Diff of the two buildlogs: -- --- b1/build.log 2024-05-02 13:13:45.436951909 +0000 +++ b2/build.log 2024-05-02 13:16:27.542054496 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu May 2 01:12:15 -12 2024 -I: pbuilder-time-stamp: 1714655535 +I: Current time: Fri May 3 03:13:59 +14 2024 +I: pbuilder-time-stamp: 1714655639 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -31,52 +31,84 @@ dpkg-source: info: applying cross-build.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/9922/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/8474/tmp/hooks/D01_modify_environment starting +debug: Running on ff4a. +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 2 13:14 /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/8474/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/8474/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='9bada5f3b5bd43988cc1b6bcb5799d9a' - 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='9922' - PS1='# ' - PS2='> ' + INVOCATION_ID=ddf8382f99d34a3e96e036693567e1f0 + 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=8474 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.hoLgcR7T/pbuilderrc_GKLU --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.hoLgcR7T/b1 --logfile b1/build.log wham-align_0.1.5-8.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.hoLgcR7T/pbuilderrc_CzpO --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.hoLgcR7T/b2 --logfile b2/build.log wham-align_0.1.5-8.dsc' + SUDO_GID=113 + SUDO_UID=107 + 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 virt64c 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 1 11:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/9922/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 2 11:24 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/8474/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -142,7 +174,7 @@ 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 0s (48.1 MB/s) +Fetched 18.4 MB in 1s (12.4 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 ... 19444 files and directories currently installed.) @@ -277,7 +309,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/wham-align-0.1.5/ && 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 > ../wham-align_0.1.5-8_source.changes +I: user script /srv/workspace/pbuilder/8474/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/8474/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/wham-align-0.1.5/ && 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 > ../wham-align_0.1.5-8_source.changes dpkg-buildpackage: info: source package wham-align dpkg-buildpackage: info: source version 0.1.5-8 dpkg-buildpackage: info: source distribution unstable @@ -287,7 +323,7 @@ debian/rules clean dh clean dh_auto_clean - make -j3 clean + make -j4 clean make[1]: Entering directory '/build/reproducible-path/wham-align-0.1.5' rm -f wham wham-build *.o make[1]: Leaving directory '/build/reproducible-path/wham-align-0.1.5' @@ -310,69 +346,12 @@ dh_autoreconf dh_auto_configure dh_auto_build - make -j3 "INSTALL=install --strip-program=true" + make -j4 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/wham-align-0.1.5' g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings hash.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings embedhash.cpp g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings main.cpp -In file included from hitset.h:31, - from hash.h:29, - from embedhash.cpp:27: -pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': -pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] - 265 | if (num > nError) { - | ~~~~^~~~~~~~ -pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': -pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] - 602 | int i, j, offset, min, tmp; - | ^~~~~~ -pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)': -pair.h:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 682 | register unsigned long long P, M, X, U, Y; - | ^ -pair.h:682:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 682 | register unsigned long long P, M, X, U, Y; - | ^ -pair.h:682:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 682 | register unsigned long long P, M, X, U, Y; - | ^ -pair.h:682:42: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 682 | register unsigned long long P, M, X, U, Y; - | ^ -pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 682 | register unsigned long long P, M, X, U, Y; - | ^ -pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] - 684 | int i, p, num, base, Cscore; - | ^~~ -pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] - 684 | int i, p, num, base, Cscore; - | ^~~~ -pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] - 685 | int a; - | ^ -pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': -pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] - 755 | int i, p, num, base, Cscore; - | ^~~ -pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] - 755 | int i, p, num, base, Cscore; - | ^~~~ -pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] - 756 | int a; - | ^ -pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': -pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] - 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); - | ~~~~~~~^~~~~~~~~~ -hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': -hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] - 86 | int size; - | ^~~~ -hash.h: In function 'uint32 murmurHash(int64*, uint32)': -hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] - 86 | uint32 sum = 0; - | ^~~ +g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings sequence.cpp In file included from hitset.h:31, from hash.h:29, from hash.cpp:27: @@ -431,61 +410,9 @@ hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ -embedhash.cpp: In member function 'int EmbedHashTable::preProcessEnd()': -embedhash.cpp:137:16: warning: unused variable 'ln2' [-Wunused-variable] - 137 | const double ln2 = log(2); - | ^~~ -embedhash.cpp: In member function 'void EmbedHashTable::setScanThreshold(double)': -embedhash.cpp:253:9: warning: unused variable 'sum' [-Wunused-variable] - 253 | int64 sum = 0; - | ^~~ -embedhash.cpp:255:9: warning: unused variable 'top' [-Wunused-variable] - 255 | int64 top = total - total * r; - | ^~~ -embedhash.cpp: In member function 'void EmbedHashTable::insert(int64*, unsigned int)': -embedhash.cpp:369:38: warning: operation on '*(((EmbedHashTable*)this)->EmbedHashTable::overflowPool + ((sizetype)(curOverflowEntry * 4)))' may be undefined [-Wsequence-point] - 369 | overflowPool[curOverflowEntry] = -embedhash.cpp:328:10: warning: unused variable 'seqOffset' [-Wunused-variable] - 328 | uint32 seqOffset; - | ^~~~~~~~~ -embedhash.cpp:330:10: warning: unused variable 'counter' [-Wunused-variable] - 330 | uint32 counter = 0; - | ^~~~~~~ -embedhash.cpp:331:11: warning: variable 'seqVector' set but not used [-Wunused-but-set-variable] - 331 | int64 * seqVector; - | ^~~~~~~~~ -embedhash.cpp:333:11: warning: unused variable 'target' [-Wunused-variable] - 333 | int64 * target = &tspace[8]; - | ^~~~~~ -embedhash.cpp:334:8: warning: unused variable 'isBloomFilter' [-Wunused-variable] - 334 | bool isBloomFilter; - | ^~~~~~~~~~~~~ -embedhash.cpp:335:12: warning: unused variable 'bloomFilter' [-Wunused-variable] - 335 | uint32 * bloomFilter; - | ^~~~~~~~~~~ -embedhash.cpp:336:10: warning: unused variable 'bloomFilterNum' [-Wunused-variable] - 336 | uint32 bloomFilterNum; - | ^~~~~~~~~~~~~~ -embedhash.cpp: In member function 'unsigned int EmbedHashTable::lookup(int64*, int64*, int, char*, strand, int, HitSet*, bool)': -embedhash.cpp:385:7: warning: unused variable 'num' [-Wunused-variable] - 385 | int num; - | ^~~ -embedhash.cpp:387:34: warning: variable 'startOffset' set but not used [-Wunused-but-set-variable] - 387 | uint32 seqOffset, entryOffset, startOffset; - | ^~~~~~~~~~~ -embedhash.cpp:389:11: warning: unused variable 'diff' [-Wunused-variable] - 389 | int64 * diff = &tspace1[8], *target = &tspace2[8]; - | ^~~~ -embedhash.cpp:392:10: warning: unused variable 'sid' [-Wunused-variable] - 392 | uint32 sid, soffset; - | ^~~ -embedhash.cpp:392:15: warning: unused variable 'soffset' [-Wunused-variable] - 392 | uint32 sid, soffset; - | ^~~~~~~ In file included from hitset.h:31, from hash.h:29, - from aligner.h:25, - from main.cpp:34: + from embedhash.cpp:27: pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 265 | if (num > nError) { @@ -671,11 +598,6 @@ hash.cpp:1137:11: warning: unused variable 'diff' [-Wunused-variable] 1137 | int64 * diff = &tspace1[8], *target = &tspace2[8]; | ^~~~ -In file included from embedhash.cpp:32: -edit_distance.h: At global scope: -edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable] - 25 | static score_mat obj_score_mat = { 1, 1, 1, 1 }; - | ^~~~~~~~~~~~~ hash.cpp: In member function 'int HashTable::sortList()': hash.cpp:1430:14: warning: variable 'pool' set but not used [-Wunused-but-set-variable] 1430 | uint32 * pool; @@ -690,6 +612,74 @@ hash.cpp:1690:5: warning: label 'restart' defined but not used [-Wunused-label] 1690 | restart: if (buckets[bucketId] == HASH_EMPTY | ^~~~~~~ +In file included from hitset.h:31, + from hash.h:29, + from aligner.h:25, + from main.cpp:34: +pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': +pair.h:265:13: warning: comparison of integer expressions of different signedness: 'int64' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] + 265 | if (num > nError) { + | ~~~~^~~~~~~~ +pair.h: In static member function 'static bool PairAligner::pairAlignDP(int64*, int64*, int, int, int, bool)': +pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] + 602 | int i, j, offset, min, tmp; + | ^~~~~~ +pair.h: In static member function 'static bool PairAligner::pairAlignBitVector64(int64*, int64*, int, int, int)': +pair.h:682:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 682 | register unsigned long long P, M, X, U, Y; + | ^ +pair.h:682:36: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 682 | register unsigned long long P, M, X, U, Y; + | ^ +pair.h:682:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 682 | register unsigned long long P, M, X, U, Y; + | ^ +pair.h:682:42: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 682 | register unsigned long long P, M, X, U, Y; + | ^ +pair.h:682:45: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 682 | register unsigned long long P, M, X, U, Y; + | ^ +pair.h:684:15: warning: unused variable 'num' [-Wunused-variable] + 684 | int i, p, num, base, Cscore; + | ^~~ +pair.h:684:20: warning: unused variable 'base' [-Wunused-variable] + 684 | int i, p, num, base, Cscore; + | ^~~~ +pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] + 685 | int a; + | ^ +pair.h: In static member function 'static bool PairAligner::pairAlignBitVector(int64*, int64*, int, int, int)': +pair.h:755:15: warning: unused variable 'num' [-Wunused-variable] + 755 | int i, p, num, base, Cscore; + | ^~~ +pair.h:755:20: warning: unused variable 'base' [-Wunused-variable] + 755 | int i, p, num, base, Cscore; + | ^~~~ +pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] + 756 | int a; + | ^ +pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': +pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] + 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); + | ~~~~~~~^~~~~~~~~~ +hitset.h: In constructor 'HitSet::HitSet(int, int, int, bool, bool)': +hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] + 86 | int size; + | ^~~~ +hash.h: In function 'uint32 murmurHash(int64*, uint32)': +hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] + 86 | uint32 sum = 0; + | ^~~ +hash.cpp: In member function 'unsigned int HashTable::lookupEmbedTable(int64*, uint32, int, char*, strand, int, HitSet*, bool)': +hash.cpp:1049:1: warning: control reaches end of non-void function [-Wreturn-type] + 1049 | } + | ^ +In file included from hash.cpp:31: +edit_distance.h: At global scope: +edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable] + 25 | static score_mat obj_score_mat = { 1, 1, 1, 1 }; + | ^~~~~~~~~~~~~ In file included from pair.h:26: rdtsc.h: In function 'long long unsigned int curtick()': rdtsc.h:32:10: warning: 'tick' is used uninitialized [-Wuninitialized] @@ -725,49 +715,6 @@ main.cpp:536:9: warning: unused variable 'threadid' [-Wunused-variable] 536 | int * threadid; | ^~~~~~~~ -hash.cpp: In member function 'unsigned int HashTable::lookupEmbedTable(int64*, uint32, int, char*, strand, int, HitSet*, bool)': -hash.cpp:1049:1: warning: control reaches end of non-void function [-Wreturn-type] - 1049 | } - | ^ -In file included from hash.cpp:31: -edit_distance.h: At global scope: -edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable] - 25 | static score_mat obj_score_mat = { 1, 1, 1, 1 }; - | ^~~~~~~~~~~~~ -In file included from pair.h:26: -rdtsc.h: In function 'long long unsigned int curtick()': -rdtsc.h:32:10: warning: 'tick' is used uninitialized [-Wuninitialized] - 32 | return tick; - | ^~~~ -rdtsc.h:20:22: note: 'tick' was declared here - 20 | unsigned long long tick; - | ^~~~ -In file included from main.cpp:38: -edit_distance.h: At global scope: -edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable] - 25 | static score_mat obj_score_mat = { 1, 1, 1, 1 }; - | ^~~~~~~~~~~~~ -main.cpp: In function 'void mergeFiles(std::string)': -main.cpp:269:21: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] - 269 | sprintf(buf, ".t%d ", i); - | ^~ -main.cpp:269:18: note: directive argument in the range [0, 2147483646] - 269 | sprintf(buf, ".t%d ", i); - | ^~~~~~~ -main.cpp:269:12: note: 'sprintf' output between 5 and 14 bytes into a destination of size 10 - 269 | sprintf(buf, ".t%d ", i); - | ~~~~~~~^~~~~~~~~~~~~~~~~ -main.cpp:276:21: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] - 276 | sprintf(buf, ".t%d", i); - | ^~ -main.cpp:276:18: note: directive argument in the range [0, 2147483646] - 276 | sprintf(buf, ".t%d", i); - | ^~~~~~ -main.cpp:276:12: note: 'sprintf' output between 4 and 13 bytes into a destination of size 10 - 276 | sprintf(buf, ".t%d", i); - | ~~~~~~~^~~~~~~~~~~~~~~~ -g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings sequence.cpp -g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings aligner.cpp In file included from hitset.h:31, from hash.h:29, from aligner.h:25, @@ -892,6 +839,128 @@ sequence.cpp:804:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 804 | if (ret != size) { | ~~~~^~~~~~~ +embedhash.cpp: In member function 'int EmbedHashTable::preProcessEnd()': +embedhash.cpp:137:16: warning: unused variable 'ln2' [-Wunused-variable] + 137 | const double ln2 = log(2); + | ^~~ +embedhash.cpp: In member function 'void EmbedHashTable::setScanThreshold(double)': +embedhash.cpp:253:9: warning: unused variable 'sum' [-Wunused-variable] + 253 | int64 sum = 0; + | ^~~ +embedhash.cpp:255:9: warning: unused variable 'top' [-Wunused-variable] + 255 | int64 top = total - total * r; + | ^~~ +embedhash.cpp: In member function 'void EmbedHashTable::insert(int64*, unsigned int)': +embedhash.cpp:369:38: warning: operation on '*(((EmbedHashTable*)this)->EmbedHashTable::overflowPool + ((sizetype)(curOverflowEntry * 4)))' may be undefined [-Wsequence-point] + 369 | overflowPool[curOverflowEntry] = +embedhash.cpp:328:10: warning: unused variable 'seqOffset' [-Wunused-variable] + 328 | uint32 seqOffset; + | ^~~~~~~~~ +embedhash.cpp:330:10: warning: unused variable 'counter' [-Wunused-variable] + 330 | uint32 counter = 0; + | ^~~~~~~ +embedhash.cpp:331:11: warning: variable 'seqVector' set but not used [-Wunused-but-set-variable] + 331 | int64 * seqVector; + | ^~~~~~~~~ +embedhash.cpp:333:11: warning: unused variable 'target' [-Wunused-variable] + 333 | int64 * target = &tspace[8]; + | ^~~~~~ +embedhash.cpp:334:8: warning: unused variable 'isBloomFilter' [-Wunused-variable] + 334 | bool isBloomFilter; + | ^~~~~~~~~~~~~ +embedhash.cpp:335:12: warning: unused variable 'bloomFilter' [-Wunused-variable] + 335 | uint32 * bloomFilter; + | ^~~~~~~~~~~ +embedhash.cpp:336:10: warning: unused variable 'bloomFilterNum' [-Wunused-variable] + 336 | uint32 bloomFilterNum; + | ^~~~~~~~~~~~~~ +embedhash.cpp: In member function 'unsigned int EmbedHashTable::lookup(int64*, int64*, int, char*, strand, int, HitSet*, bool)': +embedhash.cpp:385:7: warning: unused variable 'num' [-Wunused-variable] + 385 | int num; + | ^~~ +embedhash.cpp:387:34: warning: variable 'startOffset' set but not used [-Wunused-but-set-variable] + 387 | uint32 seqOffset, entryOffset, startOffset; + | ^~~~~~~~~~~ +embedhash.cpp:389:11: warning: unused variable 'diff' [-Wunused-variable] + 389 | int64 * diff = &tspace1[8], *target = &tspace2[8]; + | ^~~~ +embedhash.cpp:392:10: warning: unused variable 'sid' [-Wunused-variable] + 392 | uint32 sid, soffset; + | ^~~ +embedhash.cpp:392:15: warning: unused variable 'soffset' [-Wunused-variable] + 392 | uint32 sid, soffset; + | ^~~~~~~ +In file included from main.cpp:38: +edit_distance.h: At global scope: +edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable] + 25 | static score_mat obj_score_mat = { 1, 1, 1, 1 }; + | ^~~~~~~~~~~~~ +main.cpp: In function 'void mergeFiles(std::string)': +main.cpp:269:21: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] + 269 | sprintf(buf, ".t%d ", i); + | ^~ +main.cpp:269:18: note: directive argument in the range [0, 2147483646] + 269 | sprintf(buf, ".t%d ", i); + | ^~~~~~~ +main.cpp:269:12: note: 'sprintf' output between 5 and 14 bytes into a destination of size 10 + 269 | sprintf(buf, ".t%d ", i); + | ~~~~~~~^~~~~~~~~~~~~~~~~ +main.cpp:276:21: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=] + 276 | sprintf(buf, ".t%d", i); + | ^~ +main.cpp:276:18: note: directive argument in the range [0, 2147483646] + 276 | sprintf(buf, ".t%d", i); + | ^~~~~~ +main.cpp:276:12: note: 'sprintf' output between 4 and 13 bytes into a destination of size 10 + 276 | sprintf(buf, ".t%d", i); + | ~~~~~~~^~~~~~~~~~~~~~~~ +In file included from embedhash.cpp:32: +edit_distance.h: At global scope: +edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable] + 25 | static score_mat obj_score_mat = { 1, 1, 1, 1 }; + | ^~~~~~~~~~~~~ +In file included from pair.h:26: +rdtsc.h: In function 'long long unsigned int curtick()': +rdtsc.h:32:10: warning: 'tick' is used uninitialized [-Wuninitialized] + 32 | return tick; + | ^~~~ +rdtsc.h:20:22: note: 'tick' was declared here + 20 | unsigned long long tick; + | ^~~~ +sequence.cpp: In member function 'int CompactSequence::build(char**, int, int, int)': +sequence.cpp:430:27: warning: 'offsetInOrgSeq' may be used uninitialized [-Wmaybe-uninitialized] + 430 | offsetInOrgSeq++; + | ~~~~~~~~~~~~~~^~ +sequence.cpp:221:33: note: 'offsetInOrgSeq' was declared here + 221 | unsigned int offsetInCmptSeq, offsetInOrgSeq; + | ^~~~~~~~~~~~~~ +sequence.cpp: In static member function 'static void CompactSequence::compose(char*, int, int64*)': +sequence.cpp:676:20: warning: 'code' may be used uninitialized [-Wmaybe-uninitialized] + 676 | forward_word = (forward_word << BITS_PER_BASE) | code; + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +sequence.cpp:630:23: note: 'code' was declared here + 630 | int64 forward_word, code; + | ^~~~ +g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings aligner.cpp +g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings interval.cpp +interval.cpp: In constructor 'IntervalTree::IntervalTree(uint32, uint32)': +interval.cpp:67:21: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] + 67 | for (int i = 0; i < numLevel - 1; i++) { + | ~~^~~~~~~~~~~~~~ +interval.cpp: In member function 'int IntervalTree::save(char*)': +interval.cpp:304:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] + 304 | if (ret != numLEntry) { + | ~~~~^~~~~~~~~~~~ +interval.cpp:310:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] + 310 | if (ret != numIEntry) { + | ~~~~^~~~~~~~~~~~ +interval.cpp: In member function 'int IntervalTree::load(char*)': +interval.cpp:359:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] + 359 | if (ret != numLEntry) { + | ~~~~^~~~~~~~~~~~ +interval.cpp:370:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] + 370 | if (ret != numIEntry) { + | ~~~~^~~~~~~~~~~~ In file included from hitset.h:31, from hash.h:29, from aligner.h:25, @@ -939,6 +1008,7 @@ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ +g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings edit_distance.cpp pair.h: In static member function 'static int128 PairAligner::Bit128RemoveSmearRightmost1(int128)': pair.h:974:23: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 974 | tmp.high = x.high ^ - x.high | (0LL - (x.low != 0)); @@ -951,6 +1021,7 @@ hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ +g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings error.cpp aligner.cpp: In member function 'int Aligner::initLookupArray()': aligner.cpp:365:37: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] 365 | if ((indexBits[i] >> j) & 0x1 == 1) { @@ -1051,6 +1122,13 @@ aligner.cpp:1426:7: warning: unused variable 'ret' [-Wunused-variable] 1426 | int ret; | ^~~ +error.cpp: In function 'void elog(int, char*, ...)': +error.cpp:31:9: warning: unused variable 'filename' [-Wunused-variable] + 31 | char *filename = __FILE__; + | ^~~~~~~~ +error.cpp:32:7: warning: unused variable 'lineno' [-Wunused-variable] + 32 | int lineno = __LINE__; + | ^~~~~~ aligner.cpp: In member function 'AlignRes Aligner::alignSingleEnd(AlignInfo*, char*)': aligner.cpp:1541:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 1541 | for (i = 0; i < nHashTable; i++) { @@ -1115,57 +1193,7 @@ aligner.cpp:1874:10: warning: unused variable 'ret' [-Wunused-variable] 1874 | int i, ret; | ^~~ -sequence.cpp: In member function 'int CompactSequence::build(char**, int, int, int)': -sequence.cpp:430:27: warning: 'offsetInOrgSeq' may be used uninitialized [-Wmaybe-uninitialized] - 430 | offsetInOrgSeq++; - | ~~~~~~~~~~~~~~^~ -sequence.cpp:221:33: note: 'offsetInOrgSeq' was declared here - 221 | unsigned int offsetInCmptSeq, offsetInOrgSeq; - | ^~~~~~~~~~~~~~ -sequence.cpp: In static member function 'static void CompactSequence::compose(char*, int, int64*)': -sequence.cpp:676:20: warning: 'code' may be used uninitialized [-Wmaybe-uninitialized] - 676 | forward_word = (forward_word << BITS_PER_BASE) | code; - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -sequence.cpp:630:23: note: 'code' was declared here - 630 | int64 forward_word, code; - | ^~~~ -In member function 'void HashTable::setLookupInfo(int, int*)', - inlined from 'int Aligner::initLookupArray()' at aligner.cpp:375:32: -hash.h:353:18: warning: 'keySpan' may be used uninitialized [-Wmaybe-uninitialized] - 353 | widthKeySpan = keySpan; - | ~~~~~~~~~~~~~^~~~~~~~~ -aligner.cpp: In member function 'int Aligner::initLookupArray()': -aligner.cpp:360:7: note: 'keySpan' was declared here - 360 | int keySpan; - | ^~~~~~~ -g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings interval.cpp -interval.cpp: In constructor 'IntervalTree::IntervalTree(uint32, uint32)': -interval.cpp:67:21: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] - 67 | for (int i = 0; i < numLevel - 1; i++) { - | ~~^~~~~~~~~~~~~~ -interval.cpp: In member function 'int IntervalTree::save(char*)': -interval.cpp:304:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] - 304 | if (ret != numLEntry) { - | ~~~~^~~~~~~~~~~~ -interval.cpp:310:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] - 310 | if (ret != numIEntry) { - | ~~~~^~~~~~~~~~~~ -interval.cpp: In member function 'int IntervalTree::load(char*)': -interval.cpp:359:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] - 359 | if (ret != numLEntry) { - | ~~~~^~~~~~~~~~~~ -interval.cpp:370:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] - 370 | if (ret != numIEntry) { - | ~~~~^~~~~~~~~~~~ -g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings edit_distance.cpp -g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings error.cpp -error.cpp: In function 'void elog(int, char*, ...)': -error.cpp:31:9: warning: unused variable 'filename' [-Wunused-variable] - 31 | char *filename = __FILE__; - | ^~~~~~~~ -error.cpp:32:7: warning: unused variable 'lineno' [-Wunused-variable] - 32 | int lineno = __LINE__; - | ^~~~~~ +g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings short.cpp edit_distance.cpp: In function 'scoreinfo edit_distance(char*, char*, int, int, char*, char*, int)': edit_distance.cpp:61:7: warning: unused variable 'i' [-Wunused-variable] 61 | int i; @@ -1183,7 +1211,6 @@ edit_distance.cpp:178:7: warning: unused variable 'kk' [-Wunused-variable] 178 | int kk = 0; | ^~ -g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings short.cpp short.cpp: In member function 'int ShortRead::preProcess(int)': short.cpp:212:16: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 212 | while (len = readLine(file, str, 256)) { @@ -1219,6 +1246,8 @@ short.cpp:510:14: note: 'sprintf' output between 4 and 268 bytes into a destination of size 256 510 | sprintf(partitions[i]->unFileName, "%s.t%d", unFileName, i); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings perfcounters.cpp +g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings model.cpp In file included from hitset.h:31, from hitset.cpp:1: pair.h: In static member function 'static ErrorVector PairAligner::pairAlignDBA(int64*, int64*, int, int, int)': @@ -1276,16 +1305,15 @@ hitset.cpp:90:8: warning: unused variable 'pairMatch' [-Wunused-variable] 90 | bool pairMatch = false; | ^~~~~~~~~ -aligner.cpp: In member function 'unsigned int Aligner::alignFirst(int64*, char*, strand, int, HitSet*, bool)': -aligner.cpp:1097:3: warning: 'ret' may be used uninitialized [-Wmaybe-uninitialized] - 1097 | if (ret == MSG_HITSETFULL) - | ^~ -aligner.cpp:1040:7: note: 'ret' was declared here - 1040 | int ret; - | ^~~ -g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings perfcounters.cpp -g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings model.cpp -g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings writer.cpp +In member function 'void HashTable::setLookupInfo(int, int*)', + inlined from 'int Aligner::initLookupArray()' at aligner.cpp:375:32: +hash.h:353:18: warning: 'keySpan' may be used uninitialized [-Wmaybe-uninitialized] + 353 | widthKeySpan = keySpan; + | ~~~~~~~~~~~~~^~~~~~~~~ +aligner.cpp: In member function 'int Aligner::initLookupArray()': +aligner.cpp:360:7: note: 'keySpan' was declared here + 360 | int keySpan; + | ^~~~~~~ model.cpp: In static member function 'static int AlignerModel::estimateNumPartition(unsigned int, int, int, bool)': model.cpp:76:16: warning: variable 'nIndex' set but not used [-Wunused-but-set-variable] 76 | unsigned int nIndex, nLookup, nBucket; @@ -1319,6 +1347,7 @@ model.cpp:198:26: warning: variable 'p2' set but not used [-Wunused-but-set-variable] 198 | double nSpace, p0, p1, p2; | ^~ +g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings writer.cpp In file included from hitset.h:31, from writer.h:26, from writer.cpp:21: @@ -1373,6 +1402,7 @@ hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ +g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings builder.cpp writer.cpp: In member function 'void SimpleWriter::writeField(int64*, int64*, strand)': writer.cpp:154:27: warning: suggest parentheses around '-' in operand of '&' [-Wparentheses] 154 | j = BITS_PER_LONGWORD - (length * BITS_PER_BASE) & BITS_LONGWORD_MASK; @@ -1425,7 +1455,6 @@ writer.cpp:619:47: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] 619 | if (!mate1Unmatch && !mate2Unmatch & sid1 == sid2) { | ~~~~~^~~~~~~ -g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/wham-align-0.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wall -pedantic -fsigned-char -O3 -Wno-write-strings builder.cpp In file included from hitset.h:31, from hash.h:29, from aligner.h:25, @@ -1496,16 +1525,23 @@ builder.cpp:277:7: warning: unused variable 'nChar' [-Wunused-variable] 277 | int nChar = sequence->getNum(); | ^~~~~ -g++ -o wham sequence.o hash.o embedhash.o main.o aligner.o interval.o edit_distance.o error.o short.o hitset.o model.o perfcounters.o writer.o -lpthread In file included from builder.cpp:34: edit_distance.h: At global scope: edit_distance.h:25:18: warning: 'obj_score_mat' defined but not used [-Wunused-variable] 25 | static score_mat obj_score_mat = { 1, 1, 1, 1 }; | ^~~~~~~~~~~~~ +aligner.cpp: In member function 'unsigned int Aligner::alignFirst(int64*, char*, strand, int, HitSet*, bool)': +aligner.cpp:1097:3: warning: 'ret' may be used uninitialized [-Wmaybe-uninitialized] + 1097 | if (ret == MSG_HITSETFULL) + | ^~ +aligner.cpp:1040:7: note: 'ret' was declared here + 1040 | int ret; + | ^~~ +g++ -o wham sequence.o hash.o embedhash.o main.o aligner.o interval.o edit_distance.o error.o short.o hitset.o model.o perfcounters.o writer.o -lpthread g++ -o wham-build sequence.o hash.o embedhash.o builder.o aligner.o interval.o edit_distance.o error.o short.o hitset.o model.o perfcounters.o writer.o -lpthread make[1]: Leaving directory '/build/reproducible-path/wham-align-0.1.5' dh_auto_test - rm -fr -- /tmp/dh-xdg-rundir-LLp3PPLq + rm -fr -- /tmp/dh-xdg-rundir-lyVHfzn0 create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/wham-align.substvars @@ -1568,16 +1604,16 @@ objcopy --compress-debug-sections debian/wham-align/usr/lib/debug/.dwz/arm-linux-gnueabihf/wham-align.debug chmod 0644 -- debian/wham-align/usr/lib/debug/.dwz/arm-linux-gnueabihf/wham-align.debug dh_strip -a - install -m0755 -d debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/fb - objcopy --only-keep-debug --compress-debug-sections debian/wham-align/usr/bin/wham-build debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/fb/f6b5862d65e43d2e5be99a514d9e909dab6666.debug - chmod 0644 -- debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/fb/f6b5862d65e43d2e5be99a514d9e909dab6666.debug - strip --remove-section=.comment --remove-section=.note debian/wham-align/usr/bin/wham-build - objcopy --add-gnu-debuglink debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/fb/f6b5862d65e43d2e5be99a514d9e909dab6666.debug debian/wham-align/usr/bin/wham-build install -m0755 -d debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/ed objcopy --only-keep-debug --compress-debug-sections debian/wham-align/usr/bin/wham debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/ed/ee901557deb3b0586aeffbc3fdea531e3a2367.debug chmod 0644 -- debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/ed/ee901557deb3b0586aeffbc3fdea531e3a2367.debug strip --remove-section=.comment --remove-section=.note debian/wham-align/usr/bin/wham objcopy --add-gnu-debuglink debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/ed/ee901557deb3b0586aeffbc3fdea531e3a2367.debug debian/wham-align/usr/bin/wham + install -m0755 -d debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/fb + objcopy --only-keep-debug --compress-debug-sections debian/wham-align/usr/bin/wham-build debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/fb/f6b5862d65e43d2e5be99a514d9e909dab6666.debug + chmod 0644 -- debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/fb/f6b5862d65e43d2e5be99a514d9e909dab6666.debug + strip --remove-section=.comment --remove-section=.note debian/wham-align/usr/bin/wham-build + objcopy --add-gnu-debuglink debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.build-id/fb/f6b5862d65e43d2e5be99a514d9e909dab6666.debug debian/wham-align/usr/bin/wham-build install -m0755 -d debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/wham-align/usr/lib/debug/.dwz/arm-linux-gnueabihf debian/.debhelper/wham-align/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/wham-align/usr/lib/debug/.dwz @@ -1589,7 +1625,7 @@ rm -f debian/wham-align/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/wham-align/DEBIAN - dpkg-shlibdeps -Tdebian/wham-align.substvars debian/wham-align/usr/bin/wham-build debian/wham-align/usr/bin/wham + dpkg-shlibdeps -Tdebian/wham-align.substvars debian/wham-align/usr/bin/wham debian/wham-align/usr/bin/wham-build dh_installdeb install -m0755 -d debian/wham-align/DEBIAN dh_gencontrol @@ -1611,8 +1647,8 @@ dh_builddeb dpkg-deb --root-owner-group --build debian/wham-align .. dpkg-deb --root-owner-group --build debian/.debhelper/wham-align/dbgsym-root .. -dpkg-deb: building package 'wham-align-dbgsym' in '../wham-align-dbgsym_0.1.5-8_armhf.deb'. dpkg-deb: building package 'wham-align' in '../wham-align_0.1.5-8_armhf.deb'. +dpkg-deb: building package 'wham-align-dbgsym' in '../wham-align-dbgsym_0.1.5-8_armhf.deb'. dpkg-genbuildinfo --build=binary -O../wham-align_0.1.5-8_armhf.buildinfo dpkg-genchanges --build=binary -O../wham-align_0.1.5-8_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1620,12 +1656,14 @@ 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/8474/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/8474/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/9922 and its subdirectories -I: Current time: Thu May 2 01:13:40 -12 2024 -I: pbuilder-time-stamp: 1714655620 +I: removing directory /srv/workspace/pbuilder/8474 and its subdirectories +I: Current time: Fri May 3 03:16:23 +14 2024 +I: pbuilder-time-stamp: 1714655783