Diff of the two buildlogs: -- --- b1/build.log 2024-12-17 15:42:34.002841014 +0000 +++ b2/build.log 2024-12-17 15:44:48.984730517 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Dec 17 03:39:37 -12 2024 -I: pbuilder-time-stamp: 1734449977 +I: Current time: Wed Dec 18 05:42:46 +14 2024 +I: pbuilder-time-stamp: 1734450166 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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/8401/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/32637/tmp/hooks/D01_modify_environment starting +debug: Running on virt64a. +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 Dec 17 15:43 /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/32637/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/32637/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='unstable' - 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]="37" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + 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=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='9b65ebfb45c14cb7abe071428a8e39b3' - 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='8401' - PS1='# ' - PS2='> ' + INVOCATION_ID=2b91b769aa494ff8811e7a6617396ced + 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=32637 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.ERNb7012/pbuilderrc_fk9D --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.ERNb7012/b1 --logfile b1/build.log wham-align_0.1.5-8.dsc' - SUDO_GID='110' - SUDO_UID='103' - 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.ERNb7012/pbuilderrc_5phI --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.ERNb7012/b2 --logfile b2/build.log wham-align_0.1.5-8.dsc' + SUDO_GID=114 + SUDO_UID=108 + 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 virt32z 6.1.0-28-armmp-lpae #1 SMP Debian 6.1.119-1 (2024-11-22) armv7l GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/8401/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/32637/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -141,7 +173,7 @@ Get: 27 http://deb.debian.org/debian unstable/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main armhf debhelper all 13.21 [919 kB] -Fetched 19.1 MB in 1s (15.4 MB/s) +Fetched 19.1 MB in 0s (43.0 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 ... 19680 files and directories currently installed.) @@ -272,7 +304,11 @@ 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/32637/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/32637/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 @@ -282,7 +318,7 @@ 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' @@ -305,11 +341,12 @@ 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 +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 embedhash.cpp:27: @@ -364,10 +401,6 @@ 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; - | ^~~ In file included from hitset.h:31, from hash.h:29, from hash.cpp:27: @@ -375,6 +408,10 @@ 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) { | ~~~~^~~~~~~~ +hash.h: In function 'uint32 murmurHash(int64*, uint32)': +hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] + 86 | uint32 sum = 0; + | ^~~ 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; @@ -426,57 +463,6 @@ 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, @@ -536,23 +522,57 @@ hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ -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; - | ^~~~ +In file included from hitset.h:31, + from hash.h:29, + from aligner.h:25, + from sequence.cpp:30: +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) { + | ~~~~^~~~~~~~ main.cpp: In function 'int getArguVal(char*)': main.cpp:159:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 159 | else if (*c = 'g' || *c == 'G') | ~~~^~~~~~~~~~~~~~~~~~ +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; + | ^ main.cpp: In function 'int align(char*, AlignInfo*, char*, int)': main.cpp:350:7: warning: unused variable 'i' [-Wunused-variable] 350 | int i, j, ret; @@ -560,6 +580,18 @@ main.cpp:350:10: warning: unused variable 'j' [-Wunused-variable] 350 | int i, j, ret; | ^ +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; + | ^~~ main.cpp: In function 'int main(int, char**)': main.cpp:523:7: warning: unused variable 'numKeys' [-Wunused-variable] 523 | int numKeys; @@ -576,6 +608,122 @@ main.cpp:536:9: warning: unused variable 'threadid' [-Wunused-variable] 536 | int * threadid; | ^~~~~~~~ +sequence.cpp: In member function 'void CompactSequence::extractFileName(char*, char*)': +sequence.cpp:97:10: warning: unused variable 'str' [-Wunused-variable] + 97 | char * str; + | ^~~ +sequence.cpp: In member function 'int CompactSequence::build(char**, int, int, int)': +sequence.cpp:238:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 238 | for (i = 0; i < numFile; i++) { + | ~~^~~~~~~~~ +sequence.cpp:309:13: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 309 | ( i = 0; i < nSeq; i++) + | ~~^~~~~~ +sequence.cpp:324:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 324 | for (i = 0; i < numFile; i++) { + | ~~^~~~~~~~~ +sequence.cpp:344:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 344 | for (j = 0; j < numError + 1; j++) { + | ~~^~~~~~~~~~~~~~ +sequence.cpp:410:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 410 | if (lenSegmentN > numError + 1) { + | ~~~~~~~~~~~~^~~~~~~~~~~~~~ +sequence.cpp:429:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 429 | if (lenSegmentN > numError + 1) { + | ~~~~~~~~~~~~^~~~~~~~~~~~~~ +sequence.cpp:223:16: warning: unused variable 'step' [-Wunused-variable] + 223 | unsigned int step, nextstep; + | ^~~~ +sequence.cpp:223:22: warning: unused variable 'nextstep' [-Wunused-variable] + 223 | unsigned int step, nextstep; + | ^~~~~~~~ +sequence.cpp: In member function 'int CompactSequence::filter(Aligner*, char**, int, char*)': +sequence.cpp:534:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 534 | for (i = 0; i < numFile; i++) { + | ~~^~~~~~~~~ +sequence.cpp:599:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 599 | if (lenSegmentN > nError + 1) + | ~~~~~~~~~~~~^~~~~~~~~~~~ +sequence.cpp:520:16: warning: unused variable 'step' [-Wunused-variable] + 520 | unsigned int step, nextstep; + | ^~~~ +sequence.cpp:520:22: warning: unused variable 'nextstep' [-Wunused-variable] + 520 | unsigned int step, nextstep; + | ^~~~~~~~ +sequence.cpp:521:9: warning: unused variable 'numFileChar' [-Wunused-variable] + 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; + | ^~~~~~~~~~~ +sequence.cpp:521:22: warning: unused variable 'numFileNSeg' [-Wunused-variable] + 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; + | ^~~~~~~~~~~ +sequence.cpp:521:35: warning: unused variable 'numFileSeq' [-Wunused-variable] + 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; + | ^~~~~~~~~~ +sequence.cpp:521:47: warning: unused variable 'nChar' [-Wunused-variable] + 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; + | ^~~~~ +sequence.cpp:521:54: warning: unused variable 'nNSegment' [-Wunused-variable] + 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; + | ^~~~~~~~~ +sequence.cpp: In member function 'int CompactSequence::save(char*)': +sequence.cpp:738:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] + 738 | if (ret != size) { + | ~~~~^~~~~~~ +sequence.cpp: In member function 'int CompactSequence::load(char*)': +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; + | ^~~~~~~ hash.cpp: In member function 'int HashTable::preProcessEnd()': hash.cpp:236:11: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32' {aka 'const unsigned int'} [-Wsign-compare] 236 | if (h >= nHistogram) @@ -627,6 +775,11 @@ hash.cpp:472:34: warning: variable 'startOffset' set but not used [-Wunused-but-set-variable] 472 | uint32 seqOffset, entryOffset, startOffset; | ^~~~~~~~~~~ +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 }; + | ^~~~~~~~~~~~~ hash.cpp: In member function 'void HashTable::preinsertEmbedTableEntry(int64*, int, int)': hash.cpp:587:11: warning: unused variable 'noheadkey' [-Wunused-variable] 587 | int64 * noheadkey = &tspace[8], *rest = &tspace[24]; @@ -720,11 +873,19 @@ hash.cpp:1690:5: warning: label 'restart' defined but not used [-Wunused-label] 1690 | restart: if (buckets[bucketId] == HASH_EMPTY | ^~~~~~~ -In file included from main.cpp:38: +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; + | ^~~~ 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 | } @@ -734,14 +895,6 @@ 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; - | ^~~~ 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); @@ -761,45 +914,48 @@ 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 +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 -In file included from hitset.h:31, - from hash.h:29, - from aligner.h:25, - from sequence.cpp:30: -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; - | ^ +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, @@ -808,28 +964,10 @@ 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::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)); - | ~~~~~~~^~~~~~~~~~ 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; | ^~~~~~ -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; - | ^~~~ 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; @@ -865,10 +1003,6 @@ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ -hash.h: In function 'uint32 murmurHash(int64*, uint32)': -hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] - 86 | uint32 sum = 0; - | ^~~ 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)); @@ -877,75 +1011,20 @@ hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ -sequence.cpp: In member function 'void CompactSequence::extractFileName(char*, char*)': -sequence.cpp:97:10: warning: unused variable 'str' [-Wunused-variable] - 97 | char * str; - | ^~~ -sequence.cpp: In member function 'int CompactSequence::build(char**, int, int, int)': -sequence.cpp:238:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 238 | for (i = 0; i < numFile; i++) { - | ~~^~~~~~~~~ hash.h: In function 'uint32 murmurHash(int64*, uint32)': hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ -sequence.cpp:309:13: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 309 | ( i = 0; i < nSeq; i++) - | ~~^~~~~~ -sequence.cpp:324:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 324 | for (i = 0; i < numFile; i++) { - | ~~^~~~~~~~~ -sequence.cpp:344:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 344 | for (j = 0; j < numError + 1; j++) { - | ~~^~~~~~~~~~~~~~ -sequence.cpp:410:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 410 | if (lenSegmentN > numError + 1) { - | ~~~~~~~~~~~~^~~~~~~~~~~~~~ -sequence.cpp:429:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 429 | if (lenSegmentN > numError + 1) { - | ~~~~~~~~~~~~^~~~~~~~~~~~~~ -sequence.cpp:223:16: warning: unused variable 'step' [-Wunused-variable] - 223 | unsigned int step, nextstep; - | ^~~~ -sequence.cpp:223:22: warning: unused variable 'nextstep' [-Wunused-variable] - 223 | unsigned int step, nextstep; - | ^~~~~~~~ -sequence.cpp: In member function 'int CompactSequence::filter(Aligner*, char**, int, char*)': -sequence.cpp:534:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 534 | for (i = 0; i < numFile; i++) { - | ~~^~~~~~~~~ -sequence.cpp:599:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 599 | if (lenSegmentN > nError + 1) - | ~~~~~~~~~~~~^~~~~~~~~~~~ -sequence.cpp:520:16: warning: unused variable 'step' [-Wunused-variable] - 520 | unsigned int step, nextstep; - | ^~~~ -sequence.cpp:520:22: warning: unused variable 'nextstep' [-Wunused-variable] - 520 | unsigned int step, nextstep; - | ^~~~~~~~ -sequence.cpp:521:9: warning: unused variable 'numFileChar' [-Wunused-variable] - 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; - | ^~~~~~~~~~~ -sequence.cpp:521:22: warning: unused variable 'numFileNSeg' [-Wunused-variable] - 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; - | ^~~~~~~~~~~ -sequence.cpp:521:35: warning: unused variable 'numFileSeq' [-Wunused-variable] - 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; - | ^~~~~~~~~~ -sequence.cpp:521:47: warning: unused variable 'nChar' [-Wunused-variable] - 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; - | ^~~~~ -sequence.cpp:521:54: warning: unused variable 'nNSegment' [-Wunused-variable] - 521 | int64 numFileChar, numFileNSeg, numFileSeq, nChar, nNSegment; - | ^~~~~~~~~ -sequence.cpp: In member function 'int CompactSequence::save(char*)': -sequence.cpp:738:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] - 738 | if (ret != size) { - | ~~~~^~~~~~~ -sequence.cpp: In member function 'int CompactSequence::load(char*)': -sequence.cpp:804:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] - 804 | if (ret != 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 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 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) { @@ -1110,49 +1189,14 @@ 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; - | ^~~~~~~~~~~~~~ -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; - | ^~~~~~~ -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 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 +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)) { + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +short.cpp: In member function 'ShortRead** ShortRead::split(int)': +short.cpp:483:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] + 483 | if (szPartition <= nRead - curRead) + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 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; @@ -1170,24 +1214,44 @@ 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 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 -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 hitset.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)) { - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +short.cpp: In member function 'int ShortRead::load(int)': +short.cpp:424:28: warning: 'code' may be used uninitialized [-Wmaybe-uninitialized] + 424 | forward_word = (forward_word << BITS_PER_BASE) | code; + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +short.cpp:310:38: note: 'code' was declared here + 310 | int64 forward_word, backward_word, code; + | ^~~~ short.cpp: In member function 'ShortRead** ShortRead::split(int)': -short.cpp:483:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] - 483 | if (szPartition <= nRead - curRead) - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ +short.cpp:503:45: warning: '.t' directive writing 2 bytes into a region of size between 1 and 256 [-Wformat-overflow=] + 503 | sprintf(partitions[i]->alFileName, "%s.t%d", alFileName, i); + | ^~ +short.cpp:503:42: note: directive argument in the range [0, 1073741823] + 503 | sprintf(partitions[i]->alFileName, "%s.t%d", alFileName, i); + | ^~~~~~~~ +short.cpp:503:14: note: 'sprintf' output between 4 and 268 bytes into a destination of size 256 + 503 | sprintf(partitions[i]->alFileName, "%s.t%d", alFileName, i); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +short.cpp:510:45: warning: '.t' directive writing 2 bytes into a region of size between 1 and 256 [-Wformat-overflow=] + 510 | sprintf(partitions[i]->unFileName, "%s.t%d", unFileName, i); + | ^~ +short.cpp:510:42: note: directive argument in the range [0, 1073741823] + 510 | sprintf(partitions[i]->unFileName, "%s.t%d", unFileName, i); + | ^~~~~~~~ +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 hitset.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 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 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; + | ^~~~~~~ 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)': @@ -1245,35 +1309,41 @@ hitset.cpp:90:8: warning: unused variable 'pairMatch' [-Wunused-variable] 90 | bool pairMatch = false; | ^~~~~~~~~ -short.cpp: In member function 'int ShortRead::load(int)': -short.cpp:424:28: warning: 'code' may be used uninitialized [-Wmaybe-uninitialized] - 424 | forward_word = (forward_word << BITS_PER_BASE) | code; - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -short.cpp:310:38: note: 'code' was declared here - 310 | int64 forward_word, backward_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 perfcounters.cpp -short.cpp: In member function 'ShortRead** ShortRead::split(int)': -short.cpp:503:45: warning: '.t' directive writing 2 bytes into a region of size between 1 and 256 [-Wformat-overflow=] - 503 | sprintf(partitions[i]->alFileName, "%s.t%d", alFileName, i); - | ^~ -short.cpp:503:42: note: directive argument in the range [0, 1073741823] - 503 | sprintf(partitions[i]->alFileName, "%s.t%d", alFileName, i); - | ^~~~~~~~ -short.cpp:503:14: note: 'sprintf' output between 4 and 268 bytes into a destination of size 256 - 503 | sprintf(partitions[i]->alFileName, "%s.t%d", alFileName, i); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -short.cpp:510:45: warning: '.t' directive writing 2 bytes into a region of size between 1 and 256 [-Wformat-overflow=] - 510 | sprintf(partitions[i]->unFileName, "%s.t%d", unFileName, i); - | ^~ -short.cpp:510:42: note: directive argument in the range [0, 1073741823] - 510 | sprintf(partitions[i]->unFileName, "%s.t%d", unFileName, i); - | ^~~~~~~~ -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 model.cpp +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; + | ^~~~~~ +model.cpp: In static member function 'static unsigned int AlignerModel::getFreeMemory()': +model.cpp:166:28: warning: format '%d' expects argument of type 'int*', but argument 3 has type 'unsigned int*' [-Wformat=] + 166 | fscanf(file, "MemTotal: %d kB\n", &memTotal); + | ~^ ~~~~~~~~~ + | | | + | int* unsigned int* + | %d +model.cpp:167:27: warning: format '%d' expects argument of type 'int*', but argument 3 has type 'unsigned int*' [-Wformat=] + 167 | fscanf(file, "MemFree: %d kB\n", &memFree); + | ~^ ~~~~~~~~ + | | | + | int* unsigned int* + | %d +model.cpp:168:27: warning: format '%d' expects argument of type 'int*', but argument 3 has type 'unsigned int*' [-Wformat=] + 168 | fscanf(file, "Buffers: %d kB\n", &memBuffer); + | ~^ ~~~~~~~~~~ + | | | + | int* unsigned int* + | %d +model.cpp:169:26: warning: format '%d' expects argument of type 'int*', but argument 3 has type 'unsigned int*' [-Wformat=] + 169 | fscanf(file, "Cached: %d kB\n", &memCache); + | ~^ ~~~~~~~~~ + | | | + | int* unsigned int* + | %d +model.cpp: In static member function 'static unsigned int AlignerModel::estimateHashtableSpace(unsigned int, int, int, int)': +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 +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 writer.h:26, from writer.cpp:21: @@ -1320,47 +1390,14 @@ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ -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; - | ^~~~~~ 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)); | ~~~~~~~^~~~~~~~~~ -model.cpp: In static member function 'static unsigned int AlignerModel::getFreeMemory()': -model.cpp:166:28: warning: format '%d' expects argument of type 'int*', but argument 3 has type 'unsigned int*' [-Wformat=] - 166 | fscanf(file, "MemTotal: %d kB\n", &memTotal); - | ~^ ~~~~~~~~~ - | | | - | int* unsigned int* - | %d -model.cpp:167:27: warning: format '%d' expects argument of type 'int*', but argument 3 has type 'unsigned int*' [-Wformat=] - 167 | fscanf(file, "MemFree: %d kB\n", &memFree); - | ~^ ~~~~~~~~ - | | | - | int* unsigned int* - | %d -model.cpp:168:27: warning: format '%d' expects argument of type 'int*', but argument 3 has type 'unsigned int*' [-Wformat=] - 168 | fscanf(file, "Buffers: %d kB\n", &memBuffer); - | ~^ ~~~~~~~~~~ - | | | - | int* unsigned int* - | %d -model.cpp:169:26: warning: format '%d' expects argument of type 'int*', but argument 3 has type 'unsigned int*' [-Wformat=] - 169 | fscanf(file, "Cached: %d kB\n", &memCache); - | ~^ ~~~~~~~~~ - | | | - | int* unsigned int* - | %d 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; | ^~~~ -model.cpp: In static member function 'static unsigned int AlignerModel::estimateHashtableSpace(unsigned int, int, int, int)': -model.cpp:198:26: warning: variable 'p2' set but not used [-Wunused-but-set-variable] - 198 | double nSpace, p0, p1, p2; - | ^~ 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; @@ -1413,14 +1450,6 @@ 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 -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; - | ^~~ In file included from hitset.h:31, from hash.h:29, from aligner.h:25, @@ -1496,11 +1525,18 @@ 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-DYvlqt0m + rm -fr -- /tmp/dh-xdg-rundir-QSGWrSyd create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/wham-align.substvars @@ -1537,10 +1573,10 @@ install -p -m0644 ./debian/wham.1 debian/wham-align/usr/share/man/man1/wham.1 man-recode --to-code UTF-8 --suffix .dh-new debian/wham-align/usr/share/man/man1/wham-build.1 man-recode --to-code UTF-8 --suffix .dh-new debian/wham-align/usr/share/man/man1/wham.1 - mv debian/wham-align/usr/share/man/man1/wham-build.1.dh-new debian/wham-align/usr/share/man/man1/wham-build.1 - chmod 0644 -- debian/wham-align/usr/share/man/man1/wham-build.1 mv debian/wham-align/usr/share/man/man1/wham.1.dh-new debian/wham-align/usr/share/man/man1/wham.1 chmod 0644 -- debian/wham-align/usr/share/man/man1/wham.1 + mv debian/wham-align/usr/share/man/man1/wham-build.1.dh-new debian/wham-align/usr/share/man/man1/wham-build.1 + chmod 0644 -- debian/wham-align/usr/share/man/man1/wham-build.1 dh_perl dh_link dh_strip_nondeterminism @@ -1608,9 +1644,9 @@ cd debian/.debhelper/wham-align/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/wham-align/dbgsym-root/DEBIAN/md5sums 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 --root-owner-group --build debian/wham-align .. dpkg-deb: building package 'wham-align' in '../wham-align_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 @@ -1619,12 +1655,14 @@ 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/32637/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/32637/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/8401 and its subdirectories -I: Current time: Tue Dec 17 03:42:29 -12 2024 -I: pbuilder-time-stamp: 1734450149 +I: removing directory /srv/workspace/pbuilder/32637 and its subdirectories +I: Current time: Wed Dec 18 05:44:44 +14 2024 +I: pbuilder-time-stamp: 1734450284