Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/c/clustalo/clustalo_1.2.4-7_all.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/clustalo-1.2.4-78v3yy4qw/clustalo_1.2.4-7_all.buildinfo Get source package info: clustalo=1.2.4-7 Source URL: http://snapshot.notset.fr/mr/package/clustalo/1.2.4-7/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-11.1 automake=1:1.16.2-4 autopoint=0.19.8.1-10 autotools-dev=20180224.1 base-files=11 base-passwd=3.5.48 bash=5.1~rc3-1 binutils=2.35.1-3 binutils-common=2.35.1-3 binutils-x86-64-linux-gnu=2.35.1-3 bsdextrautils=2.36.1-1 bsdutils=1:2.36.1-1 build-essential=12.8 bzip2=1.0.8-4 coreutils=8.32-4+b1 cpp=4:10.2.0-1 cpp-10=10.2.0-18 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 doxygen=1.8.20-4 dpkg=1.20.5 dpkg-dev=1.20.5 dwz=0.13-5 file=1:5.39-3 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 g++-10=10.2.0-18 gcc=4:10.2.0-1 gcc-10=10.2.0-18 gcc-10-base=10.2.0-18 gettext=0.19.8.1-10 gettext-base=0.19.8.1-10 graphviz=2.42.2-4+b2 grep=3.6-1 groff-base=1.22.4-5 gzip=1.10-2 hostname=3.23 init-system-helpers=1.59 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-8 libann0=1.1.2+doc-7 libarchive-zip-perl=1.68-1 libargtable2-0=13-1+b1 libargtable2-dev=13-1+b1 libargtable2-docs=13-1 libasan6=10.2.0-18 libatomic1=10.2.0-18 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-3.1 libaudit1=1:2.8.5-3.1 libbinutils=2.35.1-3 libblkid1=2.36.1-1 libbrotli1=1.0.9-2+b1 libbsd0=0.10.0-1 libbz2-1.0=1.0.8-4 libc-bin=2.31-4 libc-dev-bin=2.31-4 libc6=2.31-4 libc6-dev=2.31-4 libcairo2=1.16.0-4 libcap-ng0=0.7.9-2.2+b1 libcc1-0=10.2.0-18 libcdt5=2.42.2-4+b2 libcgraph6=2.42.2-4+b2 libclang-cpp9=1:9.0.1-15+b1 libclang1-9=1:9.0.1-15+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=2.35.1-3 libctf0=2.35.1-3 libdatrie1=0.2.12-3 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.255 libdebhelper-perl=13.2.1 libdpkg-perl=1.20.5 libedit2=3.1-20191231-1 libelf1=0.182-1 libexpat1=2.2.10-1 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=10.2.0-18 libgcc-s1=10.2.0-18 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=2:6.2.1+dfsg-1 libgomp1=10.2.0-18 libgpg-error0=1.38-2 libgraphite2-3=1.3.14-1 libgssapi-krb5-2=1.18.3-2 libgts-0.7-5=0.7.6+darcs121130-4+b1 libgvc6=2.42.2-4+b2 libgvpr2=2.42.2-4+b2 libharfbuzz0b=2.6.7-1 libice6=2:1.0.10-1 libicu67=67.1-4 libisl22=0.22.1-1 libitm1=10.2.0-18 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=1.18.3-2 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-2 libkrb5support0=1.18.3-2 liblab-gamut1=2.42.2-4+b2 libllvm9=1:9.0.1-15+b1 liblsan0=10.2.0-18 libltdl7=2.4.6-14 liblz4-1=1.9.2-2 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmount1=2.36.1-1 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libnss-nis=3.1-4 libnss-nisplus=1.3-4 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+b2 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 libquadmath0=10.2.0-18 libseccomp2=2.5.0-3 libselinux1=3.1-2+b1 libsigsegv2=2.12-2 libsm6=2:1.2.3-1 libsmartcols1=2.36.1-1 libssl1.1=1.1.1h-1 libstdc++-10-dev=10.2.0-18 libstdc++6=10.2.0-18 libsub-override-perl=0.09-2 libsystemd0=246.6-4 libthai-data=0.1.28-3 libthai0=0.1.28-3 libtiff5=4.1.0+git191117-2 libtinfo6=6.2+20201114-1 libtirpc-common=1.2.6-3 libtirpc-dev=1.2.6-3 libtirpc3=1.2.6-3 libtool=2.4.6-14 libtsan0=10.2.0-18 libubsan1=10.2.0-18 libuchardet0=0.0.7-1 libudev1=246.6-4 libunistring2=0.9.10-4 libuuid1=2.36.1-1 libwebp6=0.6.1-2+b1 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 linux-libc-dev=5.9.9-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-4 make=4.3-4 man-db=2.9.3-2 mawk=1.3.4.20200120-2 ncurses-base=6.2+20201114-1 ncurses-bin=6.2+20201114-1 node-jquery=3.5.1+dfsg+~3.5.4-1 patch=2.7.6-6 perl=5.32.0-5 perl-base=5.32.0-5 perl-modules-5.32=5.32.0-5 po-debconf=1.0.21 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 ucf=3.0043 util-linux=2.36.1-1 x11-common=1:7.7+21 xz-utils=5.2.4-1+b1 zlib1g=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20201123T152838Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d clustalo=1.2.4-7 && mkdir -p /build/clustalo-4Mwvmp && dpkg-source --no-check -x /*.dsc /build/clustalo-4Mwvmp/clustalo-1.2.4 && chown -R builduser:builduser /build/clustalo-4Mwvmp" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/clustalo-4Mwvmp/clustalo-1.2.4 && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1606119291" dpkg-buildpackage -uc -a amd64 --build=all" --customize-hook=sync-out /build/clustalo-4Mwvmp /tmp/clustalo-1.2.4-78v3yy4qw bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20201123T152838Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.AeFbYToti6 as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.AeFbYToti6 Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-1). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20201123T152838Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201123T152838Z unstable/main amd64 fakeroot amd64 1.25.3-1.1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (1022 kB/s) Selecting previously unselected package libfakeroot:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4691 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1.1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1.1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1.1_amd64.deb ... Unpacking fakeroot (1.25.3-1.1) ... Setting up libfakeroot:amd64 (1.25.3-1.1) ... Setting up fakeroot (1.25.3-1.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-4) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20201123T152838Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.AeFbYToti6 Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20201123T152838Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Fetched 22.6 MB in 20s (1117 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.AeFbYToti6 I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d clustalo=1.2.4-7 && mkdir -p /build/clustalo-4Mwvmp && dpkg-source --no-check -x /*.dsc /build/clustalo-4Mwvmp/clustalo-1.2.4 && chown -R builduser:builduser /build/clustalo-4Mwvmp"' exec /tmp/mmdebstrap.AeFbYToti6 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://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main clustalo 1.2.4-7 (dsc) [2153 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main clustalo 1.2.4-7 (tar) [1171 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main clustalo 1.2.4-7 (diff) [10.9 kB] Fetched 1184 kB in 3s (340 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'clustalo_1.2.4-7.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting clustalo in /build/clustalo-4Mwvmp/clustalo-1.2.4 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 I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/clustalo-4Mwvmp/clustalo-1.2.4 && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1606119291" dpkg-buildpackage -uc -a amd64 --build=all"' exec /tmp/mmdebstrap.AeFbYToti6 dpkg-buildpackage: info: source package clustalo dpkg-buildpackage: info: source version 1.2.4-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/build/clustalo-4Mwvmp/clustalo-1.2.4' dh_clean rm -f _configs.sed rm -rf doc make[1]: Leaving directory '/build/clustalo-4Mwvmp/clustalo-1.2.4' debian/rules binary-indep dh binary-indep dh_update_autotools_config -i dh_autoreconf -i 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 -i ./configure --build=x86_64-linux-gnu --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/x86_64-linux-gnu --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 checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking minix/config.h usability... no checking minix/config.h presence... no checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking whether make sets $(MAKE)... (cached) yes checking how to print strings... printf checking for a sed that does not truncate output... /bin/sed checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for gcc... (cached) gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ISO C89... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking dependency style of gcc... (cached) none checking how to run the C preprocessor... gcc -E checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking how to run the C++ preprocessor... g++ -E checking for ANSI C header files... (cached) yes checking assert.h usability... yes checking assert.h presence... yes checking for assert.h... yes checking ctype.h usability... yes checking ctype.h presence... yes checking for ctype.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking math.h usability... yes checking math.h presence... yes checking for math.h... yes checking for memory.h... (cached) yes checking stdarg.h usability... yes checking stdarg.h presence... yes checking for stdarg.h... yes checking stdio.h usability... yes checking stdio.h presence... yes checking for stdio.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking time.h usability... yes checking time.h presence... yes checking for time.h... yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for size_t... yes checking for inline... inline checking for log in -lm... yes checking for log2 in -lm... yes checking argtable2.h usability... yes checking argtable2.h presence... yes checking for argtable2.h... yes checking for arg_parse in -largtable2... yes checking for OpenMP flag of C compiler... -fopenmp checking whether byte ordering is bigendian... no checking for ntohs... yes checking for ntohl... yes checking for ntons... no checking for ntonl... no checking size of unsigned short... 2 checking size of unsigned int... 4 checking size of unsigned long... 8 checking size of unsigned long long... 8 checking for stroul... no checking for strtoull... yes checking for ftello... yes checking for fseeko... yes checking for ftello64... yes checking for fseeko64... yes checking for ftell64... no checking for fseek64... no checking for off_t... yes checking size of fpos_t... 16 checking if malloc debugging is wanted... no checking whether to build with debug information... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating clustalo.pc config.status: creating Doxyfile config.status: creating src/clustal/Makefile config.status: creating src/hhalign/Makefile config.status: creating src/kmpp/Makefile config.status: creating src/squid/Makefile config.status: creating src/config.h config.status: executing src/clustal-omega-config.h commands config.status: creating src/clustal-omega-config.h - prefix CLUSTAL_OMEGA for src/config.h defines config.status: executing depfiles commands config.status: executing libtool commands debian/rules override_dh_auto_build-indep make[1]: Entering directory '/build/clustalo-4Mwvmp/clustalo-1.2.4' # nothing to do here make[1]: Leaving directory '/build/clustalo-4Mwvmp/clustalo-1.2.4' debian/rules override_dh_auto_test-indep make[1]: Entering directory '/build/clustalo-4Mwvmp/clustalo-1.2.4' echo "Do not run build time test" Do not run build time test make[1]: Leaving directory '/build/clustalo-4Mwvmp/clustalo-1.2.4' create-stamp debian/debhelper-build-stamp dh_testroot -i dh_prep -i debian/rules override_dh_auto_install-indep make[1]: Entering directory '/build/clustalo-4Mwvmp/clustalo-1.2.4' # Generate doxygen doc mkdir -p doc doxygen Doxyfile warning: Tag 'SYMBOL_CACHE_SIZE' at line 289 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'SHOW_DIRECTORIES' at line 473 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'HTML_ALIGN_MEMBERS' at line 799 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'XML_SCHEMA' at line 1136 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'XML_DTD' at line 1142 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'PERL_PATH' at line 1307 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'MSCGEN_PATH' at line 1329 of file 'Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: argument 'a4wide' for option PAPER_TYPE is not a valid enum value Using the default: a4! warning: doxygen no longer ships with the FreeSans font. You may want to clear or change DOT_FONTNAME. Otherwise you run the risk that the wrong font is being used for dot generated graphs. /build/clustalo-4Mwvmp/clustalo-1.2.4/src/clustal-omega.c:755: warning: argument 'pdSeqWeights_p' from the argument list of AlignmentOrder has multiple @param documentation sections /build/clustalo-4Mwvmp/clustalo-1.2.4/src/clustal-omega.c:755: warning: The following parameters of AlignmentOrder(int **piOrderLR_p, double **pdSeqWeights_p, mseq_t *prMSeq, int iPairDistType, char *pcDistmatInfile, char *pcDistmatOutfile, int iClusteringType, int iClustersizes, char *pcGuidetreeInfile, char *pcGuidetreeOutfile, char *pcClusterFile, bool bUseMbed, bool bPercID) are not documented: parameter 'iClustersizes' parameter 'pcClusterFile' parameter 'bPercID' /build/clustalo-4Mwvmp/clustalo-1.2.4/src/clustal-omega.h:169: warning: argument 'pdSeqWeights_p' from the argument list of AlignmentOrder has multiple @param documentation sections /build/clustalo-4Mwvmp/clustalo-1.2.4/src/clustal-omega.h:169: warning: The following parameters of AlignmentOrder(int **piOrderLR_p, double **pdSeqWeights_p, mseq_t *prMSeq, int iPairDistType, char *pcDistmatInfile, char *pcDistmatOutfile, int iClusteringType, int iClustersizes, char *pcGuidetreeInfile, char *pcGuidetreeOutfile, char *pcClusterFile, bool bUseMbed, bool bPercID) are not documented: parameter 'iClustersizes' parameter 'pcClusterFile' parameter 'bPercID' /build/clustalo-4Mwvmp/clustalo-1.2.4/src/clustal/mbed.c:666: warning: The following parameter of BisectingKmeans(bisecting_kmeans_result_t **prKMeansResult_p, const int iNObjs, const int iDim, double **ppdVectors, const int iMinRequiredObjsPerCluster, const int iMaxAllowedObjsPerCluster, char ***ppcClusterSplits_p) is not documented: parameter 'ppcClusterSplits_p' /build/clustalo-4Mwvmp/clustalo-1.2.4/src/clustal/mbed.c:1162: warning: The following parameters of Mbed(tree_t **prMbedTree_p, mseq_t *prMSeq, const int iPairDistType, const char *pcGuidetreeOut, int iClustersizes, const char *pcClusterFile) are not documented: parameter 'iClustersizes' parameter 'pcClusterFile' /build/clustalo-4Mwvmp/clustalo-1.2.4/src/clustal/mbed.h:27: warning: The following parameters of Mbed(tree_t **prMbedTree_p, mseq_t *prMSeq, const int iPairDistType, const char *pcGuidetreeOut, int iClustersizes, const char *pcClusterFile) are not documented: parameter 'iClustersizes' parameter 'pcClusterFile' /build/clustalo-4Mwvmp/clustalo-1.2.4/src/clustal/pair_dist.c:263: warning: Unsupported xml/html tag found /build/clustalo-4Mwvmp/clustalo-1.2.4/src/clustal/pair_dist.c:269: warning: Unsupported xml/html tag found /build/clustalo-4Mwvmp/clustalo-1.2.4/src/clustal/pair_dist.c:277: warning: The following parameter of PairDistances(symmatrix_t **distmat, mseq_t *mseq, int pairdist_type, bool bPercID, int istart, const unsigned long int iend, int jstart, const unsigned long int jend, char *fdist_in, char *fdist_out) is not documented: parameter 'bPercID' /build/clustalo-4Mwvmp/clustalo-1.2.4/src/clustal/pair_dist.c:263: warning: Unsupported xml/html tag found /build/clustalo-4Mwvmp/clustalo-1.2.4/src/clustal/pair_dist.c:269: warning: Unsupported xml/html tag found /build/clustalo-4Mwvmp/clustalo-1.2.4/src/clustal/pair_dist.h:36: warning: The following parameter of PairDistances(symmatrix_t **distmat, mseq_t *mseq, int pairdist_type, bool bPercID, int istart, const unsigned long int iend, int jstart, const unsigned long int jend, char *fdist_in, char *fdist_out) is not documented: parameter 'bPercID' /build/clustalo-4Mwvmp/clustalo-1.2.4/src/clustal/seq.c:420: warning: The following parameters of ReadSequences(mseq_t *prMSeq, char *seqfile, int iSeqType, int iSeqFmt, bool bIsProfile, bool bDealignInputSeqs, int iMaxNumSeq, int iMaxSeqLen, char *pcHMMBatch) are not documented: parameter 'iSeqFmt' parameter 'bIsProfile' parameter 'bDealignInputSeqs' parameter 'pcHMMBatch' /build/clustalo-4Mwvmp/clustalo-1.2.4/src/clustal/seq.c:1112: warning: The following parameters of SeqsAreAligned(mseq_t *prMSeq, bool bIsProfile, bool bDealignInputSeqs) are not documented: parameter 'bIsProfile' parameter 'bDealignInputSeqs' /build/clustalo-4Mwvmp/clustalo-1.2.4/src/clustal/seq.c:884: warning: The following parameter of WriteAlignment(mseq_t *mseq, const char *pcAlnOutfile, int outfmt, int iWrap, bool bResno) is not documented: parameter 'bResno' /build/clustalo-4Mwvmp/clustalo-1.2.4/src/clustal/seq.h:136: warning: The following parameters of ReadSequences(mseq_t *prMSeq, char *seqfile, int iSeqType, int iSeqFmt, bool bIsProfile, bool bDealignInputSeqs, int iMaxNumSeq, int iMaxSeqLen, char *pcHMMBatch) are not documented: parameter 'iSeqFmt' parameter 'bIsProfile' parameter 'bDealignInputSeqs' parameter 'pcHMMBatch' /build/clustalo-4Mwvmp/clustalo-1.2.4/src/clustal/seq.h:171: warning: The following parameters of SeqsAreAligned(mseq_t *prMSeq, bool bIsProfile, bool bDealignInputSeqs) are not documented: parameter 'bIsProfile' parameter 'bDealignInputSeqs' /build/clustalo-4Mwvmp/clustalo-1.2.4/src/clustal/seq.h:156: warning: The following parameter of WriteAlignment(mseq_t *mseq, const char *pcAlnOutfile, int outfmt, int iWrap, bool bResno) is not documented: parameter 'bResno' /build/clustalo-4Mwvmp/clustalo-1.2.4/src/clustal/symmatrix.c:248: warning: documented empty return type of SymMatrixGetValueP /build/clustalo-4Mwvmp/clustalo-1.2.4/src/clustal/symmatrix.c:316: warning: The following parameter of SymMatrixPrint(symmatrix_t *symmat, char **labels, const char *path, bool bPercID) is not documented: parameter 'bPercID' /build/clustalo-4Mwvmp/clustalo-1.2.4/src/clustal/symmatrix.h:74: warning: documented empty return type of SymMatrixGetValueP /build/clustalo-4Mwvmp/clustalo-1.2.4/src/clustal/symmatrix.h:80: warning: The following parameter of SymMatrixPrint(symmatrix_t *symmat, char **labels, const char *path, bool bPercID) is not documented: parameter 'bPercID' find doc -name "*.md5" -delete make[1]: Leaving directory '/build/clustalo-4Mwvmp/clustalo-1.2.4' dh_install -i dh_installdocs -i dh_installchangelogs -i dh_installexamples -i dh_installman -i dh_perl -i dh_link -i dh_strip_nondeterminism -i dh_compress -i dh_fixperms -i dh_missing -i dh_installdeb -i dh_gencontrol -i dpkg-gencontrol: warning: Depends field of package libclustalo-doc: substitution variable ${js:Depends} used, but is not defined dh_md5sums -i dh_builddeb -i dpkg-deb: building package 'libclustalo-doc' in '../libclustalo-doc_1.2.4-7_all.deb'. dpkg-genbuildinfo --build=all dpkg-genchanges --build=all >../clustalo_1.2.4-7_all.changes dpkg-genchanges: info: binary-only arch-indep upload (source code and arch-specific packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/clustalo-4Mwvmp /tmp/clustalo-1.2.4-78v3yy4qw I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.AeFbYToti6... I: success in 708.7857 seconds md5: libclustalo-doc_1.2.4-7_all.deb: OK sha1: libclustalo-doc_1.2.4-7_all.deb: OK sha256: libclustalo-doc_1.2.4-7_all.deb: OK Checksums: OK