Diff of the two buildlogs: -- --- b1/build.log 2023-06-06 16:24:49.915761150 +0000 +++ b2/build.log 2023-06-06 16:27:22.369081158 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Jun 6 04:15:50 -12 2023 -I: pbuilder-time-stamp: 1686068150 +I: Current time: Tue Jul 9 12:48:04 +14 2024 +I: pbuilder-time-stamp: 1720478884 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./wise_2.4.1.orig.tar.gz] I: copying [./wise_2.4.1-23.debian.tar.xz] I: Extracting source -gpgv: Signature made Sat Apr 18 04:13:39 2020 -12 +gpgv: Signature made Sun Apr 19 06:13:39 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -40,135 +40,167 @@ dpkg-source: info: applying cross.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/760477/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1379294/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jul 9 12:48 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/1379294/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1379294/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=15 ' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='192e54c9d6524dde9b9cec9c8ef824d3' - 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='760477' - PS1='# ' - PS2='> ' + INVOCATION_ID=f63dbfa8fade4d92ad1502b04f834741 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1379294 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.kgfa4w3K/pbuilderrc_Lbtk --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.kgfa4w3K/b1 --logfile b1/build.log wise_2.4.1-23.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://78.137.99.97:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.kgfa4w3K/pbuilderrc_TXdf --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.kgfa4w3K/b2 --logfile b2/build.log --extrapackages usrmerge wise_2.4.1-23.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos1-amd64 5.10.0-23-amd64 #1 SMP Debian 5.10.179-1 (2023-05-12) x86_64 GNU/Linux + Linux i-capture-the-hostname 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 09:23 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 01:20 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 22:02 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname - -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 35664 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 85600 Mar 22 22:02 findmnt - -rwsr-xr-x 1 root root 35128 Mar 22 20:35 fusermount - -rwxr-xr-x 1 root root 203152 Jan 24 02:43 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 01:33 hostname - -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln - -rwxr-xr-x 1 root root 53024 Mar 23 00:40 login - -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls - -rwxr-xr-x 1 root root 207168 Mar 22 22:02 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 22:02 more - -rwsr-xr-x 1 root root 59704 Mar 22 22:02 mount - -rwxr-xr-x 1 root root 18744 Mar 22 22:02 mountpoint - -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 09:23 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 07:55 sed - lrwxrwxrwx 1 root root 4 Jan 5 01:20 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 22:02 su - -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync - -rwxr-xr-x 1 root root 531984 Apr 6 02:25 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 20:35 ulockmgr_server - -rwsr-xr-x 1 root root 35128 Mar 22 22:02 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 22:02 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 01:33 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/760477/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1265648 Apr 24 2023 bash + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 44016 Sep 21 2022 cat + -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown + -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp + -rwxr-xr-x 1 root root 125640 Jan 6 2023 dash + -rwxr-xr-x 1 root root 121904 Sep 21 2022 date + -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd + -rwxr-xr-x 1 root root 102200 Sep 21 2022 df + -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir + -rwxr-xr-x 1 root root 88656 Mar 24 2023 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 2022 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 2022 domainname -> hostname + -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 2023 egrep + -rwxr-xr-x 1 root root 35664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 2023 fgrep + -rwxr-xr-x 1 root root 85600 Mar 24 2023 findmnt + -rwsr-xr-x 1 root root 35128 Mar 23 2023 fusermount + -rwxr-xr-x 1 root root 203152 Jan 25 2023 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22680 Dec 20 2022 hostname + -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln + -rwxr-xr-x 1 root root 53024 Mar 24 2023 login + -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls + -rwxr-xr-x 1 root root 207168 Mar 24 2023 lsblk + -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 59712 Mar 24 2023 more + -rwsr-xr-x 1 root root 59704 Mar 24 2023 mount + -rwxr-xr-x 1 root root 18744 Mar 24 2023 mountpoint + -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 2022 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 2023 rbash -> bash + -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm + -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 27560 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 126424 Jan 6 2023 sed + lrwxrwxrwx 1 root root 9 Jul 9 12:48 sh -> /bin/bash + -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty + -rwsr-xr-x 1 root root 72000 Mar 24 2023 su + -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync + -rwxr-xr-x 1 root root 531984 Apr 7 2023 tar + -rwxr-xr-x 1 root root 14520 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch + -rwxr-xr-x 1 root root 35664 Sep 21 2022 true + -rwxr-xr-x 1 root root 14568 Mar 23 2023 ulockmgr_server + -rwsr-xr-x 1 root root 35128 Mar 24 2023 umount + -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 72024 Mar 24 2023 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 2022 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/1379294/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -385,7 +417,7 @@ Get: 169 http://deb.debian.org/debian bookworm/main amd64 texlive-luatex all 2022.20230122-3 [22.7 MB] Get: 170 http://deb.debian.org/debian bookworm/main amd64 texlive-plain-generic all 2022.20230122-4 [28.9 MB] Get: 171 http://deb.debian.org/debian bookworm/main amd64 texlive-extra-utils all 2022.20230122-4 [59.0 MB] -Fetched 233 MB in 6s (37.9 MB/s) +Fetched 233 MB in 3s (74.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libfftw3-double3: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 ... 19591 files and directories currently installed.) @@ -1129,8 +1161,19 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/wise-2.4.1/ && 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 > ../wise_2.4.1-23_source.changes +I: user script /srv/workspace/pbuilder/1379294/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +removed '/etc/unsupported-skip-usrmerge-conversion' +The system has been successfully converted. +I: user script /srv/workspace/pbuilder/1379294/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/wise-2.4.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../wise_2.4.1-23_source.changes dpkg-buildpackage: info: source package wise dpkg-buildpackage: info: source version 2.4.1-23 dpkg-buildpackage: info: source distribution unstable @@ -1214,7 +1257,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/wise-2.4.1' dh_auto_build --sourcedirectory=src -- all - cd src && make -j15 "INSTALL=install --strip-program=true" all + cd src && make -j16 "INSTALL=install --strip-program=true" all make[2]: Entering directory '/build/wise-2.4.1/src' (cd base ; make CC="cc" CFLAGS="-g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c `pkg-config --cflags glib-2.0`" libwisebase.a ) make[3]: Entering directory '/build/wise-2.4.1/src/base' @@ -1259,10 +1302,6 @@ cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c prior.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c tophits.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c trace.c -cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c aligneval.c -cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c alignio.c -cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c cluster.c -cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c dayhoff.c prior.c: In function ‘P7ReadPrior’: prior.c:102:12: warning: implicit declaration of function ‘strcmp’ [-Wimplicit-function-declaration] 102 | if (strcmp(sptr, "DIRICHLET") == 0) pri->strategy = PRI_DCHLET; @@ -1271,14 +1310,15 @@ 9 | #include "funcs.h" +++ |+#include 10 | #include "squid.h" +cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c aligneval.c +cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c alignio.c +cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c cluster.c +cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c dayhoff.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c file.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c getopt.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c gnuregex.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c interleaved.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c iupac.c -cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c msf.c -cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c revcomp.c -cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c selex.c gnuregex.c: In function ‘re_match_2’: gnuregex.c:3752:31: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 3752 | if ((int) old_regend[r] >= (int) regstart[r]) @@ -1400,6 +1440,9 @@ gnuregex.c:4278:11: note: in expansion of macro ‘POP_FAILURE_POINT’ 4278 | POP_FAILURE_POINT (d, p, | ^~~~~~~~~~~~~~~~~ +cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c msf.c +cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c revcomp.c +cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c selex.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c sqerror.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c sqio.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c sre_ctype.c @@ -1469,10 +1512,7 @@ cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ complexsequence.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ complexevalset.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ complexconsensi.c -packaln.dy: In function ‘Wise2_read_simple_PackAln’: -packaln.dy:88:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] - 88 | fgets(buffer,MAXLINE,ifp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~ +cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ sequence.c aln.dy: In function ‘Wise2_mapped_ascii_AlnBlock’: aln.dy:867:19: warning: too many arguments for format [-Wformat-extra-args] 867 | fprintf(ofp," {%3.2f} ",(double)(*score_to_double)(cuml),cuml); @@ -1481,7 +1521,10 @@ matrixdebug.dy:208:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 208 | fgets(buffer,MAXLINE,in); | ^~~~~~~~~~~~~~~~~~~~~~~~ -cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ sequence.c +packaln.dy: In function ‘Wise2_read_simple_PackAln’: +packaln.dy:88:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] + 88 | fgets(buffer,MAXLINE,ifp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~ cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ sequencestream.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ seqalign.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ hitlist.c @@ -1547,6 +1590,44 @@ cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ hsptwohitscan.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ proteinindexcons.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ dnaindexcons.c +cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ staticseq.c +hspthreadeddb.dy: In function ‘Wise2_threadeddb_scan_worker’: +hspthreadeddb.dy:154:77: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 154 | fprintf(stderr,"For segment %d, finished query with %d (%d) linear\n",seg,(int)seg->lm,seg->lm->len); + | ^ +hspthreadeddb.dy:154:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Wise2_HSPDatabaseSegment *’ [-Wformat=] + 154 | fprintf(stderr,"For segment %d, finished query with %d (%d) linear\n",seg,(int)seg->lm,seg->lm->len); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~ + | | + | Wise2_HSPDatabaseSegment * +hsplookupthreaded.dy: In function ‘Wise2_one_off_ordered_HSPscan_scan_query_direct’: +hsplookupthreaded.dy:263:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] + 263 | fprintf(stderr,"retrieved array with %d elements\n",current_oph); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~ + | | + | long int +subseqhash.dy: In function ‘Wise2_is_populated_subseqhash_ghash’: +subseqhash.dy:111:29: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] + 111 | if( g_hash_table_lookup(h,(gconstpointer)seq_number) == NULL ) { + | ^ +subseqhash.dy: In function ‘Wise2_lookup_subseqhash_ghash’: +subseqhash.dy:128:85: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] + 128 | return new_linkedl_SeqLookupResultInterface((SeqLookupPos *)g_hash_table_lookup(h,(gconstpointer)seq_number)); + | ^ +subseqhash.dy: In function ‘Wise2_add_seq_subseqhash_ghash’: +subseqhash.dy:160:54: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] + 160 | if((ret = (SeqLookupPos *) g_hash_table_lookup(h,(gconstpointer)seq_number)) == NULL ) { + | ^ +subseqhash.dy:161:29: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] + 161 | g_hash_table_insert(h,(gpointer)seq_number,p); + | ^ +subseqhash.dy: In function ‘Wise2_add_direct_number_subseqhash_ghash’: +subseqhash.dy:188:52: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] + 188 | if((ret = (SeqLookupPos *) g_hash_table_lookup(h,(gconstpointer)seq_number)) == NULL ) { + | ^ +subseqhash.dy:189:27: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] + 189 | g_hash_table_insert(h,(gpointer)seq_number,p); + | ^ hsp2hitscan.dy: In function ‘Wise2_one_off_two_hit_HSPscan_query_direct’: hsp2hitscan.dy:209:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 209 | fprintf(stderr,"START %d.%03du %d.%03ds \n", @@ -1579,12 +1660,12 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} -hsplookupthreaded.dy: In function ‘Wise2_one_off_ordered_HSPscan_scan_query_direct’: -hsplookupthreaded.dy:263:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] - 263 | fprintf(stderr,"retrieved array with %d elements\n",current_oph); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~ - | | - | long int +shadowseqindex.dy: In function ‘Wise2_dump_stats_ShadowSequenceIndex’: +shadowseqindex.dy:285:15: warning: format ‘%f’ expects argument of type ‘double’, but argument 4 has type ‘long unsigned int’ [-Wformat=] + 285 | fprintf(ofp,"Head memory %d [%.2f Mbytes]\n",total_head,(total_head*sizeof(ShadowArraySeqHead))/100000); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + | | + | long unsigned int hsp2hitscan.dy:273:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 273 | fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1678,44 +1759,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} -subseqhash.dy: In function ‘Wise2_is_populated_subseqhash_ghash’: -subseqhash.dy:111:29: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] - 111 | if( g_hash_table_lookup(h,(gconstpointer)seq_number) == NULL ) { - | ^ -subseqhash.dy: In function ‘Wise2_lookup_subseqhash_ghash’: -subseqhash.dy:128:85: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] - 128 | return new_linkedl_SeqLookupResultInterface((SeqLookupPos *)g_hash_table_lookup(h,(gconstpointer)seq_number)); - | ^ -subseqhash.dy: In function ‘Wise2_add_seq_subseqhash_ghash’: -subseqhash.dy:160:54: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] - 160 | if((ret = (SeqLookupPos *) g_hash_table_lookup(h,(gconstpointer)seq_number)) == NULL ) { - | ^ -subseqhash.dy:161:29: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] - 161 | g_hash_table_insert(h,(gpointer)seq_number,p); - | ^ -subseqhash.dy: In function ‘Wise2_add_direct_number_subseqhash_ghash’: -subseqhash.dy:188:52: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] - 188 | if((ret = (SeqLookupPos *) g_hash_table_lookup(h,(gconstpointer)seq_number)) == NULL ) { - | ^ -subseqhash.dy:189:27: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] - 189 | g_hash_table_insert(h,(gpointer)seq_number,p); - | ^ -shadowseqindex.dy: In function ‘Wise2_dump_stats_ShadowSequenceIndex’: -shadowseqindex.dy:285:15: warning: format ‘%f’ expects argument of type ‘double’, but argument 4 has type ‘long unsigned int’ [-Wformat=] - 285 | fprintf(ofp,"Head memory %d [%.2f Mbytes]\n",total_head,(total_head*sizeof(ShadowArraySeqHead))/100000); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - | | - | long unsigned int -cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ staticseq.c -hspthreadeddb.dy: In function ‘Wise2_threadeddb_scan_worker’: -hspthreadeddb.dy:154:77: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 154 | fprintf(stderr,"For segment %d, finished query with %d (%d) linear\n",seg,(int)seg->lm,seg->lm->len); - | ^ -hspthreadeddb.dy:154:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Wise2_HSPDatabaseSegment *’ [-Wformat=] - 154 | fprintf(stderr,"For segment %d, finished query with %d (%d) linear\n",seg,(int)seg->lm,seg->lm->len); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~ - | | - | Wise2_HSPDatabaseSegment * ar ru libdyna_glib.a subseqhash.o intallocator.o proteinstreamedindex.o shadowseq.o shadowseqindex.o hsphandler.o hspscaninterface.o hsp2hitscan.o hsplookupscan.o hsplookupthreaded.o hspthreadeddb.o hspscanruntime.o hsptwohitscan.o proteinindexcons.o dnaindexcons.o staticseq.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating libdyna_glib.a @@ -1790,16 +1833,6 @@ cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ anonobj.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ transferinterface.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ directsocketwrite.c -functionserver.dy: In function ‘Wise2_main_loop_forking_FunctionServer’: -functionserver.dy:129:11: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] - 129 | write(new_socket,buf,9); - | ^~~~~~~~~~~~~~~~~~~~~~~ -functionserver.dy:141:9: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] - 141 | write(new_socket,buf,6); - | ^~~~~~~~~~~~~~~~~~~~~~~ -functionserver.dy:183:9: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] - 183 | write(new_socket,buf,5); - | ^~~~~~~~~~~~~~~~~~~~~~~ functionclient.dy: In function ‘Wise2_new_FunctionProxyCoordinator’: functionclient.dy:193:24: warning: passing argument 2 of ‘connect’ from incompatible pointer type [-Wincompatible-pointer-types] 193 | connect(out->socket, &server, sizeof(server)); @@ -1810,6 +1843,16 @@ /usr/include/x86_64-linux-gnu/sys/socket.h:126:52: note: expected ‘const struct sockaddr *’ but argument is of type ‘struct sockaddr_in *’ 126 | extern int connect (int __fd, __CONST_SOCKADDR_ARG __addr, socklen_t __len); | ^ +functionserver.dy: In function ‘Wise2_main_loop_forking_FunctionServer’: +functionserver.dy:129:11: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] + 129 | write(new_socket,buf,9); + | ^~~~~~~~~~~~~~~~~~~~~~~ +functionserver.dy:141:9: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] + 141 | write(new_socket,buf,6); + | ^~~~~~~~~~~~~~~~~~~~~~~ +functionserver.dy:183:9: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] + 183 | write(new_socket,buf,5); + | ^~~~~~~~~~~~~~~~~~~~~~~ ar ru libwisesocket.a functionserver.o functionclient.o anonobj.o transferinterface.o directsocketwrite.o ar: `u' modifier ignored since `D' is the default (see `U') ar: creating libwisesocket.a @@ -1833,6 +1876,7 @@ cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_interface.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_fasta.c +cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_sanger_project.c kmer_hash.dy: In function ‘Wise2_free_KmerHashIndex’: kmer_hash.dy:318:19: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 318 | fprintf(stderr, "min_kmer: %016lx\n", khi->min_kmer); @@ -1869,8 +1913,25 @@ kmer_assembly.dy:367:20: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 367 | fprintf(stderr," [%ld] is %d label\n",kal->sequence_label[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_sanger_project.c kmer_assembly_error.dy: In function ‘Wise2_mark_tangles_KmerAssembly’: +kmer_assembly_error.dy:93:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] + 93 | fprintf(stderr,"Marking node (%ld) [%s] as next tangled\n",node->number,buffer); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ + | | + | kmer_t {aka long long int} +kmer_assembly_error.dy:105:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] + 105 | fprintf(stderr,"Marking node (%ld) [%s] as prev tangled\n",node->number,buffer); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ + | | + | kmer_t {aka long long int} +kmer_assembly_error.dy: In function ‘Wise2_extend_indel_path_KmerAssembly’: +kmer_assembly_error.dy:351:24: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int *’ [-Wformat=] + 351 | fprintf(stderr,"in considering indel (%d, path %d), real (%c) and error (%c) do not agree at position %d,%d\n",delete_length,current_path,real->base,error->base,real_pos,error_pos); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ + | | + | int * +cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_cons.c +cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models compressed_protein_index.c kmer_assembly_untangler.dy: In function ‘Wise2_show_KmerAssemblyPath’: kmer_assembly_untangler.dy:52:65: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 52 | fprintf(ofp,"%3d memory %d, from [%s] to [%s], base %c\n",i,(int)kap->stack[i],back,forw,kap->stack[i]->base); @@ -1901,24 +1962,7 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} -kmer_assembly_error.dy:93:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] - 93 | fprintf(stderr,"Marking node (%ld) [%s] as next tangled\n",node->number,buffer); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ - | | - | kmer_t {aka long long int} -kmer_assembly_error.dy:105:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] - 105 | fprintf(stderr,"Marking node (%ld) [%s] as prev tangled\n",node->number,buffer); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ - | | - | kmer_t {aka long long int} -cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_cons.c kmer_assembly_untangler.dy: In function ‘Wise2_old_attempt_forward_untangle_KmerAssembly’: -kmer_assembly_error.dy: In function ‘Wise2_extend_indel_path_KmerAssembly’: -kmer_assembly_error.dy:351:24: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int *’ [-Wformat=] - 351 | fprintf(stderr,"in considering indel (%d, path %d), real (%c) and error (%c) do not agree at position %d,%d\n",delete_length,current_path,real->base,error->base,real_pos,error_pos); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ - | | - | int * kmer_assembly_untangler.dy:444:20: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 444 | fprintf(stderr,"looking at node %ld with path length %d, next length %d depth %d\n",current->next->number,pathlen,current->next->next_len,current->sequence_label_len); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~ @@ -1944,7 +1988,6 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | kmer_t {aka long long int} -cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models compressed_protein_index.c compressed_protein_index.dy: In function ‘Wise2_add_direct_number_CompressedProteinIndex’: compressed_protein_index.dy:223:10: warning: returning ‘void *’ from a function with return type ‘boolean’ {aka ‘int’} makes integer from pointer without a cast [-Wint-conversion] 223 | return NULL; @@ -1978,14 +2021,15 @@ cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ bigdba.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ dbadisplay.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include estwise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. -dnal.c: In function ‘show_version’: -dnal.c:106:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - 106 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); - | ^~~~~~~~~~~~ +cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneparser21.c psw.c: In function ‘show_version’: psw.c:261:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 261 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ +pswdb.c: In function ‘show_version’: +pswdb.c:97:106: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 97 | fprintf(stdout,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); + | ^~~~~~~~~~~~ dbac.c: In function ‘show_version’: dbac.c:364:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 364 | fprintf(ofp," Compiled %s\n",COMPILE_DATE); @@ -1997,20 +2041,19 @@ | | | | int size_t {aka long unsigned int} | %ld -pswdb.c: In function ‘show_version’: -pswdb.c:97:106: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - 97 | fprintf(stdout,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); - | ^~~~~~~~~~~~ -cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneparser21.c -cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneparameter.c -estwise.c: In function ‘show_version’: -estwise.c:559:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - 559 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +dnal.c: In function ‘show_version’: +dnal.c:106:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 106 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ +cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneparameter.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genestats.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewisehsp.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneutil.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneoutput.c +estwise.c: In function ‘show_version’: +estwise.c:559:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 559 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); + | ^~~~~~~~~~~~ cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ threestatemodel.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genefrequency.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ splicesitemodeler.c @@ -2033,7 +2076,6 @@ phasemodel.dy:241:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fgets(name,10000,ifp); | ^~~~~~~~~~~~~~~~~~~~~ -cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genedisplay.c phasemodel.dy:241:3: warning: ‘fgets’ writing 10000 bytes into a region of size 2000 overflows the destination [-Wstringop-overflow=] 241 | fgets(name,10000,ifp); | ^~~~~~~~~~~~~~~~~~~~~ @@ -2050,8 +2092,10 @@ /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) | ^~~~~ +cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genedisplay.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estwise3.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estslim3.c +cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estloop3.c genedisplay.dy: In function ‘Wise2_write_intron_desc’: genedisplay.dy:493:20: warning: too many arguments for format [-Wformat-extra-args] 493 | sprintf(buffer," Intron ??? ",in_number); @@ -2061,7 +2105,6 @@ /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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estloop3.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estfrag3.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estslimloop.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ gwquickdb.c @@ -2075,33 +2118,33 @@ cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneparser4.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estquick3.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include genewise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. +cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include genewisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ genewise.c: In function ‘show_version’: genewise.c:860:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 860 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ -cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include genewisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ genewisedb.c: In function ‘show_version’: genewisedb.c:1005:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 1005 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include estwisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genomewise.c -cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genomewise9.c genomewise.c: In function ‘show_version’: genomewise.c:18:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 18 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ +cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genomewise9.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genome_evidence.c estwisedb.c: In function ‘show_version’: estwisedb.c:838:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 838 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ est_evidence.c -cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ sywise.c est_evidence.dy: In function ‘Wise2_new_est_GenomeEvidenceUnit’: est_evidence.dy:142:16: warning: assignment to ‘int (*)(void *)’ from incompatible pointer type ‘Wise2_EstEvidence * (*)(Wise2_EstEvidence *)’ [-Wincompatible-pointer-types] 142 | in->geu_free = free_EstEvidence; | ^ +cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ sywise.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ sywise20.c sywise.c: In function ‘show_version’: sywise.c:14:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] @@ -2110,29 +2153,36 @@ cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ syexonmodel.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pseudowise.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pseudowise7.c -cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` promoterwise.c pseudowise.c: In function ‘show_version’: pseudowise.c:15:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 15 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ +cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` promoterwise.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ localdba.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` localcishit.c +cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ localcispara.c promoterwise.c: In function ‘show_version’: promoterwise.c:17:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 17 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ -cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ localcispara.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ motifmatrix.c cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ motifmatrixdp.c +cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ transfactor.c +cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pairwiseshortdna.c +cc -g -O2 -ffile-prefix-map=/build/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c motifmatrix.c: In function ‘Wise2_MotifConsMatrix_alloc_matrix’: motifmatrix.c:408:24: warning: assignment to ‘char’ from ‘void *’ makes integer from pointer without a cast [-Wint-conversion] 408 | for(i=0;i kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tcrm1000 -mkdir: cannot create directory ‘././nonexistent’: Permission denied +mkdir: kataloogi ``././nonexistent'' ei õnnestu luua: Permission denied mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tcrm1000 This is METAFONT, Version 2.71828182 (TeX Live 2022/Debian) (preloaded base=mf) @@ -5655,18 +5698,18 @@ chmod -R u\+rw,go=rX debian/wise-doc/usr/share/doc install -p -m0644 debian/copyright debian/wise-doc/usr/share/doc/wise-doc/copyright install -m0755 -d debian/wise-doc/usr/share/doc-base/ + install -p -m0644 debian/wise-doc.doc-base.wise debian/wise-doc/usr/share/doc-base/wise-doc.wise install -p -m0644 debian/wise-doc.doc-base.dynamite debian/wise-doc/usr/share/doc-base/wise-doc.wise-dynamite install -p -m0644 debian/wise-doc.doc-base.api debian/wise-doc/usr/share/doc-base/wise-doc.wise-api - install -p -m0644 debian/wise-doc.doc-base.wise debian/wise-doc/usr/share/doc-base/wise-doc.wise install -m0755 -d debian/wise-data/usr/share/doc/wise-data install -p -m0644 debian/copyright debian/wise-data/usr/share/doc/wise-data/copyright dh_installchangelogs + install -m0755 -d debian/wise-doc/usr/share/doc/wise-doc + install -p -m0644 debian/.debhelper/generated/wise-doc/dh_installchangelogs.dch.trimmed debian/wise-doc/usr/share/doc/wise-doc/changelog.Debian install -m0755 -d debian/wise-data/usr/share/doc/wise-data install -p -m0644 debian/.debhelper/generated/wise-data/dh_installchangelogs.dch.trimmed debian/wise-data/usr/share/doc/wise-data/changelog.Debian install -m0755 -d debian/wise/usr/share/doc/wise install -p -m0644 debian/.debhelper/generated/wise/dh_installchangelogs.dch.trimmed debian/wise/usr/share/doc/wise/changelog.Debian - install -m0755 -d debian/wise-doc/usr/share/doc/wise-doc - install -p -m0644 debian/.debhelper/generated/wise-doc/dh_installchangelogs.dch.trimmed debian/wise-doc/usr/share/doc/wise-doc/changelog.Debian debian/rules override_dh_installexamples-indep make[1]: Entering directory '/build/wise-2.4.1' dh_installexamples @@ -5729,40 +5772,40 @@ install -p -m0644 ./debian/manpages.d/scanwise.1 debian/wise/usr/share/man/man1/scanwise.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/scanwise_server.1 debian/wise/usr/share/man/man1/scanwise_server.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/estwisedb.1 man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/dba.1 man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/dnal.1 man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/estwise.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/scanwise_server.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/genomewise.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/estwisedb.1 man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/genewise.1 man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/genewisedb.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/genomewise.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/promoterwise.1 man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/psw.1 man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/pswdb.1 man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/scanwise.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/promoterwise.1 - mv debian/wise/usr/share/man/man1/scanwise_server.1.dh-new debian/wise/usr/share/man/man1/scanwise_server.1 - chmod 0644 -- debian/wise/usr/share/man/man1/scanwise_server.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/scanwise_server.1 mv debian/wise/usr/share/man/man1/dnal.1.dh-new debian/wise/usr/share/man/man1/dnal.1 chmod 0644 -- debian/wise/usr/share/man/man1/dnal.1 mv debian/wise/usr/share/man/man1/estwise.1.dh-new debian/wise/usr/share/man/man1/estwise.1 chmod 0644 -- debian/wise/usr/share/man/man1/estwise.1 mv debian/wise/usr/share/man/man1/dba.1.dh-new debian/wise/usr/share/man/man1/dba.1 chmod 0644 -- debian/wise/usr/share/man/man1/dba.1 - mv debian/wise/usr/share/man/man1/genomewise.1.dh-new debian/wise/usr/share/man/man1/genomewise.1 - chmod 0644 -- debian/wise/usr/share/man/man1/genomewise.1 + mv debian/wise/usr/share/man/man1/genewisedb.1.dh-new debian/wise/usr/share/man/man1/genewisedb.1 + chmod 0644 -- debian/wise/usr/share/man/man1/genewisedb.1 + mv debian/wise/usr/share/man/man1/estwisedb.1.dh-new debian/wise/usr/share/man/man1/estwisedb.1 + chmod 0644 -- debian/wise/usr/share/man/man1/estwisedb.1 mv debian/wise/usr/share/man/man1/genewise.1.dh-new debian/wise/usr/share/man/man1/genewise.1 chmod 0644 -- debian/wise/usr/share/man/man1/genewise.1 - mv debian/wise/usr/share/man/man1/psw.1.dh-new debian/wise/usr/share/man/man1/psw.1 - chmod 0644 -- debian/wise/usr/share/man/man1/psw.1 mv debian/wise/usr/share/man/man1/pswdb.1.dh-new debian/wise/usr/share/man/man1/pswdb.1 chmod 0644 -- debian/wise/usr/share/man/man1/pswdb.1 - mv debian/wise/usr/share/man/man1/estwisedb.1.dh-new debian/wise/usr/share/man/man1/estwisedb.1 - chmod 0644 -- debian/wise/usr/share/man/man1/estwisedb.1 + mv debian/wise/usr/share/man/man1/genomewise.1.dh-new debian/wise/usr/share/man/man1/genomewise.1 + chmod 0644 -- debian/wise/usr/share/man/man1/genomewise.1 mv debian/wise/usr/share/man/man1/scanwise.1.dh-new debian/wise/usr/share/man/man1/scanwise.1 chmod 0644 -- debian/wise/usr/share/man/man1/scanwise.1 - mv debian/wise/usr/share/man/man1/genewisedb.1.dh-new debian/wise/usr/share/man/man1/genewisedb.1 - chmod 0644 -- debian/wise/usr/share/man/man1/genewisedb.1 + mv debian/wise/usr/share/man/man1/psw.1.dh-new debian/wise/usr/share/man/man1/psw.1 + chmod 0644 -- debian/wise/usr/share/man/man1/psw.1 + mv debian/wise/usr/share/man/man1/scanwise_server.1.dh-new debian/wise/usr/share/man/man1/scanwise_server.1 + chmod 0644 -- debian/wise/usr/share/man/man1/scanwise_server.1 mv debian/wise/usr/share/man/man1/promoterwise.1.dh-new debian/wise/usr/share/man/man1/promoterwise.1 chmod 0644 -- debian/wise/usr/share/man/man1/promoterwise.1 dh_perl @@ -5773,11 +5816,11 @@ cd debian/wise-doc cd debian/wise-data chmod a-x usr/share/doc/wise/changelog.Debian usr/share/man/man1/dba.1 usr/share/man/man1/dnal.1 usr/share/man/man1/estwise.1 usr/share/man/man1/estwisedb.1 usr/share/man/man1/genewise.1 usr/share/man/man1/genewisedb.1 usr/share/man/man1/genomewise.1 usr/share/man/man1/promoterwise.1 usr/share/man/man1/psw.1 usr/share/man/man1/pswdb.1 usr/share/man/man1/scanwise.1 usr/share/man/man1/scanwise_server.1 - chmod a-x usr/share/doc/wise-data/changelog.Debian chmod a-x usr/share/doc/wise-doc/changelog.Debian usr/share/doc/wise/api.pdf usr/share/doc/wise/dynamite.pdf usr/share/doc/wise/wise2.pdf + chmod a-x usr/share/doc/wise-data/changelog.Debian gzip -9nf usr/share/doc/wise/changelog.Debian usr/share/man/man1/dba.1 usr/share/man/man1/dnal.1 usr/share/man/man1/estwise.1 usr/share/man/man1/estwisedb.1 usr/share/man/man1/genewise.1 usr/share/man/man1/genewisedb.1 usr/share/man/man1/genomewise.1 usr/share/man/man1/promoterwise.1 usr/share/man/man1/psw.1 usr/share/man/man1/pswdb.1 usr/share/man/man1/scanwise.1 usr/share/man/man1/scanwise_server.1 - gzip -9nf usr/share/doc/wise-data/changelog.Debian gzip -9nf usr/share/doc/wise-doc/changelog.Debian usr/share/doc/wise/api.pdf usr/share/doc/wise/dynamite.pdf usr/share/doc/wise/wise2.pdf + gzip -9nf usr/share/doc/wise-data/changelog.Debian cd '/build/wise-2.4.1' cd '/build/wise-2.4.1' cd '/build/wise-2.4.1' @@ -5785,18 +5828,18 @@ debian/rules override_dh_fixperms make[1]: Entering directory '/build/wise-2.4.1' dh_fixperms - find debian/wise-data ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s - find debian/wise-doc ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/wise ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s - find debian/wise-data/usr/share/doc -type f -a -true -a ! -regex 'debian/wise-data/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 - find debian/wise-doc/usr/share/doc -type f -a -true -a ! -regex 'debian/wise-doc/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 + find debian/wise-doc ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s + find debian/wise-data ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/wise/usr/share/doc -type f -a -true -a ! -regex 'debian/wise/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 - find debian/wise-data/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 - find debian/wise-doc/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 + find debian/wise-doc/usr/share/doc -type f -a -true -a ! -regex 'debian/wise-doc/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 + find debian/wise-data/usr/share/doc -type f -a -true -a ! -regex 'debian/wise-data/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/wise/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 - find debian/wise-data -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 + find debian/wise-doc/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 + find debian/wise-data/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/wise-doc -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/wise/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 + find debian/wise-data -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/wise -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/wise/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian -iname "*.hmm" -exec chmod -x \{\} \; @@ -5808,26 +5851,26 @@ objcopy --compress-debug-sections debian/wise/usr/lib/debug/.dwz/x86_64-linux-gnu/wise.debug chmod 0644 -- debian/wise/usr/lib/debug/.dwz/x86_64-linux-gnu/wise.debug dh_strip - install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/fd - objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/estwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/fd/c453f002b1d767767f8ad8f2e56a4f4eb56d26.debug - chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/fd/c453f002b1d767767f8ad8f2e56a4f4eb56d26.debug - strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/estwise - objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/fd/c453f002b1d767767f8ad8f2e56a4f4eb56d26.debug debian/wise/usr/bin/estwise - install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/d3 - objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genewise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/d3/47d162b31fefda0ce1edfb499489405e4b1f40.debug - chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/d3/47d162b31fefda0ce1edfb499489405e4b1f40.debug - strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genewise - objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/d3/47d162b31fefda0ce1edfb499489405e4b1f40.debug debian/wise/usr/bin/genewise install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/06 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genewisedb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/06/1e6026b43be958314a239e7188fb67b1e95ba6.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/06/1e6026b43be958314a239e7188fb67b1e95ba6.debug strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genewisedb objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/06/1e6026b43be958314a239e7188fb67b1e95ba6.debug debian/wise/usr/bin/genewisedb + install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/d3 + objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genewise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/d3/47d162b31fefda0ce1edfb499489405e4b1f40.debug + chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/d3/47d162b31fefda0ce1edfb499489405e4b1f40.debug + strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genewise + objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/d3/47d162b31fefda0ce1edfb499489405e4b1f40.debug debian/wise/usr/bin/genewise install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/6a objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/estwisedb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/6a/1f40c39e3739e5da95499ecb89a23a1fffca68.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/6a/1f40c39e3739e5da95499ecb89a23a1fffca68.debug strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/estwisedb objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/6a/1f40c39e3739e5da95499ecb89a23a1fffca68.debug debian/wise/usr/bin/estwisedb + install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/fd + objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/estwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/fd/c453f002b1d767767f8ad8f2e56a4f4eb56d26.debug + chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/fd/c453f002b1d767767f8ad8f2e56a4f4eb56d26.debug + strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/estwise + objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/fd/c453f002b1d767767f8ad8f2e56a4f4eb56d26.debug debian/wise/usr/bin/estwise install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/f2 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/scanwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/f2/3f35a6566ab1a478e0525a240c6914996ccbaa.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/f2/3f35a6566ab1a478e0525a240c6914996ccbaa.debug @@ -5843,26 +5886,26 @@ chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/e7/8eba56cc06ec0b8b733b5d97206701d2e61107.debug strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/pswdb objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/e7/8eba56cc06ec0b8b733b5d97206701d2e61107.debug debian/wise/usr/bin/pswdb - install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/dc - objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/promoterwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/dc/14ae6585ba57e6d505812184dda701ede882f3.debug - chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/dc/14ae6585ba57e6d505812184dda701ede882f3.debug - strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/promoterwise - objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/dc/14ae6585ba57e6d505812184dda701ede882f3.debug debian/wise/usr/bin/promoterwise install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/c1 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/psw debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/c1/891bc726cb0cacd9ba320170c6871ad69c4d7a.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/c1/891bc726cb0cacd9ba320170c6871ad69c4d7a.debug strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/psw objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/c1/891bc726cb0cacd9ba320170c6871ad69c4d7a.debug debian/wise/usr/bin/psw - install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a1 - objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/dba debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a1/f98bc2a4fdf444829d2dac07defbf8623b36d9.debug - chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a1/f98bc2a4fdf444829d2dac07defbf8623b36d9.debug - strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/dba - objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a1/f98bc2a4fdf444829d2dac07defbf8623b36d9.debug debian/wise/usr/bin/dba + install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/dc + objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/promoterwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/dc/14ae6585ba57e6d505812184dda701ede882f3.debug + chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/dc/14ae6585ba57e6d505812184dda701ede882f3.debug + strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/promoterwise + objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/dc/14ae6585ba57e6d505812184dda701ede882f3.debug debian/wise/usr/bin/promoterwise install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/87 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genomewise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/87/251e29cb08d465c5194af0c247e097a8690a6e.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/87/251e29cb08d465c5194af0c247e097a8690a6e.debug strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genomewise objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/87/251e29cb08d465c5194af0c247e097a8690a6e.debug debian/wise/usr/bin/genomewise + install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a1 + objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/dba debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a1/f98bc2a4fdf444829d2dac07defbf8623b36d9.debug + chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a1/f98bc2a4fdf444829d2dac07defbf8623b36d9.debug + strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/dba + objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a1/f98bc2a4fdf444829d2dac07defbf8623b36d9.debug debian/wise/usr/bin/dba install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/42 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/dnal debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/42/40d51c5fa7bcb811194a6416c3d27ea085f613.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/42/40d51c5fa7bcb811194a6416c3d27ea085f613.debug @@ -5881,7 +5924,7 @@ rm -f debian/wise-data/DEBIAN/shlibs dh_shlibdeps install -m0755 -d debian/wise/DEBIAN - dpkg-shlibdeps -Tdebian/wise.substvars debian/wise/usr/bin/estwise debian/wise/usr/bin/genewise debian/wise/usr/bin/genewisedb debian/wise/usr/bin/estwisedb debian/wise/usr/bin/scanwise debian/wise/usr/bin/scanwise_server debian/wise/usr/bin/pswdb debian/wise/usr/bin/promoterwise debian/wise/usr/bin/psw debian/wise/usr/bin/dba debian/wise/usr/bin/genomewise debian/wise/usr/bin/dnal + dpkg-shlibdeps -Tdebian/wise.substvars debian/wise/usr/bin/genewisedb debian/wise/usr/bin/genewise debian/wise/usr/bin/estwisedb debian/wise/usr/bin/estwise debian/wise/usr/bin/scanwise debian/wise/usr/bin/scanwise_server debian/wise/usr/bin/pswdb debian/wise/usr/bin/psw debian/wise/usr/bin/promoterwise debian/wise/usr/bin/genomewise debian/wise/usr/bin/dba debian/wise/usr/bin/dnal dh_installdeb install -m0755 -d debian/wise/DEBIAN install -m0755 -d debian/wise-doc/DEBIAN @@ -5900,33 +5943,33 @@ echo misc:Depends= >> debian/wise-data.substvars echo misc:Pre-Depends= >> debian/wise-data.substvars dpkg-gencontrol -pwise-data -ldebian/changelog -Tdebian/wise-data.substvars -Pdebian/wise-data + chmod 0644 -- debian/wise-doc/DEBIAN/control + chmod 0644 -- debian/wise-data/DEBIAN/control chmod 0644 -- debian/.debhelper/wise/dbgsym-root/DEBIAN/control dpkg-gencontrol -pwise -ldebian/changelog -Tdebian/wise.substvars -Pdebian/wise - chmod 0644 -- debian/wise-doc/DEBIAN/control chmod 0644 -- debian/wise/DEBIAN/control - chmod 0644 -- debian/wise-data/DEBIAN/control dh_md5sums + install -m0755 -d debian/wise/DEBIAN install -m0755 -d debian/wise-data/DEBIAN install -m0755 -d debian/wise-doc/DEBIAN + cd debian/wise >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/wise-data >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums - install -m0755 -d debian/wise/DEBIAN cd debian/wise-doc >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums - cd debian/wise >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums - chmod 0644 -- debian/wise-doc/DEBIAN/md5sums chmod 0644 -- debian/wise-data/DEBIAN/md5sums + chmod 0644 -- debian/wise-doc/DEBIAN/md5sums chmod 0644 -- debian/wise/DEBIAN/md5sums install -m0755 -d debian/.debhelper/wise/dbgsym-root/DEBIAN cd debian/.debhelper/wise/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/wise/dbgsym-root/DEBIAN/md5sums dh_builddeb - dpkg-deb --root-owner-group --build debian/wise-data .. - dpkg-deb --root-owner-group --build debian/.debhelper/wise/dbgsym-root .. dpkg-deb --root-owner-group --build debian/wise .. + dpkg-deb --root-owner-group --build debian/.debhelper/wise/dbgsym-root .. dpkg-deb --root-owner-group --build debian/wise-doc .. -dpkg-deb: building package 'wise-data' in '../wise-data_2.4.1-23_all.deb'. -dpkg-deb: building package 'wise-dbgsym' in '../wise-dbgsym_2.4.1-23_amd64.deb'. + dpkg-deb --root-owner-group --build debian/wise-data .. dpkg-deb: building package 'wise' in '../wise_2.4.1-23_amd64.deb'. +dpkg-deb: building package 'wise-dbgsym' in '../wise-dbgsym_2.4.1-23_amd64.deb'. dpkg-deb: building package 'wise-doc' in '../wise-doc_2.4.1-23_all.deb'. +dpkg-deb: building package 'wise-data' in '../wise-data_2.4.1-23_all.deb'. dpkg-genbuildinfo --build=binary -O../wise_2.4.1-23_amd64.buildinfo dpkg-genchanges --build=binary -O../wise_2.4.1-23_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -5934,12 +5977,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/1379294/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1379294/tmp/hooks/B01_cleanup finished 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/760477 and its subdirectories -I: Current time: Tue Jun 6 04:24:49 -12 2023 -I: pbuilder-time-stamp: 1686068689 +I: removing directory /srv/workspace/pbuilder/1379294 and its subdirectories +I: Current time: Tue Jul 9 12:50:34 +14 2024 +I: pbuilder-time-stamp: 1720479034