Diff of the two buildlogs: -- --- b1/build.log 2024-05-04 05:57:40.413439982 +0000 +++ b2/build.log 2024-05-04 05:58:59.922053918 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri May 3 17:53:39 -12 2024 -I: pbuilder-time-stamp: 1714802019 +I: Current time: Sat May 4 19:57:51 +14 2024 +I: pbuilder-time-stamp: 1714802271 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -33,52 +33,84 @@ dpkg-source: info: applying mayhem.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/29538/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/28010/tmp/hooks/D01_modify_environment starting +debug: Running on virt32z. +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 May 4 05:58 /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/28010/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/28010/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='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='armhf' + 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]="21" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='5f2686ea7da54b21ace68ec73a5e3ead' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='29538' - PS1='# ' - PS2='> ' + INVOCATION_ID=5b537683214c432ea7073664d0c8169d + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + 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=28010 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.6gM1z0Qz/pbuilderrc_z8pM --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.6gM1z0Qz/b1 --logfile b1/build.log probcons_1.12-14.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + 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.6gM1z0Qz/pbuilderrc_V89O --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.6gM1z0Qz/b2 --logfile b2/build.log probcons_1.12-14.dsc' + SUDO_GID=110 + SUDO_UID=103 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux virt64b 6.1.0-20-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-armmp-lpae #1 SMP Debian 6.1.85-1 (2024-04-11) armv7l GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 2 11:24 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/29538/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 1 11:24 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/28010/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -144,7 +176,7 @@ Get: 28 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf debhelper all 13.15.3 [901 kB] -Fetched 18.4 MB in 1s (32.6 MB/s) +Fetched 18.4 MB in 0s (77.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19441 files and directories currently installed.) @@ -279,7 +311,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/probcons-1.12/ && 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 > ../probcons_1.12-14_source.changes +I: user script /srv/workspace/pbuilder/28010/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/28010/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/probcons-1.12/ && 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 > ../probcons_1.12-14_source.changes dpkg-buildpackage: info: source package probcons dpkg-buildpackage: info: source version 1.12-14 dpkg-buildpackage: info: source distribution unstable @@ -289,7 +325,7 @@ debian/rules clean dh clean dh_auto_clean - make -j3 clean + make -j4 clean make[1]: Entering directory '/build/reproducible-path/probcons-1.12' rm -f probcons probcons-RNA pc-compare pc-project pc-makegnuplot make[1]: Leaving directory '/build/reproducible-path/probcons-1.12' @@ -308,11 +344,12 @@ sed -i s/Defaults.h/Defaults-RNA.h/ Main-RNA.cc cp debian/Defaults-RNA.h Defaults-RNA.h dh_auto_build - make -j3 "INSTALL=install --strip-program=true" + make -j4 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/probcons-1.12' g++ -O3 -W -Wall -pedantic -DNDEBUG -DNumInsertStates=2 -DVERSION="1.12" -funroll-loops -g -O2 -ffile-prefix-map=/build/reproducible-path/probcons-1.12=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -lm -o probcons Main.cc -Wl,-z,relro -Wl,-z,now g++ -O3 -W -Wall -pedantic -DNDEBUG -DNumInsertStates=1 -DVERSION="1.12" -funroll-loops -g -O2 -ffile-prefix-map=/build/reproducible-path/probcons-1.12=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -lm -o probcons-RNA Main-RNA.cc -Wl,-z,relro -Wl,-z,now g++ -O3 -W -Wall -pedantic -DNDEBUG -DNumInsertStates=2 -DVERSION="1.12" -funroll-loops -g -O2 -ffile-prefix-map=/build/reproducible-path/probcons-1.12=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -o pc-compare CompareToRef.cc -Wl,-z,relro -Wl,-z,now +g++ -O3 -W -Wall -pedantic -DNDEBUG -DNumInsertStates=2 -DVERSION="1.12" -funroll-loops -g -O2 -ffile-prefix-map=/build/reproducible-path/probcons-1.12=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -o pc-project ProjectPairwise.cc -Wl,-z,relro -Wl,-z,now In file included from MultiSequence.h:18, from CompareToRef.cc:9: Sequence.h: In member function 'Sequence* Sequence::Clone() const': @@ -324,25 +361,40 @@ 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ In file included from MultiSequence.h:18, - from Main.cc:8: + from ProjectPairwise.cc:9: Sequence.h: In member function 'Sequence* Sequence::Clone() const': Sequence.h:293:21: warning: implicitly-declared 'SafeVector& SafeVector::operator=(const SafeVector&)' is deprecated [-Wdeprecated-copy] 293 | *(ret->data) = *data; | ^~~~ -In file included from Main.cc:7: +In file included from ProjectPairwise.cc:8: SafeVector.h:29:3: note: because 'SafeVector' has user-provided 'SafeVector::SafeVector(const SafeVector&) [with TYPE = char]' 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ In file included from MultiSequence.h:18, + from Main.cc:8: +Sequence.h: In member function 'Sequence* Sequence::Clone() const': +Sequence.h:293:21: warning: implicitly-declared 'SafeVector& SafeVector::operator=(const SafeVector&)' is deprecated [-Wdeprecated-copy] + 293 | *(ret->data) = *data; + | ^~~~ +In file included from MultiSequence.h:18, from Main-RNA.cc:8: Sequence.h: In member function 'Sequence* Sequence::Clone() const': Sequence.h:293:21: warning: implicitly-declared 'SafeVector& SafeVector::operator=(const SafeVector&)' is deprecated [-Wdeprecated-copy] 293 | *(ret->data) = *data; | ^~~~ +In file included from Main.cc:7: +SafeVector.h:29:3: note: because 'SafeVector' has user-provided 'SafeVector::SafeVector(const SafeVector&) [with TYPE = char]' + 29 | SafeVector (const SafeVector &source) : std::vector(source) {} + | ^~~~~~~~~~ In file included from Main-RNA.cc:7: SafeVector.h:29:3: note: because 'SafeVector' has user-provided 'SafeVector::SafeVector(const SafeVector&) [with TYPE = char]' 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ +In file included from Main-RNA.cc:11: +ProbabilisticModel.h: In member function 'void ProbabilisticModel::ComputeNewParameters(Sequence*, Sequence*, const VF&, const VF&, VF&, VF&, VF&, VVF&, VF&, bool) const': +ProbabilisticModel.h:493:38: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 493 | if (enableTrainEmissions && i != 1 || j != 1){ + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ In file included from Main.cc:11: ProbabilisticModel.h: In member function 'void ProbabilisticModel::ComputeNewParameters(Sequence*, Sequence*, const VF&, const VF&, VF&, VF&, VF&, VVF&, VF&, bool) const': ProbabilisticModel.h:493:38: warning: suggest parentheses around '&&' within '||' [-Wparentheses] @@ -352,15 +404,17 @@ ProbabilisticModel.h:1027:18: warning: variable 'postPtr' set but not used [-Wunused-but-set-variable] 1027 | VF::iterator postPtr = posterior.begin(); | ^~~~~~~ -In file included from Main-RNA.cc:11: -ProbabilisticModel.h: In member function 'void ProbabilisticModel::ComputeNewParameters(Sequence*, Sequence*, const VF&, const VF&, VF&, VF&, VF&, VVF&, VF&, bool) const': -ProbabilisticModel.h:493:38: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 493 | if (enableTrainEmissions && i != 1 || j != 1){ - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ ProbabilisticModel.h: In member function 'VF* ProbabilisticModel::BuildPosterior(MultiSequence*, MultiSequence*, const SafeVector >&, float) const': ProbabilisticModel.h:1027:18: warning: variable 'postPtr' set but not used [-Wunused-but-set-variable] 1027 | VF::iterator postPtr = posterior.begin(); | ^~~~~~~ +Main-RNA.cc: In function 'void PrintParameters(const char*, const VF&, const VF&, const VF&, const VVF&, const VF&, const char*)': +Main-RNA.cc:282:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation] + 282 | for (int i = 0; i < NumMatrixTypes; i++) fprintf (file, "%.10f ", initDistrib[i]); fprintf (file, "\n"); + | ^~~ +Main-RNA.cc:282:88: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' + 282 | for (int i = 0; i < NumMatrixTypes; i++) fprintf (file, "%.10f ", initDistrib[i]); fprintf (file, "\n"); + | ^~~~~~~ Main.cc: In function 'void PrintParameters(const char*, const VF&, const VF&, const VF&, const VVF&, const VF&, const char*)': Main.cc:282:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 282 | for (int i = 0; i < NumMatrixTypes; i++) fprintf (file, "%.10f ", initDistrib[i]); fprintf (file, "\n"); @@ -368,18 +422,37 @@ Main.cc:282:88: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 282 | for (int i = 0; i < NumMatrixTypes; i++) fprintf (file, "%.10f ", initDistrib[i]); fprintf (file, "\n"); | ^~~~~~~ +Main-RNA.cc:283:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation] + 283 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapOpen[i]); fprintf (file, "\n"); + | ^~~ +Main-RNA.cc:283:87: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' + 283 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapOpen[i]); fprintf (file, "\n"); + | ^~~~~~~ Main.cc:283:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 283 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapOpen[i]); fprintf (file, "\n"); | ^~~ Main.cc:283:87: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 283 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapOpen[i]); fprintf (file, "\n"); | ^~~~~~~ +Main-RNA.cc:284:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation] + 284 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapExtend[i]); fprintf (file, "\n"); + | ^~~ +Main-RNA.cc:284:89: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' + 284 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapExtend[i]); fprintf (file, "\n"); + | ^~~~~~~ Main.cc:284:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 284 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapExtend[i]); fprintf (file, "\n"); | ^~~ Main.cc:284:89: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 284 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapExtend[i]); fprintf (file, "\n"); | ^~~~~~~ +Main-RNA.cc: In function 'MultiSequence* DoAlign(MultiSequence*, const ProbabilisticModel&, VF&, VF&, VF&, VVF&, VF&)': +Main-RNA.cc:400:13: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 400 | if (enableVerbose) + | ^~ +Main-RNA.cc:403:15: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 403 | delete alignment.first; + | ^~~~~~ Main.cc: In function 'MultiSequence* DoAlign(MultiSequence*, const ProbabilisticModel&, VF&, VF&, VF&, VVF&, VF&)': Main.cc:400:13: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 400 | if (enableVerbose) @@ -387,69 +460,32 @@ Main.cc:403:15: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 403 | delete alignment.first; | ^~~~~~ -Main.cc: In function 'void ReadParameters()': -Main.cc:893:40: warning: implicitly-declared 'SafeVector >& SafeVector >::operator=(const SafeVector >&)' is deprecated [-Wdeprecated-copy] +Main-RNA.cc: In function 'void ReadParameters()': +Main-RNA.cc:893:40: warning: implicitly-declared 'SafeVector >& SafeVector >::operator=(const SafeVector >&)' is deprecated [-Wdeprecated-copy] 893 | emitPairs = VVF (256, VF (256, 1e-10)); | ^ SafeVector.h:29:3: note: because 'SafeVector >' has user-provided 'SafeVector::SafeVector(const SafeVector&) [with TYPE = SafeVector]' 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ -Main.cc:894:29: warning: implicitly-declared 'SafeVector& SafeVector::operator=(const SafeVector&)' is deprecated [-Wdeprecated-copy] +Main.cc: In function 'void ReadParameters()': +Main.cc:893:40: warning: implicitly-declared 'SafeVector >& SafeVector >::operator=(const SafeVector >&)' is deprecated [-Wdeprecated-copy] + 893 | emitPairs = VVF (256, VF (256, 1e-10)); + | ^ +Main-RNA.cc:894:29: warning: implicitly-declared 'SafeVector& SafeVector::operator=(const SafeVector&)' is deprecated [-Wdeprecated-copy] 894 | emitSingle = VF (256, 1e-5); | ^ SafeVector.h:29:3: note: because 'SafeVector' has user-provided 'SafeVector::SafeVector(const SafeVector&) [with TYPE = float]' 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ -Main-RNA.cc: In function 'void PrintParameters(const char*, const VF&, const VF&, const VF&, const VVF&, const VF&, const char*)': -Main-RNA.cc:282:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation] - 282 | for (int i = 0; i < NumMatrixTypes; i++) fprintf (file, "%.10f ", initDistrib[i]); fprintf (file, "\n"); - | ^~~ -Main-RNA.cc:282:88: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' - 282 | for (int i = 0; i < NumMatrixTypes; i++) fprintf (file, "%.10f ", initDistrib[i]); fprintf (file, "\n"); - | ^~~~~~~ -Main-RNA.cc:283:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation] - 283 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapOpen[i]); fprintf (file, "\n"); - | ^~~ -Main-RNA.cc:283:87: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' - 283 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapOpen[i]); fprintf (file, "\n"); - | ^~~~~~~ -Main-RNA.cc:284:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation] - 284 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapExtend[i]); fprintf (file, "\n"); - | ^~~ -Main-RNA.cc:284:89: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' - 284 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapExtend[i]); fprintf (file, "\n"); - | ^~~~~~~ -Main-RNA.cc: In function 'MultiSequence* DoAlign(MultiSequence*, const ProbabilisticModel&, VF&, VF&, VF&, VVF&, VF&)': -Main-RNA.cc:400:13: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - 400 | if (enableVerbose) - | ^~ -Main-RNA.cc:403:15: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 403 | delete alignment.first; - | ^~~~~~ -Main-RNA.cc: In function 'void ReadParameters()': -Main-RNA.cc:893:40: warning: implicitly-declared 'SafeVector >& SafeVector >::operator=(const SafeVector >&)' is deprecated [-Wdeprecated-copy] - 893 | emitPairs = VVF (256, VF (256, 1e-10)); - | ^ SafeVector.h:29:3: note: because 'SafeVector >' has user-provided 'SafeVector::SafeVector(const SafeVector&) [with TYPE = SafeVector]' 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ -Main-RNA.cc:894:29: warning: implicitly-declared 'SafeVector& SafeVector::operator=(const SafeVector&)' is deprecated [-Wdeprecated-copy] +Main.cc:894:29: warning: implicitly-declared 'SafeVector& SafeVector::operator=(const SafeVector&)' is deprecated [-Wdeprecated-copy] 894 | emitSingle = VF (256, 1e-5); | ^ SafeVector.h:29:3: note: because 'SafeVector' has user-provided 'SafeVector::SafeVector(const SafeVector&) [with TYPE = float]' 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ -g++ -O3 -W -Wall -pedantic -DNDEBUG -DNumInsertStates=2 -DVERSION="1.12" -funroll-loops -g -O2 -ffile-prefix-map=/build/reproducible-path/probcons-1.12=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -o pc-project ProjectPairwise.cc -Wl,-z,relro -Wl,-z,now -In file included from MultiSequence.h:18, - from ProjectPairwise.cc:9: -Sequence.h: In member function 'Sequence* Sequence::Clone() const': -Sequence.h:293:21: warning: implicitly-declared 'SafeVector& SafeVector::operator=(const SafeVector&)' is deprecated [-Wdeprecated-copy] - 293 | *(ret->data) = *data; - | ^~~~ -In file included from ProjectPairwise.cc:8: -SafeVector.h:29:3: note: because 'SafeVector' has user-provided 'SafeVector::SafeVector(const SafeVector&) [with TYPE = char]' - 29 | SafeVector (const SafeVector &source) : std::vector(source) {} - | ^~~~~~~~~~ g++ -O3 -W -Wall -pedantic -DNDEBUG -DNumInsertStates=2 -DVERSION="1.12" -funroll-loops -g -O2 -ffile-prefix-map=/build/reproducible-path/probcons-1.12=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -o pc-makegnuplot MakeGnuPlot.cc -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/probcons-1.12' make[1]: Leaving directory '/build/reproducible-path/probcons-1.12' @@ -478,16 +514,16 @@ dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: debian/probcons-extra/usr/bin/pc-compare contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/probcons/usr/bin/probcons-RNA contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/probcons/usr/bin/probcons contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/probcons/usr/bin/probcons-RNA contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'probcons' in '../probcons_1.12-14_armhf.deb'. -dpkg-deb: building package 'probcons-extra' in '../probcons-extra_1.12-14_armhf.deb'. dpkg-deb: building package 'probcons-dbgsym' in '../probcons-dbgsym_1.12-14_armhf.deb'. dpkg-deb: building package 'probcons-extra-dbgsym' in '../probcons-extra-dbgsym_1.12-14_armhf.deb'. +dpkg-deb: building package 'probcons-extra' in '../probcons-extra_1.12-14_armhf.deb'. +dpkg-deb: building package 'probcons' in '../probcons_1.12-14_armhf.deb'. dpkg-genbuildinfo --build=binary -O../probcons_1.12-14_armhf.buildinfo dpkg-genchanges --build=binary -O../probcons_1.12-14_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -495,12 +531,14 @@ 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/28010/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/28010/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/29538 and its subdirectories -I: Current time: Fri May 3 17:57:34 -12 2024 -I: pbuilder-time-stamp: 1714802254 +I: removing directory /srv/workspace/pbuilder/28010 and its subdirectories +I: Current time: Sat May 4 19:58:56 +14 2024 +I: pbuilder-time-stamp: 1714802336