Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/h/hmmer2/hmmer2_2.3.2+dfsg-7_all.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/hmmer2-2.3.2+dfsg-7ln1vyy9j/hmmer2_2.3.2+dfsg-7_all.buildinfo Get source package info: hmmer2=2.3.2+dfsg-7 Source URL: http://snapshot.notset.fr/mr/package/hmmer2/2.3.2+dfsg-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=1:1.16.2-3 autopoint=0.19.8.1-10 autotools-dev=20180224.1 base-files=11 base-passwd=3.5.47 bash=5.0-7 binutils=2.35-2 binutils-common=2.35-2 binutils-x86-64-linux-gnu=2.35-2 bsdextrautils=2.36-3 bsdutils=1:2.36-3 build-essential=12.8 bzip2=1.0.8-4 coreutils=8.32-3 cpp=4:10.1.0-1 cpp-10=10.2.0-6 dash=0.5.10.2-7 debconf=1.5.74 debhelper=13.2 debianutils=4.11.1 dh-autoreconf=19 dh-exec=0.23.2 dh-strip-nondeterminism=1.9.0-1 diffutils=1:3.7-3 dpkg=1.20.5 dpkg-dev=1.20.5 dwz=0.13-5 file=1:5.38-5 findutils=4.7.0-1 g++=4:10.1.0-1 g++-10=10.2.0-6 gcc=4:10.1.0-1 gcc-10=10.2.0-6 gcc-10-base=10.2.0-6 gettext=0.19.8.1-10 gettext-base=0.19.8.1-10 grep=3.4-1 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 libacl1=2.2.53-8 libarchive-zip-perl=1.68-1 libasan6=10.2.0-6 libatomic1=10.2.0-6 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-3 libaudit1=1:2.8.5-3+b1 libbinutils=2.35-2 libblkid1=2.36-3 libbz2-1.0=1.0.8-4 libc-bin=2.31-3 libc-dev-bin=2.31-3 libc6=2.31-3 libc6-dev=2.31-3 libcap-ng0=0.7.9-2.2 libcc1-0=10.2.0-6 libcroco3=0.6.13-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35-2 libctf0=2.35-2 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.253 libdebhelper-perl=13.2 libdpkg-perl=1.20.5 libelf1=0.180-1+b1 libffi7=3.3-4 libfile-stripnondeterminism-perl=1.9.0-1 libgcc-10-dev=10.2.0-6 libgcc-s1=10.2.0-6 libgcrypt20=1.8.6-2 libgdbm-compat4=1.18.1-5.1 libgdbm6=1.18.1-5.1 libglib2.0-0=2.64.4-1 libgmp10=2:6.2.0+dfsg-6 libgomp1=10.2.0-6 libgpg-error0=1.38-2 libicu67=67.1-4 libisl22=0.22.1-1 libitm1=10.2.0-6 liblsan0=10.2.0-6 liblz4-1=1.9.2-2 liblzma5=5.2.4-1+b1 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 libpam-modules=1.3.1-5 libpam-modules-bin=1.3.1-5 libpam-runtime=1.3.1-5 libpam0g=1.3.1-5 libpcre2-8-0=10.34-7 libpcre3=2:8.39-13 libperl4-corelibs-perl=0.004-2 libperl5.30=5.30.3-4 libpipeline1=1.5.3-1 libquadmath0=10.2.0-6 libseccomp2=2.4.3-1+b1 libselinux1=3.1-2 libsigsegv2=2.12-2 libsmartcols1=2.36-3 libsquid-dev=1.9g+cvs20050121-12 libsquid1=1.9g+cvs20050121-12 libstdc++-10-dev=10.2.0-6 libstdc++6=10.2.0-6 libsub-override-perl=0.09-2 libsystemd0=246.4-1 libtinfo6=6.2-1 libtool=2.4.6-14 libtsan0=10.2.0-6 libubsan1=10.2.0-6 libuchardet0=0.0.7-1 libudev1=246.4-1 libunistring2=0.9.10-4 libuuid1=2.36-3 libxml2=2.9.10+dfsg-6 libzstd1=1.4.5+dfsg-4 linux-libc-dev=5.8.7-1 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=6.2-1 ncurses-bin=6.2-1 patch=2.7.6-6 perl=5.30.3-4 perl-base=5.30.3-4 perl-modules-5.30=5.30.3-4 pkg-config=0.29.2-1 po-debconf=1.0.21 rename=1.13-1 sed=4.7-1 sensible-utils=0.0.12+nmu1 sysvinit-utils=2.96-4 tar=1.30+dfsg-7 util-linux=2.36-3 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/20200910T144906Z/ 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 hmmer2=2.3.2+dfsg-7 && mkdir -p /build/hmmer2-C8muUe && dpkg-source --no-check -x /*.dsc /build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg && chown -R builduser:builduser /build/hmmer2-C8muUe" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1597225470" dpkg-buildpackage -uc -a amd64 --build=all" --customize-hook=sync-out /build/hmmer2-C8muUe /tmp/hmmer2-2.3.2+dfsg-7ln1vyy9j bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20200910T144906Z 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.BRR1KM5ZE8 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.BRR1KM5ZE8 Reading package lists... Building dependency tree... util-linux is already the newest version (2.36-3). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 132 kB of archives. After this operation, 393 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20200910T144906Z unstable/main amd64 libfakeroot amd64 1.24-1 [45.7 kB] Get:2 http://snapshot.notset.fr/archive/debian/20200910T144906Z unstable/main amd64 fakeroot amd64 1.24-1 [85.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 132 kB in 0s (682 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 ... 4576 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.24-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.24-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.24-1_amd64.deb ... Unpacking fakeroot (1.24-1) ... Setting up libfakeroot:amd64 (1.24-1) ... Setting up fakeroot (1.24-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-3) ... 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/20200910T144906Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.BRR1KM5ZE8 Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20200910T144906Z 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 (1104 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.BRR1KM5ZE8 I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d hmmer2=2.3.2+dfsg-7 && mkdir -p /build/hmmer2-C8muUe && dpkg-source --no-check -x /*.dsc /build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg && chown -R builduser:builduser /build/hmmer2-C8muUe"' exec /tmp/mmdebstrap.BRR1KM5ZE8 Reading package lists... NOTICE: 'hmmer2' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/hmmer2.git Please use: git clone https://salsa.debian.org/med-team/hmmer2.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 348 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main hmmer2 2.3.2+dfsg-7 (dsc) [2268 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main hmmer2 2.3.2+dfsg-7 (tar) [332 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main hmmer2 2.3.2+dfsg-7 (diff) [14.2 kB] Fetched 348 kB in 1s (677 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'hmmer2_2.3.2+dfsg-7.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting hmmer2 in /build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg dpkg-source: info: unpacking hmmer2_2.3.2+dfsg.orig.tar.xz dpkg-source: info: unpacking hmmer2_2.3.2+dfsg-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying version2-manpage dpkg-source: info: applying userguidepdf dpkg-source: info: applying spelling.patch dpkg-source: info: applying use_debian_packaged_biosquid.patch dpkg-source: info: applying build_libhmmer.a_with-fPIC.patch dpkg-source: info: applying add-runstatedir-option.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1597225470" dpkg-buildpackage -uc -a amd64 --build=all"' exec /tmp/mmdebstrap.BRR1KM5ZE8 dpkg-buildpackage: info: source package hmmer2 dpkg-buildpackage: info: source version 2.3.2+dfsg-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . debian/rules clean dh clean dh_clean debian/rules binary-indep dh binary-indep dh_update_autotools_config -i dh_autoreconf -i debian/rules override_dh_auto_configure make[1]: Entering directory '/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg' dh_auto_configure -- --enable-threads --enable-lfs # --enable-pvm ./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 --enable-threads --enable-lfs configure: configuring HMMER for your system. configure: This is a full source distribution - using full config checking for gcc... gcc checking for C compiler default output... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... 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 ANSI C... none needed checking for ranlib... ranlib checking for ar... /usr/bin/ar checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking whether your make is GNU make... yes, it is. configure: configured for optional LFS, large file support configure: enabled POSIX multithreading support checking for pthread_setconcurrency... no checking for pthread_attr_setscope... yes checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... gcc checking for ntohs... yes checking for ntohl... yes checking for htons... yes checking for htonl... yes configure: creating ./config.status config.status: creating src/Makefile config.status: creating testsuite/Makefile config.status: creating Makefile config.status: creating src/config.h # avoid duplicated definition of PACKAGE_NAME (basically conflicting with biosquid when used together) sed -i -e '/^#define PACKAGE_NAME /i #ifndef PACKAGE_NAME' \ -e '/^#define PACKAGE_NAME /a #endif' \ -e '/^#define PACKAGE_VERSION /i #ifndef PACKAGE_VERSION' \ -e '/^#define PACKAGE_VERSION /a #endif' \ -e '/^#define _LARGEFILE_SOURCE /i #ifndef _LARGEFILE_SOURCE' \ -e '/^#define _LARGEFILE_SOURCE /a #endif' \ -e '/^#define _LARGEFILE64_SOURCE /i #ifndef _LARGEFILE64_SOURCE' \ -e '/^#define _LARGEFILE64_SOURCE /a #endif' \ -e '/^#define VERSION /i #ifndef VERSION' \ -e '/^#define VERSION /a #endif' \ src/config.h make[1]: Leaving directory '/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg' dh_auto_build -i make -j4 make[1]: Entering directory '/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg' make[2]: Entering directory '/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg/src' gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -c hmmalign.c gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -c alphabet.c gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -c core_algorithms.c gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -c debug.c gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -c display.c gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -c emit.c gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -c emulation.c gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -c fast_algorithms.c gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -c histogram.c gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -c hmmio.c gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -c mathsupport.c histogram.c: In function ‘ExtremeValueSetHistogram’: histogram.c:725:23: warning: implicit declaration of function ‘IncompleteGamma’ [-Wimplicit-function-declaration] 725 | h->chip = (float) IncompleteGamma((double)(nbins-1-ndegrees)/2., | ^~~~~~~~~~~~~~~ mathsupport.c: In function ‘Logp_cvec’: mathsupport.c:229:15: warning: implicit declaration of function ‘Gammln’ [-Wimplicit-function-declaration] 229 | lnp += Gammln(alpha[x] + cvec[x]); | ^~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -c masks.c gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -c misc.c gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -c modelmakers.c gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -c plan7.c gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -c plan9.c gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -c postprob.c gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -c prior.c gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -c pvm.c gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -c threads.c gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -c tophits.c gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -c trace.c gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -c hmmbuild.c gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -c hmmcalibrate.c gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -c hmmconvert.c gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -c hmmemit.c gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -c hmmfetch.c gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -c hmmindex.c gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -c hmmpfam.c gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -c hmmsearch.c gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmalign hmmalign.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `pkg-config --libs libsquid` -lm gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmcalibrate hmmcalibrate.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `pkg-config --libs libsquid` -lm gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmconvert hmmconvert.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `pkg-config --libs libsquid` -lm gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmemit hmmemit.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `pkg-config --libs libsquid` -lm gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmfetch hmmfetch.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `pkg-config --libs libsquid` -lm gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmindex hmmindex.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `pkg-config --libs libsquid` -lm gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmbuild hmmbuild.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `pkg-config --libs libsquid` -lm gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmpfam hmmpfam.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `pkg-config --libs libsquid` -lm gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -o hmmsearch hmmsearch.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o `pkg-config --libs libsquid` -lm make[2]: Leaving directory '/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg/src' make[2]: Entering directory '/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg/src' /usr/bin/ar rcv libhmmer.a alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o a - alphabet.o a - core_algorithms.o a - debug.o a - display.o a - emit.o a - emulation.o a - fast_algorithms.o a - histogram.o a - hmmio.o a - mathsupport.o a - masks.o a - misc.o a - modelmakers.o a - plan7.o a - plan9.o a - postprob.o a - prior.o a - pvm.o a - threads.o a - tophits.o a - trace.o ranlib libhmmer.a chmod 644 libhmmer.a make[2]: Leaving directory '/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg/src' make[2]: Entering directory '/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg/testsuite' gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -I../src -c alignalign_test.c gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -I../src -c evd_test.c gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -I../src -c masks_test.c gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -I../src -c parsingviterbi_test.c gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -I../src -c tophits_test.c gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -I../src -c trace_test.c gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -I../src -c viterbi_exercise.c gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -I../src -c weeviterbi_test.c gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o alignalign_test -L../src alignalign_test.o -lhmmer `pkg-config --libs libsquid` -lm gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o evd_test -L../src evd_test.o -lhmmer `pkg-config --libs libsquid` -lm gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o masks_test -L../src masks_test.o -lhmmer `pkg-config --libs libsquid` -lm gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o parsingviterbi_test -L../src parsingviterbi_test.o -lhmmer `pkg-config --libs libsquid` -lm gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o tophits_test -L../src tophits_test.o -lhmmer `pkg-config --libs libsquid` -lm gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o trace_test -L../src trace_test.o -lhmmer `pkg-config --libs libsquid` -lm gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o viterbi_exercise -L../src viterbi_exercise.o -lhmmer `pkg-config --libs libsquid` -lm gcc -g -O2 -fdebug-prefix-map=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o weeviterbi_test -L../src weeviterbi_test.o -lhmmer `pkg-config --libs libsquid` -lm make[2]: Leaving directory '/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg/testsuite' make[1]: Leaving directory '/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg' dh_auto_test make -j4 check VERBOSE=1 make[2]: Entering directory '/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg' (cd testsuite; make check) make[3]: Entering directory '/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg/testsuite' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. Running test suite exercises. Warning: some tests may take several minutes to complete. ./sqc 2 exercises.sqc . ../src exercise 1 [ hmmalign] ... ok. exercise 2 [ hmmalign/h] ... ok. exercise 3 [ hmmalign/m] ... ok. exercise 4 [ hmmalign/o] ... ok. exercise 5 [ hmmalign/q] ... ok. exercise 6 [ hmmalign/informat] ... ok. exercise 7 [ hmmalign/selex] ... ok. exercise 8 [ hmmalign/a2m] ... ok. exercise 9 [ hmmalign/clustal] ... ok. exercise 10 [ hmmalign/msf] ... ok. exercise 11 [ hmmalign/phylip] ... ok. exercise 12 [ hmmalign/oneline] ... ok. exercise 13 [ hmmalign/withali] ... ok. exercise 14 [ hmmalign/mapali] ... ok. exercise 15 [ hmmbuild] ... ok. exercise 16 [ hmmbuild/h] ... ok. exercise 17 [ hmmbuild/F] ... ok. exercise 18 [ hmmbuild/n] ... ok. exercise 19 [ hmmbuild/o] ... ok. exercise 20 [ hmmbuild/A] ... ok. exercise 21 [ hmmbuild/f] ... ok. exercise 22 [ hmmbuild/g] ... ok. exercise 23 [ hmmbuild/s] ... ok. exercise 24 [ hmmbuild/fast] ... ok. exercise 25 [ hmmbuild/hand] ... ok. exercise 26 [ hmmbuild/null] ... ok. exercise 27 [ hmmbuild/pam] ... ok. exercise 28 [ hmmbuild/prior] ... ok. exercise 29 [ hmmbuild/wblosum] ... ok. exercise 30 [ hmmbuild/wgsc] ... ok. exercise 31 [ hmmbuild/wme] ... ok. exercise 32 [ hmmbuild/wpb] ... ok. exercise 33 [ hmmbuild/wvoronoi] ... ok. exercise 34 [ hmmbuild/wnone] ... ok. exercise 35 [ hmmbuild/noeff] ... ok. exercise 36 [ hmmbuild/pbswitch] ... ok. exercise 37 [ hmmbuild/amino] ... ok. exercise 38 [ hmmbuild/nucleic] ... ok. exercise 39 [ hmmbuild/archpri] ... ok. exercise 40 [ hmmbuild/binary] ... ok. exercise 41 [ hmmbuild/cfile] ... ok. exercise 42 [ hmmbuild/gapmax] ... ok. exercise 43 [ hmmbuild/idlevel] ... ok. exercise 44 [ hmmbuild/informat] ... ok. exercise 45 [ hmmbuild/pamwgt] ... ok. exercise 46 [ hmmbuild/swentry] ... ok. exercise 47 [ hmmbuild/swexit] ... ok. exercise 48 [ hmmbuild/verbose] ... ok. exercise 49 [ hmmcalibrate] ... ok. exercise 50 [ hmmcalibrate/h] ... ok. exercise 51 [ hmmcalibrate/fixed] ... ok. exercise 52 [ hmmcalibrate/mean] ... ok. exercise 53 [ hmmcalibrate/hist] ... ok. exercise 54 [ hmmcalibrate/num] ... ok. exercise 55 [ hmmcalibrate/sd] ... ok. exercise 56 [ hmmcalibrate/seed] ... ok. exercise 57 [ hmmconvert] ... ok. exercise 58 [ hmmconvert/h] ... ok. exercise 59 [ hmmconvert/F] ... ok. exercise 60 [ hmmconvert/a] ... ok. exercise 61 [ hmmconvert/A] ... ok. exercise 62 [ hmmconvert/b] ... ok. exercise 63 [ hmmconvert/p] ... ok. exercise 64 [ hmmconvert/P] ... ok. exercise 65 [ hmmemit] ... ok. exercise 66 [ hmmemit/a] ... ok. exercise 67 [ hmmemit/c] ... ok. exercise 68 [ hmmemit/h] ... ok. exercise 69 [ hmmemit/n] ... ok. exercise 70 [ hmmemit/o] ... ok. exercise 71 [ hmmemit/q] ... ok. exercise 72 [ hmmemit/seed] ... ok. exercise 73 [ hmmindex] ... ok. exercise 74 [ hmmindex/h] ... ok. exercise 75 [ hmmfetch] ... ok. exercise 76 [ hmmfetch/h] ... ok. exercise 77 [ hmmfetch/n] ... ok. exercise 78 [ hmmpfam] ... ok. exercise 79 [ hmmpfam/h] ... ok. exercise 80 [ hmmpfam/n] ... ok. exercise 81 [ hmmpfam/A] ... ok. exercise 82 [ hmmpfam/E] ... ok. exercise 83 [ hmmpfam/T] ... ok. exercise 84 [ hmmpfam/Z] ... ok. exercise 85 [ hmmpfam/acc] ... ok. exercise 86 [ hmmpfam/compat] ... ok. exercise 87 [ hmmpfam/cut_ga] ... ok. exercise 88 [ hmmpfam/cut_nc] ... ok. exercise 89 [ hmmpfam/cut_tc] ... ok. exercise 90 [ hmmpfam/domE] ... ok. exercise 91 [ hmmpfam/domT] ... ok. exercise 92 [ hmmpfam/forward] ... ok. exercise 93 [ hmmpfam/informat] ... ok. exercise 94 [ hmmpfam/null2] ... ok. exercise 95 [ hmmpfam/xnu] ... ok. exercise 96 [ hmmsearch] ... ok. exercise 97 [ hmmsearch/h] ... ok. exercise 98 [ hmmsearch/A] ... ok. exercise 99 [ hmmsearch/E] ... ok. exercise 100 [ hmmsearch/T] ... ok. exercise 101 [ hmmsearch/Z] ... ok. exercise 102 [ hmmsearch/compat] ... ok. exercise 103 [ hmmsearch/cut_ga] ... ok. exercise 104 [ hmmsearch/cut_nc] ... ok. exercise 105 [ hmmsearch/cut_tc] ... ok. exercise 106 [ hmmsearch/domE] ... ok. exercise 107 [ hmmsearch/domT] ... ok. exercise 108 [ hmmsearch/forward] ... ok. exercise 109 [ hmmsearch/informat] ... ok. exercise 110 [ hmmsearch/null2] ... ok. exercise 111 [ hmmsearch/xnu] ... ok. exercise 112 [ align_align] ... ok. exercise 113 [ evd] ... ok. exercise 114 [ masks] ... ok. exercise 115 [ parsingv] ... ok. exercise 116 [ tophits] ... ok. exercise 117 [ trace] ... ok. exercise 118 [ viterbi] ... ok. exercise 119 [ weeviterbi] ... ok. exercise 120 [ test1/conversion] ... ok. All 120 exercises at level <= 2 passed. System information: Sat Oct 9 00:29:19 UTC 2021 Linux c46ad8d52efd 5.10.0-8-amd64 #1 SMP Debian 5.10.46-4 (2021-08-03) x86_64 GNU/Linux make[3]: Leaving directory '/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg/testsuite' make[2]: Leaving directory '/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg' rm -f testsuite/*.ssi cd testsuite && make clean make[2]: Entering directory '/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg/testsuite' rm -f *.o *~ Makefile.bak core alignalign_test evd_test masks_test parsingviterbi_test tophits_test trace_test viterbi_exercise weeviterbi_test TAGS gmon.out make[2]: Leaving directory '/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg/testsuite' make[1]: Leaving directory '/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -i dh_prep -i debian/rules override_dh_auto_install make[1]: Entering directory '/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg' dh_auto_install -- prefix=/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg/debian/tmp make -j4 install DESTDIR=/build/hmmer2-C8muUe/hmmer2-2.3.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/build/hmmer2-C8muUe/hmmer2-2.3.2\+dfsg/debian/tmp make[2]: Entering directory '/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg' mkdir -p /build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg/debian/tmp/bin mkdir -p /build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg/debian/tmp/share/man/man1 for file in hmmalign hmmbuild hmmcalibrate hmmconvert hmmemit hmmfetch hmmindex hmmpfam hmmsearch ; do\ cp src/$file /build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg/debian/tmp/bin/;\ done for file in hmmer hmmalign hmmbuild hmmcalibrate hmmconvert hmmemit hmmfetch hmmindex hmmpfam hmmsearch; do\ cp documentation/man/$file.man /build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg/debian/tmp/share/man/man1/$file.1;\ done make[2]: Leaving directory '/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg' # lkajan: rename binaries and man pages like this: s/hmm/hmm2/ - except hmmer.1, rename that to hmmer2.1: rename 's/^hmm/hmm2/;' /build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg/debian/tmp/bin/* cd /build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg/debian/tmp/bin; rename 's/^hmm/hmm2/;' * cd /build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg/debian/tmp/share/man/man1; rename 's/^hmm/hmm2/;' * mv /build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg/debian/tmp/share/man/man1/hmm2er.1 /build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg/debian/tmp/share/man/man1/hmmer2.1 # lkajan: resolve man page hypen issue: sed -i -e 's/--/\\-\\-/g;s/-\([[:alpha:]]\)\b/\\-\1/g;' /build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg/debian/tmp/share/man/man1/* make[1]: Leaving directory '/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg' dh_install -i dh_installdocs -i debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg' dh_installchangelogs -k NOTES make[1]: Leaving directory '/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg' debian/rules override_dh_installexamples make[1]: Entering directory '/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg' dh_installexamples mkdir -p /build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples; sed -i "s#hmm#hmm2#g" testsuite/exercises.sqc cp -a testsuite/* /build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples/; mkdir /build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples/tutorial; cp -a tutorial/* /build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples/tutorial; sed -i "s#../tut#./tut#g" /build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples/exercises.sqc find /build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples -name 'Makefile' | xargs sed -i "s^/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg^.^g" make[1]: Leaving directory '/build/hmmer2-C8muUe/hmmer2-2.3.2+dfsg' 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 hmmer2-doc: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums -i dh_builddeb -i dpkg-deb: building package 'hmmer2-doc' in '../hmmer2-doc_2.3.2+dfsg-7_all.deb'. dpkg-genbuildinfo --build=all dpkg-genchanges --build=all >../hmmer2_2.3.2+dfsg-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/hmmer2-C8muUe /tmp/hmmer2-2.3.2+dfsg-7ln1vyy9j I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.BRR1KM5ZE8... I: success in 333.2659 seconds md5: hmmer2-doc_2.3.2+dfsg-7_all.deb: OK sha1: hmmer2-doc_2.3.2+dfsg-7_all.deb: OK sha256: hmmer2-doc_2.3.2+dfsg-7_all.deb: OK Checksums: OK