Diff of the two buildlogs: -- --- b1/build.log 2023-05-10 05:07:07.246174329 +0000 +++ b2/build.log 2023-05-10 05:14:03.727938916 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue May 9 17:01:27 -12 2023 -I: pbuilder-time-stamp: 1683694887 +I: Current time: Wed Jun 12 01:30:11 +14 2024 +I: pbuilder-time-stamp: 1718105411 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 @@ -40,52 +40,84 @@ dpkg-source: info: applying cross.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/21667/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2962/tmp/hooks/D01_modify_environment starting +debug: Running on codethink9-arm64. +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 Jun 12 01:30 /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/2962/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2962/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='arm64' - DEBIAN_FRONTEND='noninteractive' + 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]="aarch64-unknown-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=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' - DISTRIBUTION='bookworm' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - 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='21667' - PS1='# ' - PS2='> ' + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-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=2962 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.YGxJyQAZ/pbuilderrc_vsKO --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.YGxJyQAZ/b1 --logfile b1/build.log wise_2.4.1-23.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + 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.YGxJyQAZ/pbuilderrc_Xxjs --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.YGxJyQAZ/b2 --logfile b2/build.log --extrapackages usrmerge wise_2.4.1-23.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink10-arm64 4.15.0-210-generic #221-Ubuntu SMP Tue Apr 18 08:32:48 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-210-generic #221-Ubuntu SMP Tue Apr 18 08:32:48 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 7 22:24 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/21667/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 11 06:48 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2962/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -301,7 +333,7 @@ Get: 168 http://deb.debian.org/debian bookworm/main arm64 texlive-luatex all 2022.20230122-3 [22.7 MB] Get: 169 http://deb.debian.org/debian bookworm/main arm64 texlive-plain-generic all 2022.20230122-4 [28.9 MB] Get: 170 http://deb.debian.org/debian bookworm/main arm64 texlive-extra-utils all 2022.20230122-4 [59.0 MB] -Fetched 227 MB in 14s (16.3 MB/s) +Fetched 227 MB in 8s (28.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libfftw3-double3:arm64. (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 ... 19616 files and directories currently installed.) @@ -1041,8 +1073,17 @@ 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/2962/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/2962/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +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 @@ -1052,16 +1093,16 @@ debian/rules clean dh clean debian/rules override_dh_clean -make[1]: Entering directory '/build/wise-2.4.1' +make[1]: Map '/build/wise-2.4.1' wordt binnengegaan /usr/bin/make -C src clean -make[2]: Entering directory '/build/wise-2.4.1/src' +make[2]: Map '/build/wise-2.4.1/src' wordt binnengegaan cd external ; /usr/bin/make clean -make[3]: Entering directory '/build/wise-2.4.1/src/external' +make[3]: Map '/build/wise-2.4.1/src/external' wordt binnengegaan (cd mott; make clean) -make[4]: Entering directory '/build/wise-2.4.1/src/external/mott' +make[4]: Map '/build/wise-2.4.1/src/external/mott' wordt binnengegaan rm -f *.[oa] -make[4]: Leaving directory '/build/wise-2.4.1/src/external/mott' -make[3]: Leaving directory '/build/wise-2.4.1/src/external' +make[4]: Map '/build/wise-2.4.1/src/external/mott' wordt verlaten +make[3]: Map '/build/wise-2.4.1/src/external' wordt verlaten if test -d dynlibsrc; then cd dynlibsrc ; rm -f *.[oa]; fi if test -d models; then cd models ; rm -f *.[oa]; fi if test -d base; then cd base ; rm -f *.[oa]; fi @@ -1074,11 +1115,11 @@ if test -x perl/Wise2/Makefile; then cd perl/Wise2/ ; /usr/bin/make clean; fi if test -d oldbin; then rm -rf oldbin; fi if test -d bin; then echo 'moving binaries to oldbin'; mv -f bin oldbin; fi -make[2]: Leaving directory '/build/wise-2.4.1/src' +make[2]: Map '/build/wise-2.4.1/src' wordt verlaten /usr/bin/make -C debian/manpages.d clean -make[2]: Entering directory '/build/wise-2.4.1/debian/manpages.d' +make[2]: Map '/build/wise-2.4.1/debian/manpages.d' wordt binnengegaan rm -f dba.1 dnal.1 estwise.1 estwisedb.1 genewise.1 genewisedb.1 genomewise.1 promoterwise.1 psw.1 pswdb.1 scanwise.1 scanwise_server.1 -make[2]: Leaving directory '/build/wise-2.4.1/debian/manpages.d' +make[2]: Map '/build/wise-2.4.1/debian/manpages.d' wordt verlaten rm -f -r src/oldbin for i in dba psw dnal genomewise pswdb scanwise estwise genewise sywise genewisedb promoterwise pseudowise estwisedb; do rm -f src/models/$i; done rm -f src/network/scanwise_server @@ -1118,18 +1159,18 @@ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) -make[1]: Leaving directory '/build/wise-2.4.1' +make[1]: Map '/build/wise-2.4.1' wordt verlaten debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_build -make[1]: Entering directory '/build/wise-2.4.1' +make[1]: Map '/build/wise-2.4.1' wordt binnengegaan dh_auto_build --sourcedirectory=src -- all cd src && make -j8 "INSTALL=install --strip-program=true" all -make[2]: Entering directory '/build/wise-2.4.1/src' +make[2]: Map '/build/wise-2.4.1/src' wordt binnengegaan (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' +make[3]: Map '/build/wise-2.4.1/src/base' wordt binnengegaan 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/aarch64-linux-gnu/glib-2.0/include wiseconfig.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/aarch64-linux-gnu/glib-2.0/include wisestring.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/aarch64-linux-gnu/glib-2.0/include wiseerror.c @@ -1138,13 +1179,13 @@ 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/aarch64-linux-gnu/glib-2.0/include wiserandom.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/aarch64-linux-gnu/glib-2.0/include wisetime.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/aarch64-linux-gnu/glib-2.0/include wiseoverlay.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/aarch64-linux-gnu/glib-2.0/include wisestreaminterface.c wisefile.dy: In function ‘Wise2_myfclose’: wisefile.dy:72:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘FILE *’ [-Wformat=] 72 | fprintf(stderr,"Closing %d\n",ofp); | ^~~~~~~~~~~~~~ ~~~ | | | FILE * +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/aarch64-linux-gnu/glib-2.0/include wisestreaminterface.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/aarch64-linux-gnu/glib-2.0/include commandline.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/aarch64-linux-gnu/glib-2.0/include linesubs.c ar ru libwisebase.a wiseconfig.o wisestring.o wiseerror.o wisememman.o wisefile.o wiserandom.o wisetime.o wiseoverlay.o wisestreaminterface.o commandline.o linesubs.o @@ -1152,9 +1193,9 @@ ar: creating libwisebase.a if test -x /bin/ranlib; then /bin/ranlib libwisebase.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libwisebase.a; else exit 0; fi -make[3]: Leaving directory '/build/wise-2.4.1/src/base' +make[3]: Map '/build/wise-2.4.1/src/base' wordt verlaten (cd HMMer2 ; 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`" libhmmer.a ) -make[3]: Entering directory '/build/wise-2.4.1/src/HMMer2' +make[3]: Map '/build/wise-2.4.1/src/HMMer2' wordt binnengegaan 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/aarch64-linux-gnu/glib-2.0/include -c alphabet.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/aarch64-linux-gnu/glib-2.0/include -c core_algorithms.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/aarch64-linux-gnu/glib-2.0/include -c debug.c @@ -1187,8 +1228,6 @@ 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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-linux-gnu/glib-2.0/include -c msf.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]) @@ -1310,6 +1349,8 @@ 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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-linux-gnu/glib-2.0/include -c sqerror.c @@ -1363,9 +1404,9 @@ if test -x /usr/bin/ranlib; then /usr/bin/ranlib libhmmer.a; else exit 0; fi if test -x ranlib; then ranlib libhmmer.a; else exit 0; fi chmod 644 libhmmer.a -make[3]: Leaving directory '/build/wise-2.4.1/src/HMMer2' +make[3]: Map '/build/wise-2.4.1/src/HMMer2' wordt verlaten (cd dynlibsrc ; 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`" libdyna.a ) -make[3]: Entering directory '/build/wise-2.4.1/src/dynlibsrc' +make[3]: Map '/build/wise-2.4.1/src/dynlibsrc' wordt binnengegaan 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/aarch64-linux-gnu/glib-2.0/include -I../base/ packaln.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/aarch64-linux-gnu/glib-2.0/include -I../base/ aln.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/aarch64-linux-gnu/glib-2.0/include -I../base/ dnamatrix.c @@ -1429,11 +1470,11 @@ 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/aarch64-linux-gnu/glib-2.0/include -I../base/ gene.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/aarch64-linux-gnu/glib-2.0/include -I../base/ transcript.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/aarch64-linux-gnu/glib-2.0/include -I../base/ translation.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/aarch64-linux-gnu/glib-2.0/include -I../base/ btcanvas.c genomicregion.dy: In function ‘Wise2_read_EMBL_FT_into_GenomicRegion’: genomicregion.dy:756:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 756 | fgets(buffer,maxlen,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/aarch64-linux-gnu/glib-2.0/include -I../base/ btcanvas.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/aarch64-linux-gnu/glib-2.0/include -I../base/ asciibtcanvas.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/aarch64-linux-gnu/glib-2.0/include -I../base/ dynlibcross.c ar ru libdyna.a packaln.o aln.o dnamatrix.o probability.o alnrange.o alnconvert.o basematrix.o shattermatrix.o matrixdebug.o dpenvelope.o dbsearchimpl.o dprunimpl.o complexsequence.o complexevalset.o complexconsensi.o sequence.o sequencestream.o seqalign.o hitlist.o hsp.o hspstream.o codon.o compmat.o codonmatrix.o codonmapper.o sequencedb.o hscore.o seqlookup.o arrayseqlookup.o genericindexresult.o linkedlist_lookpos.o singlenumberspace.o histogram.o searchstatinterface.o searchstatlookup.o proteindb.o protein.o pairbase.o pairbaseseq.o genomicdb.o randommodel.o randomdb.o genomic.o cdna.o cdnadb.o dna.o embl.o genomicregion.o gene.o transcript.o translation.o btcanvas.o asciibtcanvas.o dynlibcross.o @@ -1441,9 +1482,9 @@ ar: creating libdyna.a if test -x /bin/ranlib; then /bin/ranlib libdyna.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libdyna.a; else exit 0; fi -make[3]: Leaving directory '/build/wise-2.4.1/src/dynlibsrc' +make[3]: Map '/build/wise-2.4.1/src/dynlibsrc' wordt verlaten (cd dynlibsrc ; 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`" libdyna_glib.a ) -make[3]: Entering directory '/build/wise-2.4.1/src/dynlibsrc' +make[3]: Map '/build/wise-2.4.1/src/dynlibsrc' wordt binnengegaan 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/aarch64-linux-gnu/glib-2.0/include -I../base/ subseqhash.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/aarch64-linux-gnu/glib-2.0/include -I../base/ intallocator.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/aarch64-linux-gnu/glib-2.0/include -I../base/ proteinstreamedindex.c @@ -1452,12 +1493,6 @@ 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/aarch64-linux-gnu/glib-2.0/include -I../base/ hsphandler.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/aarch64-linux-gnu/glib-2.0/include -I../base/ hspscaninterface.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/aarch64-linux-gnu/glib-2.0/include -I../base/ hsp2hitscan.c -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 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 ) { @@ -1480,6 +1515,12 @@ 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/aarch64-linux-gnu/glib-2.0/include -I../base/ hsplookupscan.c 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=] @@ -1610,12 +1651,6 @@ 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/aarch64-linux-gnu/glib-2.0/include -I../base/ hspthreadeddb.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/aarch64-linux-gnu/glib-2.0/include -I../base/ hspscanruntime.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/aarch64-linux-gnu/glib-2.0/include -I../base/ hsptwohitscan.c -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 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); @@ -1625,6 +1660,12 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~ | | | 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 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/aarch64-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/aarch64-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/aarch64-linux-gnu/glib-2.0/include -I../base/ staticseq.c @@ -1633,12 +1674,12 @@ ar: creating libdyna_glib.a if test -x /bin/ranlib; then /bin/ranlib libdyna_glib.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libdyna_glib.a; else exit 0; fi -make[3]: Leaving directory '/build/wise-2.4.1/src/dynlibsrc' +make[3]: Map '/build/wise-2.4.1/src/dynlibsrc' wordt verlaten (cd external ; 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`" all ) -make[3]: Entering directory '/build/wise-2.4.1/src/external' +make[3]: Map '/build/wise-2.4.1/src/external' wordt binnengegaan (cd mott; 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 -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include " all) -make[4]: Entering directory '/build/wise-2.4.1/src/external/mott' -make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. +make[4]: Map '/build/wise-2.4.1/src/external/mott' wordt binnengegaan +make[4]: Waarschuwing: taakserver is onbeschikbaar: '-j1' wordt gebruikt. Voeg '+' toe aan de ouderregel. 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/aarch64-linux-gnu/glib-2.0/include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mott_api.o mott_api.c mott_api.c: In function ‘InitPvaluesMott’: mott_api.c:64:3: warning: implicit declaration of function ‘free’ [-Wimplicit-function-declaration] @@ -1693,10 +1734,10 @@ ar: creating libmott.a if test -x /bin/ranlib; then /bin/ranlib libmott.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libmott.a; else exit 0; fi -make[4]: Leaving directory '/build/wise-2.4.1/src/external/mott' -make[3]: Leaving directory '/build/wise-2.4.1/src/external' +make[4]: Map '/build/wise-2.4.1/src/external/mott' wordt verlaten +make[3]: Map '/build/wise-2.4.1/src/external' wordt verlaten (cd socket ; 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`" libwisesocket.a ) -make[3]: Entering directory '/build/wise-2.4.1/src/socket' +make[3]: Map '/build/wise-2.4.1/src/socket' wordt binnengegaan 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/aarch64-linux-gnu/glib-2.0/include -I../base/ functionserver.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/aarch64-linux-gnu/glib-2.0/include -I../base/ functionclient.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/aarch64-linux-gnu/glib-2.0/include -I../base/ anonobj.c @@ -1727,9 +1768,9 @@ ar: creating libwisesocket.a if test -x /bin/ranlib; then /bin/ranlib libwisesocket.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libwisesocket.a; else exit 0; fi -make[3]: Leaving directory '/build/wise-2.4.1/src/socket' +make[3]: Map '/build/wise-2.4.1/src/socket' wordt verlaten (cd dnaindex ; 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`" all ) -make[3]: Entering directory '/build/wise-2.4.1/src/dnaindex' +make[3]: Map '/build/wise-2.4.1/src/dnaindex' wordt binnengegaan 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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_index_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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_direct.c @@ -1779,9 +1820,6 @@ 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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_contig.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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_error.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/aarch64-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/aarch64-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/aarch64-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_sanger_project.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); @@ -1812,6 +1850,7 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | 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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_interface.c kmer_assembly_untangler.dy: In function ‘Wise2_old_attempt_forward_untangle_KmerAssembly’: 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); @@ -1838,6 +1877,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | 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/aarch64-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/aarch64-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); @@ -1861,9 +1902,9 @@ 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; | ^~~~ -make[3]: Leaving directory '/build/wise-2.4.1/src/dnaindex' +make[3]: Map '/build/wise-2.4.1/src/dnaindex' wordt verlaten (cd network ; 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`" all ) -make[3]: Entering directory '/build/wise-2.4.1/src/network' +make[3]: Map '/build/wise-2.4.1/src/network' wordt binnengegaan 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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../socket -I../dynlibsrc -I../dnaindex wise_proteinindex_server.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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../socket -I../dynlibsrc -I../dnaindex net_hspscan.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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../socket -I../dynlibsrc -I../dnaindex client_multihspscan.c @@ -1872,9 +1913,9 @@ 28 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ cc -g -o scanwise_server wise_proteinindex_server.o net_hspscan.o ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o -ldyna_glib -ldyna -lwisesocket -lwisebase -Wl,-z,relro -Wl,-z,now -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config --libs glib-2.0` -lpthread -make[3]: Leaving directory '/build/wise-2.4.1/src/network' +make[3]: Map '/build/wise-2.4.1/src/network' wordt verlaten (cd models ; 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`" EXTRALIBS="-lm" HMMER_DEFINE="HMMER_INTERNAL" HMMER_INCLUDE="../HMMer2/" HMMER_LIBS="../HMMer2/" all ) -make[3]: Entering directory '/build/wise-2.4.1/src/models' +make[3]: Map '/build/wise-2.4.1/src/models' wordt binnengegaan 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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ dnal.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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ dnaalign.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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ seqaligndisplay.c @@ -1893,6 +1934,8 @@ | ^~~~~~~~~~~~ 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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pswdb.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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ dbac.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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ dba.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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ slimdba.c 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); @@ -1908,8 +1951,6 @@ | | | | int size_t {aka long unsigned int} | %ld -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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ dba.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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ slimdba.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/aarch64-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/aarch64-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/aarch64-linux-gnu/glib-2.0/include estwise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. @@ -1960,11 +2001,6 @@ /usr/include/aarch64-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) | ^~~~~ -In function ‘fgets’, - inlined from ‘Wise2_read_fasta_PhasedProtein’ at phasemodel.dy:241:3: -/usr/include/aarch64-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ cdparser.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/aarch64-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estwise3.c @@ -1972,6 +2008,11 @@ genedisplay.dy:493:20: warning: too many arguments for format [-Wformat-extra-args] 493 | sprintf(buffer," Intron ??? ",in_number); | ^~~~~~~~~~~~~~~~ +In function ‘fgets’, + inlined from ‘Wise2_read_fasta_PhasedProtein’ at phasemodel.dy:241:3: +/usr/include/aarch64-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/aarch64-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/aarch64-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estfrag3.c @@ -1998,27 +2039,27 @@ | ^~~~~~~~~~~~ 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/aarch64-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/aarch64-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/aarch64-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); - | ^~~~~~~~~~~~ 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); | ^~~~~~~~~~~~ +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/aarch64-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genome_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/aarch64-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/aarch64-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/aarch64-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/aarch64-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] 14 | 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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ sywise20.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/aarch64-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/aarch64-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pseudowise7.c @@ -2028,18 +2069,18 @@ | ^~~~~~~~~~~~ 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/aarch64-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/aarch64-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` localcishit.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/aarch64-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/aarch64-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/aarch64-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ motifmatrixdp.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 dba.1 docbook-to-man dnal.sgml > dnal.1 docbook-to-man estwise.sgml > estwise.1 @@ -2120,7 +2161,7 @@ docbook-to-man pswdb.sgml > pswdb.1 docbook-to-man scanwise.sgml > scanwise.1 docbook-to-man scanwise_server.sgml > scanwise_server.1 -make[2]: Leaving directory '/build/wise-2.4.1/debian/manpages.d' +make[2]: Map '/build/wise-2.4.1/debian/manpages.d' wordt verlaten find src/models/ src/dynlibsrc/ -name '*.tex' -print0 | LC_ALL=C sort -z | xargs -0 cat | perl docs/gettex.pl > docs/temp.tex cat docs/wise2api.tex docs/temp.tex docs/apiend.tex > docs/api.tex sed -i 's/ sw_wrap / sw\\_wrap /' docs/api.tex @@ -3176,7 +3217,7 @@ [107] [108] (./api.aux) kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tctt1000 -mkdir: cannot create directory ‘././nonexistent’: Permission denied +mkdir: kan map ‘././nonexistent’ niet aanmaken: Toegang geweigerd mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tctt1000 This is METAFONT, Version 2.71828182 (TeX Live 2022/Debian) (preloaded base=mf) @@ -3219,7 +3260,7 @@ (see the transcript file for additional information) kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tcrm1000 -mkdir: cannot create directory ‘././nonexistent’: Permission denied +mkdir: kan map ‘././nonexistent’ niet aanmaken: Toegang geweigerd 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) @@ -5526,16 +5567,16 @@ mv docs/dynamite.html docs/dynamite mv docs/wise2.html docs/wise2 dh_auto_build -make[1]: Leaving directory '/build/wise-2.4.1' +make[1]: Map '/build/wise-2.4.1' wordt verlaten rm -f debian/wise-data.debhelper.log debian/wise-doc.debhelper.log debian/wise.debhelper.log debian/rules override_dh_auto_test -make[1]: Entering directory '/build/wise-2.4.1' +make[1]: Map '/build/wise-2.4.1' wordt binnengegaan echo "Since a patch was used to adapt the binaries to the Debian locations of data files the test suite will not run in the build directory any more." Since a patch was used to adapt the binaries to the Debian locations of data files the test suite will not run in the build directory any more. echo "A autopkgtest was added as compensation." A autopkgtest was added as compensation. # make -C src test -make[1]: Leaving directory '/build/wise-2.4.1' +make[1]: Map '/build/wise-2.4.1' wordt verlaten create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/wise.substvars debian/wise-doc.substvars debian/wise-data.substvars @@ -5568,8 +5609,8 @@ 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.api debian/wise-doc/usr/share/doc-base/wise-doc.wise-api - 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.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 -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 @@ -5580,7 +5621,7 @@ 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 debian/rules override_dh_installexamples-indep -make[1]: Entering directory '/build/wise-2.4.1' +make[1]: Map '/build/wise-2.4.1' wordt binnengegaan dh_installexamples install -m0755 -d debian/wise-data/usr/share/doc/wise-data/examples cp --reflink=auto -a ./src/test/basic_cdna.out debian/wise-data/usr/share/doc/wise-data/examples @@ -5614,7 +5655,7 @@ cp --reflink=auto -a ./src/test/wrong.out debian/wise-data/usr/share/doc/wise-data/examples cp --reflink=auto -a ./src/test/wrong_est.out debian/wise-data/usr/share/doc/wise-data/examples sed -i -e 's?"../bin/$do"?"$do"?' -e 's?#!/usr/local/bin/perl?/usr/bin/perl?' debian/wise-data/usr/share/doc/wise-data/examples/testman.pl -make[1]: Leaving directory '/build/wise-2.4.1' +make[1]: Map '/build/wise-2.4.1' wordt verlaten dh_installexamples -Nwise-doc -Nwise-data dh_installman install -m0755 -d debian/wise/usr/share/man/man1/ @@ -5643,28 +5684,28 @@ 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/dba.1 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 debian/wise/usr/share/man/man1/estwisedb.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/genomewise.1 debian/wise/usr/share/man/man1/promoterwise.1 man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/genewise.1 debian/wise/usr/share/man/man1/genewisedb.1 man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/psw.1 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 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 debian/wise/usr/share/man/man1/promoterwise.1 mv debian/wise/usr/share/man/man1/estwise.1.dh-new debian/wise/usr/share/man/man1/estwise.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/estwise.1 debian/wise/usr/share/man/man1/estwisedb.1 - mv debian/wise/usr/share/man/man1/scanwise.1.dh-new debian/wise/usr/share/man/man1/scanwise.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.1 debian/wise/usr/share/man/man1/scanwise_server.1 - mv debian/wise/usr/share/man/man1/psw.1.dh-new 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/psw.1 debian/wise/usr/share/man/man1/pswdb.1 - mv debian/wise/usr/share/man/man1/genomewise.1.dh-new debian/wise/usr/share/man/man1/genomewise.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/genomewise.1 debian/wise/usr/share/man/man1/promoterwise.1 mv debian/wise/usr/share/man/man1/genewise.1.dh-new debian/wise/usr/share/man/man1/genewise.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/genewise.1 debian/wise/usr/share/man/man1/genewisedb.1 + mv debian/wise/usr/share/man/man1/genomewise.1.dh-new debian/wise/usr/share/man/man1/genomewise.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/genomewise.1 debian/wise/usr/share/man/man1/promoterwise.1 + mv debian/wise/usr/share/man/man1/scanwise.1.dh-new debian/wise/usr/share/man/man1/scanwise.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.1 debian/wise/usr/share/man/man1/scanwise_server.1 mv debian/wise/usr/share/man/man1/dba.1.dh-new debian/wise/usr/share/man/man1/dba.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/dba.1 debian/wise/usr/share/man/man1/dnal.1 + mv debian/wise/usr/share/man/man1/psw.1.dh-new 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/psw.1 debian/wise/usr/share/man/man1/pswdb.1 dh_perl dh_link dh_strip_nondeterminism @@ -5672,25 +5713,25 @@ cd debian/wise cd debian/wise-doc cd debian/wise-data + 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 - 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 + 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 - 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 - 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/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 cd '/build/wise-2.4.1' + 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 cd '/build/wise-2.4.1' - 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 cd '/build/wise-2.4.1' rm -f debian/wise-data.debhelper.log debian/wise-doc.debhelper.log debian/rules override_dh_fixperms -make[1]: Entering directory '/build/wise-2.4.1' +make[1]: Map '/build/wise-2.4.1' wordt binnengegaan dh_fixperms 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-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-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-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/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/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 @@ -5700,7 +5741,7 @@ 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 \{\} \; -make[1]: Leaving directory '/build/wise-2.4.1' +make[1]: Map '/build/wise-2.4.1' wordt verlaten dh_missing dh_dwz install -m0755 -d debian/wise/usr/lib/debug/.dwz/aarch64-linux-gnu @@ -5713,11 +5754,6 @@ chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/c0/88713aace23a0d7b9caec576fc98e74f420cb8.debug strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/scanwise objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/c0/88713aace23a0d7b9caec576fc98e74f420cb8.debug debian/wise/usr/bin/scanwise - install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a8 - objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/scanwise_server debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a8/f4fec5ad51fb0673a33f2478e5133afb85beff.debug - chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a8/f4fec5ad51fb0673a33f2478e5133afb85beff.debug - strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/scanwise_server - objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a8/f4fec5ad51fb0673a33f2478e5133afb85beff.debug debian/wise/usr/bin/scanwise_server install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/45 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/pswdb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/45/7e9023d6c8a28a2873c88ac233ed5ff098ca29.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/45/7e9023d6c8a28a2873c88ac233ed5ff098ca29.debug @@ -5728,31 +5764,36 @@ chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/1b/81212812d42e3b1868f1dab134e90938d49e6d.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/1b/81212812d42e3b1868f1dab134e90938d49e6d.debug debian/wise/usr/bin/psw + install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a8 + objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/scanwise_server debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a8/f4fec5ad51fb0673a33f2478e5133afb85beff.debug + chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a8/f4fec5ad51fb0673a33f2478e5133afb85beff.debug + strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/scanwise_server + objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a8/f4fec5ad51fb0673a33f2478e5133afb85beff.debug debian/wise/usr/bin/scanwise_server install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/be objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/promoterwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/be/554d786eaf6d1b34bfb92fa4305d3d8b2745c6.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/be/554d786eaf6d1b34bfb92fa4305d3d8b2745c6.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/be/554d786eaf6d1b34bfb92fa4305d3d8b2745c6.debug debian/wise/usr/bin/promoterwise - install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/38 - objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genomewise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/38/e6a64dcb97dd04a98b39d29b15ef97ab7d77d5.debug - chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/38/e6a64dcb97dd04a98b39d29b15ef97ab7d77d5.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/38/e6a64dcb97dd04a98b39d29b15ef97ab7d77d5.debug debian/wise/usr/bin/genomewise - install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/41 - objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genewisedb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/41/5a9b1d9ae52026c07b00068519dd83a26c82c0.debug - chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/41/5a9b1d9ae52026c07b00068519dd83a26c82c0.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/41/5a9b1d9ae52026c07b00068519dd83a26c82c0.debug debian/wise/usr/bin/genewisedb install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b3 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genewise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b3/4201f245edac45d6a7a3320bb63da1bfcc06f9.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b3/4201f245edac45d6a7a3320bb63da1bfcc06f9.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/b3/4201f245edac45d6a7a3320bb63da1bfcc06f9.debug debian/wise/usr/bin/genewise + install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/41 + objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genewisedb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/41/5a9b1d9ae52026c07b00068519dd83a26c82c0.debug + chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/41/5a9b1d9ae52026c07b00068519dd83a26c82c0.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/41/5a9b1d9ae52026c07b00068519dd83a26c82c0.debug debian/wise/usr/bin/genewisedb install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b9 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/estwisedb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b9/03cd7b29f6d2950c69da70e4ab472e2545a0ee.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b9/03cd7b29f6d2950c69da70e4ab472e2545a0ee.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/b9/03cd7b29f6d2950c69da70e4ab472e2545a0ee.debug debian/wise/usr/bin/estwisedb + install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/38 + objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genomewise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/38/e6a64dcb97dd04a98b39d29b15ef97ab7d77d5.debug + chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/38/e6a64dcb97dd04a98b39d29b15ef97ab7d77d5.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/38/e6a64dcb97dd04a98b39d29b15ef97ab7d77d5.debug debian/wise/usr/bin/genomewise install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/fb objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/estwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/fb/ac30688c40c85207f8288ec689019fdf799531.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/fb/ac30688c40c85207f8288ec689019fdf799531.debug @@ -5781,7 +5822,7 @@ rm -f debian/wise-data/DEBIAN/shlibs dh_shlibdeps install -m0755 -d debian/wise/DEBIAN - dpkg-shlibdeps -Tdebian/wise.substvars debian/wise/usr/bin/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/genewisedb debian/wise/usr/bin/genewise debian/wise/usr/bin/estwisedb debian/wise/usr/bin/estwise debian/wise/usr/bin/dba debian/wise/usr/bin/dnal + dpkg-shlibdeps -Tdebian/wise.substvars debian/wise/usr/bin/scanwise debian/wise/usr/bin/pswdb debian/wise/usr/bin/psw debian/wise/usr/bin/scanwise_server debian/wise/usr/bin/promoterwise debian/wise/usr/bin/genewise debian/wise/usr/bin/genewisedb debian/wise/usr/bin/estwisedb debian/wise/usr/bin/genomewise debian/wise/usr/bin/estwise 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 @@ -5800,33 +5841,33 @@ 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-data/DEBIAN/control - chmod 0644 -- debian/wise-doc/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-data/DEBIAN/control chmod 0644 -- debian/wise/DEBIAN/control dh_md5sums - install -m0755 -d debian/wise-doc/DEBIAN 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 + install -m0755 -d debian/wise-data/DEBIAN cd debian/wise-doc >/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 - chmod 0644 -- debian/wise-data/DEBIAN/md5sums chmod 0644 -- debian/wise-doc/DEBIAN/md5sums + chmod 0644 -- debian/wise-data/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 .. - dpkg-deb --root-owner-group --build debian/.debhelper/wise/dbgsym-root .. dpkg-deb --root-owner-group --build debian/wise-doc .. dpkg-deb --root-owner-group --build debian/wise-data .. -dpkg-deb: building package 'wise-dbgsym' in '../wise-dbgsym_2.4.1-23_arm64.deb'. -dpkg-deb: building package 'wise' in '../wise_2.4.1-23_arm64.deb'. -dpkg-deb: building package 'wise-data' in '../wise-data_2.4.1-23_all.deb'. -dpkg-deb: building package 'wise-doc' in '../wise-doc_2.4.1-23_all.deb'. + dpkg-deb --root-owner-group --build debian/.debhelper/wise/dbgsym-root .. +dpkg-deb: pakket 'wise' wordt gebouwd in '../wise_2.4.1-23_arm64.deb'. +dpkg-deb: pakket 'wise-dbgsym' wordt gebouwd in '../wise-dbgsym_2.4.1-23_arm64.deb'. +dpkg-deb: pakket 'wise-doc' wordt gebouwd in '../wise-doc_2.4.1-23_all.deb'. +dpkg-deb: pakket 'wise-data' wordt gebouwd in '../wise-data_2.4.1-23_all.deb'. dpkg-genbuildinfo --build=binary -O../wise_2.4.1-23_arm64.buildinfo dpkg-genchanges --build=binary -O../wise_2.4.1-23_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -5834,12 +5875,14 @@ 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/2962/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2962/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/21667 and its subdirectories -I: Current time: Tue May 9 17:07:06 -12 2023 -I: pbuilder-time-stamp: 1683695226 +I: removing directory /srv/workspace/pbuilder/2962 and its subdirectories +I: Current time: Wed Jun 12 01:37:02 +14 2024 +I: pbuilder-time-stamp: 1718105822