Thu Jun 1 16:59:34 UTC 2023 I: starting to build libpsortb/bookworm/amd64 on jenkins on '2023-06-01 16:59' Thu Jun 1 16:59:34 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_30/43/console.log Thu Jun 1 16:59:34 UTC 2023 I: Downloading source for bookworm/libpsortb=1.0+dfsg-5 --2023-06-01 16:59:34-- http://cdn-fastly.deb.debian.org/debian/pool/main/libp/libpsortb/libpsortb_1.0%2bdfsg-5.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2188 (2.1K) [text/prs.lines.tag] Saving to: ‘libpsortb_1.0+dfsg-5.dsc’ 0K .. 100% 132M=0s 2023-06-01 16:59:35 (132 MB/s) - ‘libpsortb_1.0+dfsg-5.dsc’ saved [2188/2188] Thu Jun 1 16:59:35 UTC 2023 I: libpsortb_1.0+dfsg-5.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: libpsortb Binary: libmodhmm0, libmodhmm-dev, libsvmloc0, libsvmloc-dev Architecture: any Version: 1.0+dfsg-5 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://www.psort.org/ Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/libpsortb Vcs-Git: https://salsa.debian.org/med-team/libpsortb.git Build-Depends: debhelper-compat (= 13), d-shlibs, libsvm-dev, libsquid-dev, libhmmer2-dev, pkg-config Package-List: libmodhmm-dev deb libdevel optional arch=any libmodhmm0 deb libs optional arch=any libsvmloc-dev deb libdevel optional arch=any libsvmloc0 deb libs optional arch=any Checksums-Sha1: 44d3705f46372837f5ecdf8fa2ad0273a6c38433 95644 libpsortb_1.0+dfsg.orig.tar.xz d777631eae370d0fae13a144ccb43adcf930e084 5168 libpsortb_1.0+dfsg-5.debian.tar.xz Checksums-Sha256: 5021b7ac656b33b8f0aa8c2e0403056a5459e1b92c17008b3ff442e262b3e2e5 95644 libpsortb_1.0+dfsg.orig.tar.xz d5221c764235817684492860128aa38c00dc8a93cd1fc47f28d4aac810362eb8 5168 libpsortb_1.0+dfsg-5.debian.tar.xz Files: f9c6cf32032da4c9e88b609fba9bb02d 95644 libpsortb_1.0+dfsg.orig.tar.xz 7a12d41f22a900cda8c0b3d08c67b451 5168 libpsortb_1.0+dfsg-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmGVMwERHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtH2LA//QBDTa+8k0cFXjUIMMZoekJYD4YxO971D 91FqLlxJMygywSmX504IYNWoqSRNZhMXo6lTG/m+/Hoy4RYU/Ndmhxw0I8XN0RKY wo5+DMg/pQTOCbOt1vF6FrpdOg4mrl/VLrPdEAygNI8EchMltRlqnvvOv1OMSd0h 4A0J/9+HJ1mFTrbRqBPmtw1QJV+5c9ZH3FRdvqbX4iz8fbEOVWDQZ4cyibzFe9Am /+LpL8yoLQ/3Zjt30Yulr3vEJFRMhuYRvl7My3i77aBUZAckdRoGj34u8eGUudvQ JgcFCEKI/jKdL7SlqiAQ5eB947h0e/dWy2G6dkK8/HmHD8Zu338a4YXjlt2azsBQ YO2ON1ferH9GB6tf78tN4Te9CTbM48wHsn2JOO/mPmCHdX35+MDOjIYDSf5srnI8 X4PeQrswK+xiPxk5AltZH/pHPrwVOlb8/5zd7NhUweeG9O5u86l63PXGC8gwPx77 zbsgM3xiHsAS9ZV+ow730Rn10dzohRqLIyhZbJDQuP2rjEjClAY0qS5NNBC9EuT6 LRm18IWLUdmK3/K3tW/8R07N/M4PHKet4Y7pxI0NPO7yYLAFRvzAazH+YihW+85g HNGpgIGrY5O499qLc0AvPXX+xZxjthAmJq6Tc8KCLFSOnwmdyL3xmxeufXy9nLC9 kKZxofbMbMU= =wNmv -----END PGP SIGNATURE----- Thu Jun 1 16:59:35 UTC 2023 I: Checking whether the package is not for us Thu Jun 1 16:59:35 UTC 2023 I: Starting 1st build on remote node ionos5-amd64.debian.net. Thu Jun 1 16:59:35 UTC 2023 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Thu Jun 1 17:02:53 UTC 2023 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Jul 3 11:22:38 -12 2024 I: pbuilder-time-stamp: 1720048958 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] tar: ./usr/share/perl5/Debian: time stamp 2025-08-04 08:27:02 is 34290261.342289657 s in the future tar: ./usr/share/man/pt/man8: time stamp 2025-08-04 08:27:02 is 34290261.287079393 s in the future tar: ./usr/share/man/pt/man5: time stamp 2025-08-04 08:27:02 is 34290261.283838274 s in the future tar: ./usr/share/man/nl/man8: time stamp 2025-08-04 08:27:02 is 34290261.276521906 s in the future tar: ./usr/share/man/nl/man5: time stamp 2025-08-04 08:27:02 is 34290261.273789454 s in the future tar: ./usr/share/man/man5: time stamp 2025-08-04 08:27:02 is 34290261.252984434 s in the future tar: ./usr/share/man/fr/man5: time stamp 2025-08-04 08:27:02 is 34290261.206881487 s in the future tar: ./usr/share/man/de/man5: time stamp 2025-08-04 08:27:02 is 34290261.192448829 s in the future tar: ./usr/share/locale/zh_CN/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290261.031700233 s in the future tar: ./usr/share/locale/vi/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290261.007810068 s in the future tar: ./usr/share/locale/uk/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.964330296 s in the future tar: ./usr/share/locale/sv/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.901921419 s in the future tar: ./usr/share/locale/sk/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.882917971 s in the future tar: ./usr/share/locale/ru/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.843335671 s in the future tar: ./usr/share/locale/pt_BR/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.806186745 s in the future tar: ./usr/share/locale/pt/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.779111183 s in the future tar: ./usr/share/locale/pl/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.75978349 s in the future tar: ./usr/share/locale/nl/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.735792111 s in the future tar: ./usr/share/locale/nb/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.718471555 s in the future tar: ./usr/share/locale/ko/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.694981265 s in the future tar: ./usr/share/locale/ja/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.666797288 s in the future tar: ./usr/share/locale/it/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.648928249 s in the future tar: ./usr/share/locale/hu/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.63550086 s in the future tar: ./usr/share/locale/gl/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.62545288 s in the future tar: ./usr/share/locale/fr/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.585088237 s in the future tar: ./usr/share/locale/eu/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.557314594 s in the future tar: ./usr/share/locale/es/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.522728551 s in the future tar: ./usr/share/locale/de/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.484587134 s in the future tar: ./usr/share/locale/da/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.462500148 s in the future tar: ./usr/share/locale/cs/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.441907561 s in the future tar: ./usr/share/locale/ca/LC_MESSAGES: time stamp 2025-08-04 08:27:02 is 34290260.420254419 s in the future tar: ./usr/share/doc/adduser/examples/adduser.local.conf.examples/skel.other: time stamp 2025-08-04 08:27:02 is 34290260.353497322 s in the future tar: ./usr/share/doc/adduser/examples/adduser.local.conf.examples/skel: time stamp 2025-08-04 08:27:02 is 34290260.353340604 s in the future tar: ./usr/share/doc/adduser/examples/adduser.local.conf.examples: time stamp 2025-08-04 08:27:02 is 34290260.353252654 s in the future tar: ./usr/share/doc/adduser/examples: time stamp 2025-08-04 08:27:02 is 34290260.351953867 s in the future tar: ./usr/share/doc/adduser: time stamp 2025-08-04 08:27:02 is 34290260.351701503 s in the future tar: ./var/lib/dpkg/info/adduser.list: time stamp 2025-08-04 08:27:02 is 34290251.646259301 s in the future tar: ./usr/share/man/de/man8: time stamp 2025-08-04 08:27:02 is 34290250.447438296 s in the future tar: ./usr/share/man/fr/man8: time stamp 2025-08-04 08:27:02 is 34290250.447251081 s in the future tar: ./usr/share/man/man8: time stamp 2025-08-04 08:27:02 is 34290250.447005675 s in the future tar: ./usr/sbin: time stamp 2025-08-04 08:27:02 is 34290250.437182669 s in the future I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [libpsortb_1.0+dfsg-5.dsc] I: copying [./libpsortb_1.0+dfsg.orig.tar.xz] I: copying [./libpsortb_1.0+dfsg-5.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Nov 17 04:51:13 2021 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./libpsortb_1.0+dfsg-5.dsc: no acceptable signature found dpkg-source: info: extracting libpsortb in libpsortb-1.0+dfsg dpkg-source: info: unpacking libpsortb_1.0+dfsg.orig.tar.xz dpkg-source: info: unpacking libpsortb_1.0+dfsg-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_libs.patch dpkg-source: info: applying use_debian_packaged_libsvm.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3633491/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='f61efbac669546348e2e9ee928f50f47' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='3633491' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.AuAiLGY3/pbuilderrc_8sti --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.AuAiLGY3/b1 --logfile b1/build.log libpsortb_1.0+dfsg-5.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos5-amd64 6.1.0-0.deb11.7-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.20-2~bpo11+1 (2023-04-23) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 23 2023 bash -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp -rwxr-xr-x 1 root root 125640 Jan 5 2023 dash -rwxr-xr-x 1 root root 121904 Sep 20 2022 date -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd -rwxr-xr-x 1 root root 102200 Sep 20 2022 df -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir -rwxr-xr-x 1 root root 88656 Mar 22 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 85600 Mar 22 2023 findmnt -rwsr-xr-x 1 root root 35128 Mar 22 2023 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 2023 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 22 2023 lsblk -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 22 2023 more -rwsr-xr-x 1 root root 59704 Mar 22 2023 mount -rwxr-xr-x 1 root root 18744 Mar 22 2023 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 22 2023 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar -rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 22 2023 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 22 2023 umount -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 22 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/3633491/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), d-shlibs, libsvm-dev, libsquid-dev, libhmmer2-dev, pkg-config dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19591 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs; however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on libsvm-dev; however: Package libsvm-dev is not installed. pbuilder-satisfydepends-dummy depends on libsquid-dev; however: Package libsquid-dev is not installed. pbuilder-satisfydepends-dummy depends on libhmmer2-dev; however: Package libhmmer2-dev is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} d-shlibs{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libhmmer2-dev{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libpkgconf3{a} libsquid-dev{a} libsquid1{a} libsub-override-perl{a} libsvm-dev{a} libsvm3{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 40 newly installed, 0 to remove and 0 not upgraded. Need to get 19.3 MB of archives. After unpacking 74.2 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 d-shlibs all 0.104 [18.6 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 22 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 24 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 libhmmer2-dev amd64 2.3.2+dfsg-8 [97.5 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 libpkgconf3 amd64 1.8.1-1 [36.1 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 libsquid1 amd64 1.9g+cvs20050121-12 [76.6 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 libsquid-dev amd64 1.9g+cvs20050121-12 [145 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libsvm3 amd64 3.24+ds-6 [43.6 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libsvm-dev amd64 3.24+ds-6 [64.2 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 pkgconf-bin amd64 1.8.1-1 [29.5 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 pkgconf amd64 1.8.1-1 [25.9 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 pkg-config amd64 1.8.1-1 [13.7 kB] Fetched 19.3 MB in 1s (31.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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 ... 19591 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../02-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.22.4-10_amd64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_amd64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.11.2-2_amd64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-3_amd64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package d-shlibs. Preparing to unpack .../15-d-shlibs_0.104_all.deb ... Unpacking d-shlibs (0.104) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../20-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../23-libelf1_0.188-2.1_amd64.deb ... Unpacking libelf1:amd64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.15-1_amd64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../25-libicu72_72.1-3_amd64.deb ... Unpacking libicu72:amd64 (72.1-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../26-libxml2_2.9.14+dfsg-1.2_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.2) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.21-12_amd64.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../28-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../29-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../30-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package libhmmer2-dev:amd64. Preparing to unpack .../31-libhmmer2-dev_2.3.2+dfsg-8_amd64.deb ... Unpacking libhmmer2-dev:amd64 (2.3.2+dfsg-8) ... Selecting previously unselected package libpkgconf3:amd64. Preparing to unpack .../32-libpkgconf3_1.8.1-1_amd64.deb ... Unpacking libpkgconf3:amd64 (1.8.1-1) ... Selecting previously unselected package libsquid1. Preparing to unpack .../33-libsquid1_1.9g+cvs20050121-12_amd64.deb ... Unpacking libsquid1 (1.9g+cvs20050121-12) ... 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Setting up libicu72:amd64 (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libmagic1:amd64 (1:5.44-3) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up autotools-dev (20220109.1) ... Setting up libpkgconf3:amd64 (1.8.1-1) ... Setting up autopoint (0.21-12) ... Setting up d-shlibs (0.104) ... Setting up pkgconf-bin (1.8.1-1) ... Setting up autoconf (2.71-3) ... Setting up libsquid1 (1.9g+cvs20050121-12) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libhmmer2-dev:amd64 (2.3.2+dfsg-8) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.2) ... Setting up libsvm3:amd64 (3.24+ds-6) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-12) ... Setting up libtool (2.4.7-5) ... Setting up libsquid-dev (1.9g+cvs20050121-12) ... Setting up pkgconf:amd64 (1.8.1-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libsvm-dev:amd64 (3.24+ds-6) ... Setting up pkg-config:amd64 (1.8.1-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.11.4) ... Processing triggers for libc-bin (2.36-9) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/libpsortb-1.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../libpsortb_1.0+dfsg-5_source.changes dpkg-buildpackage: info: source package libpsortb dpkg-buildpackage: info: source version 1.0+dfsg-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: Consider adding 'AC_CONFIG_MACRO_DIRS([m4])' to configure.ac, libtoolize: and rerunning libtoolize and aclocal. libtoolize: Consider adding '-I m4' to ACLOCAL_AMFLAGS in Makefile.am. configure.ac:7: warning: The macro `AC_CONFIG_HEADER' is obsolete. configure.ac:7: You should run autoupdate. ./lib/autoconf/status.m4:719: AC_CONFIG_HEADER is expanded from... configure.ac:7: the top level configure.ac:17: warning: The macro `AC_PROG_LIBTOOL' is obsolete. configure.ac:17: You should run autoupdate. aclocal.m4:122: AC_PROG_LIBTOOL is expanded from... configure.ac:17: the top level configure.ac:47: warning: The macro `AC_HEADER_STDC' is obsolete. configure.ac:47: You should run autoupdate. ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... configure.ac:47: the top level configure.ac:55: warning: The macro `AC_HEADER_TIME' is obsolete. configure.ac:55: You should run autoupdate. ./lib/autoconf/headers.m4:743: AC_HEADER_TIME is expanded from... configure.ac:55: the top level configure.ac:12: installing './compile' configure.ac:17: installing './config.guess' configure.ac:17: installing './config.sub' configure.ac:8: installing './install-sh' configure.ac:8: installing './missing' modhmm0.92b/Makefile.am: installing './depcomp' dh_auto_configure ./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 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free 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 for g++... g++ 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 the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking for gcc... gcc checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... 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 whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E 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 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 file... file 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 stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/time.h... yes 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 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 for main in -lm... yes checking for egrep... (cached) /bin/grep -E checking for float.h... yes checking for limits.h... yes checking for memory.h... yes checking for netinet/in.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for _Bool... yes checking for stdbool.h that conforms to C99... yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... yes checking whether struct tm is in sys/time.h or time.h... time.h checking for _LARGEFILE_SOURCE value needed for large files... no checking for GNU libc compatible malloc... yes checking for GNU libc compatible realloc... yes checking whether lstat correctly handles trailing slash... yes checking whether stat accepts an empty string... no checking for strftime... yes checking for vprintf... yes checking for working strtod... yes checking for atexit... yes checking for floor... yes checking for memmove... yes checking for memset... yes checking for pow... yes checking for sqrt... yes checking for strchr... yes checking for strcspn... yes checking for strerror... yes checking for strpbrk... yes checking for strrchr... yes checking for strspn... yes checking for strstr... yes checking for strtol... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating svmloc/Makefile config.status: creating modhmm0.92b/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands dh_auto_build make -j16 make[1]: Entering directory '/build/libpsortb-1.0+dfsg' make all-recursive make[2]: Entering directory '/build/libpsortb-1.0+dfsg' Making all in svmloc make[3]: Entering directory '/build/libpsortb-1.0+dfsg/svmloc' /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o binding.lo binding.cpp /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o svmloc.lo svmloc.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c svmloc.cpp -fPIC -DPIC -o .libs/svmloc.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c binding.cpp -fPIC -DPIC -o .libs/binding.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c binding.cpp -o binding.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c svmloc.cpp -o svmloc.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 0:0:0 -lsvm -Wl,-z,relro -Wl,-z,now -o libsvmloc.la -rpath /usr/lib/x86_64-linux-gnu binding.lo svmloc.lo -lm libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/12/crtbeginS.o .libs/binding.o .libs/svmloc.o -lsvm -L/usr/lib/gcc/x86_64-linux-gnu/12 -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/12/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/12/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libsvmloc.so.0 -o .libs/libsvmloc.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libsvmloc.so.0" && ln -s "libsvmloc.so.0.0.0" "libsvmloc.so.0") libtool: link: (cd ".libs" && rm -f "libsvmloc.so" && ln -s "libsvmloc.so.0.0.0" "libsvmloc.so") libtool: link: ar cr .libs/libsvmloc.a binding.o svmloc.o libtool: link: ranlib .libs/libsvmloc.a libtool: link: ( cd ".libs" && rm -f "libsvmloc.la" && ln -s "../libsvmloc.la" "libsvmloc.la" ) make[3]: Leaving directory '/build/libpsortb-1.0+dfsg/svmloc' Making all in modhmm0.92b make[3]: Entering directory '/build/libpsortb-1.0+dfsg/modhmm0.92b' /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o core_algorithms_multialpha.lo core_algorithms_multialpha.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o debug_funcs.lo debug_funcs.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hmmsearch.lo hmmsearch.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o readhmm.lo readhmm.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o readhmm_multialpha.lo readhmm_multialpha.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o readseqs_multialpha.lo readseqs_multialpha.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o std_calculation_funcs.lo std_calculation_funcs.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o std_funcs.lo std_funcs.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o training_algorithms_multialpha.lo training_algorithms_multialpha.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c core_algorithms_multialpha.c -fPIC -DPIC -o .libs/core_algorithms_multialpha.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c debug_funcs.c -fPIC -DPIC -o .libs/debug_funcs.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c readhmm.c -fPIC -DPIC -o .libs/readhmm.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c std_calculation_funcs.c -fPIC -DPIC -o .libs/std_calculation_funcs.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c readhmm_multialpha.c -fPIC -DPIC -o .libs/readhmm_multialpha.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c hmmsearch.c -fPIC -DPIC -o .libs/hmmsearch.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c readseqs_multialpha.c -fPIC -DPIC -o .libs/readseqs_multialpha.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c std_funcs.c -fPIC -DPIC -o .libs/std_funcs.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c training_algorithms_multialpha.c -fPIC -DPIC -o .libs/training_algorithms_multialpha.o debug_funcs.c: In function 'dump_viterbi_path': debug_funcs.c:320:38: warning: implicit declaration of function 'get_mtx_index' [-Wimplicit-function-declaration] 320 | dump_viterbi_path(viterbi_mtxp + get_mtx_index(row-1, cur->prev, row_size), hmmp, | ^~~~~~~~~~~~~ debug_funcs.c: In function 'dump_replacement_letters': debug_funcs.c:861:14: warning: format '%c' expects argument of type 'int', but argument 2 has type 'struct letter_s' [-Wformat=] 861 | printf("%c ", (*(replacement_letters->letters + i))); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int struct letter_s debug_funcs.c: In function 'dump_replacement_letters_multi': debug_funcs.c:915:16: warning: format '%c' expects argument of type 'int', but argument 2 has type 'struct letter_s' [-Wformat=] 915 | printf("%c ", (*(replacement_letters->letters_1 + i))); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int struct letter_s debug_funcs.c:918:16: warning: format '%c' expects argument of type 'int', but argument 2 has type 'struct letter_s' [-Wformat=] 918 | printf("%c ", (*(replacement_letters->letters_2 + i))); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int struct letter_s debug_funcs.c:921:16: warning: format '%c' expects argument of type 'int', but argument 2 has type 'struct letter_s' [-Wformat=] 921 | printf("%c ", (*(replacement_letters->letters_3 + i))); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int struct letter_s debug_funcs.c:924:16: warning: format '%c' expects argument of type 'int', but argument 2 has type 'struct letter_s' [-Wformat=] 924 | printf("%c ", (*(replacement_letters->letters_4 + i))); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int struct letter_s readhmm.c: In function 'readhmm': readhmm.c:121:28: warning: assignment to 'struct transition_s *' from incompatible pointer type 'int *' [-Wincompatible-pointer-types] 121 | hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); | ^ readhmm.c: In function 'readanhmm': readhmm.c:397:28: warning: assignment to 'struct transition_s *' from incompatible pointer type 'int *' [-Wincompatible-pointer-types] 397 | hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); | ^ core_algorithms_multialpha.c: In function 'msa_forward_multi': core_algorithms_multialpha.c:1192:87: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1192 | a_index = get_alphabet_index((msa_seq_infop->msa_seq_1 + (c * (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ | | | char * In file included from core_algorithms_multialpha.c:7: funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ core_algorithms_multialpha.c:1199:93: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1199 | a_index_2 = get_alphabet_index((msa_seq_infop->msa_seq_2 + (c * (hmmp->a_size_2+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ | | | char * funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ core_algorithms_multialpha.c:1208:93: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1208 | a_index_3 = get_alphabet_index((msa_seq_infop->msa_seq_3 + (c * (hmmp->a_size_3+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ | | | char * funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ core_algorithms_multialpha.c:1217:93: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1217 | a_index_4 = get_alphabet_index((msa_seq_infop->msa_seq_4 + (c * (hmmp->a_size_4+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ | | | char * funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ readhmm.c: In function 'readhmm': readhmm.c:69:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 69 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ core_algorithms_multialpha.c: In function 'msa_backward_multi': core_algorithms_multialpha.c:1419:87: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1419 | a_index = get_alphabet_index((msa_seq_infop->msa_seq_1 + (c * (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ | | | char * readseqs_multialpha.c: In function 'get_sequence_fasta_multi': readseqs_multialpha.c:83:39: warning: assignment to 'char' from 'char *' makes integer from pointer without a cast [-Wint-conversion] 83 | (seq_infop->seqs + seq_nr)->name[0] = "s"; | ^ readseqs_multialpha.c: In function 'get_sequence_std_multi': readseqs_multialpha.c:121:55: warning: unknown escape sequence: '\s' 121 | if(line[0] == '<' || line[0] == '#' || line[0] == '\s' || line[0] == '\n' || line[0] == '/') { | ^~~~ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ core_algorithms_multialpha.c:1426:93: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1426 | a_index_2 = get_alphabet_index((msa_seq_infop->msa_seq_2 + (c * (hmmp->a_size_2+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ | | | char * funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ core_algorithms_multialpha.c:1435:93: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1435 | a_index_3 = get_alphabet_index((msa_seq_infop->msa_seq_3 + (c * (hmmp->a_size_3+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ | | | char * funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ core_algorithms_multialpha.c:1444:93: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1444 | a_index_4 = get_alphabet_index((msa_seq_infop->msa_seq_4 + (c * (hmmp->a_size_4+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ | | | char * funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ readhmm.c: In function 'readanhmm': readhmm.c:345:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 345 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ core_algorithms_multialpha.c: In function 'msa_viterbi_multi': core_algorithms_multialpha.c:1608:87: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1608 | a_index = get_alphabet_index((msa_seq_infop->msa_seq_1 + (c * (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ | | | char * funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ core_algorithms_multialpha.c:1615:93: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1615 | a_index_2 = get_alphabet_index((msa_seq_infop->msa_seq_2 + (c * (hmmp->a_size_2+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ | | | char * funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ core_algorithms_multialpha.c:1624:93: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1624 | a_index_3 = get_alphabet_index((msa_seq_infop->msa_seq_3 + (c * (hmmp->a_size_3+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ | | | char * funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ core_algorithms_multialpha.c:1633:93: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1633 | a_index_4 = get_alphabet_index((msa_seq_infop->msa_seq_4 + (c * (hmmp->a_size_4+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ | | | char * readseqs_multialpha.c: In function 'get_sequences_msa_std_multi': readseqs_multialpha.c:372:18: warning: unknown escape sequence: '\s' 372 | else if(i == '\s' && i == '\n') { | ^~~~ readseqs_multialpha.c:389:22: warning: implicit declaration of function 'read_multi_prior_file_multi'; did you mean 'read_prior_file_multi'? [-Wimplicit-function-declaration] 389 | read_priorfile = read_multi_prior_file_multi(&em_di_1, hmmp, priorfile_a1, 1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ | read_prior_file_multi funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ readhmm.c: In function 'read_module': readhmm.c:751:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 751 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm.c:786:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 786 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm.c:821:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 821 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm.c:850:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 850 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm.c:854:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 854 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ core_algorithms_multialpha.c: In function 'msa_one_best_multi': core_algorithms_multialpha.c:1892:87: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1892 | a_index = get_alphabet_index((msa_seq_infop->msa_seq_1 + (c * (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ | | | char * funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ core_algorithms_multialpha.c:1899:93: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1899 | a_index_2 = get_alphabet_index((msa_seq_infop->msa_seq_2 + (c * (hmmp->a_size_2+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ | | | char * funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ readhmm.c: In function 'read_prior_files': readhmm.c:1231:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1231 | fgets(ps, 2048, priorfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ core_algorithms_multialpha.c:1908:93: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1908 | a_index_3 = get_alphabet_index((msa_seq_infop->msa_seq_3 + (c * (hmmp->a_size_3+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ | | | char * funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ core_algorithms_multialpha.c:1917:93: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1917 | a_index_4 = get_alphabet_index((msa_seq_infop->msa_seq_4 + (c * (hmmp->a_size_4+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ | | | char * funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ std_funcs.c: In function 'get_replacement_letter_index_single': std_funcs.c:683:62: warning: comparison between pointer and integer 683 | if(((replacement_letters->letters + a_index)->letter)[0] == c) { | ^~ readhmm_multialpha.c: In function 'copy_hmm_struct': readhmm_multialpha.c:273:34: warning: assignment to 'struct transition_s *' from incompatible pointer type 'int *' [-Wincompatible-pointer-types] 273 | retrain_hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); | ^ hmmsearch.c: In function 'get_scores': hmmsearch.c:535:19: warning: assignment to 'struct helix_site *' from incompatible pointer type 'helix_sites *' [-Wincompatible-pointer-types] 535 | hSites->helix = (helix_sites *) malloc(sizeof (helix_sites) * helices); | ^ hmmsearch.c: In function 'get_nullmodel_score_multi': hmmsearch.c:656:42: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] 656 | printf("Could not find letter %s when scoring null model\n", &seq[l]); | ~^ ~~~~~~~ | | | | char * struct letter_s * hmmsearch.c:674:44: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] 674 | printf("Could not find letter %s when scoring null model\n", &seq_2[l]); | ~^ ~~~~~~~~~ | | | | char * struct letter_s * hmmsearch.c:693:44: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] 693 | printf("Could not find letter %s when scoring null model\n", &seq_3[l]); | ~^ ~~~~~~~~~ | | | | char * struct letter_s * readhmm_multialpha.c: In function 'readhmm_multialpha': readhmm_multialpha.c:469:28: warning: assignment to 'struct transition_s *' from incompatible pointer type 'int *' [-Wincompatible-pointer-types] 469 | hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); | ^ hmmsearch.c:712:44: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] 712 | printf("Could not find letter %s when scoring null model\n", &seq[l]); | ~^ ~~~~~~~ | | | | char * struct letter_s * readseqs_multialpha.c: In function 'get_sequence_std_multi': readseqs_multialpha.c:286:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 286 | fgets(line, MAX_LINE, seqfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ std_funcs.c: In function 'get_reverse_msa_seq': std_funcs.c:2076:74: warning: assignment to 'int *' from 'int' makes pointer from integer without a cast [-Wint-conversion] 2076 | *(reverse_msa_seq_infop->gaps + (msa_seq_infop->msa_seq_length + i)) = END; | ^ std_calculation_funcs.c: In function 'update_labelings': std_calculation_funcs.c:1295:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1295 | cur_address = (int)((cur_rowp+v)->labeling); | ^ std_calculation_funcs.c:1309:12: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1309 | if((int)((cur_rowp+w)->labeling) == cur_address && (cur_rowp + w)->is_updated == NO) { | ^ std_calculation_funcs.c: In function 'deallocate_row_labelings': std_calculation_funcs.c:1425:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1425 | cur_address = (int)((prev_rowp+v)->labeling); | ^ std_calculation_funcs.c:1430:12: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1430 | if((int)((prev_rowp+w)->labeling) == cur_address) { | ^ std_funcs.c: In function 'get_reverse_msa_seq_multi': std_funcs.c:2184:74: warning: assignment to 'int *' from 'int' makes pointer from integer without a cast [-Wint-conversion] 2184 | *(reverse_msa_seq_infop->gaps + (msa_seq_infop->msa_seq_length + i)) = END; | ^ readseqs_multialpha.c: In function 'get_sequences_msa_std_multi': readseqs_multialpha.c:625:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 625 | fgets(line, MAX_LINE, seqfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readseqs_multialpha.c:754:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 754 | fgets(line, MAX_LINE, seqfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readseqs_multialpha.c:874:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 874 | fgets(line, MAX_LINE, seqfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readseqs_multialpha.c:995:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 995 | fgets(line, MAX_LINE, seqfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ std_funcs.c: In function 'update_shares_prior_multi': std_funcs.c:2471:5: warning: 'return' with no value, in function returning non-void 2471 | return; | ^~~~~~ std_funcs.c:2457:5: note: declared here 2457 | int update_shares_prior_multi(struct emission_dirichlet_s *em_di, struct hmm_multi_s *hmmp, | ^~~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:326:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 326 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c: In function 'read_module_multi': readhmm_multialpha.c:1042:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1042 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1077:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1077 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1111:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1111 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1140:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1140 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1143:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1143 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1169:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1169 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1172:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1172 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1198:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1198 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1202:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1202 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ training_algorithms_multialpha.c: In function 'msa_baum_welch_dirichlet_multi': training_algorithms_multialpha.c:701:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] 701 | alphabet = hmmp->alphabet; | ^ training_algorithms_multialpha.c:710:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] 710 | alphabet = hmmp->alphabet_2; | ^ training_algorithms_multialpha.c:719:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] 719 | alphabet = hmmp->alphabet_3; | ^ training_algorithms_multialpha.c:728:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] 728 | alphabet = hmmp->alphabet_4; | ^ readhmm_multialpha.c:1229:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1229 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1236:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1236 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ training_algorithms_multialpha.c: In function 'extended_msa_baum_welch_dirichlet_multi': training_algorithms_multialpha.c:1639:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] 1639 | alphabet = hmmp->alphabet; | ^ training_algorithms_multialpha.c:1646:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] 1646 | alphabet = hmmp->alphabet_2; | ^ training_algorithms_multialpha.c:1653:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] 1653 | alphabet = hmmp->alphabet_3; | ^ training_algorithms_multialpha.c:1660:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] 1660 | alphabet = hmmp->alphabet_4; | ^ training_algorithms_multialpha.c:1784:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] 1784 | alphabet = hmmp->alphabet; | ^ training_algorithms_multialpha.c:1791:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] 1791 | alphabet = hmmp->alphabet_2; | ^ training_algorithms_multialpha.c:1798:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] 1798 | alphabet = hmmp->alphabet_3; | ^ training_algorithms_multialpha.c:1805:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] 1805 | alphabet = hmmp->alphabet_4; | ^ std_funcs.c: In function 'get_nr_alphabets': std_funcs.c:2731:10: warning: 'fgets' writing 4000 bytes into a region of size 1000 overflows the destination [-Wstringop-overflow=] 2731 | if(fgets(s, MAX_LINE, hmmfile) != NULL) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ std_funcs.c:2724:8: note: destination object 's' of size 1000 2724 | char s[1000]; | ^ In file included from /usr/include/stdio.h:906, from std_funcs.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:209:1: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)' 209 | fgets (char *__restrict __s, int __n, FILE *__restrict __stream) | ^~~~~ std_funcs.c:2738:8: warning: 'fgets' writing 4000 bytes into a region of size 1000 overflows the destination [-Wstringop-overflow=] 2738 | if(fgets(s, MAX_LINE, hmmfile) != NULL) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ std_funcs.c:2724:8: note: destination object 's' of size 1000 2724 | char s[1000]; | ^ /usr/include/x86_64-linux-gnu/bits/stdio2.h:209:1: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)' 209 | fgets (char *__restrict __s, int __n, FILE *__restrict __stream) | ^~~~~ training_algorithms_multialpha.c: In function 'add_to_E_multi': training_algorithms_multialpha.c:3564:5: warning: implicit declaration of function 'add_to_E_continuous' [-Wimplicit-function-declaration] 3564 | add_to_E_continuous(E, Eka_base, msa_seq, p, k, a_size, emissions); | ^~~~~~~~~~~~~~~~~~~ training_algorithms_multialpha.c:3589:43: warning: passing argument 9 of 'add_to_E_subst_mtx_dot_product_nr_occ' makes pointer from integer without a cast [-Wint-conversion] 3589 | alphabet); | ^~~~~~~~ | | | int In file included from training_algorithms_multialpha.c:10: funcs.h:257:103: note: expected 'char *' but argument is of type 'int' 257 | int k, int a_size, int normalize, double *subst_mtx, char *alphabet); | ~~~~~~^~~~~~~~ training_algorithms_multialpha.c:3593:49: warning: passing argument 9 of 'add_to_E_subst_mtx_dot_product_prior_nr_occ' makes pointer from integer without a cast [-Wint-conversion] 3593 | alphabet); | ^~~~~~~~ | | | int funcs.h:259:102: note: expected 'char *' but argument is of type 'int' 259 | int k, int a_size, int normalize, double *subst_mtx, char *alphabet); | ~~~~~~^~~~~~~~ training_algorithms_multialpha.c:3618:36: warning: passing argument 9 of 'add_to_E_subst_mtx_dot_product' makes pointer from integer without a cast [-Wint-conversion] 3618 | alphabet); | ^~~~~~~~ | | | int funcs.h:238:96: note: expected 'char *' but argument is of type 'int' 238 | int k, int a_size, int normalize, double *subst_mtx, char *alphabet); | ~~~~~~^~~~~~~~ training_algorithms_multialpha.c:3622:42: warning: passing argument 9 of 'add_to_E_subst_mtx_dot_product_prior' makes pointer from integer without a cast [-Wint-conversion] 3622 | alphabet); | ^~~~~~~~ | | | int funcs.h:240:102: note: expected 'char *' but argument is of type 'int' 240 | int k, int a_size, int normalize, double *subst_mtx, char *alphabet); | ~~~~~~^~~~~~~~ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c hmmsearch.c -o hmmsearch.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c debug_funcs.c -o debug_funcs.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c readhmm.c -o readhmm.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c std_calculation_funcs.c -o std_calculation_funcs.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c readseqs_multialpha.c -o readseqs_multialpha.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c readhmm_multialpha.c -o readhmm_multialpha.o >/dev/null 2>&1 In function 'fgets', inlined from 'get_nr_alphabets' at std_funcs.c:2731:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:215:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 215 | return __fgets_chk_warn (__s, sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'fgets', inlined from 'get_nr_alphabets' at std_funcs.c:2738:8: /usr/include/x86_64-linux-gnu/bits/stdio2.h:215:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 215 | return __fgets_chk_warn (__s, sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c std_funcs.c -o std_funcs.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c core_algorithms_multialpha.c -o core_algorithms_multialpha.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c training_algorithms_multialpha.c -o training_algorithms_multialpha.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 0:0:0 -Wl,-z,relro -Wl,-z,now -o libmodhmm.la -rpath /usr/lib/x86_64-linux-gnu core_algorithms_multialpha.lo debug_funcs.lo hmmsearch.lo readhmm.lo readhmm_multialpha.lo readseqs_multialpha.lo std_calculation_funcs.lo std_funcs.lo training_algorithms_multialpha.lo -lm libtool: link: gcc -shared -fPIC -DPIC .libs/core_algorithms_multialpha.o .libs/debug_funcs.o .libs/hmmsearch.o .libs/readhmm.o .libs/readhmm_multialpha.o .libs/readseqs_multialpha.o .libs/std_calculation_funcs.o .libs/std_funcs.o .libs/training_algorithms_multialpha.o -lm -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libmodhmm.so.0 -o .libs/libmodhmm.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libmodhmm.so.0" && ln -s "libmodhmm.so.0.0.0" "libmodhmm.so.0") libtool: link: (cd ".libs" && rm -f "libmodhmm.so" && ln -s "libmodhmm.so.0.0.0" "libmodhmm.so") libtool: link: ar cr .libs/libmodhmm.a core_algorithms_multialpha.o debug_funcs.o hmmsearch.o readhmm.o readhmm_multialpha.o readseqs_multialpha.o std_calculation_funcs.o std_funcs.o training_algorithms_multialpha.o libtool: link: ranlib .libs/libmodhmm.a libtool: link: ( cd ".libs" && rm -f "libmodhmm.la" && ln -s "../libmodhmm.la" "libmodhmm.la" ) make[3]: Leaving directory '/build/libpsortb-1.0+dfsg/modhmm0.92b' make[3]: Entering directory '/build/libpsortb-1.0+dfsg' make[3]: Leaving directory '/build/libpsortb-1.0+dfsg' make[2]: Leaving directory '/build/libpsortb-1.0+dfsg' make[1]: Leaving directory '/build/libpsortb-1.0+dfsg' dh_auto_test make -j16 check "TESTSUITEFLAGS=-j16 --verbose" VERBOSE=1 make[1]: Entering directory '/build/libpsortb-1.0+dfsg' Making check in svmloc make[2]: Entering directory '/build/libpsortb-1.0+dfsg/svmloc' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/libpsortb-1.0+dfsg/svmloc' Making check in modhmm0.92b make[2]: Entering directory '/build/libpsortb-1.0+dfsg/modhmm0.92b' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/libpsortb-1.0+dfsg/modhmm0.92b' make[2]: Entering directory '/build/libpsortb-1.0+dfsg' make[2]: Leaving directory '/build/libpsortb-1.0+dfsg' make[1]: Leaving directory '/build/libpsortb-1.0+dfsg' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/libpsortb-1.0+dfsg' dh_auto_install make -j1 install DESTDIR=/build/libpsortb-1.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/libpsortb-1.0+dfsg' Making install in svmloc make[3]: Entering directory '/build/libpsortb-1.0+dfsg/svmloc' make[4]: Entering directory '/build/libpsortb-1.0+dfsg/svmloc' /bin/mkdir -p '/build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu' /bin/bash ../libtool --mode=install /usr/bin/install -c libsvmloc.la '/build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libsvmloc.so.0.0.0 /build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libsvmloc.so.0.0.0 libtool: install: (cd /build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libsvmloc.so.0.0.0 libsvmloc.so.0 || { rm -f libsvmloc.so.0 && ln -s libsvmloc.so.0.0.0 libsvmloc.so.0; }; }) libtool: install: (cd /build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libsvmloc.so.0.0.0 libsvmloc.so || { rm -f libsvmloc.so && ln -s libsvmloc.so.0.0.0 libsvmloc.so; }; }) libtool: install: /usr/bin/install -c .libs/libsvmloc.lai /build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libsvmloc.la libtool: install: /usr/bin/install -c .libs/libsvmloc.a /build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libsvmloc.a libtool: install: chmod 644 /build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libsvmloc.a libtool: install: ranlib /build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libsvmloc.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/libpsortb-1.0+dfsg/svmloc' make[3]: Leaving directory '/build/libpsortb-1.0+dfsg/svmloc' Making install in modhmm0.92b make[3]: Entering directory '/build/libpsortb-1.0+dfsg/modhmm0.92b' make[4]: Entering directory '/build/libpsortb-1.0+dfsg/modhmm0.92b' /bin/mkdir -p '/build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu' /bin/bash ../libtool --mode=install /usr/bin/install -c libmodhmm.la '/build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libmodhmm.so.0.0.0 /build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libmodhmm.so.0.0.0 libtool: install: (cd /build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libmodhmm.so.0.0.0 libmodhmm.so.0 || { rm -f libmodhmm.so.0 && ln -s libmodhmm.so.0.0.0 libmodhmm.so.0; }; }) libtool: install: (cd /build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libmodhmm.so.0.0.0 libmodhmm.so || { rm -f libmodhmm.so && ln -s libmodhmm.so.0.0.0 libmodhmm.so; }; }) libtool: install: /usr/bin/install -c .libs/libmodhmm.lai /build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libmodhmm.la libtool: install: /usr/bin/install -c .libs/libmodhmm.a /build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libmodhmm.a libtool: install: chmod 644 /build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libmodhmm.a libtool: install: ranlib /build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libmodhmm.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/libpsortb-1.0+dfsg/modhmm0.92b' make[3]: Leaving directory '/build/libpsortb-1.0+dfsg/modhmm0.92b' make[3]: Entering directory '/build/libpsortb-1.0+dfsg' make[4]: Entering directory '/build/libpsortb-1.0+dfsg' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/libpsortb-1.0+dfsg' make[3]: Leaving directory '/build/libpsortb-1.0+dfsg' make[2]: Leaving directory '/build/libpsortb-1.0+dfsg' d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-la \ debian/tmp/usr/lib/*/libmodhmm.so Library package automatic movement utility set -e install -d -m 755 debian/libmodhmm-dev/usr/lib/x86_64-linux-gnu install -d -m 755 debian/libmodhmm0/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libmodhmm.a debian/libmodhmm-dev/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libmodhmm.so debian/libmodhmm-dev/usr/lib/x86_64-linux-gnu mv /build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libmodhmm.so.0 debian/libmodhmm0/usr/lib/x86_64-linux-gnu mv /build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libmodhmm.so.0.0.0 debian/libmodhmm0/usr/lib/x86_64-linux-gnu PKGDEV=libmodhmm-dev PKGSHL=libmodhmm0 d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-la \ debian/tmp/usr/lib/*/libsvmloc.so Library package automatic movement utility --> libsvm-dev package exists. set -e install -d -m 755 debian/libsvmloc-dev/usr/lib/x86_64-linux-gnu install -d -m 755 debian/libsvmloc0/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libsvmloc.a debian/libsvmloc-dev/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libsvmloc.so debian/libsvmloc-dev/usr/lib/x86_64-linux-gnu mv /build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libsvmloc.so.0 debian/libsvmloc0/usr/lib/x86_64-linux-gnu mv /build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libsvmloc.so.0.0.0 debian/libsvmloc0/usr/lib/x86_64-linux-gnu PKGDEV=libsvmloc-dev PKGSHL=libsvmloc0 find debian -name "lib*.la" -delete make[1]: Leaving directory '/build/libpsortb-1.0+dfsg' dh_installdocs dh_installchangelogs dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'libmodhmm0-dbgsym' in '../libmodhmm0-dbgsym_1.0+dfsg-5_amd64.deb'. dpkg-deb: building package 'libsvmloc-dev' in '../libsvmloc-dev_1.0+dfsg-5_amd64.deb'. dpkg-deb: building package 'libmodhmm0' in '../libmodhmm0_1.0+dfsg-5_amd64.deb'. dpkg-deb: building package 'libsvmloc0-dbgsym' in '../libsvmloc0-dbgsym_1.0+dfsg-5_amd64.deb'. dpkg-deb: building package 'libmodhmm-dev' in '../libmodhmm-dev_1.0+dfsg-5_amd64.deb'. dpkg-deb: building package 'libsvmloc0' in '../libsvmloc0_1.0+dfsg-5_amd64.deb'. dpkg-genbuildinfo --build=binary -O../libpsortb_1.0+dfsg-5_amd64.buildinfo dpkg-genchanges --build=binary -O../libpsortb_1.0+dfsg-5_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3633491 and its subdirectories I: Current time: Wed Jul 3 11:25:53 -12 2024 I: pbuilder-time-stamp: 1720049153 Thu Jun 1 17:02:53 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net. Thu Jun 1 17:02:53 UTC 2023 I: Preparing to do remote build '2' on ionos11-amd64.debian.net. Thu Jun 1 17:04:07 UTC 2023 I: Deleting $TMPDIR on ionos11-amd64.debian.net. Thu Jun 1 17:04:07 UTC 2023 I: libpsortb_1.0+dfsg-5_amd64.changes: Format: 1.8 Date: Wed, 17 Nov 2021 17:48:38 +0100 Source: libpsortb Binary: libmodhmm-dev libmodhmm0 libmodhmm0-dbgsym libsvmloc-dev libsvmloc0 libsvmloc0-dbgsym Architecture: amd64 Version: 1.0+dfsg-5 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: libmodhmm-dev - library for constructing, training and scoring hidden Markov mode libmodhmm0 - library for constructing, training and scoring hidden Markov mode libsvmloc-dev - PSORTb adapted library for svm machine-learning library (dev) libsvmloc0 - PSORTb adapted library for svm machine-learning library Closes: 999795 Changes: libpsortb (1.0+dfsg-5) unstable; urgency=medium . * Versioned Build-Depends: d-shlibs (>= 0.84) * Drop needless override for d-shlibs Closes: #999795 * Standards-Version: 4.6.0 (routine-update) Checksums-Sha1: 9ec0d8a4ca55003471d8e27fc3987a16f55e9385 80660 libmodhmm-dev_1.0+dfsg-5_amd64.deb 8a028c461d546b3a4161773c1f8e5ce45c2401d9 234272 libmodhmm0-dbgsym_1.0+dfsg-5_amd64.deb d04a716b086e59b6cd6f1f6779ed31fbb340e772 80684 libmodhmm0_1.0+dfsg-5_amd64.deb ba634833666655befe5910e4d17148103034f654 6992 libpsortb_1.0+dfsg-5_amd64.buildinfo e55003d7a8eaa679e34475811c51fa5e6fb24db4 12296 libsvmloc-dev_1.0+dfsg-5_amd64.deb 2d60a6bbd09bd5aecf0a7828a0174e449658b15d 102200 libsvmloc0-dbgsym_1.0+dfsg-5_amd64.deb 37f7eed931eb641f77ae7381785ad2bb3b017000 13316 libsvmloc0_1.0+dfsg-5_amd64.deb Checksums-Sha256: 9dc19f11c8e48c2f04ab132d61adf55a9f811835c315d3b87b332f29a38f1876 80660 libmodhmm-dev_1.0+dfsg-5_amd64.deb 1cfc55e979b13ad0df88663e633e0917f76c847e6df409d1bdfc678b6d7e883a 234272 libmodhmm0-dbgsym_1.0+dfsg-5_amd64.deb 6d2c771ed2fc8781bea93be3af4bbcbdad5261f5ff621f9854af645124b1d67f 80684 libmodhmm0_1.0+dfsg-5_amd64.deb 2f4bebd433232113e3ea45c3304ec17f6ac948e78a4f939f94b7940a1af46a70 6992 libpsortb_1.0+dfsg-5_amd64.buildinfo ea5e176534f75185e3f047365f596c9868458b3020e408c16fa5196f775434b4 12296 libsvmloc-dev_1.0+dfsg-5_amd64.deb 36678a6381e45f84152a71c4b11a2af1a2912abefab073b1533c305a71727159 102200 libsvmloc0-dbgsym_1.0+dfsg-5_amd64.deb 50d2a626b9fe8472fdc26cf3d7c177b2e0684ab8f2d2c6f7355134fa6a2fc05d 13316 libsvmloc0_1.0+dfsg-5_amd64.deb Files: 4244ddf7443c62b1d37ec5026c295dc0 80660 libdevel optional libmodhmm-dev_1.0+dfsg-5_amd64.deb 604f670bc37c38b1db1190156350bae4 234272 debug optional libmodhmm0-dbgsym_1.0+dfsg-5_amd64.deb c8085d49e515b170d440032cce698207 80684 libs optional libmodhmm0_1.0+dfsg-5_amd64.deb 833c3198acbfd16bad0ec6589de560f4 6992 science optional libpsortb_1.0+dfsg-5_amd64.buildinfo 1732eb11c4e977cb00cdbfc28f3e2a5e 12296 libdevel optional libsvmloc-dev_1.0+dfsg-5_amd64.deb 4bf5adb32414eb6eca2970b71dd58244 102200 debug optional libsvmloc0-dbgsym_1.0+dfsg-5_amd64.deb f31b7075f7a243cc838c3720adc0dde7 13316 libs optional libsvmloc0_1.0+dfsg-5_amd64.deb Thu Jun 1 17:04:08 UTC 2023 I: diffoscope 242 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.AuAiLGY3/libpsortb_1.0+dfsg-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.AuAiLGY3/libpsortb_1.0+dfsg-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.AuAiLGY3/libpsortb_1.0+dfsg-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.AuAiLGY3/b1/libpsortb_1.0+dfsg-5_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.AuAiLGY3/b2/libpsortb_1.0+dfsg-5_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.446s) 0.446s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.031s) 0.031s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.001s) 0.001s 1 call specialize Thu Jun 1 17:04:12 UTC 2023 I: diffoscope 242 found no differences in the changes files, and a .buildinfo file also exists. Thu Jun 1 17:04:12 UTC 2023 I: libpsortb from bookworm built successfully and reproducibly on amd64. Thu Jun 1 17:04:13 UTC 2023 I: Submitting .buildinfo files to external archives: Thu Jun 1 17:04:13 UTC 2023 I: Submitting 8.0K b1/libpsortb_1.0+dfsg-5_amd64.buildinfo.asc Thu Jun 1 17:04:14 UTC 2023 I: Submitting 8.0K b2/libpsortb_1.0+dfsg-5_amd64.buildinfo.asc Thu Jun 1 17:04:15 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Jun 1 17:04:15 UTC 2023 I: Done submitting .buildinfo files. Thu Jun 1 17:04:15 UTC 2023 I: Removing signed libpsortb_1.0+dfsg-5_amd64.buildinfo.asc files: removed './b1/libpsortb_1.0+dfsg-5_amd64.buildinfo.asc' removed './b2/libpsortb_1.0+dfsg-5_amd64.buildinfo.asc'