clustalo →
1.2.4-7 →
armhf → 2020-11-25 06:16:15
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testbuildd
+==============================================================================+
| clustalo 1.2.4-7 (armhf) Wed, 25 Nov 2020 05:53:49 +0000 |
+==============================================================================+
Package: clustalo
Version: 1.2.4-7
Source Version: 1.2.4-7
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-8cd5ad43-5324-4663-a365-a2bbe356d845' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.9 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.9 MB]
Fetched 24.8 MB in 27s (920 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'clustalo' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/clustalo.git
Please use:
git clone https://salsa.debian.org/med-team/clustalo.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1184 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main clustalo 1.2.4-7 (dsc) [2153 B]
Get:2 http://172.17.0.1/private bullseye-staging/main clustalo 1.2.4-7 (tar) [1171 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main clustalo 1.2.4-7 (diff) [10.9 kB]
Fetched 1184 kB in 1s (2365 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/clustalo-tzyHsH/clustalo-1.2.4' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/clustalo-tzyHsH' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-YND9uR/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-YND9uR/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-YND9uR/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-YND9uR/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-YND9uR/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-YND9uR/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-YND9uR/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-YND9uR/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (2846 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
bsdextrautils krb5-locales netbase sensible-utils
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 16 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-YND9uR/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (11.0 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12725 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), libargtable2-dev, doxygen, graphviz, sphinx-common
Filtered Build-Depends: debhelper-compat (= 13), libargtable2-dev, doxygen, graphviz, sphinx-common
dpkg-deb: building package 'sbuild-build-depends-clustalo-dummy' in '/<<BUILDDIR>>/resolver-YND9uR/apt_archive/sbuild-build-depends-clustalo-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-clustalo-dummy sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-YND9uR/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-YND9uR/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-YND9uR/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-YND9uR/apt_archive ./ Sources [529 B]
Get:5 copy:/<<BUILDDIR>>/resolver-YND9uR/apt_archive ./ Packages [608 B]
Fetched 2470 B in 1s (3171 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install clustalo build dependencies (apt-based resolver)
--------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
krb5-locales netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev debhelper dh-autoreconf
dh-strip-nondeterminism doxygen dwz file fontconfig fontconfig-config
fonts-dejavu-core gettext gettext-base graphviz groff-base intltool-debian
libarchive-zip-perl libargtable2-0 libargtable2-dev libargtable2-docs
libbrotli1 libbsd0 libcairo2 libcdt5 libcgraph6 libclang-cpp9 libclang1-9
libcroco3 libdatrie1 libdebhelper-perl libedit2 libelf1 libexpat1
libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0
libgd3 libglib2.0-0 libgraphite2-3 libgts-0.7-5 libgvc6 libgvpr2
libharfbuzz0b libice6 libicu67 libjbig0 libjpeg62-turbo libjs-jquery
libjs-sphinxdoc libjs-underscore liblab-gamut1 libllvm9 libltdl7
libmagic-mgc libmagic1 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0
libpathplan4 libpipeline1 libpixman-1-0 libpng16-16 libsigsegv2 libsm6
libsub-override-perl libthai-data libthai0 libtiff5 libtool libuchardet0
libwebp6 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0
libxcb1 libxdmcp6 libxext6 libxml2 libxmu6 libxpm4 libxrender1 libxt6
libz3-4 m4 man-db node-jquery po-debconf sphinx-common ucf x11-common
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make doxygen-latex
doxygen-doc doxygen-gui gettext-doc libasprintf-dev libgettextpo-dev gsfonts
graphviz-doc groff libgd-tools libtool-doc gfortran | fortran95-compiler
gcj-jdk m4-doc apparmor less www-browser libmail-box-perl
Recommended packages:
curl | wget | lynx fonts-liberation libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs libgts-bin javascript-common libltdl-dev
libmail-sendmail-perl python3-sphinx
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev debhelper dh-autoreconf
dh-strip-nondeterminism doxygen dwz file fontconfig fontconfig-config
fonts-dejavu-core gettext gettext-base graphviz groff-base intltool-debian
libarchive-zip-perl libargtable2-0 libargtable2-dev libargtable2-docs
libbrotli1 libbsd0 libcairo2 libcdt5 libcgraph6 libclang-cpp9 libclang1-9
libcroco3 libdatrie1 libdebhelper-perl libedit2 libelf1 libexpat1
libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0
libgd3 libglib2.0-0 libgraphite2-3 libgts-0.7-5 libgvc6 libgvpr2
libharfbuzz0b libice6 libicu67 libjbig0 libjpeg62-turbo libjs-jquery
libjs-sphinxdoc libjs-underscore liblab-gamut1 libllvm9 libltdl7
libmagic-mgc libmagic1 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0
libpathplan4 libpipeline1 libpixman-1-0 libpng16-16 libsigsegv2 libsm6
libsub-override-perl libthai-data libthai0 libtiff5 libtool libuchardet0
libwebp6 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0
libxcb1 libxdmcp6 libxext6 libxml2 libxmu6 libxpm4 libxrender1 libxt6
libz3-4 m4 man-db node-jquery po-debconf sbuild-build-depends-clustalo-dummy
sphinx-common ucf x11-common
0 upgraded, 97 newly installed, 0 to remove and 16 not upgraded.
Need to get 68.7 MB of archives.
After this operation, 261 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-YND9uR/apt_archive ./ sbuild-build-depends-clustalo-dummy 0.invalid.0 [896 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.3-2 [1269 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-5 [262 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-5 [113 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-5 [67.0 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf ucf all 3.0043 [74.0 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-4 [801 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.2.1 [188 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.9.0-1 [15.2 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.182-1 [162 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.66.3-1 [1176 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-4 [8289 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-6.2 [578 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.2.1 [1007 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libedit2 armhf 3.1-20191231-1 [79.2 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libz3-4 armhf 4.8.9-1 [5548 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libllvm9 armhf 1:9.0.1-15+rpi1+b1 [13.1 MB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libclang-cpp9 armhf 1:9.0.1-15+rpi1+b1 [7099 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libclang1-9 armhf 1:9.0.1-15+rpi1+b1 [5584 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf doxygen armhf 1.8.20-4 [3439 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.10-1 [73.3 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.9-2 [259 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libpng16-16 armhf 1.6.37-3 [276 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libfreetype6 armhf 2.10.2+dfsg-4 [345 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf fonts-dejavu-core all 2.37-2 [1069 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf fontconfig-config all 2.13.1-4.2 [281 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libfontconfig1 armhf 2.13.1-4.2 [328 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf fontconfig armhf 2.13.1-4.2 [416 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libcdt5 armhf 2.42.2-4+b1 [59.8 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libcgraph6 armhf 2.42.2-4+b1 [78.8 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libjpeg62-turbo armhf 1:2.0.5-1.1 [121 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libjbig0 armhf 2.1-3.1+b2 [27.6 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libwebp6 armhf 0.6.1-2 [228 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libtiff5 armhf 4.1.0+git191117-2 [250 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libxau6 armhf 1:1.0.8-1+b2 [19.1 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libxcb1 armhf 1.14-2 [135 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libx11-data all 2:1.6.12-1 [311 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libx11-6 armhf 2:1.6.12-1 [700 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf libxpm4 armhf 1:3.5.12-1 [43.6 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf libgd3 armhf 2.3.0-2 [116 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf libgts-0.7-5 armhf 0.7.6+darcs121130-4 [134 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf libpixman-1-0 armhf 0.36.0-1 [458 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libxcb-render0 armhf 1.14-2 [110 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libxcb-shm0 armhf 1.14-2 [101 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf libxext6 armhf 2:1.3.3-1+b2 [47.8 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf libxrender1 armhf 1:0.9.10-1 [29.9 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf libcairo2 armhf 1.16.0-4 [599 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf libltdl7 armhf 2.4.6-14 [388 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf libfribidi0 armhf 1.0.8-2 [63.5 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libgraphite2-3 armhf 1.3.14-1 [70.3 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf libharfbuzz0b armhf 2.6.7-1 [1366 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf libthai-data all 0.1.28-3 [170 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf libdatrie1 armhf 0.2.12-3+b5 [36.5 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf libthai0 armhf 0.1.28-3 [51.0 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf libpango-1.0-0 armhf 1.46.2-3 [172 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf libpangoft2-1.0-0 armhf 1.46.2-3 [55.7 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf libpangocairo-1.0-0 armhf 1.46.2-3 [46.7 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf libpathplan4 armhf 2.42.2-4+b1 [62.1 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf libgvc6 armhf 2.42.2-4+b1 [587 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf libgvpr2 armhf 2.42.2-4+b1 [185 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf liblab-gamut1 armhf 2.42.2-4+b1 [221 kB]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf x11-common all 1:7.7+21 [252 kB]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf libice6 armhf 2:1.0.10-1 [51.7 kB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf libsm6 armhf 2:1.2.3-1 [32.9 kB]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf libxt6 armhf 1:1.2.0-1 [159 kB]
Get:87 http://172.17.0.1/private bullseye-staging/main armhf libxmu6 armhf 2:1.1.2-2+b3 [52.1 kB]
Get:88 http://172.17.0.1/private bullseye-staging/main armhf libxaw7 armhf 2:1.0.13-1+b2 [163 kB]
Get:89 http://172.17.0.1/private bullseye-staging/main armhf graphviz armhf 2.42.2-4+b1 [498 kB]
Get:90 http://172.17.0.1/private bullseye-staging/main armhf libargtable2-0 armhf 13-1 [15.9 kB]
Get:91 http://172.17.0.1/private bullseye-staging/main armhf libargtable2-docs all 13-1 [2621 kB]
Get:92 http://172.17.0.1/private bullseye-staging/main armhf libargtable2-dev armhf 13-1 [55.7 kB]
Get:93 http://172.17.0.1/private bullseye-staging/main armhf node-jquery all 3.5.1+dfsg+~3.5.4-1 [390 kB]
Get:94 http://172.17.0.1/private bullseye-staging/main armhf libjs-jquery all 3.5.1+dfsg+~3.5.4-1 [3844 B]
Get:95 http://172.17.0.1/private bullseye-staging/main armhf libjs-underscore all 1.9.1~dfsg-1 [99.4 kB]
Get:96 http://172.17.0.1/private bullseye-staging/main armhf libjs-sphinxdoc all 3.3.1-1 [124 kB]
Get:97 http://172.17.0.1/private bullseye-staging/main armhf sphinx-common all 3.3.1-1 [575 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 68.7 MB in 20s (3351 kB/s)
Selecting previously unselected package libuchardet0:armhf.
(Reading database ... 12725 files and directories currently installed.)
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invoke-rc.d: could not determine current runlevel
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Setting up automake (1:1.16.2-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up fontconfig (2.13.1-4.2) ...
Regenerating fonts cache... done.
Setting up gettext (0.19.8.1-10) ...
Setting up libxpm4:armhf (1:3.5.12-1) ...
Setting up libxrender1:armhf (1:0.9.10-1) ...
Setting up libclang1-9 (1:9.0.1-15+rpi1+b1) ...
Setting up libclang-cpp9 (1:9.0.1-15+rpi1+b1) ...
Setting up libpango-1.0-0:armhf (1.46.2-3) ...
Setting up libxext6:armhf (2:1.3.3-1+b2) ...
Setting up man-db (2.9.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libcairo2:armhf (1.16.0-4) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up doxygen (1.8.20-4) ...
Setting up libgd3:armhf (2.3.0-2) ...
Setting up libxt6:armhf (1:1.2.0-1) ...
Setting up libjs-sphinxdoc (3.3.1-1) ...
Setting up libpangoft2-1.0-0:armhf (1.46.2-3) ...
Setting up libpangocairo-1.0-0:armhf (1.46.2-3) ...
Setting up libxmu6:armhf (2:1.1.2-2+b3) ...
Setting up po-debconf (1.0.21) ...
Setting up libxaw7:armhf (2:1.0.13-1+b2) ...
Setting up sphinx-common (3.3.1-1) ...
Setting up libgvc6 (2.42.2-4+b1) ...
Setting up graphviz (2.42.2-4+b1) ...
Setting up dh-autoreconf (19) ...
Setting up debhelper (13.2.1) ...
Setting up sbuild-build-depends-clustalo-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.31-4+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.35.1-2+rpi1 dpkg-dev_1.20.5+rpi1 g++-10_10.2.0-16+rpi1 gcc-10_10.2.0-16+rpi1 libc6-dev_2.31-4+rpi1 libstdc++-10-dev_10.2.0-16+rpi1 libstdc++6_10.2.0-16+rpi1 linux-libc-dev_5.7.10-1+rpi1
Package versions: adduser_3.118 apt_2.1.11 aptitude_0.8.13-2 aptitude-common_0.8.13-2 autoconf_2.69-11.1 automake_1:1.16.2-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.48 bash_5.1~rc2-1 binutils_2.35.1-2+rpi1 binutils-arm-linux-gnueabihf_2.35.1-2+rpi1 binutils-common_2.35.1-2+rpi1 bsdextrautils_2.36-3 bsdutils_1:2.36-3 build-essential_12.8 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.0-1+rpi1 cpp-10_10.2.0-16+rpi1 dash_0.5.11+git20200708+dd9ef66-2 debconf_1.5.74 debhelper_13.2.1 debianutils_4.11.2 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 doxygen_1.8.20-4 dpkg_1.20.5+rpi1 dpkg-dev_1.20.5+rpi1 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.25.3-1 file_1:5.38-5 findutils_4.7.0+git20201010-2 fontconfig_2.13.1-4.2 fontconfig-config_2.13.1-4.2 fonts-dejavu-core_2.37-2 g++_4:10.2.0-1+rpi1 g++-10_10.2.0-16+rpi1 gcc_4:10.2.0-1+rpi1 gcc-10_10.2.0-16+rpi1 gcc-10-base_10.2.0-16+rpi1 gcc-6-base_6.5.0-1+rpi3 gcc-7-base_7.5.0-6+rpi1+b1 gcc-8-base_8.4.0-4+rpi1+b1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 graphviz_2.42.2-4+b1 grep_3.6-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 krb5-locales_1.17-10 libacl1_2.2.53-8 libapt-pkg6.0_2.1.11 libarchive-zip-perl_1.68-1 libargtable2-0_13-1 libargtable2-dev_13-1 libargtable2-docs_13-1 libasan6_10.2.0-16+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.0-16+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3.1 libaudit1_1:2.8.5-3.1 libbinutils_2.35.1-2+rpi1 libblkid1_2.36-3 libboost-iostreams1.71.0_1.71.0-7 libbrotli1_1.0.9-2 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-4 libc-bin_2.31-4+rpi1 libc-dev-bin_2.31-4+rpi1 libc6_2.31-4+rpi1 libc6-dev_2.31-4+rpi1 libcairo2_1.16.0-4 libcap-ng0_0.7.9-2.2 libcc1-0_10.2.0-16+rpi1 libcdt5_2.42.2-4+b1 libcgraph6_2.42.2-4+b1 libclang-cpp9_1:9.0.1-15+rpi1+b1 libclang1-9_1:9.0.1-15+rpi1+b1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35.1-2+rpi1 libctf0_2.35.1-2+rpi1 libcwidget4_0.5.18-5 libdatrie1_0.2.12-3+b5 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.255 libdebhelper-perl_13.2.1 libdpkg-perl_1.20.5+rpi1 libedit2_3.1-20191231-1 libelf1_0.182-1 libexpat1_2.2.10-1 libext2fs2_1.45.6-1 libfakeroot_1.25.3-1 libffi7_3.3-5 libfile-stripnondeterminism-perl_1.9.0-1 libfontconfig1_2.13.1-4.2 libfreetype6_2.10.2+dfsg-4 libfribidi0_1.0.8-2 libgcc-10-dev_10.2.0-16+rpi1 libgcc-s1_10.2.0-16+rpi1 libgcrypt20_1.8.7-2 libgd3_2.3.0-2 libgdbm-compat4_1.18.1-5.1 libgdbm6_1.18.1-5.1 libglib2.0-0_2.66.3-1 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.15-4 libgomp1_10.2.0-16+rpi1 libgpg-error0_1.38-2 libgraphite2-3_1.3.14-1 libgssapi-krb5-2_1.17-10+b3 libgts-0.7-5_0.7.6+darcs121130-4 libgvc6_2.42.2-4+b1 libgvpr2_2.42.2-4+b1 libharfbuzz0b_2.6.7-1 libhogweed6_3.6-2 libice6_2:1.0.10-1 libicu67_67.1-4 libidn2-0_2.3.0-3 libisl22_0.22.1-1 libjbig0_2.1-3.1+b2 libjpeg62-turbo_1:2.0.5-1.1 libjs-jquery_3.5.1+dfsg+~3.5.4-1 libjs-sphinxdoc_3.3.1-1 libjs-underscore_1.9.1~dfsg-1 libk5crypto3_1.17-10+b3 libkeyutils1_1.6.1-2 libkrb5-3_1.17-10+b3 libkrb5support0_1.17-10+b3 libksba8_1.4.0-2 liblab-gamut1_2.42.2-4+b1 libldap-2.4-2_2.4.56+dfsg-1+rpi1 libldap-common_2.4.56+dfsg-1+rpi1 libllvm9_1:9.0.1-15+rpi1+b1 libltdl7_2.4.6-14 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.36-3 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncursesw6_6.2+20200918-1 libnettle8_3.6-2 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnss-nis_3.1-4 libnss-nisplus_1.3-4 libp11-kit0_0.23.21-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpango-1.0-0_1.46.2-3 libpangocairo-1.0-0_1.46.2-3 libpangoft2-1.0-0_1.46.2-3 libpathplan4_2.42.2-4+b1 libpcre2-8-0_10.34-7 libpcre3_2:8.39-13 libperl5.32_5.32.0-5 libpipeline1_1.5.3-1 libpixman-1-0_0.36.0-1 libpng16-16_1.6.37-3 libreadline8_8.1~rc2-2 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.5.0-3+rpi1 libselinux1_3.1-2 libsemanage-common_3.1-1 libsemanage1_3.1-1 libsepol1_3.1-1 libsigc++-2.0-0v5_2.10.4-2 libsigsegv2_2.12-2 libsm6_2:1.2.3-1 libsmartcols1_2.36-3 libsqlite3-0_3.33.0-1 libss2_1.45.6-1 libssl1.1_1.1.1h-1 libstdc++-10-dev_10.2.0-16+rpi1 libstdc++6_10.2.0-16+rpi1 libsub-override-perl_0.09-2 libsystemd0_246.6-2+rpi1 libtasn1-6_4.16.0-2 libthai-data_0.1.28-3 libthai0_0.1.28-3 libtiff5_4.1.0+git191117-2 libtinfo6_6.2+20200918-1 libtirpc-common_1.2.6-3 libtirpc-dev_1.2.6-3 libtirpc3_1.2.6-3 libtool_2.4.6-14 libubsan1_10.2.0-16+rpi1 libuchardet0_0.0.7-1 libudev1_246.6-2+rpi1 libunistring2_0.9.10-4 libuuid1_2.36-3 libwebp6_0.6.1-2 libx11-6_2:1.6.12-1 libx11-data_2:1.6.12-1 libxapian30_1.4.17-1 libxau6_1:1.0.8-1+b2 libxaw7_2:1.0.13-1+b2 libxcb-render0_1.14-2 libxcb-shm0_1.14-2 libxcb1_1.14-2 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1+b2 libxml2_2.9.10+dfsg-6.2 libxmu6_2:1.1.2-2+b3 libxpm4_1:3.5.12-1 libxrender1_1:0.9.10-1 libxt6_1:1.2.0-1 libz3-4_4.8.9-1 libzstd1_1.4.5+dfsg-4+rpi1 linux-libc-dev_5.7.10-1+rpi1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.3-4 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mount_2.36-3 ncurses-base_6.2+20200918-1 ncurses-bin_6.2+20200918-1 netbase_6.2 node-jquery_3.5.1+dfsg+~3.5.4-1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.32.0-5 perl-base_5.32.0-5 perl-modules-5.32_5.32.0-5 pinentry-curses_1.1.0-4 po-debconf_1.0.21 raspbian-archive-keyring_20120528.2 readline-common_8.1~rc2-2 sbuild-build-depends-clustalo-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sphinx-common_3.3.1-1 sysvinit-utils_2.96-5 tar_1.30+dfsg-7 tzdata_2020d-1 ucf_3.0043 util-linux_2.36-3 x11-common_1:7.7+21 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.6xp83VeY/trustedkeys.kbx': General error
gpgv: Signature made Mon Nov 23 08:15:40 2020 UTC
gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./clustalo_1.2.4-7.dsc
dpkg-source: info: extracting clustalo in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking clustalo_1.2.4.orig.tar.gz
dpkg-source: info: unpacking clustalo_1.2.4-7.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying clustalo-log-format-calls.patch
dpkg-source: info: applying array_out_of_bounds.patch
dpkg-source: info: applying memory_leak.patch
dpkg-source: info: applying fix_syntax.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-8cd5ad43-5324-4663-a365-a2bbe356d845
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package clustalo
dpkg-buildpackage: info: source version 1.2.4-7
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh 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 binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
configure.ac:150: 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:150: the top level
configure.ac:150: 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:150: the top level
configure.ac:172: 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:172: the top level
configure.ac:150: 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:150: the top level
configure.ac:150: 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:150: the top level
configure.ac:172: 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:172: the top level
configure.ac:150: 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:150: the top level
configure.ac:150: 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:150: the top level
configure.ac:172: 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:172: the top level
libtoolize: putting auxiliary files in '.'.
libtoolize: copying file './ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, '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:133: installing './compile'
configure.ac:115: installing './missing'
src/Makefile.am: installing './depcomp'
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-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking
configure:
Welcome to Clustal Omega - version 1.2.4 (AndreaGiacomo)
+NMMMMMMMMMS=
MMMMM? :MMMMM8
IMMMMS MMMMM,
~MMMMN ,MMMMM
=MMMMM MMMMM
?MMMMM +MMMMM
MMMMMS MMMMM
MMMMM MMMMM:
MMMMM MMMMM+
MMMMM MMMMM~
MMMMM MMMMM
MMMMMZ MMMMM
MMMMM ,MMMMZ
MMMM8 MMMM+
MMMMS MMMM,
MMMMO MMMM
,N SMMM MMM8 +8
,M7 M+ M+ :M8
,MMMMMMMMMMMMI MMMMMMMMMMMM8
,MMMMMMMMMMMM8 MMMMMMMMMMMM8
,MMMMMMMMMMMMN MMMMMMMMMMMM8
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether make supports the include directive... yes (GNU style)
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
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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
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dh_auto_build -a
make -j4
make[1]: Entering directory '/<<PKGBUILDDIR>>'
Making all in src
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make all-recursive
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Making all in hhalign
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libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c hhalign.cpp -fPIC -DPIC -o .libs/hhalign.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c hhalign.cpp -o hhalign.o >/dev/null 2>&1
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libtool: link: ar cr .libs/libhhalign.a .libs/hhalign.o
libtool: link: ranlib .libs/libhhalign.a
libtool: link: ( cd ".libs" && rm -f "libhhalign.la" && ln -s "../libhhalign.la" "libhhalign.la" )
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Making all in squid
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/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o clustal.lo clustal.c
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c a2m.c -o a2m.o >/dev/null 2>&1
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c aligneval.c -o aligneval.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c clustal.c -o clustal.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o dayhoff.lo dayhoff.c
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c cluster.c -o cluster.o >/dev/null 2>&1
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c dayhoff.c -o dayhoff.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o file.lo file.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c file.c -fPIC -DPIC -o .libs/file.o
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o getopt.lo getopt.c
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gki.lo gki.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c gki.c -fPIC -DPIC -o .libs/gki.o
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsi.lo gsi.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c file.c -o file.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gsi64.lo gsi64.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c gki.c -o gki.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hsregex.lo hsregex.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c hsregex.c -fPIC -DPIC -o .libs/hsregex.o
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c gsi.c -o gsi.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c iupac.c -fPIC -DPIC -o .libs/iupac.o
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c iupac.c -o iupac.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c msa.c -fPIC -DPIC -o .libs/msa.o
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c msf.c -fPIC -DPIC -o .libs/msf.o
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c phylip.c -fPIC -DPIC -o .libs/phylip.o
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c squidcore.c -o squidcore.o >/dev/null 2>&1
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c sre_random.c -fPIC -DPIC -o .libs/sre_random.o
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Making all in kmpp
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libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c KmUtils.cpp -fPIC -DPIC -o .libs/KmUtils.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c KmUtils.cpp -o KmUtils.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c KmTree.cpp -o KmTree.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c KMeans.cpp -o KMeans.o >/dev/null 2>&1
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libtool: link: ar cr .libs/libkmpp.a .libs/KMeans.o .libs/KmTree.o .libs/KmUtils.o
libtool: link: ranlib .libs/libkmpp.a
libtool: link: ( cd ".libs" && rm -f "libkmpp.la" && ln -s "../libkmpp.la" "libkmpp.la" )
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/kmpp'
Making all in clustal
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/clustal'
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hhalign_wrapper.lo hhalign_wrapper.c
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ktuple_pair.lo ktuple_pair.c
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c log.c -fPIC -DPIC -o .libs/log.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c ktuple_pair.c -fPIC -DPIC -o .libs/ktuple_pair.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c list.c -fPIC -DPIC -o .libs/list.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c list.c -o list.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c log.c -o log.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o muscle_upgma.lo muscle_upgma.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c muscle_upgma.c -fPIC -DPIC -o .libs/muscle_upgma.o
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o muscle_tree.lo muscle_tree.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c muscle_tree.c -fPIC -DPIC -o .libs/muscle_tree.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c muscle_upgma.c -o muscle_upgma.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c ktuple_pair.c -o ktuple_pair.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mbed.lo mbed.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c mbed.c -fPIC -DPIC -o .libs/mbed.o
muscle_tree.c: In function 'AssertAreNeighbors':
muscle_tree.c:811:1: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
811 | AssertAreNeighbors(unsigned uNodeIndex1, unsigned uNodeIndex2, tree_t *tree)
| ^~~~~~~~~~~~~~~~~~
muscle_tree.c:811:1: note: non-delegitimized UNSPEC UNSPEC_PIC_SYM (1) found in variable location
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pair_dist.lo pair_dist.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c pair_dist.c -fPIC -DPIC -o .libs/pair_dist.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c muscle_tree.c -o muscle_tree.o >/dev/null 2>&1
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c mbed.c -o mbed.o >/dev/null 2>&1
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c progress.c -fPIC -DPIC -o .libs/progress.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c progress.c -o progress.o >/dev/null 2>&1
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c seq.c -fPIC -DPIC -o .libs/seq.o
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o symmatrix.lo symmatrix.c
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o tree.lo tree.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c symmatrix.c -fPIC -DPIC -o .libs/symmatrix.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c tree.c -fPIC -DPIC -o .libs/tree.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c tree.c -o tree.o >/dev/null 2>&1
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libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c util.c -o util.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c seq.c -o seq.o >/dev/null 2>&1
/bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o weights.lo weights.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -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 cr .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
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'
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o main.o main.cpp
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mymain.o mymain.c
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o clustal-omega.lo clustal-omega.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c clustal-omega.c -fPIC -DPIC -o .libs/clustal-omega.o
clustal-omega.c: In function 'PrintLongVersion':
clustal-omega.c:152:49: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
152 | PACKAGE_VERSION, PACKAGE_CODENAME, __DATE__);
| ^~~~~~~~
libtool: compile: gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -static -Wl,-z,relro -Wl,-z,now -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 cr .libs/libclustalo.a clustal-omega.o .libs/libclustalo.lax/libclustal.a/hhalign_wrapper.o .libs/libclustalo.lax/libclustal.a/ktuple_pair.o .libs/libclustalo.lax/libclustal.a/list.o .libs/libclustalo.lax/libclustal.a/log.o .libs/libclustalo.lax/libclustal.a/mbed.o .libs/libclustalo.lax/libclustal.a/muscle_tree.o .libs/libclustalo.lax/libclustal.a/muscle_upgma.o .libs/libclustalo.lax/libclustal.a/pair_dist.o .libs/libclustalo.lax/libclustal.a/progress.o .libs/libclustalo.lax/libclustal.a/seq.o .libs/libclustalo.lax/libclustal.a/symmatrix.o .libs/libclustalo.lax/libclustal.a/tree.o .libs/libclustalo.lax/libclustal.a/util.o .libs/libclustalo.lax/libclustal.a/weights.o .libs/libclustalo.lax/libhhalign.a/hhalign.o .libs/libclustalo.lax/libsquid.a/a2m.o .libs/libclustalo.lax/libsquid.a/aligneval.o .libs/libclustalo.lax/libsquid.a/alignio.o .libs/libclustalo.lax/libsquid.a/clustal.o .libs/libclustalo.lax/libsquid.a/cluster.o .libs/libclustalo.lax/libsquid.a/dayhoff.o .libs/libclustalo.lax/libsquid.a/eps.o .libs/libclustalo.lax/libsquid.a/file.o .libs/libclustalo.lax/libsquid.a/getopt.o .libs/libclustalo.lax/libsquid.a/gki.o .libs/libclustalo.lax/libsquid.a/gsi.o .libs/libclustalo.lax/libsquid.a/gsi64.o .libs/libclustalo.lax/libsquid.a/hsregex.o .libs/libclustalo.lax/libsquid.a/iupac.o .libs/libclustalo.lax/libsquid.a/msa.o .libs/libclustalo.lax/libsquid.a/msf.o .libs/libclustalo.lax/libsquid.a/phylip.o .libs/libclustalo.lax/libsquid.a/revcomp.o .libs/libclustalo.lax/libsquid.a/rk.o .libs/libclustalo.lax/libsquid.a/selex.o .libs/libclustalo.lax/libsquid.a/seqencode.o .libs/libclustalo.lax/libsquid.a/shuffle.o .libs/libclustalo.lax/libsquid.a/sqerror.o .libs/libclustalo.lax/libsquid.a/sqio.o .libs/libclustalo.lax/libsquid.a/squidcore.o .libs/libclustalo.lax/libsquid.a/sre_ctype.o .libs/libclustalo.lax/libsquid.a/sre_math.o .libs/libclustalo.lax/libsquid.a/sre_random.o .libs/libclustalo.lax/libsquid.a/sre_string.o .libs/libclustalo.lax/libsquid.a/ssi.o .libs/libclustalo.lax/libsquid.a/stack.o .libs/libclustalo.lax/libsquid.a/stockholm.o .libs/libclustalo.lax/libsquid.a/stopwatch.o .libs/libclustalo.lax/libsquid.a/translate.o .libs/libclustalo.lax/libsquid.a/types.o .libs/libclustalo.lax/libsquid.a/vectorops.o .libs/libclustalo.lax/libsquid.a/weight.o .libs/libclustalo.lax/libkmpp.a/KMeans.o .libs/libclustalo.lax/libkmpp.a/KmTree.o .libs/libclustalo.lax/libkmpp.a/KmUtils.o
libtool: link: ranlib .libs/libclustalo.a
libtool: link: rm -fr .libs/libclustalo.lax
libtool: link: ( cd ".libs" && rm -f "libclustalo.la" && ln -s "../libclustalo.la" "libclustalo.la" )
/bin/bash ../libtool --tag=CXX --mode=link g++ -O3 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o clustalo main.o mymain.o libclustalo.la -largtable2 -lm
libtool: link: g++ -O3 -fopenmp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o clustalo main.o mymain.o ./.libs/libclustalo.a /usr/lib/arm-linux-gnueabihf/libargtable2.so -lm -fopenmp
/usr/bin/ld: ./.libs/libclustalo.a(clustal-omega.o): in function `AlnToHHMFile':
./src/clustal-omega.c:393: 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>>'
debian/rules override_dh_auto_test-arch
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
make -j4 check VERBOSE=1
make[2]: Entering directory '/<<PKGBUILDDIR>>'
Making check in src
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
Making check in hhalign
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/hhalign'
make[4]: Nothing to be done for 'check'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/hhalign'
Making check in squid
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/squid'
make[4]: Nothing to be done for 'check'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/squid'
Making check in kmpp
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/kmpp'
make[4]: Nothing to be done for 'check'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/kmpp'
Making check in clustal
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/clustal'
make[4]: Nothing to be done for 'check'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/clustal'
make[4]: Entering directory '/<<PKGBUILDDIR>>/src'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Nothing to be done for 'check-am'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
# Run additional test from python-biopython package to verify that
# this will work as well
src/clustalo -i debian/tests/biopython_testdata/f002 --guidetree-out temp_test.dnd -o temp_test.aln --outfmt clustal --force
rm temp_test.aln temp_test.dnd
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
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: 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_install -a
dh_installdocs -a
dh_installchangelogs -a
dh_installexamples -a
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_dwz -a -a
dh_strip -a -a
dh_makeshlibs -a -a
dh_shlibdeps -a -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
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/clustalo/usr/bin/clustalo was not linked against ld-linux-armhf.so.3 (it uses none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: Depends field of package libclustalo-dev: substitution variable ${shlibs:Depends} used, but is not defined
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'clustalo-dbgsym' in '../clustalo-dbgsym_1.2.4-7_armhf.deb'.
dpkg-deb: building package 'clustalo' in '../clustalo_1.2.4-7_armhf.deb'.
dpkg-deb: building package 'libclustalo-dev' in '../libclustalo-dev_1.2.4-7_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../clustalo_1.2.4-7_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2020-11-25T06:16:06Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
clustalo_1.2.4-7_armhf.changes:
-------------------------------
Format: 1.8
Date: Mon, 23 Nov 2020 09:14:51 +0100
Source: clustalo
Binary: clustalo clustalo-dbgsym libclustalo-dev
Architecture: armhf
Version: 1.2.4-7
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Michael R. Crusoe <crusoe@debian.org>
Description:
clustalo - General-purpose multiple sequence alignment program for proteins
libclustalo-dev - Library to embed Clustal Omega
Closes: 975511
Changes:
clustalo (1.2.4-7) unstable; urgency=medium
.
* Team upload.
* debian/rules: fix segfaults on s390x by compiling with -O0, courtesy
Christian Ehrhardt <christian.ehrhardt@canonical.com>. Closes: #975511
* Standards-Version: 4.5.1 (routine-update)
* debhelper-compat 13 (routine-update)
* debian/control: mark libclustalo-doc as Multi-Arch: foreign, thanks to the
Multiarch hinter
* debian/docs: use installed path for README to appease dh-missing
Checksums-Sha1:
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bcbb796bb79c03dd4ffaed241d9ee4e865e3e495 7126 clustalo_1.2.4-7_armhf.buildinfo
779446570159fe84d065a858a193fe61a0b1d9ed 221740 clustalo_1.2.4-7_armhf.deb
14729293b8934232dfeb42ca911408f64bf0ffb8 274132 libclustalo-dev_1.2.4-7_armhf.deb
Checksums-Sha256:
7bc912acbedb0fcab3f4a71106d4c7a5f473da7e6f8acf422acfb13fa86a714f 698572 clustalo-dbgsym_1.2.4-7_armhf.deb
893206643c53913a51d9b8b520979beb33ad0c40b1bb5909a91f65041caea257 7126 clustalo_1.2.4-7_armhf.buildinfo
d6b9d8d6bab18d6fe548b034cc91226b9590bd015f8ad886b4113bc635d59752 221740 clustalo_1.2.4-7_armhf.deb
edd0d187788ce2ffec4f9919dd495eb156e99143311afd8c88c9855791b31efe 274132 libclustalo-dev_1.2.4-7_armhf.deb
Files:
2b68e5b4c46412d397e1f061844f1894 698572 debug optional clustalo-dbgsym_1.2.4-7_armhf.deb
2231f4644721e5741c414dfc1c21ce21 7126 science optional clustalo_1.2.4-7_armhf.buildinfo
edcb9db4deeb102457fbb9ece5850faf 221740 science optional clustalo_1.2.4-7_armhf.deb
83a15ae500678bd4b2088f5fcad99311 274132 libdevel optional libclustalo-dev_1.2.4-7_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
clustalo-dbgsym_1.2.4-7_armhf.deb
---------------------------------
new Debian package, version 2.0.
size 698572 bytes: control archive=536 bytes.
374 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: clustalo-dbgsym
Source: clustalo
Version: 1.2.4-7
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 737
Depends: clustalo (= 1.2.4-7)
Section: debug
Priority: optional
Description: debug symbols for clustalo
Build-Ids: 2d6c06f50561c7f14b9e63917640c42eb849884c
drwxr-xr-x root/root 0 2020-11-23 08:14 ./
drwxr-xr-x root/root 0 2020-11-23 08:14 ./usr/
drwxr-xr-x root/root 0 2020-11-23 08:14 ./usr/lib/
drwxr-xr-x root/root 0 2020-11-23 08:14 ./usr/lib/debug/
drwxr-xr-x root/root 0 2020-11-23 08:14 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2020-11-23 08:14 ./usr/lib/debug/.build-id/2d/
-rw-r--r-- root/root 743504 2020-11-23 08:14 ./usr/lib/debug/.build-id/2d/6c06f50561c7f14b9e63917640c42eb849884c.debug
drwxr-xr-x root/root 0 2020-11-23 08:14 ./usr/share/
drwxr-xr-x root/root 0 2020-11-23 08:14 ./usr/share/doc/
lrwxrwxrwx root/root 0 2020-11-23 08:14 ./usr/share/doc/clustalo-dbgsym -> clustalo
clustalo_1.2.4-7_armhf.deb
--------------------------
new Debian package, version 2.0.
size 221740 bytes: control archive=940 bytes.
706 bytes, 14 lines control
547 bytes, 8 lines md5sums
Package: clustalo
Version: 1.2.4-7
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 545
Depends: libargtable2-0 (>= 7), libc6 (>= 2.29), libgcc-s1 (>= 3.5), libgomp1 (>= 6), 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, primarily for amino-acid sequences. It produces high quality MSAs
and is capable of handling data sets of hundreds of thousands of sequences
in reasonable time, using multiple processors where available.
drwxr-xr-x root/root 0 2020-11-23 08:14 ./
drwxr-xr-x root/root 0 2020-11-23 08:14 ./usr/
drwxr-xr-x root/root 0 2020-11-23 08:14 ./usr/bin/
-rwxr-xr-x root/root 522968 2020-11-23 08:14 ./usr/bin/clustalo
drwxr-xr-x root/root 0 2020-11-23 08:14 ./usr/share/
drwxr-xr-x root/root 0 2020-11-23 08:14 ./usr/share/doc/
drwxr-xr-x root/root 0 2020-11-23 08:14 ./usr/share/doc/clustalo/
-rw-r--r-- root/root 10994 2020-11-23 08:14 ./usr/share/doc/clustalo/README.gz
-rw-r--r-- root/root 1633 2020-11-23 08:14 ./usr/share/doc/clustalo/changelog.Debian.gz
-rw-r--r-- root/root 1730 2016-12-21 15:00 ./usr/share/doc/clustalo/changelog.gz
-rw-r--r-- root/root 1230 2020-11-23 08:14 ./usr/share/doc/clustalo/copyright
drwxr-xr-x root/root 0 2020-11-23 08:14 ./usr/share/doc/clustalo/examples/
-rw-r--r-- root/root 2269 2020-11-23 07:51 ./usr/share/doc/clustalo/examples/example.fa
-rw-r--r-- root/root 1742 2020-11-23 07:51 ./usr/share/doc/clustalo/examples/f002
drwxr-xr-x root/root 0 2020-11-23 08:14 ./usr/share/man/
drwxr-xr-x root/root 0 2020-11-23 08:14 ./usr/share/man/man1/
-rw-r--r-- root/root 1083 2020-11-23 08:14 ./usr/share/man/man1/clustalo.1.gz
libclustalo-dev_1.2.4-7_armhf.deb
---------------------------------
new Debian package, version 2.0.
size 274132 bytes: control archive=1532 bytes.
509 bytes, 14 lines control
2409 bytes, 33 lines md5sums
Package: libclustalo-dev
Source: clustalo
Version: 1.2.4-7
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 924
Depends: libargtable2-dev, clustalo (= 1.2.4-7)
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 Omega usage with an API.
drwxr-xr-x root/root 0 2020-11-23 08:14 ./
drwxr-xr-x root/root 0 2020-11-23 08:14 ./usr/
drwxr-xr-x root/root 0 2020-11-23 08:14 ./usr/include/
drwxr-xr-x root/root 0 2020-11-23 08:14 ./usr/include/clustalo/
-rw-r--r-- root/root 9523 2020-11-23 08:14 ./usr/include/clustalo/clustal-omega-config.h
-rw-r--r-- root/root 4740 2020-11-23 08:14 ./usr/include/clustalo/clustal-omega.h
drwxr-xr-x root/root 0 2020-11-23 08:14 ./usr/include/clustalo/clustal/
-rw-r--r-- root/root 1159 2020-11-23 08:14 ./usr/include/clustalo/clustal/hhalign_wrapper.h
-rw-r--r-- root/root 1251 2020-11-23 08:14 ./usr/include/clustalo/clustal/ktuple_pair.h
-rw-r--r-- root/root 1787 2020-11-23 08:14 ./usr/include/clustalo/clustal/log.h
-rw-r--r-- root/root 866 2020-11-23 08:14 ./usr/include/clustalo/clustal/mbed.h
-rw-r--r-- root/root 4112 2020-11-23 08:14 ./usr/include/clustalo/clustal/muscle_tree.h
-rw-r--r-- root/root 1303 2020-11-23 08:14 ./usr/include/clustalo/clustal/pair_dist.h
-rw-r--r-- root/root 1257 2020-11-23 08:14 ./usr/include/clustalo/clustal/progress.h
-rw-r--r-- root/root 4032 2020-11-23 08:14 ./usr/include/clustalo/clustal/seq.h
-rw-r--r-- root/root 2310 2020-11-23 08:14 ./usr/include/clustalo/clustal/symmatrix.h
-rw-r--r-- root/root 1066 2020-11-23 08:14 ./usr/include/clustalo/clustal/tree.h
-rw-r--r-- root/root 2308 2020-11-23 08:14 ./usr/include/clustalo/clustal/util.h
-rw-r--r-- root/root 741 2020-11-23 08:14 ./usr/include/clustalo/clustal/weights.h
drwxr-xr-x root/root 0 2020-11-23 08:14 ./usr/include/clustalo/hhalign/
-rw-r--r-- root/root 2961 2020-11-23 08:14 ./usr/include/clustalo/hhalign/general.h
-rw-r--r-- root/root 859 2020-11-23 08:14 ./usr/include/clustalo/hhalign/hhfunc.h
drwxr-xr-x root/root 0 2020-11-23 08:14 ./usr/include/clustalo/squid/
-rw-r--r-- root/root 1381 2020-11-23 08:14 ./usr/include/clustalo/squid/gki.h
-rw-r--r-- root/root 3473 2020-11-23 08:14 ./usr/include/clustalo/squid/gsi64.h
-rw-r--r-- root/root 13442 2020-11-23 08:14 ./usr/include/clustalo/squid/msa.h
-rw-r--r-- root/root 1264 2020-11-23 08:14 ./usr/include/clustalo/squid/rk.h
-rw-r--r-- root/root 10390 2020-11-23 08:14 ./usr/include/clustalo/squid/sqfuncs.h
-rw-r--r-- root/root 19594 2020-11-23 08:14 ./usr/include/clustalo/squid/squid.h
-rw-r--r-- root/root 489 2020-11-23 08:14 ./usr/include/clustalo/squid/sre_random.h
-rw-r--r-- root/root 7610 2020-11-23 08:14 ./usr/include/clustalo/squid/ssi.h
-rw-r--r-- root/root 1868 2020-11-23 08:14 ./usr/include/clustalo/squid/stockholm.h
-rw-r--r-- root/root 1937 2020-11-23 08:14 ./usr/include/clustalo/squid/stopwatch.h
-rw-r--r-- root/root 1434 2020-11-23 08:14 ./usr/include/clustalo/squid/vectorops.h
-rw-r--r-- root/root 333 2020-11-23 08:14 ./usr/include/clustalo/squid/version.h
drwxr-xr-x root/root 0 2020-11-23 08:14 ./usr/lib/
drwxr-xr-x root/root 0 2020-11-23 08:14 ./usr/lib/arm-linux-gnueabihf/
-rw-r--r-- root/root 803918 2020-11-23 08:14 ./usr/lib/arm-linux-gnueabihf/libclustalo.a
drwxr-xr-x root/root 0 2020-11-23 08:14 ./usr/lib/arm-linux-gnueabihf/pkgconfig/
-rw-r--r-- root/root 250 2020-11-23 08:14 ./usr/lib/arm-linux-gnueabihf/pkgconfig/clustalo.pc
drwxr-xr-x root/root 0 2020-11-23 08:14 ./usr/share/
drwxr-xr-x root/root 0 2020-11-23 08:14 ./usr/share/doc/
drwxr-xr-x root/root 0 2020-11-23 08:14 ./usr/share/doc/libclustalo-dev/
-rw-r--r-- root/root 1633 2020-11-23 08:14 ./usr/share/doc/libclustalo-dev/changelog.Debian.gz
-rw-r--r-- root/root 1730 2016-12-21 15:00 ./usr/share/doc/libclustalo-dev/changelog.gz
-rw-r--r-- root/root 1230 2020-11-23 08:14 ./usr/share/doc/libclustalo-dev/copyright
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 29056
Build-Time: 845
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 440
Job: clustalo_1.2.4-7
Machine Architecture: armhf
Package: clustalo
Package-Time: 1337
Source-Version: 1.2.4-7
Space: 29056
Status: successful
Version: 1.2.4-7
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Finished at 2020-11-25T06:16:06Z
Build needed 00:22:17, 29056k disc space