Neff = new(float[par.maxResLen]); // diversity of subalignment i
^
hhalignment-C.h:2265:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
wi = new(float[N_in+2]); /* FIXME: FS */
^
hhalignment-C.h:2275:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
n = new(int*[L+2]);
^
hhalignment-C.h: In member function 'void Alignment::MergeMasterSlave(Hit&, char*)':
hhalignment-C.h:2546:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
int* imatch=new(int[hit.j2+1]);
^
hhalignment-C.h:2678:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
char* new_seq=new(char[2*maxcol]);
^
hhalignment-C.h:2691:23: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq[N_in]=new(char[h]);
^
hhalignment-C.h:2694:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
X[N_in]=new(char[h]);
^
hhalignment-C.h:2696:35: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
I[N_in]=new(short unsigned int[h]);
^
hhalignment-C.h:2698:47: warning: non-constant array new length must be specified without parentheses around the type-id [-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: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
X[N_in]=new(char[L+2]);
^
hhalignment-C.h: In member function 'void Alignment::GetPositionSpecificWeights(float**)':
hhalignment-C.h:2779:19: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
n = new(int*[L+2]);
^
hhalignment-C.h: In member function 'void Alignment::Transfer(char**, int)':
hhalignment-C.h:2896:59: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
I[k] = new(short unsigned int[iLen+2+GOOD_MEASURE]);
^
hhalignment-C.h:2897:45: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
X[k] = new(char[iLen+2+GOOD_MEASURE]);
^
hhalignment-C.h:2898:47: warning: non-constant array new length must be specified without parentheses around the type-id [-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: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
bMM=new(char*[Nq]);
^
hhhit-C.h:180:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
bMI=new(char*[Nq]);
^
hhhit-C.h:181:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
bIM=new(char*[Nq]);
^
hhhit-C.h:182:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
bDG=new(char*[Nq]);
^
hhhit-C.h:183:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
bGD=new(char*[Nq]);
^
hhhit-C.h:184:25: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
cell_off=new(char*[Nq]);
^
hhhit-C.h:187:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
bMM[i]=new(char[Nt]);
^
hhhit-C.h:188:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
bMI[i]=new(char[Nt]);
^
hhhit-C.h:189:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
bIM[i]=new(char[Nt]);
^
hhhit-C.h:190:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
bGD[i]=new(char[Nt]);
^
hhhit-C.h:191:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
bDG[i]=new(char[Nt]);
^
hhhit-C.h:192:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
cell_off[i]=new(char[Nt]);
^
hhhit-C.h: In member function 'void Hit::AllocateForwardMatrix(int, int)':
hhhit-C.h:239:23: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
F_MM=new(double*[Nq]);
^
hhhit-C.h:240:23: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
F_MI=new(double*[Nq]);
^
hhhit-C.h:241:23: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
F_DG=new(double*[Nq]);
^
hhhit-C.h:242:23: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
F_IM=new(double*[Nq]);
^
hhhit-C.h:243:23: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
F_GD=new(double*[Nq]);
^
hhhit-C.h:244:25: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
scale=new(double[Nq+1]); // need Nq+3?
^
hhhit-C.h:247:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
F_MM[i] = new(double[Nt]);
^
hhhit-C.h:248:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
F_MI[i] = new(double[Nt]);
^
hhhit-C.h:249:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
F_DG[i] = new(double[Nt]);
^
hhhit-C.h:250:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
F_IM[i] = new(double[Nt]);
^
hhhit-C.h:251:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
F_GD[i] = new(double[Nt]);
^
hhhit-C.h: In member function 'void Hit::AllocateBackwardMatrix(int, int)':
hhhit-C.h:296:23: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
B_MM=new(double*[Nq]);
^
hhhit-C.h:303:31: warning: non-constant array new length must be specified without parentheses around the type-id [-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: non-constant array new length must be specified without parentheses around the type-id [-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: non-constant array new length must be specified without parentheses around the type-id [-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: non-constant array new length must be specified without parentheses around the type-id [-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: non-constant array new length must be specified without parentheses around the type-id [-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: non-constant array new length must be specified without parentheses around the type-id [-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: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
if (t.Xcons) Xcons = new( char[q.L+2]); // for template consensus sequence aligned to query
^
hhhit-C.h:1127:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
S = new( float[nsteps+1]);
^
hhhit-C.h:1128:30: warning: non-constant array new length must be specified without parentheses around the type-id [-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: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double* scale_cum = new(double[q.L+2]);
^
hhhit-C.h:1247:39: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double* sumF=new(double[q.L+t.L]);
^
hhhit-C.h:1371:40: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
if (t.Xcons) Xcons = new( char[q.L+2]); // for template consensus sequence aligned to query
^
hhhit-C.h:1372:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
S = new( float[nsteps+1]);
^
hhhit-C.h:1373:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
S_ss = new( float[nsteps+1]);
^
hhhit-C.h: In member function 'void Hit::BacktraceMAC(HMM&, HMM&)':
hhhit-C.h:1475:40: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
if (t.Xcons) Xcons = new( char[q.L+2]); // for template consensus sequence aligned to query
^
hhhit-C.h:1476:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
S = new( float[nsteps+1]);
^
hhhit-C.h:1477:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
S_ss = new( float[nsteps+1]);
^
hhhit-C.h:1478:37: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
P_posterior = new( float[nsteps+1]);
^
hhhit-C.h: In member function 'void Hit::InitializeBacktrace(HMM&, HMM&)':
hhhit-C.h:1683:54: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
longname=new(char[strlen(t.longname)+1])();
^
hhhit-C.h:1684:50: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
name =new(char[strlen(t.name)+1])();
^
hhhit-C.h:1685:50: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
file =new(char[strlen(t.file)+1])();
^
hhhit-C.h:1696:43: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
sname=new(char*[t.n_display])(); // Call Compare only once with irep=1
^
hhhit-C.h:1697:43: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
seq =new(char*[t.n_display])(); // Call Compare only once with irep=1
^
hhhit-C.h:1730:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
this->i = new( int[i2+j2+2])();
^
hhhit-C.h:1731:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
this->j = new( int[i2+j2+2])();
^
hhhit-C.h:1732:35: warning: non-constant array new length must be specified without parentheses around the type-id [-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: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
h = new(int[maxseqdis]); //h[k] = next position of sequence k to be written
^
hhhalfalignment-C.h:67:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
s = new(char*[maxseqdis]); //s[k][h] = character in column h, sequence k of output alignment
^
hhhalfalignment-C.h:68:26: warning: non-constant array new length must be specified without parentheses around the type-id [-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: non-constant array new length must be specified without parentheses around the type-id [-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: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
lq = new(short unsigned int[qa->n+2]);
^
hhfullalignment-C.h:360:39: warning: non-constant array new length must be specified without parentheses around the type-id [-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: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Z = new(float*[N]);
^
hhhitlist-C.h:1288:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Z[k] = new(float[N]);
^
hhhitlist-C.h:1293:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
C = new(float*[N]);
^
hhhitlist-C.h:1296:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
C[k] = new(float[N]);
^
hhhitlist-C.h:1303:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Zq = new(float[N]);
^
hhhitlist-C.h:1304:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Ztq = new(float[N]);
^
hhhitlist-C.h:1305:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Zrq = new(float[N]);
^
hhhitlist-C.h:1306:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
fold = new(char*[N]);
^
hhhitlist-C.h:1307:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
fam = new(char*[N]);
^
hhhitlist-C.h:1308:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Prob = new(float[N]);
^
hhhitlist-C.h:1309:18: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
ll = new(int[N]);
^
hhhitlist-C.h:1310:19: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
w = new(float[N]);
^
hhhitlist-C.h:1373:37: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Csub = new(double*[M]);
^
hhhitlist-C.h:1374:37: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Cinv = new(double*[M]);
^
hhhitlist-C.h:1377:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Csub[m] = new(double[M]);
^
hhhitlist-C.h:1378:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Cinv[m] = new(double[M]);
^
hhhitlist-C.h:1453:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Csub = new(double*[M]);
^
hhhitlist-C.h:1456:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Csub[m] = new(double[M]);
^
hhhitlist-C.h:1470:38: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Cinv = new(double*[M]);
^
hhhitlist-C.h:1471:51: warning: non-constant array new length must be specified without parentheses around the type-id [-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: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Z = new(float*[N]);
^
hhhitlist-C.h:1653:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Z[k] = new(float[N]);
^
hhhitlist-C.h:1658:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
C = new(float*[N]);
^
hhhitlist-C.h:1661:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
C[k] = new(float[N]);
^
hhhitlist-C.h:1668:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Zq = new(float[N]);
^
hhhitlist-C.h:1669:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Ztq = new(float[N]);
^
hhhitlist-C.h:1670:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Zrq = new(float[N]);
^
hhhitlist-C.h:1671:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
fold = new(char*[N]);
^
hhhitlist-C.h:1672:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
fam = new(char*[N]);
^
hhhitlist-C.h:1673:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Prob = new(float[N]);
^
hhhitlist-C.h:1674:18: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
ll = new(int[N]);
^
hhhitlist-C.h:1675:19: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
w = new(float[N]);
^
hhhitlist-C.h:1739:37: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Csub = new(double*[M]);
^
hhhitlist-C.h:1740:37: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Cinv = new(double*[M]);
^
hhhitlist-C.h:1743:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Csub[m] = new(double[M]);
^
hhhitlist-C.h:1744:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Cinv[m] = new(double[M]);
^
hhhitlist-C.h:1821:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Csub = new(double*[M]);
^
hhhitlist-C.h:1824:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Csub[m] = new(double[M]);
^
hhhitlist-C.h:1838:38: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Cinv = new(double*[M]);
^
hhhitlist-C.h:1839:51: warning: non-constant array new length must be specified without parentheses around the type-id [-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: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Z = new(float*[N]);
^
hhhitlist-C.h:2023:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Z[k] = new(float[N]);
^
hhhitlist-C.h:2028:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
C = new(float*[N]);
^
hhhitlist-C.h:2031:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
C[k] = new(float[N]);
^
hhhitlist-C.h:2038:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Zq = new(float[N]);
^
hhhitlist-C.h:2039:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Ztq = new(float[N]);
^
hhhitlist-C.h:2040:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Zrq = new(float[N]);
^
hhhitlist-C.h:2041:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
fold = new(char*[N]);
^
hhhitlist-C.h:2042:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
fam = new(char*[N]);
^
hhhitlist-C.h:2043:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Prob = new(float[N]);
^
hhhitlist-C.h:2044:18: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
ll = new(int[N]);
^
hhhitlist-C.h:2045:19: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
w = new(float[N]);
^
hhhitlist-C.h:2114:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Csub = new(double*[M]);
^
hhhitlist-C.h:2115:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Cinv = new(double*[M]);
^
hhhitlist-C.h:2118:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Csub[m] = new(double[M]);
^
hhhitlist-C.h:2119:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Cinv[m] = new(double[M]);
^
hhhitlist-C.h:2186:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Csub = new(double*[M]);
^
hhhitlist-C.h:2189:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Csub[m] = new(double[M]);
^
hhhitlist-C.h:2203:38: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Cinv = new(double*[M]);
^
hhhitlist-C.h:2204:51: warning: non-constant array new length must be specified without parentheses around the type-id [-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: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Z = new(float*[N]);
^
hhhitlist-C.h:2388:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Z[k] = new(float[N]);
^
hhhitlist-C.h:2393:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
C = new(float*[N]);
^
hhhitlist-C.h:2396:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
C[k] = new(float[N]);
^
hhhitlist-C.h:2403:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Zq = new(float[N]);
^
hhhitlist-C.h:2404:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Ztq = new(float[N]);
^
hhhitlist-C.h:2405:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Zrq = new(float[N]);
^
hhhitlist-C.h:2406:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
fold = new(char*[N]);
^
hhhitlist-C.h:2407:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
fam = new(char*[N]);
^
hhhitlist-C.h:2408:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Prob = new(float[N]);
^
hhhitlist-C.h:2409:18: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
ll = new(int[N]);
^
hhhitlist-C.h:2410:19: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
w = new(float[N]);
^
hhhitlist-C.h:2472:37: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Csub = new(double*[M]);
^
hhhitlist-C.h:2475:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Csub[m] = new(double[M]);
^
hhhitlist-C.h:2538:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** Csub = new(double*[M]);
^
hhhitlist-C.h:2541:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
Csub[m] = new(double[M]);
^
hhhitlist-C.h: In member function 'void HitList::InvertMatrix(double**, double**, int)':
hhhitlist-C.h:2840:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double** V = new(double*[N]);
^
hhhitlist-C.h:2841:29: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla]
double* s = new(double[N]);
^
hhhitlist-C.h:2842:43: warning: non-constant array new length must be specified without parentheses around the type-id [-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: non-constant array new length must be specified without parentheses around the type-id [-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-strong -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-strong -Wformat -Werror=format-security -Wl,-z,relro -o libhhalign.la hhalign.lo -largtable2 -lm
libtool: link: ar cru .libs/libhhalign.a .libs/hhalign.o
ar: `u' modifier ignored since `D' is the default (see `U')
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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -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-strong -Wformat -Werror=format-security -c phylip.c -o phylip.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-strong -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-strong -Wformat -Werror=format-security -c revcomp.c -o revcomp.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-strong -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-strong -Wformat -Werror=format-security -c rk.c -o rk.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-strong -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-strong -Wformat -Werror=format-security -c selex.c -o selex.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-strong -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-strong -Wformat -Werror=format-security -c seqencode.c -o seqencode.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-strong -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-strong -Wformat -Werror=format-security -c shuffle.c -o shuffle.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-strong -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-strong -Wformat -Werror=format-security -c sqerror.c -o sqerror.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-strong -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-strong -Wformat -Werror=format-security -c sqio.c -o sqio.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-strong -Wformat -Werror=format-security -c squidcore.c -fPIC -DPIC -o .libs/squidcore.o
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c sre_ctype.c -fPIC -DPIC -o .libs/sre_ctype.o
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector-strong -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-strong -Wformat -Werror=format-security -c sre_math.c -o sre_math.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-strong -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-strong -Wformat -Werror=format-security -c sre_random.c -o sre_random.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-strong -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-strong -Wformat -Werror=format-security -c sre_string.c -o sre_string.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-strong -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-strong -Wformat -Werror=format-security -c ssi.c -o ssi.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-strong -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-strong -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-strong -Wformat -Werror=format-security -c stopwatch.c -o stopwatch.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-strong -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-strong -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-strong -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-strong -Wformat -Werror=format-security -c weight.c -o weight.o >/dev/null 2>&1
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ar: `u' modifier ignored since `D' is the default (see `U')
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libtool: link: ( cd ".libs" && rm -f "libsquid.la" && ln -s "../libsquid.la" "libsquid.la" )
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Making all in kmpp
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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-strong -Wformat -Werror=format-security -c util.c -fPIC -DPIC -o .libs/util.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c util.c -o util.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o weights.lo weights.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fstack-protector-strong -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-strong -Wformat -Werror=format-security -c weights.c -o weights.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=link gcc -fopenmp -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -o libclustal.la hhalign_wrapper.lo ktuple_pair.lo list.lo log.lo muscle_upgma.lo muscle_tree.lo mbed.lo pair_dist.lo progress.lo seq.lo symmatrix.lo tree.lo util.lo weights.lo -largtable2 -lm
libtool: link: ar cru .libs/libclustal.a .libs/hhalign_wrapper.o .libs/ktuple_pair.o .libs/list.o .libs/log.o .libs/muscle_upgma.o .libs/muscle_tree.o .libs/mbed.o .libs/pair_dist.o .libs/progress.o .libs/seq.o .libs/symmatrix.o .libs/tree.o .libs/util.o .libs/weights.o
ar: `u' modifier ignored since `D' is the default (see `U')
libtool: link: ranlib .libs/libclustal.a
libtool: link: ( cd ".libs" && rm -f "libclustal.la" && ln -s "../libclustal.la" "libclustal.la" )
make[4]: Leaving directory '/«PKGBUILDDIR»/src/clustal'
make[4]: Entering directory '/«PKGBUILDDIR»/src'
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o clustal-omega.lo clustal-omega.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c clustal-omega.c -fPIC -DPIC -o .libs/clustal-omega.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c clustal-omega.c -o clustal-omega.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=link gcc -O3 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -static -Wl,-z,relro -o libclustalo.la -rpath /usr/lib/arm-linux-gnueabihf clustal-omega.lo clustal/libclustal.la hhalign/libhhalign.la squid/libsquid.la kmpp/libkmpp.la -largtable2 -lm
libtool: link: (cd .libs/libclustalo.lax/libclustal.a && ar x "/«PKGBUILDDIR»/src/clustal/.libs/libclustal.a")
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
ar: `u' modifier ignored since `D' is the default (see `U')
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-strong -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-strong -Wformat -Werror=format-security -c -o mymain.o mymain.c
/bin/bash ../libtool --tag=CXX --mode=link g++ -O3 -fopenmp -g -O2 -fstack-protector-strong -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-strong -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 -j1 check
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 --with linktree
dh_testroot -a
dh_prep -a
dh_installdirs -a
debian/rules override_dh_auto_install-arch
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_install -a
make -j1 install DESTDIR=/«PKGBUILDDIR»/debian/tmp AM_UPDATE_INFO_DIR=no
make[2]: Entering directory '/«PKGBUILDDIR»'
Making install in src
make[3]: Entering directory '/«PKGBUILDDIR»/src'
Making install in hhalign
make[4]: Entering directory '/«PKGBUILDDIR»/src/hhalign'
make[5]: Entering directory '/«PKGBUILDDIR»/src/hhalign'
make[5]: 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[5]: Leaving directory '/«PKGBUILDDIR»/src/hhalign'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/hhalign'
Making install in squid
make[4]: Entering directory '/«PKGBUILDDIR»/src/squid'
make[5]: Entering directory '/«PKGBUILDDIR»/src/squid'
make[5]: 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[5]: Leaving directory '/«PKGBUILDDIR»/src/squid'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/squid'
Making install in kmpp
make[4]: Entering directory '/«PKGBUILDDIR»/src/kmpp'
make[5]: Entering directory '/«PKGBUILDDIR»/src/kmpp'
make[5]: Nothing to be done for 'install-exec-am'.
make[5]: Nothing to be done for 'install-data-am'.
make[5]: Leaving directory '/«PKGBUILDDIR»/src/kmpp'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/kmpp'
Making install in clustal
make[4]: Entering directory '/«PKGBUILDDIR»/src/clustal'
make[5]: Entering directory '/«PKGBUILDDIR»/src/clustal'
make[5]: 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[5]: Leaving directory '/«PKGBUILDDIR»/src/clustal'
make[4]: Leaving directory '/«PKGBUILDDIR»/src/clustal'
make[4]: Entering directory '/«PKGBUILDDIR»/src'
make[5]: 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[5]: Leaving directory '/«PKGBUILDDIR»/src'
make[4]: Leaving directory '/«PKGBUILDDIR»/src'
make[3]: Leaving directory '/«PKGBUILDDIR»/src'
make[3]: Entering directory '/«PKGBUILDDIR»'
make[4]: Entering directory '/«PKGBUILDDIR»'
make[4]: 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[4]: Leaving directory '/«PKGBUILDDIR»'
make[3]: Leaving directory '/«PKGBUILDDIR»'
make[2]: Leaving directory '/«PKGBUILDDIR»'
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_linktree -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/clustalo/usr/bin/clustalo contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
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 'libclustalo-dev' in '../libclustalo-dev_1.2.1-2_armhf.deb'.
dpkg-deb: building package 'clustalo' in '../clustalo_1.2.1-2_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../clustalo_1.2.1-2_armhf.changes
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build clustalo-1.2.1
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20151130-0857
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build Chroot │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
clustalo_1.2.1-2_armhf.changes:
───────────────────────────────
Format: 1.8
Date: Tue, 24 Nov 2015 17:58:56 +0100
Source: clustalo
Binary: clustalo libclustalo-dev libclustalo-doc
Architecture: armhf
Version: 1.2.1-2
Distribution: stretch-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 for library to embed Clustal Omega
Closes: 806007
Changes:
clustalo (1.2.1-2) unstable; urgency=medium
.
[ Steffen Möller]
* Added debian/upstream/edam
.
[ Andreas Tille ]
* cme fix dpkg-control
* debian/rules: enable building architecture independent package only
Closes: #806007
* more verbose descriptions
* use linktree to get rid of jquery.js copy
* fix order in debian/copyright
Checksums-Sha1:
6311763bf7a578ea6c3cef46213599b0371b70a5 219272 clustalo_1.2.1-2_armhf.deb
4f528ee232a52f3030e66e3a975b25459365379b 273606 libclustalo-dev_1.2.1-2_armhf.deb
Checksums-Sha256:
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a38190246671fb48d948f918dbd0665f2035e0cd9c1d82f44af672b6643f4e0c 273606 libclustalo-dev_1.2.1-2_armhf.deb
Files:
c05ea9bb090e311f60d7b105108f65ff 219272 science optional clustalo_1.2.1-2_armhf.deb
56d1161f74ac7f07cb2d677912fdfdf3 273606 libdevel optional libclustalo-dev_1.2.1-2_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
clustalo_1.2.1-2_armhf.deb
──────────────────────────
new debian package, version 2.0.
size 219272 bytes: control archive=768 bytes.
651 bytes, 14 lines control
399 bytes, 6 lines md5sums
Package: clustalo
Version: 1.2.1-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 542
Depends: libargtable2-0 (>= 7), libc6 (>= 2.4), libgcc1 (>= 1:4.4.0), libgomp1 (>= 4.9), libstdc++6 (>= 5.2)
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 2015-11-30 08:57 ./
drwxr-xr-x root/root 0 2015-11-30 08:57 ./usr/
drwxr-xr-x root/root 0 2015-11-30 08:57 ./usr/bin/
-rwxr-xr-x root/root 527920 2015-11-30 08:57 ./usr/bin/clustalo
drwxr-xr-x root/root 0 2015-11-30 08:57 ./usr/share/
drwxr-xr-x root/root 0 2015-11-30 08:57 ./usr/share/doc/
drwxr-xr-x root/root 0 2015-11-30 08:57 ./usr/share/doc/clustalo/
-rw-r--r-- root/root 10994 2013-08-27 12:07 ./usr/share/doc/clustalo/README.gz
-rw-r--r-- root/root 626 2015-11-24 17:15 ./usr/share/doc/clustalo/changelog.Debian.gz
-rw-r--r-- root/root 744 2012-06-27 14:48 ./usr/share/doc/clustalo/changelog.gz
-rw-r--r-- root/root 1174 2015-11-24 17:15 ./usr/share/doc/clustalo/copyright
drwxr-xr-x root/root 0 2015-11-30 08:57 ./usr/share/man/
drwxr-xr-x root/root 0 2015-11-30 08:57 ./usr/share/man/man1/
-rw-r--r-- root/root 1083 2015-11-30 08:57 ./usr/share/man/man1/clustalo.1.gz
libclustalo-dev_1.2.1-2_armhf.deb
─────────────────────────────────
new debian package, version 2.0.
size 273606 bytes: control archive=1478 bytes.
504 bytes, 15 lines control
2409 bytes, 33 lines md5sums
Package: libclustalo-dev
Source: clustalo
Version: 1.2.1-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 919
Depends: libargtable2-dev, clustalo (= 1.2.1-2)
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 2015-11-30 08:57 ./
drwxr-xr-x root/root 0 2015-11-30 08:57 ./usr/
drwxr-xr-x root/root 0 2015-11-30 08:57 ./usr/include/
drwxr-xr-x root/root 0 2015-11-30 08:57 ./usr/include/clustalo/
-rw-r--r-- root/root 9529 2015-11-30 08:57 ./usr/include/clustalo/clustal-omega-config.h
-rw-r--r-- root/root 4640 2015-11-30 08:57 ./usr/include/clustalo/clustal-omega.h
drwxr-xr-x root/root 0 2015-11-30 08:57 ./usr/include/clustalo/clustal/
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-rw-r--r-- root/root 3936 2015-11-30 08:57 ./usr/include/clustalo/clustal/seq.h
-rw-r--r-- root/root 2310 2015-11-30 08:57 ./usr/include/clustalo/clustal/symmatrix.h
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-rw-r--r-- root/root 2308 2015-11-30 08:57 ./usr/include/clustalo/clustal/util.h
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drwxr-xr-x root/root 0 2015-11-30 08:57 ./usr/include/clustalo/squid/
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drwxr-xr-x root/root 0 2015-11-30 08:57 ./usr/lib/
drwxr-xr-x root/root 0 2015-11-30 08:57 ./usr/lib/arm-linux-gnueabihf/
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drwxr-xr-x root/root 0 2015-11-30 08:57 ./usr/lib/arm-linux-gnueabihf/pkgconfig/
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drwxr-xr-x root/root 0 2015-11-30 08:57 ./usr/share/
drwxr-xr-x root/root 0 2015-11-30 08:57 ./usr/share/doc/
drwxr-xr-x root/root 0 2015-11-30 08:57 ./usr/share/doc/libclustalo-dev/
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-rw-r--r-- root/root 744 2012-06-27 14:48 ./usr/share/doc/libclustalo-dev/changelog.gz
-rw-r--r-- root/root 1174 2015-11-24 17:15 ./usr/share/doc/libclustalo-dev/copyright
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 23516
Build-Time: 575
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 524
Job: clustalo_1.2.1-2
Machine Architecture: armhf
Package: clustalo
Package-Time: 1166
Source-Version: 1.2.1-2
Space: 23516
Status: successful
Version: 1.2.1-2
────────────────────────────────────────────────────────────────────────────────
Finished at 20151130-0857
Build needed 00:19:26, 23516k disc space