Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/p/psortb/psortb_3.0.6+dfsg-2+b1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/psortb-3.0.6+dfsg-2+b1y0ei7qmv/psortb_3.0.6+dfsg-2+b1_amd64.buildinfo Get source package info: psortb=3.0.6+dfsg-2 Source URL: http://snapshot.notset.fr/mr/package/psortb/3.0.6+dfsg-2/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~rc2-1 binutils=2.35.1-2 binutils-common=2.35.1-2 binutils-x86-64-linux-gnu=2.35.1-2 bioperl=1.7.7-2 bsdextrautils=2.36-3+b2 bsdutils=1:2.36-3+b2 build-essential=12.8 bzip2=1.0.8-4 coreutils=8.32-4+b1 cpp=4:10.2.0-1 cpp-10=10.2.0-16 dash=0.5.10.2-7 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 dpkg=1.20.5 dpkg-dev=1.20.5 dwz=0.13-5 file=1:5.38-5 findutils=4.7.0+git20201010-2 g++=4:10.2.0-1 g++-10=10.2.0-16 gcc=4:10.2.0-1 gcc-10=10.2.0-16 gcc-10-base=10.2.0-16 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 libalgorithm-diff-perl=1.200-1 libarchive-zip-perl=1.68-1 libasan6=10.2.0-16 libatomic1=10.2.0-16 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 libbio-perl-perl=1.7.7-2 libblkid1=2.36-3+b2 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 libcap-ng0=0.7.9-2.2 libcapture-tiny-perl=0.48-1 libcc1-0=10.2.0-16 libclass-data-inheritable-perl=0.08-3 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 libctf0=2.35.1-2 libdata-stag-perl=0.14-2 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.255 libdebhelper-perl=13.2.1 libdevel-stacktrace-perl=2.0400-1 libdpkg-perl=1.20.5 libelf1=0.182-1 libexception-class-perl=1.44-1 libexpat1=2.2.10-1 libffi7=3.3-4 libfile-stripnondeterminism-perl=1.9.0-1 libgcc-10-dev=10.2.0-16 libgcc-s1=10.2.0-16 libgcrypt20=1.8.7-2 libgdbm-compat4=1.18.1-5.1 libgdbm6=1.18.1-5.1 libgfortran5=10.2.0-16 libglib2.0-0=2.66.2-1 libgmp10=2:6.2.0+dfsg-6 libgomp1=10.2.0-16 libgpg-error0=1.38-2 libgssapi-krb5-2=1.17-10 libhmmer2-dev=2.3.2+dfsg-7 libicu67=67.1-4 libio-string-perl=1.08-3 libisl22=0.22.1-1 libitm1=10.2.0-16 libk5crypto3=1.17-10 libkeyutils1=1.6.1-2 libkrb5-3=1.17-10 libkrb5support0=1.17-10 liblmdb0=0.9.24-1 liblsan0=10.2.0-16 liblz4-1=1.9.2-2 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.38-5 libmagic1=1:5.38-5 libmbedcrypto3=2.16.5-1 libmbedtls12=2.16.5-1 libmbedx509-0=2.16.5-1 libmodhmm-dev=1.0+dfsg-3 libmodhmm0=1.0+dfsg-3 libmount1=2.36-3+b2 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libncursesw6=6.2+20200918-1 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 libpcre2-8-0=10.34-7 libpcre3=2:8.39-13 libperl5.32=5.32.0-4 libpipeline1=1.5.3-1 libpython3-stdlib=3.8.6-1 libpython3.8-minimal=3.8.6-1 libpython3.8-stdlib=3.8.6-1 libquadmath0=10.2.0-16 libreadline8=8.0-4 libseccomp2=2.4.4-1+b1 libselinux1=3.1-2+b1 libsigsegv2=2.12-2 libsmartcols1=2.36-3+b2 libsqlite3-0=3.33.0-1 libsquid-dev=1.9g+cvs20050121-12 libsquid1=1.9g+cvs20050121-12 libssl1.1=1.1.1h-1 libstdc++-10-dev=10.2.0-16 libstdc++6=10.2.0-16 libsub-override-perl=0.09-2 libsub-uplevel-perl=0.2800-1 libsvm-dev=3.24+ds-6 libsvm3=3.24+ds-6 libsvmloc-dev=1.0+dfsg-3 libsvmloc0=1.0+dfsg-3 libsystemd0=246.6-2 libtest-deep-perl=1.130-1 libtest-differences-perl=0.67-1 libtest-exception-perl=0.43-1 libtest-most-perl=0.37-1 libtest-warn-perl=0.36-1 libtext-diff-perl=1.45-1 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 libtsan0=10.2.0-16 libubsan1=10.2.0-16 libuchardet0=0.0.7-1 libudev1=246.6-2 libunistring2=0.9.10-4 libuuid1=2.36-3+b2 libxml2=2.9.10+dfsg-6.2 libzstd1=1.4.5+dfsg-4 linux-libc-dev=5.9.1-1 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 mime-support=3.64 ncbi-blast+=2.10.1+ds-1 ncbi-blast+-legacy=2.10.1+ds-1 ncbi-data=6.1.20170106+dfsg1-9 ncurses-base=6.2+20200918-1 ncurses-bin=6.2+20200918-1 patch=2.7.6-6 perl=5.32.0-4 perl-base=5.32.0-4 perl-modules-5.32=5.32.0-4 pftools=3+dfsg-3 pkg-config=0.29.2-1 po-debconf=1.0.21 python3=3.8.6-1 python3-minimal=3.8.6-1 python3.8=3.8.6-1 python3.8-minimal=3.8.6-1 readline-common=8.0-4 sed=4.7-1 sensible-utils=0.0.12+nmu1 sysvinit-utils=2.96-5 tar=1.30+dfsg-7 util-linux=2.36-3+b2 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/20201114T093457Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20201108T155128Z/ 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 psortb=3.0.6+dfsg-2 && mkdir -p /build/psortb-hGdyRV && dpkg-source --no-check -x /*.dsc /build/psortb-hGdyRV/psortb-3.0.6+dfsg && cd /build/psortb-hGdyRV/psortb-3.0.6+dfsg && { printf '%s' 'psortb (3.0.6+dfsg-2+b1) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild against perl 5.32.0 -- all / amd64 / i386 Build Daemon (x86-conova-01) Sun, 08 Nov 2020 20:38:45 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/psortb-hGdyRV" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/psortb-hGdyRV/psortb-3.0.6+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1604867925" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/psortb-hGdyRV /tmp/psortb-3.0.6+dfsg-2+b1y0ei7qmv bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20201108T155128Z 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.J3T1LRgb37 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.J3T1LRgb37 Reading package lists... Building dependency tree... util-linux is already the newest version (2.36-3+b2). 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/20201108T155128Z unstable/main amd64 libfakeroot amd64 1.25.3-1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201108T155128Z unstable/main amd64 fakeroot amd64 1.25.3-1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (1050 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 ... 4664 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1_amd64.deb ... Unpacking fakeroot (1.25.3-1) ... Setting up libfakeroot:amd64 (1.25.3-1) ... Setting up fakeroot (1.25.3-1) ... 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/20201114T093457Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20201108T155128Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.J3T1LRgb37 Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201114T093457Z unstable InRelease [146 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20201108T155128Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20201114T093457Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20201114T093457Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20201114T093457Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20201114T093457Z unstable/main amd64 Packages [11.5 MB] Fetched 34.2 MB in 29s (1171 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.J3T1LRgb37 I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d psortb=3.0.6+dfsg-2 && mkdir -p /build/psortb-hGdyRV && dpkg-source --no-check -x /*.dsc /build/psortb-hGdyRV/psortb-3.0.6+dfsg && cd /build/psortb-hGdyRV/psortb-3.0.6+dfsg && { printf '%s' 'psortb (3.0.6+dfsg-2+b1) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild against perl 5.32.0 -- all / amd64 / i386 Build Daemon (x86-conova-01) Sun, 08 Nov 2020 20:38:45 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/psortb-hGdyRV"' exec /tmp/mmdebstrap.J3T1LRgb37 Reading package lists... NOTICE: 'psortb' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/psortb.git Please use: git clone https://salsa.debian.org/med-team/psortb.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 17.0 MB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main psortb 3.0.6+dfsg-2 (dsc) [2092 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main psortb 3.0.6+dfsg-2 (tar) [17.0 MB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main psortb 3.0.6+dfsg-2 (diff) [6812 B] Fetched 17.0 MB in 13s (1279 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'psortb_3.0.6+dfsg-2.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting psortb in /build/psortb-hGdyRV/psortb-3.0.6+dfsg dpkg-source: info: unpacking psortb_3.0.6+dfsg.orig.tar.xz dpkg-source: info: unpacking psortb_3.0.6+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying biosquid_includes.patch dpkg-source: info: applying fix_hmmer_interface.patch dpkg-source: info: applying fix_build_Algorithm-SVM.patch dpkg-source: info: applying remove-bundled-party-libsvm.patch dpkg-source: info: applying path_to_conf.patch dpkg-source: info: applying fix_module_path.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/psortb-hGdyRV/psortb-3.0.6+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1604867925" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.J3T1LRgb37 dpkg-buildpackage: info: source package psortb dpkg-buildpackage: info: source version 3.0.6+dfsg-2+b1 dpkg-buildpackage: info: source distribution sid dpkg-buildpackage: info: source changed by all / amd64 / i386 Build Daemon (x86-conova-01) dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/psortb-hGdyRV/psortb-3.0.6+dfsg' dh_auto_clean if [ -x psort/bin/psort.debsave ] ; then \ mv psort/bin/psort.debsave psort/bin/psort ; \ fi make[1]: Leaving directory '/build/psortb-hGdyRV/psortb-3.0.6+dfsg' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_configure make[1]: Entering directory '/build/psortb-hGdyRV/psortb-3.0.6+dfsg' cp -a psort/bin/psort psort/bin/psort.debsave dh_auto_configure perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -fdebug-prefix-map=/build/psortb-hGdyRV/psortb-3.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "LD=x86_64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/build/psortb-hGdyRV/psortb-3.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now" External Module XML::RPC, XML Based RPC client, is not installed on this computer. The XML::RPC in PSortb needs it for making calls to remote PSortb servers, if you don't plan to do this, ignore this warning We think we've found blastall, please enter the path if this isn't correct [/usr/bin/] /usr/bin/ We think we've found pfscan, please enter the path if this isn't correct [/usr/bin/] /usr/bin/ Where do you plan to install the psort configuration files? [/usr/local/psortb] /usr/local/psortb Checking if your kit is complete... Looks good hmmer was not found in the dynamic linker path, is there somewhere else we should check? [/usr/local/lib] /usr/local/lib We're still not finding hmmer either in your dynamic linker path (/etc/ld.so.conf) or in /usr/local/lib. Do you want to continue anyways? [Y/n] [Y] Y squid was not found in the dynamic linker path, is there somewhere else we should check? [/usr/local/lib] /usr/local/lib We're still not finding squid either in your dynamic linker path (/etc/ld.so.conf) or in /usr/local/lib. Do you want to continue anyways? [Y/n] [Y] Y Checking if your kit is complete... Looks good Writing MYMETA.yml and MYMETA.json svmloc was not found in the dynamic linker path, is there somewhere else we should check? [/usr/local/lib] /usr/local/lib We're still not finding svmloc either in your dynamic linker path (/etc/ld.so.conf) or in /usr/local/lib. Do you want to continue anyways? [Y/n] [Y] Y Checking if your kit is complete... Looks good Writing MYMETA.yml and MYMETA.json modhmm was not found in the dynamic linker path, is there somewhere else we should check? [/usr/local/lib] /usr/local/lib We're still not finding modhmm either in your dynamic linker path (/etc/ld.so.conf) or in /usr/local/lib. Do you want to continue anyways? [Y/n] [Y] Y Writing MYMETA.yml and MYMETA.json Generating a Unix-style Makefile Writing Makefile for Bio::Tools::PSort Writing MYMETA.yml and MYMETA.json Updating psort/bin/psort with path hints Making sclblast databases Building a new DB, current time: 10/15/2021 15:54:00 New DB name: /build/psortb-hGdyRV/psortb-3.0.6+dfsg/psort/conf/analysis/sclblast/gramneg/sclblast New DB title: sclblast Sequence type: Protein Keep MBits: T Maximum file size: 1000000000B Error: NCBI C++ Exception: T0 "c++/include/corelib/ncbidiag.hpp", line 2143: Error: (CSeqIdException::eFormat) ncbi::objects::CSeq_id::Set() - Malformatted ID 15596049[Extracellular] Program failed, try executing the command manually. Building a new DB, current time: 10/15/2021 15:54:01 New DB name: /build/psortb-hGdyRV/psortb-3.0.6+dfsg/psort/conf/analysis/sclblast/grampos/sclblast New DB title: sclblast Sequence type: Protein Keep MBits: T Maximum file size: 1000000000B BLAST Database creation error: Error: Duplicate seq_ids are found: LCL|145559529 Program failed, try executing the command manually. Building a new DB, current time: 10/15/2021 15:54:02 New DB name: /build/psortb-hGdyRV/psortb-3.0.6+dfsg/psort/conf/analysis/sclblast/archaea/sclblast New DB title: sclblast Sequence type: Protein Keep MBits: T Maximum file size: 1000000000B FASTA-Reader: Ignoring invalid residues at position(s): On line 46049: 38 FASTA-Reader: Ignoring invalid residues at position(s): On line 87237: 23 FASTA-Reader: Title ends with at least 50 valid amino acid characters. Was the sequence accidentally put in the title line? FASTA-Reader: Ignoring invalid residues at position(s): On line 87252: 4 FASTA-Reader: Ignoring invalid residues at position(s): On line 87263: 8 BLAST Database creation error: Error: Duplicate seq_ids are found: LCL|15596641 Program failed, try executing the command manually. Ready for make, next steps you must run: $ make $ make test $ make install RECOMMENDED: cp -r psort /usr/local/psortb PSortb will then be available at /usr/local/psortb/bin/psort or in your path depending on your configuration make[1]: Leaving directory '/build/psortb-hGdyRV/psortb-3.0.6+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/psortb-hGdyRV/psortb-3.0.6+dfsg' # hack around the issue that configure injects wrong root dir /usr/local/psortb mv psort/bin/psort.debsave psort/bin/psort dh_auto_build make -j4 make[2]: Entering directory '/build/psortb-hGdyRV/psortb-3.0.6+dfsg' make[3]: Entering directory '/build/psortb-hGdyRV/psortb-3.0.6+dfsg/algorithm-hmm' Running Mkbootstrap for HMM () "/usr/bin/perl" "/usr/share/perl/5.32.0/ExtUtils/xsubpp" -C++ -typemap '/usr/share/perl/5.32/ExtUtils/typemap' -typemap '/build/psortb-hGdyRV/psortb-3.0.6+dfsg/algorithm-hmm/typemap' HMM.xs > HMM.xsc chmod 644 "HMM.bs" g++ -c -Isrc/include `pkg-config --cflags libsquid` `pkg-config --cflags libhmmer2` -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/psortb-hGdyRV/psortb-3.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"0.02\" -DXS_VERSION=\"0.02\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.32/CORE" hmm-binding.cpp cp lib/Algorithm/HMM/Hit.pm ../blib/lib/Algorithm/HMM/Hit.pm cp lib/Algorithm/HMM/Report.pm ../blib/lib/Algorithm/HMM/Report.pm cp lib/Algorithm/HMM/Hit/Domain.pm ../blib/lib/Algorithm/HMM/Hit/Domain.pm cp lib/Algorithm/HMM.pm ../blib/lib/Algorithm/HMM.pm AutoSplitting ../blib/lib/Algorithm/HMM.pm (../blib/lib/auto/Algorithm/HMM) cp lib/Algorithm/HMM/Hit/Global.pm ../blib/lib/Algorithm/HMM/Hit/Global.pm "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- HMM.bs ../blib/arch/auto/Algorithm/HMM/HMM.bs 644 cp lib/Bio/Tools/Motif.pm blib/lib/Bio/Tools/Motif.pm cp lib/Bio/Tools/PSort/Report.pm blib/lib/Bio/Tools/PSort/Report.pm cp lib/Bio/Tools/PSort/ModuleI.pm blib/lib/Bio/Tools/PSort/ModuleI.pm cp lib/Bio/Tools/PSort/Profile.pm blib/lib/Bio/Tools/PSort/Profile.pm cp lib/Bio/Tools/PSort/Module/Rules.pm blib/lib/Bio/Tools/PSort/Module/Rules.pm cp lib/Bio/Tools/PSort/Report/Formatter/html.pm blib/lib/Bio/Tools/PSort/Report/Formatter/html.pm cp lib/Bio/Tools/PSort/Profile/Match.pm blib/lib/Bio/Tools/PSort/Profile/Match.pm cp lib/Bio/Tools/PSort.pm blib/lib/Bio/Tools/PSort.pm cp lib/Bio/Tools/PSort/Module/Motif.pm blib/lib/Bio/Tools/PSort/Module/Motif.pm cp lib/Bio/Tools/Motif/Match.pm blib/lib/Bio/Tools/Motif/Match.pm cp lib/Bio/Tools/PSort/Module/SVMLoc.pm blib/lib/Bio/Tools/PSort/Module/SVMLoc.pm cp lib/Bio/Tools/PSort/Install.pm blib/lib/Bio/Tools/PSort/Install.pm cp lib/Bio/Tools/PSort/Module/SCLBlast.pm blib/lib/Bio/Tools/PSort/Module/SCLBlast.pm cp lib/Bio/Tools/PSort/Module/Null.pm blib/lib/Bio/Tools/PSort/Module/Null.pm cp lib/Bio/Tools/Motif/Pattern.pm blib/lib/Bio/Tools/Motif/Pattern.pm cp lib/Bio/Tools/PSort/Report/Formatter/terse.pm blib/lib/Bio/Tools/PSort/Report/Formatter/terse.pm cp lib/Bio/Tools/PSort/Report/Formatter/normal.pm blib/lib/Bio/Tools/PSort/Report/Formatter/normal.pm cp lib/Bio/Tools/PSort/Module/Bayesian.pm blib/lib/Bio/Tools/PSort/Module/Bayesian.pm cp lib/Bio/Tools/PSort/Report/Formatter.pm blib/lib/Bio/Tools/PSort/Report/Formatter.pm cp lib/Bio/Tools/PSort/Module/SVMLocApache.pm blib/lib/Bio/Tools/PSort/Module/SVMLocApache.pm cp lib/Bio/Tools/PSort/Report/Result.pm blib/lib/Bio/Tools/PSort/Report/Result.pm cp lib/Bio/Tools/PSort/Module/OMPMotif.pm blib/lib/Bio/Tools/PSort/Module/OMPMotif.pm cp lib/Bio/Tools/PSort/Module/ModHMM.pm blib/lib/Bio/Tools/PSort/Module/ModHMM.pm cp lib/Bio/Tools/PSort/Module/Signal.pm blib/lib/Bio/Tools/PSort/Module/Signal.pm cp lib/Bio/Tools/PSort/Module/Profile.pm blib/lib/Bio/Tools/PSort/Module/Profile.pm cp lib/Bio/Tools/PSort/Pathway.pm blib/lib/Bio/Tools/PSort/Pathway.pm cp lib/Bio/Tools/PSort/Module/HMMTOP.pm blib/lib/Bio/Tools/PSort/Module/HMMTOP.pm cp lib/Bio/Tools/PSort/Module/OutputI.pm blib/lib/Bio/Tools/PSort/Module/OutputI.pm cp lib/Bio/Tools/PSort/Module/InputI.pm blib/lib/Bio/Tools/PSort/Module/InputI.pm cp lib/Bio/Tools/PSort/Constants.pm blib/lib/Bio/Tools/PSort/Constants.pm cp lib/Bio/Tools/PSort/Module/AnalysisI.pm blib/lib/Bio/Tools/PSort/Module/AnalysisI.pm cp lib/Bio/Tools/PSort/Report/Formatter/long.pm blib/lib/Bio/Tools/PSort/Report/Formatter/long.pm cp lib/Bio/Tools/Run/SCLBlastLocal.pm blib/lib/Bio/Tools/Run/SCLBlastLocal.pm cp lib/Bio/Tools/Run/SCLBlast.pm blib/lib/Bio/Tools/Run/SCLBlast.pm cp lib/Bio/Tools/Signal/Report.pm blib/lib/Bio/Tools/Signal/Report.pm cp lib/Bio/Tools/Run/SCLBlast/Hit.pm blib/lib/Bio/Tools/Run/SCLBlast/Hit.pm cp lib/Bio/Tools/Run/HMMTOP/Helix.pm blib/lib/Bio/Tools/Run/HMMTOP/Helix.pm cp lib/Bio/Tools/Run/SCLBlast/Report.pm blib/lib/Bio/Tools/Run/SCLBlast/Report.pm cp lib/Bio/Tools/Run/HMMTOP.pm blib/lib/Bio/Tools/Run/HMMTOP.pm cp lib/Bio/Tools/Run/HMMTOP/Report.pm blib/lib/Bio/Tools/Run/HMMTOP/Report.pm cp lib/Bio/Tools/SVMLoc.pm blib/lib/Bio/Tools/SVMLoc.pm cp lib/Bio/Tools/Signal.pm blib/lib/Bio/Tools/Signal.pm cp lib/Bio/Tools/PSort/XMLRPC/Client.pm blib/lib/Bio/Tools/PSort/XMLRPC/Client.pm Please specify prototyping behavior for HMM.xs (see perlxs manual) mv HMM.xsc HMM.c g++ -c -Isrc/include `pkg-config --cflags libsquid` `pkg-config --cflags libhmmer2` -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/psortb-hGdyRV/psortb-3.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"0.02\" -DXS_VERSION=\"0.02\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.32/CORE" HMM.c hmm-binding.cpp: In member function ‘HMMReport* HMM::search(char*)’: hmm-binding.cpp:136:71: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 136 | PostprocessSignificantHit(ghit, dhit, trace, model, dseq, seqlen, "SEQ", | ^~~~~ rm -f ../blib/arch/auto/Algorithm/HMM/HMM.so x86_64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/build/psortb-hGdyRV/psortb-3.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -shared -L/usr/local/lib -fstack-protector-strong HMM.o hmm-binding.o -o ../blib/arch/auto/Algorithm/HMM/HMM.so \ -lm -lpthread -lstdc++ -L/usr/local/lib -lhmmer -lsquid \ chmod 755 ../blib/arch/auto/Algorithm/HMM/HMM.so Manifying 5 pod documents make[3]: Leaving directory '/build/psortb-hGdyRV/psortb-3.0.6+dfsg/algorithm-hmm' make[3]: Entering directory '/build/psortb-hGdyRV/psortb-3.0.6+dfsg/bio-tools-psort-svmloc' Running Mkbootstrap for SVMLoc () "/usr/bin/perl" "/usr/share/perl/5.32.0/ExtUtils/xsubpp" -C++ -typemap '/usr/share/perl/5.32/ExtUtils/typemap' -typemap '/build/psortb-hGdyRV/psortb-3.0.6+dfsg/bio-tools-psort-svmloc/typemap' SVMLoc.xs > SVMLoc.xsc cp lib/Bio/Tools/PSort/SVMLoc/DataSet.pm ../blib/lib/Bio/Tools/PSort/SVMLoc/DataSet.pm cp lib/Bio/Tools/PSort/SVMLoc.pm ../blib/lib/Bio/Tools/PSort/SVMLoc.pm AutoSplitting ../blib/lib/Bio/Tools/PSort/SVMLoc.pm (../blib/lib/auto/Bio/Tools/PSort/SVMLoc) chmod 644 "SVMLoc.bs" "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- SVMLoc.bs ../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.bs 644 Please specify prototyping behavior for SVMLoc.xs (see perlxs manual) mv SVMLoc.xsc SVMLoc.c g++ -c -Wall -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/psortb-hGdyRV/psortb-3.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.32/CORE" SVMLoc.c rm -f ../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.so x86_64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/build/psortb-hGdyRV/psortb-3.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -shared -L/usr/local/lib -fstack-protector-strong SVMLoc.o -o ../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.so \ -L/usr/local/lib -lsvmloc -lm -lsvm -lstdc++ \ chmod 755 ../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.so Manifying 2 pod documents make[3]: Leaving directory '/build/psortb-hGdyRV/psortb-3.0.6+dfsg/bio-tools-psort-svmloc' make[3]: Entering directory '/build/psortb-hGdyRV/psortb-3.0.6+dfsg/bio-tools-psort-modhmm' Running Mkbootstrap for ModHMM () chmod 644 "ModHMM.bs" "/usr/bin/perl" "/usr/share/perl/5.32.0/ExtUtils/xsubpp" -typemap '/usr/share/perl/5.32/ExtUtils/typemap' -typemap '/build/psortb-hGdyRV/psortb-3.0.6+dfsg/bio-tools-psort-modhmm/typemap' modhmm.xs > modhmm.xsc cc -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/psortb-hGdyRV/psortb-3.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.32/CORE" binding.c "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- ModHMM.bs ../blib/arch/auto/Bio/Tools/PSort/ModHMM/ModHMM.bs 644 cp lib/Bio/Tools/PSort/ModHMM.pm ../blib/lib/Bio/Tools/PSort/ModHMM.pm AutoSplitting ../blib/lib/Bio/Tools/PSort/ModHMM.pm (../blib/lib/auto/Bio/Tools/PSort/ModHMM) binding.c: In function ‘helix_DESTROY’: binding.c:52:6: warning: implicit declaration of function ‘free’ [-Wimplicit-function-declaration] 52 | free(hSites->helix); | ^~~~ binding.c:52:6: warning: incompatible implicit declaration of built-in function ‘free’ binding.c:4:1: note: include ‘’ or provide a declaration of ‘free’ 3 | #include "modhmm0.92b/structs.h" +++ |+#include 4 | binding.c:55:2: warning: incompatible implicit declaration of built-in function ‘free’ 55 | free(hSites); | ^~~~ binding.c:55:2: note: include ‘’ or provide a declaration of ‘free’ mv modhmm.xsc modhmm.c cc -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/psortb-hGdyRV/psortb-3.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.32/CORE" modhmm.c modhmm.c: In function ‘XS_Bio__Tools__PSort__ModHMM_find_helices’: modhmm.c:179:11: warning: implicit declaration of function ‘find_helices’; did you mean ‘get_helices’? [-Wimplicit-function-declaration] 179 | RETVAL = find_helices(seq, hmmfile, repfile, path); | ^~~~~~~~~~~~ | get_helices rm -f ../blib/arch/auto/Bio/Tools/PSort/ModHMM/ModHMM.so x86_64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/build/psortb-hGdyRV/psortb-3.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -shared -L/usr/local/lib -fstack-protector-strong modhmm.o binding.o -o ../blib/arch/auto/Bio/Tools/PSort/ModHMM/ModHMM.so \ -lm -lstdc++ -L/usr/local/lib -lmodhmm \ chmod 755 ../blib/arch/auto/Bio/Tools/PSort/ModHMM/ModHMM.so Manifying 1 pod document make[3]: Leaving directory '/build/psortb-hGdyRV/psortb-3.0.6+dfsg/bio-tools-psort-modhmm' Manifying 18 pod documents make[2]: Leaving directory '/build/psortb-hGdyRV/psortb-3.0.6+dfsg' make[1]: Leaving directory '/build/psortb-hGdyRV/psortb-3.0.6+dfsg' dh_auto_test -a make -j4 test TEST_VERBOSE=1 make[1]: Entering directory '/build/psortb-hGdyRV/psortb-3.0.6+dfsg' make[2]: Entering directory '/build/psortb-hGdyRV/psortb-3.0.6+dfsg/algorithm-hmm' "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- HMM.bs ../blib/arch/auto/Algorithm/HMM/HMM.bs 644 Manifying 5 pod documents make[2]: Leaving directory '/build/psortb-hGdyRV/psortb-3.0.6+dfsg/algorithm-hmm' make[2]: Entering directory '/build/psortb-hGdyRV/psortb-3.0.6+dfsg/bio-tools-psort-svmloc' "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- SVMLoc.bs ../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.bs 644 Manifying 2 pod documents make[2]: Leaving directory '/build/psortb-hGdyRV/psortb-3.0.6+dfsg/bio-tools-psort-svmloc' make[2]: Entering directory '/build/psortb-hGdyRV/psortb-3.0.6+dfsg/bio-tools-psort-modhmm' "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- ModHMM.bs ../blib/arch/auto/Bio/Tools/PSort/ModHMM/ModHMM.bs 644 Manifying 1 pod document make[2]: Leaving directory '/build/psortb-hGdyRV/psortb-3.0.6+dfsg/bio-tools-psort-modhmm' make[2]: Entering directory '/build/psortb-hGdyRV/psortb-3.0.6+dfsg/algorithm-hmm' "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- HMM.bs ../blib/arch/auto/Algorithm/HMM/HMM.bs 644 PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, '../blib/lib', '../blib/arch')" t/*.t t/hmm.t .. 1..5 ok 1 - use Algorithm::HMM; ok 2 Creating new Algorithm::HMM ok 3 - Ensuring we could load a model Saving model... ok 4 - Testing saving a model Loading saved model... ok 5 - Testing reloading a model ok All tests successful. Files=1, Tests=5, 1 wallclock secs ( 0.03 usr 0.01 sys + 0.17 cusr 0.02 csys = 0.23 CPU) Result: PASS make[2]: Leaving directory '/build/psortb-hGdyRV/psortb-3.0.6+dfsg/algorithm-hmm' make[2]: Entering directory '/build/psortb-hGdyRV/psortb-3.0.6+dfsg/bio-tools-psort-svmloc' "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- SVMLoc.bs ../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.bs 644 PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, '../blib/lib', '../blib/arch')" t/*.t t/svmloc.t .. 1..15 ok 1 - use Bio::Tools::PSort::SVMLoc; ok 2 - use Bio::Tools::PSort::SVMLoc::DataSet; ok 3 - Loaded SVMLoc Creating new Bio::Tools::PSort::SVMLoc ok 4 - Creating SVMLoc object Checking predictions on loaded model ok 5 - Classify seq 1 ok 6 - Classify seq 2 ok 7 - Classify seq 3 Creating second Bio::Tools::PSort::SVMLoc ok 8 - Creating SVMLoc object 2 Creating new Bio::Tools::PSort::SVMLoc::DataSet objects ok 9 - Dataset 1 created ok 10 - Dataset 2 created ok 11 - Dataset 3 created Adding attributes to Bio::Tools::PSort::SVMLoc::DataSet objects ok 12 Checking predictions on second loaded model ok 13 - Classify seq 1 on model 2 ok 14 - Classify seq 2 on model 2 ok 15 - Classify seq 3 on model 2 Everything looks ok! ok All tests successful. Files=1, Tests=15, 1 wallclock secs ( 0.04 usr 0.00 sys + 0.30 cusr 0.05 csys = 0.39 CPU) Result: PASS make[2]: Leaving directory '/build/psortb-hGdyRV/psortb-3.0.6+dfsg/bio-tools-psort-svmloc' make[2]: Entering directory '/build/psortb-hGdyRV/psortb-3.0.6+dfsg/bio-tools-psort-modhmm' "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- ModHMM.bs ../blib/arch/auto/Bio/Tools/PSort/ModHMM/ModHMM.bs 644 PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, '../blib/lib', '../blib/arch')" t/*.t t/modhmm.t .. 1..4 ok 1 - use Bio::Tools::PSort::ModHMM; ok 2 - Loading ModHMM Running sequence through Bio::Tools::PSort::ModHMM ok 3 - Running sequence through ModHMM Retreiving TM helix sites ok 4 - Retreiving TM helix sites ok All tests successful. Files=1, Tests=4, 0 wallclock secs ( 0.04 usr 0.00 sys + 0.33 cusr 0.03 csys = 0.40 CPU) Result: PASS make[2]: Leaving directory '/build/psortb-hGdyRV/psortb-3.0.6+dfsg/bio-tools-psort-modhmm' PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, 'blib/lib', 'blib/arch')" t/*.t t/psort.t .. 1..2 ok 1 - PSort module loaded Creating new Bio::Tools::PSort ok 2 - PSort object made ok All tests successful. Files=1, Tests=2, 1 wallclock secs ( 0.04 usr 0.02 sys + 0.23 cusr 0.01 csys = 0.30 CPU) Result: PASS make[1]: Leaving directory '/build/psortb-hGdyRV/psortb-3.0.6+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -a dh_prep -a dh_auto_install -a make -j4 install DESTDIR=/build/psortb-hGdyRV/psortb-3.0.6\+dfsg/debian/psortb AM_UPDATE_INFO_DIR=no PREFIX=/usr make[1]: Entering directory '/build/psortb-hGdyRV/psortb-3.0.6+dfsg' make[2]: Entering directory '/build/psortb-hGdyRV/psortb-3.0.6+dfsg/algorithm-hmm' "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- HMM.bs ../blib/arch/auto/Algorithm/HMM/HMM.bs 644 Manifying 5 pod documents make[2]: Leaving directory '/build/psortb-hGdyRV/psortb-3.0.6+dfsg/algorithm-hmm' make[2]: Entering directory '/build/psortb-hGdyRV/psortb-3.0.6+dfsg/bio-tools-psort-svmloc' "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- SVMLoc.bs ../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.bs 644 Manifying 2 pod documents make[2]: Leaving directory '/build/psortb-hGdyRV/psortb-3.0.6+dfsg/bio-tools-psort-svmloc' make[2]: Entering directory '/build/psortb-hGdyRV/psortb-3.0.6+dfsg/bio-tools-psort-modhmm' "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- ModHMM.bs ../blib/arch/auto/Bio/Tools/PSort/ModHMM/ModHMM.bs 644 Manifying 1 pod document make[2]: Leaving directory '/build/psortb-hGdyRV/psortb-3.0.6+dfsg/bio-tools-psort-modhmm' Manifying 18 pod documents Files found in blib/arch: installing files in blib/lib into architecture dependent library tree Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/auto/Algorithm/HMM/HMM.so Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/auto/Bio/Tools/PSort/ModHMM/ModHMM.so Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.so Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Algorithm/HMM.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Algorithm/HMM/Report.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Algorithm/HMM/Hit.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Algorithm/HMM/Hit/Global.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Algorithm/HMM/Hit/Domain.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/Motif.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/SVMLoc.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/Signal.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/Run/SCLBlast.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/Run/HMMTOP.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/Run/SCLBlastLocal.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/Run/HMMTOP/Helix.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/Run/HMMTOP/Report.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/Run/SCLBlast/Report.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/Run/SCLBlast/Hit.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Profile.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Pathway.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/ModHMM.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Report.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Install.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/SVMLoc.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/ModuleI.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Constants.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Profile/Match.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Module/Motif.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Module/Profile.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Module/AnalysisI.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Module/ModHMM.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Module/SCLBlast.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Module/OutputI.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Module/OMPMotif.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Module/HMMTOP.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Module/SVMLocApache.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Module/Null.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Module/InputI.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Module/Bayesian.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Module/SVMLoc.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Module/Signal.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Module/Rules.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/XMLRPC/Client.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Report/Formatter.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Report/Result.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Report/Formatter/long.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Report/Formatter/normal.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Report/Formatter/terse.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/Report/Formatter/html.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/PSort/SVMLoc/DataSet.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/Signal/Report.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/Motif/Match.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/Bio/Tools/Motif/Pattern.pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/auto/Algorithm/HMM/autosplit.ix Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/auto/Bio/Tools/PSort/ModHMM/autosplit.ix Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/lib/x86_64-linux-gnu/perl5/5.32/auto/Bio/Tools/PSort/SVMLoc/autosplit.ix Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort.3pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::Motif::Match.3pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::ModHMM.3pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Algorithm::HMM::Hit::Domain.3pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::Motif::Pattern.3pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::SVMLoc.3pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::Signal.3pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Module::InputI.3pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Module::OMPMotif.3pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::Motif.3pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::SVMLoc.3pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::SVMLoc::DataSet.3pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Module::Null.3pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::ModuleI.3pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Profile::Match.3pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Module::OutputI.3pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Algorithm::HMM.3pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Algorithm::HMM::Hit::Global.3pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Pathway.3pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Algorithm::HMM::Report.3pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Profile.3pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Module::AnalysisI.3pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Module::Motif.3pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::Run::HMMTOP.3pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Bio::Tools::PSort::Module::Profile.3pm Installing /build/psortb-hGdyRV/psortb-3.0.6+dfsg/debian/psortb/usr/share/man/man3/Algorithm::HMM::Hit.3pm make[1]: Leaving directory '/build/psortb-hGdyRV/psortb-3.0.6+dfsg' dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_lintian -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a debian/rules override_dh_fixperms make[1]: Entering directory '/build/psortb-hGdyRV/psortb-3.0.6+dfsg' dh_fixperms chmod +x debian/psortb/usr/lib/psort/conf/analysis/signal/archaea/check-sig make[1]: Leaving directory '/build/psortb-hGdyRV/psortb-3.0.6+dfsg' dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'psortb' in '../psortb_3.0.6+dfsg-2+b1_amd64.deb'. dpkg-deb: building package 'psortb-dbgsym' in '../psortb-dbgsym_3.0.6+dfsg-2+b1_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../psortb_3.0.6+dfsg-2+b1_amd64.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) I: running special hook: sync-out /build/psortb-hGdyRV /tmp/psortb-3.0.6+dfsg-2+b1y0ei7qmv I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.J3T1LRgb37... I: success in 881.4337 seconds md5: psortb-dbgsym_3.0.6+dfsg-2+b1_amd64.deb: OK md5: psortb_3.0.6+dfsg-2+b1_amd64.deb: OK sha1: psortb-dbgsym_3.0.6+dfsg-2+b1_amd64.deb: OK sha1: psortb_3.0.6+dfsg-2+b1_amd64.deb: OK sha256: psortb-dbgsym_3.0.6+dfsg-2+b1_amd64.deb: OK sha256: psortb_3.0.6+dfsg-2+b1_amd64.deb: OK Checksums: OK