Diff of the two buildlogs: -- --- b1/build.log 2025-03-10 14:36:31.147039843 +0000 +++ b2/build.log 2025-03-10 14:40:23.072679381 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Apr 12 08:56:55 -12 2026 -I: pbuilder-time-stamp: 1776027415 +I: Current time: Tue Mar 11 04:36:33 +14 2025 +I: pbuilder-time-stamp: 1741617393 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -40,54 +40,86 @@ dpkg-source: info: applying gcc-14.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/121021/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/33451/tmp/hooks/D01_modify_environment starting +debug: Running on ionos2-i386. +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 Mar 10 14:36 /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/33451/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/33451/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='i386' + 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]="37" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='719dc7dd58be48c3977c6bd87b72fc48' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='121021' - PS1='# ' - PS2='> ' + INVOCATION_ID=4794985264f54c41bc34dd89a5bf9a33 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-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=33451 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.VzFt06We/pbuilderrc_JPl5 --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.VzFt06We/b1 --logfile b1/build.log wise_2.4.1-25.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.VzFt06We/pbuilderrc_GBtQ --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.VzFt06We/b2 --logfile b2/build.log wise_2.4.1-25.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos6-i386 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/121021/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/33451/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -373,7 +405,7 @@ Get: 200 http://deb.debian.org/debian unstable/main i386 texlive-luatex all 2024.20250114-1 [28.0 MB] Get: 201 http://deb.debian.org/debian unstable/main i386 texlive-plain-generic all 2024.20250114-1 [28.9 MB] Get: 202 http://deb.debian.org/debian unstable/main i386 texlive-extra-utils all 2024.20250114-1 [67.6 MB] -Fetched 251 MB in 6s (42.7 MB/s) +Fetched 251 MB in 3s (75.2 MB/s) Preconfiguring packages ... Selecting previously unselected package m4. (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 ... 19769 files and directories currently installed.) @@ -1041,8 +1073,8 @@ Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' -Local time is now: Sun Apr 12 20:57:39 UTC 2026. -Universal Time is now: Sun Apr 12 20:57:39 UTC 2026. +Local time is now: Mon Mar 10 14:37:26 UTC 2025. +Universal Time is now: Mon Mar 10 14:37:26 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libsysprof-capture-4-dev:i386 (48~beta-2) ... @@ -1258,7 +1290,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/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_2.4.1-25_source.changes +I: user script /srv/workspace/pbuilder/33451/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/33451/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/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_2.4.1-25_source.changes dpkg-buildpackage: info: source package wise dpkg-buildpackage: info: source version 2.4.1-25 dpkg-buildpackage: info: source distribution unstable @@ -1345,7 +1381,7 @@ # Also, it pre-depends on the libwisebase library, otherwise # linking fails. dh_auto_build --sourcedirectory=src/base -- libwisebase.a - cd src/base && make -j22 "INSTALL=install --strip-program=true" libwisebase.a + cd src/base && make -j10 "INSTALL=install --strip-program=true" libwisebase.a make[2]: Entering directory '/build/reproducible-path/wise-2.4.1/src/base' cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread wiseconfig.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread wisestring.c @@ -1357,13 +1393,13 @@ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread wiseoverlay.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread wisestreaminterface.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread commandline.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread linesubs.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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread 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 ar: `u' modifier ignored since `D' is the default (see `U') ar: creating libwisebase.a @@ -1371,7 +1407,7 @@ if test -x /usr/bin/ranlib; then /usr/bin/ranlib libwisebase.a; else exit 0; fi make[2]: Leaving directory '/build/reproducible-path/wise-2.4.1/src/base' dh_auto_build --sourcedirectory=src/dyc -- dyc - cd src/dyc && make -j22 "INSTALL=install --strip-program=true" dyc + cd src/dyc && make -j10 "INSTALL=install --strip-program=true" dyc make[2]: Entering directory '/build/reproducible-path/wise-2.4.1/src/dyc' cc -pthread -c -g -DUNIX -I../base/ -I../base/ dyc.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ dyna2.c @@ -1393,11 +1429,6 @@ cc -pthread -c -g -DUNIX -I../base/ -I../base/ ftext.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ funcinfo.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ objectinfo.c -cc -pthread -c -g -DUNIX -I../base/ -I../base/ exprtree.c -cc -pthread -c -g -DUNIX -I../base/ -I../base/ compugen.c -cc -pthread -c -g -DUNIX -I../base/ -I../base/ docugen.c -cc -pthread -c -g -DUNIX -I../base/ -I../base/ input.c -cc -pthread -c -g -DUNIX -I../base/ -I../base/ dpimpl.c dynashadow.dy: In function ‘optimised_shadow_GenericMatrix’: dynashadow.dy:2180:31: warning: passing argument 2 of ‘write_main_shadow_block’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2180 | write_main_shadow_block(dfp,gm,"DC_OPT_SHADOW_MATRIX","mat","DC_OPT_SHADOW_SPECIAL","DC_OPT_SHADOW_MATRIX_SP","DC_OPT_SHADOW_SPECIAL_SP",7,TRUE,TRUE,0,TRUE); @@ -1412,6 +1443,11 @@ dynashadow.h:189:63: note: expected ‘GenericMatrix *’ but argument is of type ‘const GenericMatrix *’ 189 | void write_special_shadow_block(DYNFILE * dfp,GenericMatrix * gm,char * matrix,char * pointer_tag,char * special,char * shadow_main_tag,char * shadow_special_tag,int shadow_length,boolean shadow_on_special,int debug); | ~~~~~~~~~~~~~~~~^~ +cc -pthread -c -g -DUNIX -I../base/ -I../base/ exprtree.c +cc -pthread -c -g -DUNIX -I../base/ -I../base/ compugen.c +cc -pthread -c -g -DUNIX -I../base/ -I../base/ docugen.c +cc -pthread -c -g -DUNIX -I../base/ -I../base/ input.c +cc -pthread -c -g -DUNIX -I../base/ -I../base/ dpimpl.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ dbthread.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ probal.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ telegraph.c @@ -1423,7 +1459,7 @@ make[2]: Leaving directory '/build/reproducible-path/wise-2.4.1/src/dyc' PATH="$PATH:/build/reproducible-path/wise-2.4.1/src/dyc" \ dh_auto_build --sourcedirectory=src -- all - cd src && make -j22 "INSTALL=install --strip-program=true" all + cd src && make -j10 "INSTALL=install --strip-program=true" all make[2]: Entering directory '/build/reproducible-path/wise-2.4.1/src' (cd base ; make CC="cc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c `pkg-config --cflags glib-2.0`" libwisebase.a ) make[3]: Entering directory '/build/reproducible-path/wise-2.4.1/src/base' @@ -1452,7 +1488,6 @@ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c cluster.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c dayhoff.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c file.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c getopt.c file.c: In function ‘EnvFileOpen’: file.c:159:26: warning: ‘%s’ directive writing up to 1022 bytes into a region of size between 1 and 1023 [-Wformat-overflow=] 159 | sprintf(full, "%s%c%s", s, DIRSLASH, fname); @@ -1468,6 +1503,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c getopt.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c gnuregex.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c interleaved.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c iupac.c @@ -1538,18 +1574,6 @@ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ shattermatrix.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ matrixdebug.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ dpenvelope.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ dbsearchimpl.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ dprunimpl.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ complexsequence.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ complexevalset.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ complexconsensi.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ sequence.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ sequencestream.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ seqalign.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hitlist.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hsp.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hspstream.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ codon.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); @@ -1562,6 +1586,18 @@ 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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ dbsearchimpl.c +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ dprunimpl.c +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ complexsequence.c +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ complexevalset.c +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ complexconsensi.c +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ sequence.c +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ sequencestream.c +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ seqalign.c +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hitlist.c +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hsp.c +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hspstream.c +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ codon.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ compmat.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ codonmatrix.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ codonmapper.c @@ -1592,12 +1628,12 @@ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ transcript.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ translation.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ btcanvas.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ asciibtcanvas.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ dynlibcross.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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ asciibtcanvas.c +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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 ar: `u' modifier ignored since `D' is the default (see `U') ar: creating libdyna.a @@ -1616,14 +1652,13 @@ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hsp2hitscan.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hsplookupscan.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hsplookupthreaded.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hspthreadeddb.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hspscanruntime.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hsptwohitscan.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ proteinindexcons.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ dnaindexcons.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ staticseq.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 ‘unsigned int’ [-Wformat=] + 285 | fprintf(ofp,"Head memory %d [%.2f Mbytes]\n",total_head,(total_head*sizeof(ShadowArraySeqHead))/100000); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + | | + | unsigned int hsp2hitscan.dy: In function ‘Wise2_one_off_two_hit_HSPscan_query_direct’: -hsplookupthreaded.dy: In function ‘Wise2_one_off_ordered_HSPscan_scan_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", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1655,11 +1690,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | long int -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 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", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1757,18 +1787,24 @@ intallocator.dy:216:15: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘unsigned int’ [-Wformat=] 216 | fprintf(ofp,"%d blocks allocated, using %ld bytes\n",ia->current_allocated_block,ia->current_allocated_block * (sizeof(IntAllocatorHeader)+(sizeof(int)*ia->size)) * IntAllocator_BLOCKSIZE); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 ‘unsigned int’ [-Wformat=] - 285 | fprintf(ofp,"Head memory %d [%.2f Mbytes]\n",total_head,(total_head*sizeof(ShadowArraySeqHead))/100000); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - | | - | unsigned 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 +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hspthreadeddb.c +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hspscanruntime.c +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hsptwohitscan.c +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ proteinindexcons.c +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ dnaindexcons.c hspthreadeddb.dy: In function ‘Wise2_threadeddb_scan_worker’: 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 * +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ staticseq.c 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 @@ -1834,9 +1870,7 @@ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models dnamapping.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models largeseqreader.c dyc -l -n Wise2_ -pthreads -dbtrace 5 -nocwarn kmer_assembly_untangler.dy -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_contig.c -Warning Errorcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_error.c - +Warning Error Could not open [methods] for MethodTypeSet reading Warning Error You have no config file called 'methods'. This is bad news for @@ -1846,36 +1880,9 @@ Warning Error kmer_assembly_untangler.dy:24: For element long - got no good default. Returning 0 -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models assembly.c Warning Error You have 14 undocumented functions -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models assembly_stream_interface.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models assembly_stream_fasta.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models assembly_sanger_project.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models assembly_stream_cons.c -dyc -l -n Wise2_ -pthreads -dbtrace 5 -nocwarn compressed_protein_index.dy -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_untangler.c -Warning Error - Could not open [methods] for MethodTypeSet reading -Warning Error - You have no config file called 'methods'. This is bad news for -dynamite matrices. I will attempt to compile, but you cannot use -logical types. 'methods' should be either in the current directory, -the $WISECONFIGDIR or your $WISEPERSONALDIR -Warning Error - You have 16 undocumented functions -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models compressed_protein_index.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); - | ^~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | kmer_t {aka long long int} -kmer_hash.dy:319:19: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] - 319 | fprintf(stderr, "max_kmer: %016lx\n", khi->max_kmer); - | ^~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | kmer_t {aka long long int} +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_contig.c kmer_assembly.dy: In function ‘Wise2_show_KmerAssemblyNode’: kmer_assembly.dy:296:15: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 296 | fprintf(ofp,"Node %ld of sequence %s \n",node->number,buffer); @@ -1901,6 +1908,32 @@ 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]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +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); + | ^~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | kmer_t {aka long long int} +kmer_hash.dy:319:19: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] + 319 | fprintf(stderr, "max_kmer: %016lx\n", khi->max_kmer); + | ^~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | kmer_t {aka long long int} +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_error.c +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models assembly.c +kmer_glib_index.dy: In function ‘Wise2_retrieve_by_kmer_KmerGlibIndex’: +kmer_glib_index.dy:77:48: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] + 77 | return (void*) g_hash_table_lookup(kgi->hash,(gconstpointer)kmer); + | ^ +kmer_glib_index.dy: In function ‘Wise2_insert_by_kmer_KmerGlibIndex’: +kmer_glib_index.dy:84:33: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] + 84 | g_hash_table_insert(kgi->hash,(gpointer)kmer,poi); + | ^ +kmer_glib_index.dy: In function ‘Wise2_retrieve_active_kmer_KmerGlibIndex’: +kmer_glib_index.dy:124:40: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 124 | kgi->active_index[kgi->kmer_pos++] = (kmer_t) key; + | ^ +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models assembly_stream_interface.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); @@ -1912,12 +1945,27 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models assembly_stream_fasta.c 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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models assembly_sanger_project.c +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models assembly_stream_cons.c +dyc -l -n Wise2_ -pthreads -dbtrace 5 -nocwarn compressed_protein_index.dy +Warning Error + Could not open [methods] for MethodTypeSet reading +Warning Error + You have no config file called 'methods'. This is bad news for +dynamite matrices. I will attempt to compile, but you cannot use +logical types. 'methods' should be either in the current directory, +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_untangler.c +the $WISECONFIGDIR or your $WISEPERSONALDIR +Warning Error + You have 16 undocumented functions +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models compressed_protein_index.c kmer_assembly_untangler.dy: In function ‘Wise2_untangle_KmerAssembly’: kmer_assembly_untangler.dy:120:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 120 | fprintf(stderr,"TANGLE: Node %ld, %s has forward %d and back %d links\n",node->number,buffer,node->next_len,node->prev_len); @@ -1961,18 +2009,6 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | kmer_t {aka long long int} -kmer_glib_index.dy: In function ‘Wise2_retrieve_by_kmer_KmerGlibIndex’: -kmer_glib_index.dy:77:48: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] - 77 | return (void*) g_hash_table_lookup(kgi->hash,(gconstpointer)kmer); - | ^ -kmer_glib_index.dy: In function ‘Wise2_insert_by_kmer_KmerGlibIndex’: -kmer_glib_index.dy:84:33: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] - 84 | g_hash_table_insert(kgi->hash,(gpointer)kmer,poi); - | ^ -kmer_glib_index.dy: In function ‘Wise2_retrieve_active_kmer_KmerGlibIndex’: -kmer_glib_index.dy:124:40: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 124 | kgi->active_index[kgi->kmer_pos++] = (kmer_t) key; - | ^ make[3]: Leaving directory '/build/reproducible-path/wise-2.4.1/src/dnaindex' (cd network ; make CC="cc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c `pkg-config --cflags glib-2.0`" all ) make[3]: Entering directory '/build/reproducible-path/wise-2.4.1/src/network' @@ -1997,34 +2033,38 @@ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ pba.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ pswdb.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ dbac.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); + | ^~~~~~~~~~~~ +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); + | ^~~~~~~~~~~~ +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); + | ^~~~~~~~~~~~ +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); + | ^~~~~~~~~~~~ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ dba.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ slimdba.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ bigdba.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ dbadisplay.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread estwise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ geneparser21.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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ geneparameter.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genestats.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genewisehsp.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ geneutil.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ geneoutput.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ threestatemodel.c -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); - | ^~~~~~~~~~~~ -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); - | ^~~~~~~~~~~~ -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); - | ^~~~~~~~~~~~ -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); - | ^~~~~~~~~~~~ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genefrequency.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ splicesitemodeler.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genewise4.c @@ -2032,10 +2072,6 @@ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genestretch6.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genewise21.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ geneloop21.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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ geneloop6.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genephase6.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ gwlite.c @@ -2045,14 +2081,10 @@ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ estwrap.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genewisemodel.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ phasemodel.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ cdparser.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genedisplay.c phasemodel.dy: In function ‘Wise2_read_fasta_PhasedProtein’: 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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ estwise3.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ estslim3.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); | ^~~~~~~~~~~~~~~~~~~~~ @@ -2069,17 +2101,21 @@ /usr/include/i386-linux-gnu/bits/stdio2.h:305:1: note: in a call to function ‘fgets’ declared with attribute ‘access (write_only, 1, 2)’ 305 | fgets (__fortify_clang_overload_arg (char *, __restrict, __s), int __n, | ^~~~~ +In function ‘fgets’, + inlined from ‘Wise2_read_fasta_PhasedProtein’ at phasemodel.dy:241:3: +/usr/include/i386-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ cdparser.c +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genedisplay.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); | ^~~~~~~~~~~~~~~~ +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ estwise3.c +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ estslim3.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ estloop3.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ estfrag3.c -In function ‘fgets’, - inlined from ‘Wise2_read_fasta_PhasedProtein’ at phasemodel.dy:241:3: -/usr/include/i386-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ estslimloop.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ gwquickdb.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ threestatedb.c @@ -2094,21 +2130,25 @@ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread genewise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread genewisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread estwisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genomewise.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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); - | ^~~~~~~~~~~~ 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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genome_evidence.c 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); | ^~~~~~~~~~~~ +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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genomewise.c +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genome_evidence.c dyc -l -D -n Wise2_ -a _api.h -b _api.t -latex -perl -pthreads -dbtrace 5 -nocwarn est_evidence.dy Warning Error Could not open [methods] for MethodTypeSet reading @@ -2149,31 +2189,27 @@ You have not documented est_utr_pot Warning Error You have 15 undocumented functions -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ sywise.c +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ sywise20.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ syexonmodel.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ pseudowise.c +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ pseudowise7.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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ pseudowise7.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` promoterwise.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ localdba.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` localcishit.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` localcishit.c +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ localcispara.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ motifmatrix.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ motifmatrixdp.c motifmatrix.c: In function ‘Wise2_MotifConsMatrix_alloc_matrix’: @@ -2183,8 +2219,11 @@ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ transfactor.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ pairwiseshortdna.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c +scanwisep.c: In function ‘show_version’: +scanwisep.c:423:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 423 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); + | ^~~~~~~~~~~~ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` hsp2aln_sw.c -cc -o dnal dnal.o dnaalign.o seqaligndisplay.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm transfactor.dy: In function ‘Wise2_read_ben_IUPAC_TransFactorSet’: transfactor.dy:680:21: warning: ‘%s’ directive writing up to 511 bytes into a region of size between 495 and 504 [-Wformat-overflow=] 680 | sprintf(sbuffer,"motif_%d_%s",motif_no,buffer); @@ -2203,18 +2242,15 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +cc -o dnal dnal.o dnaalign.o seqaligndisplay.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm cc -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm -scanwisep.c: In function ‘show_version’: -scanwisep.c:423:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - 423 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); - | ^~~~~~~~~~~~ cc -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm cc -o dba dbac.o dba.o slimdba.o bigdba.o dbadisplay.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ est_evidence.c cc -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o ../network/client_multihspscan.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase -lm -lpthread -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` cc -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm `pkg-config --libs glib-2.0` -lpthread -cc -g -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm cc -g -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm +cc -g -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm cc -g -o estwise estwise.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` cc -o genewise genewise.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` cc -g -o genewisedb genewisedb.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` @@ -6134,18 +6170,18 @@ 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.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 -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 -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/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-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-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/reproducible-path/wise-2.4.1' dh_installexamples @@ -6208,42 +6244,30 @@ 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/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/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/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/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 + 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/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/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/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 + 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/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/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/estwise.1 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/promoterwise.1.dh-new debian/wise/usr/share/man/man1/promoterwise.1 - chmod 0644 -- debian/wise/usr/share/man/man1/promoterwise.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 + 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/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/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 + 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 - chmod 0644 -- debian/wise/usr/share/man/man1/dba.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/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 dh_perl dh_link dh_strip_nondeterminism @@ -6253,8 +6277,8 @@ cd debian/wise-data 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/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 + 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/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/reproducible-path/wise-2.4.1' @@ -6270,11 +6294,11 @@ 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/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/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/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 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 @@ -6297,56 +6321,56 @@ chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/0e/21006b1f24702f0334522becf571c65183ccd3.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/0e/21006b1f24702f0334522becf571c65183ccd3.debug debian/wise/usr/bin/promoterwise + install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a4 + objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genewisedb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a4/e756ab0deb5511959ae66eb61da4f475a15abd.debug + chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a4/e756ab0deb5511959ae66eb61da4f475a15abd.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/a4/e756ab0deb5511959ae66eb61da4f475a15abd.debug debian/wise/usr/bin/genewisedb + install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/97 + objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/dnal debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/97/926e3a985789aa6f79ee3bb63579a4f9ccdf44.debug + chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/97/926e3a985789aa6f79ee3bb63579a4f9ccdf44.debug + strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/dnal + objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/97/926e3a985789aa6f79ee3bb63579a4f9ccdf44.debug debian/wise/usr/bin/dnal install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/02 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/estwisedb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/02/7b7bff96100a160122a85f40d2c852f4f1566b.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/02/7b7bff96100a160122a85f40d2c852f4f1566b.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/02/7b7bff96100a160122a85f40d2c852f4f1566b.debug debian/wise/usr/bin/estwisedb - 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/scanwise_server debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/6a/11d5c45466a3d7b5acdf75f4741da3285eb56d.debug - chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/6a/11d5c45466a3d7b5acdf75f4741da3285eb56d.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/6a/11d5c45466a3d7b5acdf75f4741da3285eb56d.debug debian/wise/usr/bin/scanwise_server - install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/f8 - objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/scanwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/f8/c89aa624943b48ac1d91df06dd6710fdad512f.debug - chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/f8/c89aa624943b48ac1d91df06dd6710fdad512f.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/f8/c89aa624943b48ac1d91df06dd6710fdad512f.debug debian/wise/usr/bin/scanwise - install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/fc - objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/pswdb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/fc/6c537aed1ef8d6edede0badebf7b0dd7c07b82.debug - chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/fc/6c537aed1ef8d6edede0badebf7b0dd7c07b82.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/fc/6c537aed1ef8d6edede0badebf7b0dd7c07b82.debug debian/wise/usr/bin/pswdb install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/5b objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/estwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/5b/22ca38aaf4ce76e185f2d42570589da1311286.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/5b/22ca38aaf4ce76e185f2d42570589da1311286.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/5b/22ca38aaf4ce76e185f2d42570589da1311286.debug debian/wise/usr/bin/estwise - install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/73 - objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genomewise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/73/a692bd38b4856b834779495cca399f19ebc1ff.debug - chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/73/a692bd38b4856b834779495cca399f19ebc1ff.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/73/a692bd38b4856b834779495cca399f19ebc1ff.debug debian/wise/usr/bin/genomewise install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/c8 objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/dba debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/c8/b66f47965563e786ba8fb661b8ffe823575c96.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/c8/b66f47965563e786ba8fb661b8ffe823575c96.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/c8/b66f47965563e786ba8fb661b8ffe823575c96.debug debian/wise/usr/bin/dba + 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/scanwise_server debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/6a/11d5c45466a3d7b5acdf75f4741da3285eb56d.debug + chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/6a/11d5c45466a3d7b5acdf75f4741da3285eb56d.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/6a/11d5c45466a3d7b5acdf75f4741da3285eb56d.debug debian/wise/usr/bin/scanwise_server install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/fe objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/psw debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/fe/867db777233e01fb5318fc58c543a4abbdeb3b.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/fe/867db777233e01fb5318fc58c543a4abbdeb3b.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/fe/867db777233e01fb5318fc58c543a4abbdeb3b.debug debian/wise/usr/bin/psw - install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/97 - objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/dnal debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/97/926e3a985789aa6f79ee3bb63579a4f9ccdf44.debug - chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/97/926e3a985789aa6f79ee3bb63579a4f9ccdf44.debug - strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/dnal - objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/97/926e3a985789aa6f79ee3bb63579a4f9ccdf44.debug debian/wise/usr/bin/dnal - install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a4 - objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genewisedb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a4/e756ab0deb5511959ae66eb61da4f475a15abd.debug - chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a4/e756ab0deb5511959ae66eb61da4f475a15abd.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/a4/e756ab0deb5511959ae66eb61da4f475a15abd.debug debian/wise/usr/bin/genewisedb + install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/f8 + objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/scanwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/f8/c89aa624943b48ac1d91df06dd6710fdad512f.debug + chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/f8/c89aa624943b48ac1d91df06dd6710fdad512f.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/f8/c89aa624943b48ac1d91df06dd6710fdad512f.debug debian/wise/usr/bin/scanwise + install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/73 + objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genomewise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/73/a692bd38b4856b834779495cca399f19ebc1ff.debug + chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/73/a692bd38b4856b834779495cca399f19ebc1ff.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/73/a692bd38b4856b834779495cca399f19ebc1ff.debug debian/wise/usr/bin/genomewise + install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/fc + objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/pswdb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/fc/6c537aed1ef8d6edede0badebf7b0dd7c07b82.debug + chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/fc/6c537aed1ef8d6edede0badebf7b0dd7c07b82.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/fc/6c537aed1ef8d6edede0badebf7b0dd7c07b82.debug debian/wise/usr/bin/pswdb install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/wise/usr/lib/debug/.dwz/i386-linux-gnu debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/wise/usr/lib/debug/.dwz @@ -6358,16 +6382,12 @@ rm -f debian/wise/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/wise/DEBIAN - dpkg-shlibdeps -Tdebian/wise.substvars debian/wise/usr/bin/genewise debian/wise/usr/bin/promoterwise debian/wise/usr/bin/estwisedb debian/wise/usr/bin/scanwise_server debian/wise/usr/bin/scanwise debian/wise/usr/bin/pswdb debian/wise/usr/bin/estwise debian/wise/usr/bin/genomewise debian/wise/usr/bin/dba debian/wise/usr/bin/psw debian/wise/usr/bin/dnal debian/wise/usr/bin/genewisedb + dpkg-shlibdeps -Tdebian/wise.substvars debian/wise/usr/bin/genewise debian/wise/usr/bin/promoterwise debian/wise/usr/bin/genewisedb debian/wise/usr/bin/dnal debian/wise/usr/bin/estwisedb debian/wise/usr/bin/estwise debian/wise/usr/bin/dba debian/wise/usr/bin/scanwise_server debian/wise/usr/bin/psw debian/wise/usr/bin/scanwise debian/wise/usr/bin/genomewise debian/wise/usr/bin/pswdb dh_installdeb install -m0755 -d debian/wise/DEBIAN install -m0755 -d debian/wise-doc/DEBIAN install -m0755 -d debian/wise-data/DEBIAN dh_gencontrol - install -m0755 -d debian/wise-data/DEBIAN - 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 -cdebian/control -Pdebian/wise-data install -m0755 -d debian/wise-doc/DEBIAN echo misc:Depends= >> debian/wise-doc.substvars echo misc:Pre-Depends= >> debian/wise-doc.substvars @@ -6377,18 +6397,22 @@ echo misc:Pre-Depends= >> debian/wise.substvars install -m0755 -d debian/.debhelper/wise/dbgsym-root/DEBIAN dpkg-gencontrol -pwise -ldebian/changelog -Tdebian/wise.substvars -cdebian/control -Pdebian/.debhelper/wise/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=wise-dbgsym "-DDepends=wise (= \${binary:Version})" "-DDescription=debug symbols for wise" "-DBuild-Ids=027b7bff96100a160122a85f40d2c852f4f1566b 069efa6a23f309dd926dd9ae4e9eef2b57a2b0c9 0e21006b1f24702f0334522becf571c65183ccd3 5b22ca38aaf4ce76e185f2d42570589da1311286 6a11d5c45466a3d7b5acdf75f4741da3285eb56d 73a692bd38b4856b834779495cca399f19ebc1ff 97926e3a985789aa6f79ee3bb63579a4f9ccdf44 a4e756ab0deb5511959ae66eb61da4f475a15abd c8b66f47965563e786ba8fb661b8ffe823575c96 f8c89aa624943b48ac1d91df06dd6710fdad512f fc6c537aed1ef8d6edede0badebf7b0dd7c07b82 fe867db777233e01fb5318fc58c543a4abbdeb3b" -DSection=debug -UMulti-Arch -UReplaces -UBreaks - chmod 0644 -- debian/wise-doc/DEBIAN/control + install -m0755 -d debian/wise-data/DEBIAN + 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 -cdebian/control -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 -cdebian/control -Pdebian/wise chmod 0644 -- debian/wise/DEBIAN/control dh_md5sums install -m0755 -d debian/wise/DEBIAN - install -m0755 -d debian/wise-doc/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-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 + cd debian/wise-doc >/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/DEBIAN/md5sums @@ -6402,8 +6426,8 @@ dpkg-deb --root-owner-group --build debian/wise-data .. dpkg-deb: building package 'wise' in '../wise_2.4.1-25_i386.deb'. dpkg-deb: building package 'wise-dbgsym' in '../wise-dbgsym_2.4.1-25_i386.deb'. -dpkg-deb: building package 'wise-doc' in '../wise-doc_2.4.1-25_all.deb'. dpkg-deb: building package 'wise-data' in '../wise-data_2.4.1-25_all.deb'. +dpkg-deb: building package 'wise-doc' in '../wise-doc_2.4.1-25_all.deb'. dpkg-genbuildinfo --build=binary -O../wise_2.4.1-25_i386.buildinfo dpkg-genchanges --build=binary -O../wise_2.4.1-25_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -6411,12 +6435,14 @@ 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/33451/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/33451/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/121021 and its subdirectories -I: Current time: Sun Apr 12 08:59:28 -12 2026 -I: pbuilder-time-stamp: 1776027568 +I: removing directory /srv/workspace/pbuilder/33451 and its subdirectories +I: Current time: Tue Mar 11 04:40:22 +14 2025 +I: pbuilder-time-stamp: 1741617622