Diff of the two buildlogs: -- --- b1/build.log 2024-05-24 05:48:31.440933563 +0000 +++ b2/build.log 2024-05-24 05:50:10.576712146 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jun 26 00:10:57 -12 2025 -I: pbuilder-time-stamp: 1750939857 +I: Current time: Fri May 24 19:48:34 +14 2024 +I: pbuilder-time-stamp: 1716529714 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -31,51 +31,83 @@ 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/56488/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3958280/tmp/hooks/D01_modify_environment starting +debug: Running on infom01-amd64. +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 24 05:48 /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/3958280/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3958280/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='amd64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + 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=amd64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='96e04bd242fb49b49fc00eb5781c48d6' - 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='56488' - PS1='# ' - PS2='> ' + INVOCATION_ID=6d4383bbebff484bbdda1464ae8e1365 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3958280 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.kFWSD6gK/pbuilderrc_R5j9 --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.kFWSD6gK/b1 --logfile b1/build.log wham-align_0.1.5-8.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + 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.kFWSD6gK/pbuilderrc_W5Re --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.kFWSD6gK/b2 --logfile b2/build.log wham-align_0.1.5-8.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom02-amd64 6.7.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.7.12-1~bpo12+1 (2024-05-06) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-21-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Jun 24 14:05 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/56488/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 22 07:42 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3958280/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -146,7 +178,7 @@ Get: 33 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] -Fetched 19.2 MB in 0s (91.9 MB/s) +Fetched 19.2 MB in 1s (13.7 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 ... 19718 files and directories currently installed.) @@ -301,7 +333,11 @@ 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/3958280/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/3958280/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 @@ -357,55 +393,24 @@ | ^~~~~~ 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 -fcf-protection -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 -fcf-protection -Wall -pedantic -fsigned-char -O3 -Wno-write-strings builder.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; - | ^~ -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)) { - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +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)': +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) { + | ~~~~^~~~~~~~ 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++) { | ~~^~~~~~~~~~~~~~ -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) - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 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) { | ~~~~^~~~~~~~~~~~ +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; + | ^~~~~~ interval.cpp:310:11: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] 310 | if (ret != numIEntry) { | ~~~~^~~~~~~~~~~~ @@ -416,17 +421,6 @@ 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 writer.h:26, - from writer.cpp:21: -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; @@ -470,64 +464,58 @@ hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ -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; -writer.cpp:148:10: warning: unused variable 'sid' [-Wunused-variable] - 148 | uint32 sid = 0, soffset = 0; - | ^~~ -writer.cpp:148:19: warning: unused variable 'soffset' [-Wunused-variable] - 148 | uint32 sid = 0, soffset = 0; - | ^~~~~~~ -writer.cpp: In member function 'void SamWriter::writeValidAlignment(int, HitSet*)': -writer.cpp:271:7: warning: unused variable 'i' [-Wunused-variable] - 271 | int i, j, k, h, lastDiff; - | ^ -writer.cpp:271:10: warning: unused variable 'j' [-Wunused-variable] - 271 | int i, j, k, h, lastDiff; - | ^ -writer.cpp:271:13: warning: unused variable 'k' [-Wunused-variable] - 271 | int i, j, k, h, lastDiff; - | ^ -writer.cpp:271:19: warning: unused variable 'lastDiff' [-Wunused-variable] - 271 | int i, j, k, h, lastDiff; - | ^~~~~~~~ -writer.cpp:272:9: warning: unused variable 'code1' [-Wunused-variable] - 272 | int64 code1, code2; - | ^~~~~ -writer.cpp:272:16: warning: unused variable 'code2' [-Wunused-variable] - 272 | int64 code1, code2; - | ^~~~~ -writer.cpp:278:10: warning: unused variable 'p' [-Wunused-variable] - 278 | double p, sump; - | ^ -writer.cpp:278:13: warning: unused variable 'sump' [-Wunused-variable] - 278 | double p, sump; - | ^~~~ -writer.cpp:279:30: warning: unused variable 'tag' [-Wunused-variable] - 279 | char qseq[128], rseq[128], tag[128]; - | ^~~ -writer.cpp:281:8: warning: unused variable 'shortread' [-Wunused-variable] - 281 | char shortread[256]; +hitset.cpp: In member function 'int HitPairSet::build(HitSet*, HitSet*, uint32, uint32, bool (*)[2], bool)': +hitset.cpp:90:8: warning: unused variable 'pairMatch' [-Wunused-variable] + 90 | bool pairMatch = false; | ^~~~~~~~~ -writer.cpp: In member function 'void SamWriter::getCIGAR(char*, char*, char*, ErrorVector)': -writer.cpp:382:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] - 382 | for (i = 0, j = 0; i < strlen(query); i++, j++) { - | ~~^~~~~~~~~~~~~~~ -writer.cpp: In member function 'void SamWriter::getMDfield(char*, char*, char*, ErrorVector)': -writer.cpp:431:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] - 431 | for (i = 0, j = 0; i < strlen(query); i++, j++) { - | ~~^~~~~~~~~~~~~~~ -writer.cpp: In member function 'void SamPairWriter::writeValidAlignment(int, HitSet*)': -writer.cpp:619:47: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] - 619 | if (!mate1Unmatch && !mate2Unmatch & sid1 == sid2) { - | ~~~~~^~~~~~~ +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) + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ +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; + | ^~~~~~ In file included from hitset.h:31, - from hitset.cpp:1: + from hash.h:29, + from hash.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) { | ~~~~^~~~~~~~ +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; + | ^~ 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; @@ -575,13 +563,14 @@ hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ -hitset.cpp: In member function 'int HitPairSet::build(HitSet*, HitSet*, uint32, uint32, bool (*)[2], bool)': -hitset.cpp:90:8: warning: unused variable 'pairMatch' [-Wunused-variable] - 90 | bool pairMatch = false; - | ^~~~~~~~~ +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 embedhash.cpp:27: + from aligner.h:25, + from aligner.cpp:25: 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) { @@ -637,10 +626,13 @@ hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ +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; + | ^ In file included from hitset.h:31, from hash.h:29, - from aligner.h:25, - from builder.cpp:31: + 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) { @@ -649,6 +641,19 @@ pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; | ^~~~~~ +edit_distance.cpp: In function 'scoreinfo edit_distance_align(int**, char**, char*, char*, int, int, char*, char*, int)': +edit_distance.cpp:181:10: warning: unused variable 'tmp_trace' [-Wunused-variable] + 181 | char tmp_trace = traceback[i][j]; + | ^~~~~~~~~ +edit_distance.cpp:132:14: warning: unused variable 'x' [-Wunused-variable] + 132 | int k = 0, x = 0, y = 0; + | ^ +edit_distance.cpp:132:21: warning: unused variable 'y' [-Wunused-variable] + 132 | int k = 0, x = 0, y = 0; + | ^ +edit_distance.cpp:178:7: warning: unused variable 'kk' [-Wunused-variable] + 178 | int kk = 0; + | ^~ 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; @@ -696,9 +701,16 @@ hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ +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; + | ^~~~ In file included from hitset.h:31, - from hash.h:29, - from hash.cpp:27: + from writer.h:26, + from writer.cpp:21: 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) { @@ -707,10 +719,6 @@ pair.h:602:15: warning: unused variable 'offset' [-Wunused-variable] 602 | int i, j, offset, min, tmp; | ^~~~~~ -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; - | ^ 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; @@ -736,19 +744,6 @@ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | int a; | ^ -edit_distance.cpp: In function 'scoreinfo edit_distance_align(int**, char**, char*, char*, int, int, char*, char*, int)': -edit_distance.cpp:181:10: warning: unused variable 'tmp_trace' [-Wunused-variable] - 181 | char tmp_trace = traceback[i][j]; - | ^~~~~~~~~ -edit_distance.cpp:132:14: warning: unused variable 'x' [-Wunused-variable] - 132 | int k = 0, x = 0, y = 0; - | ^ -edit_distance.cpp:132:21: warning: unused variable 'y' [-Wunused-variable] - 132 | int k = 0, x = 0, y = 0; - | ^ -edit_distance.cpp:178:7: warning: unused variable 'kk' [-Wunused-variable] - 178 | int kk = 0; - | ^~ 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; @@ -763,25 +758,247 @@ 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; + | ^~~~ +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; +writer.cpp:148:10: warning: unused variable 'sid' [-Wunused-variable] + 148 | uint32 sid = 0, soffset = 0; + | ^~~ +writer.cpp:148:19: warning: unused variable 'soffset' [-Wunused-variable] + 148 | uint32 sid = 0, soffset = 0; + | ^~~~~~~ +writer.cpp: In member function 'void SamWriter::writeValidAlignment(int, HitSet*)': +writer.cpp:271:7: warning: unused variable 'i' [-Wunused-variable] + 271 | int i, j, k, h, lastDiff; + | ^ +writer.cpp:271:10: warning: unused variable 'j' [-Wunused-variable] + 271 | int i, j, k, h, lastDiff; + | ^ +writer.cpp:271:13: warning: unused variable 'k' [-Wunused-variable] + 271 | int i, j, k, h, lastDiff; + | ^ +writer.cpp:271:19: warning: unused variable 'lastDiff' [-Wunused-variable] + 271 | int i, j, k, h, lastDiff; + | ^~~~~~~~ +writer.cpp:272:9: warning: unused variable 'code1' [-Wunused-variable] + 272 | int64 code1, code2; + | ^~~~~ +writer.cpp:272:16: warning: unused variable 'code2' [-Wunused-variable] + 272 | int64 code1, code2; + | ^~~~~ +writer.cpp:278:10: warning: unused variable 'p' [-Wunused-variable] + 278 | double p, sump; + | ^ +writer.cpp:278:13: warning: unused variable 'sump' [-Wunused-variable] + 278 | double p, sump; + | ^~~~ +writer.cpp:279:30: warning: unused variable 'tag' [-Wunused-variable] + 279 | char qseq[128], rseq[128], tag[128]; + | ^~~ +writer.cpp:281:8: warning: unused variable 'shortread' [-Wunused-variable] + 281 | char shortread[256]; + | ^~~~~~~~~ +writer.cpp: In member function 'void SamWriter::getCIGAR(char*, char*, char*, ErrorVector)': +writer.cpp:382:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] + 382 | for (i = 0, j = 0; i < strlen(query); i++, j++) { + | ~~^~~~~~~~~~~~~~~ +writer.cpp: In member function 'void SamWriter::getMDfield(char*, char*, char*, ErrorVector)': +writer.cpp:431:24: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] + 431 | for (i = 0, j = 0; i < strlen(query); i++, j++) { + | ~~^~~~~~~~~~~~~~~ +writer.cpp: In member function 'void SamPairWriter::writeValidAlignment(int, HitSet*)': +writer.cpp:619:47: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] + 619 | if (!mate1Unmatch && !mate2Unmatch & sid1 == sid2) { + | ~~~~~^~~~~~~ +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, 2147483646] + 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, 2147483646] + 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); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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) + | ~~^~~~~~~~~~~~~ +hash.cpp:285:33: warning: comparison of integer expressions of different signedness: 'uint32' {aka 'unsigned int'} and 'int' [-Wsign-compare] + 285 | if (useEmbedTables() && tmp > embedShreshold) { + | ~~~~^~~~~~~~~~~~~~~~ +hash.cpp: In member function 'void HashTable::setScanThreshold(double)': +hash.cpp:343:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] + 343 | for (int i = 0; i < nHistogram - 1; i++) { + | ~~^~~~~~~~~~~~~~~~ +hash.cpp: In member function 'void HashTable::insert(int64*, unsigned int)': +hash.cpp:460:38: warning: operation on '*(((HashTable*)this)->HashTable::overflowPool + ((sizetype)(((long unsigned int)curOverflowEntry) * 4)))' may be undefined [-Wsequence-point] + 460 | overflowPool[curOverflowEntry] = +hash.cpp:411:10: warning: unused variable 'seqOffset' [-Wunused-variable] + 411 | uint32 seqOffset; + | ^~~~~~~~~ +hash.cpp:413:10: warning: unused variable 'counter' [-Wunused-variable] + 413 | uint32 counter = 0; + | ^~~~~~~ +hash.cpp:414:11: warning: variable 'seqVector' set but not used [-Wunused-but-set-variable] + 414 | int64 * seqVector; + | ^~~~~~~~~ +hash.cpp:416:11: warning: unused variable 'target' [-Wunused-variable] + 416 | int64 * target = &tspace[8]; + | ^~~~~~ +hash.cpp:417:8: warning: unused variable 'isBloomFilter' [-Wunused-variable] + 417 | bool isBloomFilter; + | ^~~~~~~~~~~~~ +hash.cpp:418:12: warning: unused variable 'bloomFilter' [-Wunused-variable] + 418 | uint32 * bloomFilter; + | ^~~~~~~~~~~ +hash.cpp:419:10: warning: unused variable 'bloomFilterNum' [-Wunused-variable] + 419 | uint32 bloomFilterNum; + | ^~~~~~~~~~~~~~ +hash.cpp: In member function 'int HashTable::buildEmbedTable()': +hash.cpp:469:33: warning: unused variable 'rest' [-Wunused-variable] + 469 | int64 * query = &ttspace[8], *rest = &ttspace[24], *rest1 = &ttspace[40], + | ^~~~ +hash.cpp:469:55: warning: unused variable 'rest1' [-Wunused-variable] + 469 | int64 * query = &ttspace[8], *rest = &ttspace[24], *rest1 = &ttspace[40], + | ^~~~~ +hash.cpp:470:8: warning: unused variable 'rest2' [-Wunused-variable] + 470 | *rest2 = &ttspace[56], *noheadkey = &ttspace[72]; + | ^~~~~ +hash.cpp:470:31: warning: unused variable 'noheadkey' [-Wunused-variable] + 470 | *rest2 = &ttspace[56], *noheadkey = &ttspace[72]; + | ^~~~~~~~~ +hash.cpp:472:34: warning: variable 'startOffset' set but not used [-Wunused-but-set-variable] + 472 | uint32 seqOffset, entryOffset, startOffset; + | ^~~~~~~~~~~ +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]; + | ^~~~~~~~~ +hash.cpp:590:8: warning: unused variable 'subkey4' [-Wunused-variable] + 590 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; + | ^~~~~~~ +hash.cpp:590:32: warning: unused variable 'subkey5' [-Wunused-variable] + 590 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; + | ^~~~~~~ +hash.cpp: In member function 'void HashTable::insertEmbedTableEntry(int64*, uint32, int, int)': +hash.cpp:662:11: warning: unused variable 'noheadkey' [-Wunused-variable] + 662 | int64 * noheadkey = &tspace[8], *rest = &tspace[24]; + | ^~~~~~~~~ +hash.cpp:665:8: warning: unused variable 'subkey4' [-Wunused-variable] + 665 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; + | ^~~~~~~ +hash.cpp:665:32: warning: unused variable 'subkey5' [-Wunused-variable] + 665 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; + | ^~~~~~~ +hash.cpp: In member function 'unsigned int HashTable::lookup(int64*, int64*, int, char*, strand, int, HitSet*, bool)': +hash.cpp:746:7: warning: unused variable 'num' [-Wunused-variable] + 746 | int num; + | ^~~ +hash.cpp:750:11: warning: unused variable 'diff' [-Wunused-variable] + 750 | int64 * diff = &tspace1[8], *target = &tspace2[8]; + | ^~~~ +hash.cpp:753:10: warning: unused variable 'sid' [-Wunused-variable] + 753 | uint32 sid, soffset; + | ^~~ +hash.cpp:753:15: warning: unused variable 'soffset' [-Wunused-variable] + 753 | uint32 sid, soffset; + | ^~~~~~~ +hash.cpp: In member function 'unsigned int HashTable::lookupEmbedTable(int64*, uint32, int, char*, strand, int, HitSet*, bool)': +hash.cpp:962:11: warning: unused variable 'noheadkey' [-Wunused-variable] + 962 | int64 * noheadkey = &tspace[8], *rest = &tspace[24]; + | ^~~~~~~~~ +hash.cpp:965:8: warning: unused variable 'subkey4' [-Wunused-variable] + 965 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; + | ^~~~~~~ +hash.cpp:965:32: warning: unused variable 'subkey5' [-Wunused-variable] + 965 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; + | ^~~~~~~ +hash.cpp:973:11: warning: unused variable 'seqVector' [-Wunused-variable] + 973 | int64 * seqVector = sequence->getSequence(); + | ^~~~~~~~~ +hash.cpp: In member function 'bool HashTable::lookup(int64*, uint32)': +hash.cpp:1052:7: warning: unused variable 'num' [-Wunused-variable] + 1052 | int num; + | ^~~ +hash.cpp:1056:11: warning: unused variable 'diff' [-Wunused-variable] + 1056 | int64 * diff = &tspace1[8], *target = &tspace2[8]; + | ^~~~ +hash.cpp:1056:32: warning: unused variable 'target' [-Wunused-variable] + 1056 | int64 * diff = &tspace1[8], *target = &tspace2[8]; + | ^~~~~~ +hash.cpp:1057:11: warning: variable 'seqVector' set but not used [-Wunused-but-set-variable] + 1057 | int64 * seqVector; + | ^~~~~~~~~ +hash.cpp:1059:10: warning: unused variable 'sid' [-Wunused-variable] + 1059 | uint32 sid, soffset; + | ^~~ +hash.cpp:1059:15: warning: unused variable 'soffset' [-Wunused-variable] + 1059 | uint32 sid, soffset; + | ^~~~~~~ +hash.cpp: In member function 'uint32 HashTable::printOverflowList(uint32, uint32, int64*)': +hash.cpp:1184:23: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] + 1184 | for (int i = 0; i < keyOffset / BITS_PER_BASE; i++) +hash.cpp:1188:23: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] + 1188 | for (int i = 0; i < (lenSeq - keyOffset - lenKey) / BITS_PER_BASE; i++) +hash.cpp:1247:27: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] + 1247 | for (int j = 0; j < strlen(set[i].str); j++) + | ~~^~~~~~~~~~~~~~~~~~~~ +hash.cpp:1254:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] + 1254 | for (int j = 0; j < strlen(set[i].str); j++) + | ~~^~~~~~~~~~~~~~~~~~~~ +hash.cpp:1137:11: warning: unused variable 'diff' [-Wunused-variable] + 1137 | int64 * diff = &tspace1[8], *target = &tspace2[8]; + | ^~~~ +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; + | ^~~~ +hash.cpp:1321:34: warning: variable 'offset' set but not used [-Wunused-but-set-variable] + 1321 | uint32 entryOffset, seqOffset, offset; + | ^~~~~~ +hash.cpp: In member function 'void HashTable::checkRepeat(uint32)': +hash.cpp:1673:34: warning: variable 'offset' set but not used [-Wunused-but-set-variable] + 1673 | uint32 entryOffset, seqOffset, offset; + | ^~~~~~ +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 aligner.cpp:25: + from builder.cpp:31: 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) { | ~~~~^~~~~~~~ -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; - | ^~~~ -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; - | ^~~~ +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) { + | ~~~~^~~~ +aligner.cpp:371:37: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] + 371 | if ((indexBits[i] >> j) & 0x1 == 1) { + | ~~~~^~~~ +aligner.cpp: In member function 'int Aligner::preProcessHashTables()': +aligner.cpp:534:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 534 | for (i = 0; i < nHashTable; i++) { + | ~~^~~~~~~~~~~~ +aligner.cpp:712:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 712 | for (i = 0; i < nHashTable; i++) { + | ~~^~~~~~~~~~~~ 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; @@ -811,10 +1028,6 @@ pair.h:685:9: warning: unused variable 'a' [-Wunused-variable] 685 | 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 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; @@ -833,29 +1046,169 @@ hitset.h:86:9: warning: variable 'size' set but not used [-Wunused-but-set-variable] 86 | int size; | ^~~~ +aligner.cpp: In member function 'int Aligner::build(char*)': +aligner.cpp:724:16: warning: unused variable 'i' [-Wunused-variable] + 724 | unsigned int i, j; + | ^ +aligner.cpp:724:19: warning: unused variable 'j' [-Wunused-variable] + 724 | unsigned int i, j; + | ^ +aligner.cpp: In member function 'int Aligner::buildHashTables(char*)': +aligner.cpp:807:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 807 | for (i = 0; i < nHashTable; i++) { + | ~~^~~~~~~~~~~~ +aligner.cpp:844:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 844 | for (i1 = 0; i1 < lenPartition * (nPartition - 1); i1 += lenPartition) { + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:864:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 864 | for (i1 = 0; i1 < lenPartition * (nPartition - 2); i1 += lenPartition) { + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:871:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 871 | for (i2 = i1; i2 < lenPartition * (nPartition - 2); + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:894:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 894 | for (i1 = 0; i1 < lenPartition * (nPartition - 3); i1 += lenPartition) { + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:901:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 901 | for (i2 = i1; i2 < lenPartition * (nPartition - 3); + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:909:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 909 | for (i3 = i2; i3 < lenPartition * (nPartition - 3); + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:928:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 928 | for (i1 = 0; i1 < lenPartition * (nPartition - 4); i1 += lenPartition) { + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:930:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 930 | for (i2 = i1; i2 < lenPartition * (nPartition - 4); + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:933:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 933 | for (i3 = i2; i3 < lenPartition * (nPartition - 4); + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:936:30: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 936 | for (i4 = i3; i4 < lenPartition * (nPartition - 4); i4 += + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:951:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 951 | for (i1 = 0; i1 < lenPartition * (nPartition - 5); i1 += lenPartition) { + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:953:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 953 | for (i2 = i1; i2 < lenPartition * (nPartition - 5); + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:956:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 956 | for (i3 = i2; i3 < lenPartition * (nPartition - 5); + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:959:30: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 959 | for (i4 = i3; i4 < lenPartition * (nPartition - 5); i4 += + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:962:32: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 962 | for (i5 = i4; i5 < lenPartition * (nPartition - 5); i5 += + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:983:19: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 983 | for (i = 0; i < nHashTable; i++) { + | ~~^~~~~~~~~~~~ +aligner.cpp:1006:19: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 1006 | for (i = 0; i < nHashTable; i++) { + | ~~^~~~~~~~~~~~ +aligner.cpp: In member function 'unsigned int Aligner::alignFirst(int64*, char*, strand, int, HitSet*, bool)': +aligner.cpp:1035:10: warning: unused variable 'offset' [-Wunused-variable] + 1035 | uint32 offset; + | ^~~~~~ +aligner.cpp:1039:7: warning: unused variable 'nHit' [-Wunused-variable] + 1039 | int nHit = 0; + | ^~~~ +aligner.cpp: In member function 'unsigned int Aligner::align(int64*, char*, strand, int, HitSet*, bool, bool)': +aligner.cpp:1119:10: warning: variable 'offset' set but not used [-Wunused-but-set-variable] + 1119 | uint32 offset; + | ^~~~~~ +aligner.cpp:1123:7: warning: variable 'nHit' set but not used [-Wunused-but-set-variable] + 1123 | int nHit = 0; + | ^~~~ +aligner.cpp: In member function 'int Aligner::check(int)': +aligner.cpp:1436:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 1436 | for (i = 0; i < num; i++) { + | ~~^~~~~ +aligner.cpp:1452:19: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 1452 | for (j = 0; j < nError; j++) { + | ~~^~~~~~~~ +aligner.cpp:1426:7: warning: unused variable 'ret' [-Wunused-variable] + 1426 | int ret; + | ^~~ +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 | } + | ^ +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++) { + | ~~^~~~~~~~~~~~ +aligner.cpp:1547:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 1547 | for (i = 0; i < res.nRead; i++) { + | ~~^~~~~~~~~~~ +aligner.cpp:1629:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] + 1629 | delete writer; + | ^~~~~~~~~~~~~ +aligner.cpp:1502:10: warning: unused variable 'file' [-Wunused-variable] + 1502 | FILE * file = NULL, *alfile = NULL, *unfile = NULL; + | ^~~~ +aligner.cpp:1502:24: warning: unused variable 'alfile' [-Wunused-variable] + 1502 | FILE * file = NULL, *alfile = NULL, *unfile = NULL; + | ^~~~~~ +aligner.cpp:1502:40: warning: unused variable 'unfile' [-Wunused-variable] + 1502 | FILE * file = NULL, *alfile = NULL, *unfile = NULL; + | ^~~~~~ +aligner.cpp:1505:7: warning: unused variable 'strand' [-Wunused-variable] + 1505 | int strand; + | ^~~~~~ +aligner.cpp:1508:9: warning: unused variable 'ratio' [-Wunused-variable] + 1508 | float ratio; + | ^~~~~ +aligner.cpp:1514:31: warning: unused variable 'strata' [-Wunused-variable] + 1514 | bool sorted = info->sorted, strata = info->strata; + | ^~~~~~ +aligner.cpp: In member function 'AlignRes Aligner::alignPairEnd(AlignInfo*, char*)': +aligner.cpp:1685:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 1685 | for (i = 0; i < res.nRead; i++) { + | ~~^~~~~~~~~~~ hash.h: In function 'uint32 murmurHash(int64*, uint32)': hash.h:86:10: warning: unused variable 'sum' [-Wunused-variable] 86 | uint32 sum = 0; | ^~~ -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, 2147483646] - 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, 2147483646] - 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); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aligner.cpp:1754:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] + 1754 | delete writer; + | ^~~~~~~~~~~~~ +aligner.cpp:1637:8: warning: unused variable 'success' [-Wunused-variable] + 1637 | bool success; + | ^~~~~~~ +aligner.cpp:1638:16: warning: unused variable 'nSuccessRead' [-Wunused-variable] + 1638 | unsigned int nSuccessRead = 0; + | ^~~~~~~~~~~~ +aligner.cpp:1639:10: warning: unused variable 'file' [-Wunused-variable] + 1639 | FILE * file = NULL; + | ^~~~ +aligner.cpp:1646:8: warning: unused variable 'mateFilename' [-Wunused-variable] + 1646 | char mateFilename[256]; + | ^~~~~~~~~~~~ +aligner.cpp:1652:31: warning: unused variable 'strata' [-Wunused-variable] + 1652 | bool sorted = info->sorted, strata = info->strata; + | ^~~~~~ +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 }; + | ^~~~~~~~~~~~~ +aligner.cpp: In member function 'AlignRes Aligner::mergeSingleEnd(AlignInfo*, int, char*)': +aligner.cpp:1851:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] + 1851 | delete writer; + | ^~~~~~~~~~~~~ +aligner.cpp:1775:10: warning: unused variable 'ret' [-Wunused-variable] + 1775 | int i, ret; + | ^~~ +aligner.cpp: In member function 'AlignRes Aligner::mergePairEnd(AlignInfo*, int, char*)': +aligner.cpp:1989:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] + 1989 | delete writer; + | ^~~~~~~~~~~~~ +aligner.cpp:1874:10: warning: unused variable 'ret' [-Wunused-variable] + 1874 | int i, ret; + | ^~~ embedhash.cpp: In member function 'int EmbedHashTable::preProcessEnd()': embedhash.cpp:137:16: warning: unused variable 'ln2' [-Wunused-variable] 137 | const double ln2 = log(2); @@ -907,17 +1260,6 @@ embedhash.cpp:392:15: warning: unused variable 'soffset' [-Wunused-variable] 392 | uint32 sid, soffset; | ^~~~~~~ -builder.cpp: In function 'int getArguVal(char*)': -builder.cpp:115:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses] - 115 | else if (*c = 'g' || *c == 'G') - | ~~~^~~~~~~~~~~~~~~~~~ -builder.cpp: In function 'int main(int, char**)': -builder.cpp:159:7: warning: unused variable 'build_mode' [-Wunused-variable] - 159 | int build_mode = BUILD_MODE_ALL; - | ^~~~~~~~~~ -builder.cpp:277:7: warning: unused variable 'nChar' [-Wunused-variable] - 277 | int nChar = sequence->getNum(); - | ^~~~~ In file included from hitset.h:31, from hash.h:29, from aligner.h:25, @@ -965,14 +1307,6 @@ pair.h:756:9: warning: unused variable 'a' [-Wunused-variable] 756 | int a; | ^ -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 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)); @@ -981,6 +1315,45 @@ 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 getArguVal(char*)': +main.cpp:159:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses] + 159 | else if (*c = 'g' || *c == 'G') + | ~~~^~~~~~~~~~~~~~~~~~ +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; + | ^ +main.cpp:350:10: warning: unused variable 'j' [-Wunused-variable] + 350 | int i, j, ret; + | ^ +main.cpp: In function 'int main(int, char**)': +main.cpp:523:7: warning: unused variable 'numKeys' [-Wunused-variable] + 523 | int numKeys; + | ^~~~~~~ +main.cpp:526:7: warning: unused variable 'nSeq' [-Wunused-variable] + 526 | int nSeq = 1; + | ^~~~ +main.cpp:532:21: warning: unused variable 'sequence' [-Wunused-variable] + 532 | CompactSequence * sequence; + | ^~~~~~~~ +main.cpp:534:15: warning: unused variable 'threadpool' [-Wunused-variable] + 534 | pthread_t * threadpool; + | ^~~~~~~~~~ +main.cpp:536:9: warning: unused variable 'threadid' [-Wunused-variable] + 536 | int * threadid; + | ^~~~~~~~ +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; @@ -1020,14 +1393,21 @@ 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)); | ~~~~~~~^~~~~~~~~~ +builder.cpp: In function 'int getArguVal(char*)': +builder.cpp:115:15: warning: suggest parentheses around assignment used as truth value [-Wparentheses] + 115 | else if (*c = 'g' || *c == 'G') + | ~~~^~~~~~~~~~~~~~~~~~ +builder.cpp: In function 'int main(int, char**)': +builder.cpp:159:7: warning: unused variable 'build_mode' [-Wunused-variable] + 159 | int build_mode = BUILD_MODE_ALL; + | ^~~~~~~~~~ +builder.cpp:277:7: warning: unused variable 'nChar' [-Wunused-variable] + 277 | int nChar = sequence->getNum(); + | ^~~~~ 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; @@ -1097,365 +1477,21 @@ 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) { - | ~~~~^~~~~~~ -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 }; - | ^~~~~~~~~~~~~ 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 }; | ^~~~~~~~~~~~~ -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) { - | ~~~~^~~~ -aligner.cpp:371:37: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] - 371 | if ((indexBits[i] >> j) & 0x1 == 1) { - | ~~~~^~~~ -aligner.cpp: In member function 'int Aligner::preProcessHashTables()': -aligner.cpp:534:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 534 | for (i = 0; i < nHashTable; i++) { - | ~~^~~~~~~~~~~~ -aligner.cpp:712:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 712 | for (i = 0; i < nHashTable; i++) { - | ~~^~~~~~~~~~~~ -aligner.cpp: In member function 'int Aligner::build(char*)': -aligner.cpp:724:16: warning: unused variable 'i' [-Wunused-variable] - 724 | unsigned int i, j; - | ^ -aligner.cpp:724:19: warning: unused variable 'j' [-Wunused-variable] - 724 | unsigned int i, j; - | ^ -aligner.cpp: In member function 'int Aligner::buildHashTables(char*)': -aligner.cpp:807:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 807 | for (i = 0; i < nHashTable; i++) { - | ~~^~~~~~~~~~~~ -aligner.cpp:844:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 844 | for (i1 = 0; i1 < lenPartition * (nPartition - 1); i1 += lenPartition) { - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:864:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 864 | for (i1 = 0; i1 < lenPartition * (nPartition - 2); i1 += lenPartition) { - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:871:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 871 | for (i2 = i1; i2 < lenPartition * (nPartition - 2); - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:894:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 894 | for (i1 = 0; i1 < lenPartition * (nPartition - 3); i1 += lenPartition) { - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:901:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 901 | for (i2 = i1; i2 < lenPartition * (nPartition - 3); - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:909:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 909 | for (i3 = i2; i3 < lenPartition * (nPartition - 3); - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:928:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 928 | for (i1 = 0; i1 < lenPartition * (nPartition - 4); i1 += lenPartition) { - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:930:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 930 | for (i2 = i1; i2 < lenPartition * (nPartition - 4); - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:933:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 933 | for (i3 = i2; i3 < lenPartition * (nPartition - 4); - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:936:30: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 936 | for (i4 = i3; i4 < lenPartition * (nPartition - 4); i4 += - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:951:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 951 | for (i1 = 0; i1 < lenPartition * (nPartition - 5); i1 += lenPartition) { - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:953:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 953 | for (i2 = i1; i2 < lenPartition * (nPartition - 5); - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:956:28: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 956 | for (i3 = i2; i3 < lenPartition * (nPartition - 5); - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:959:30: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 959 | for (i4 = i3; i4 < lenPartition * (nPartition - 5); i4 += - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:962:32: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 962 | for (i5 = i4; i5 < lenPartition * (nPartition - 5); i5 += - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aligner.cpp:983:19: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 983 | for (i = 0; i < nHashTable; i++) { - | ~~^~~~~~~~~~~~ -aligner.cpp:1006:19: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 1006 | for (i = 0; i < nHashTable; i++) { - | ~~^~~~~~~~~~~~ -aligner.cpp: In member function 'unsigned int Aligner::alignFirst(int64*, char*, strand, int, HitSet*, bool)': -aligner.cpp:1035:10: warning: unused variable 'offset' [-Wunused-variable] - 1035 | uint32 offset; - | ^~~~~~ -aligner.cpp:1039:7: warning: unused variable 'nHit' [-Wunused-variable] - 1039 | int nHit = 0; - | ^~~~ -aligner.cpp: In member function 'unsigned int Aligner::align(int64*, char*, strand, int, HitSet*, bool, bool)': -aligner.cpp:1119:10: warning: variable 'offset' set but not used [-Wunused-but-set-variable] - 1119 | uint32 offset; - | ^~~~~~ -aligner.cpp:1123:7: warning: variable 'nHit' set but not used [-Wunused-but-set-variable] - 1123 | int nHit = 0; - | ^~~~ -aligner.cpp: In member function 'int Aligner::check(int)': -aligner.cpp:1436:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 1436 | for (i = 0; i < num; i++) { - | ~~^~~~~ -aligner.cpp:1452:19: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 1452 | for (j = 0; j < nError; j++) { - | ~~^~~~~~~~ -aligner.cpp:1426:7: warning: unused variable 'ret' [-Wunused-variable] - 1426 | int ret; - | ^~~ -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') - | ~~~^~~~~~~~~~~~~~~~~~ -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++) { - | ~~^~~~~~~~~~~~ -aligner.cpp:1547:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 1547 | for (i = 0; i < res.nRead; i++) { - | ~~^~~~~~~~~~~ -aligner.cpp:1629:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] - 1629 | delete writer; - | ^~~~~~~~~~~~~ -aligner.cpp:1502:10: warning: unused variable 'file' [-Wunused-variable] - 1502 | FILE * file = NULL, *alfile = NULL, *unfile = NULL; - | ^~~~ -aligner.cpp:1502:24: warning: unused variable 'alfile' [-Wunused-variable] - 1502 | FILE * file = NULL, *alfile = NULL, *unfile = NULL; - | ^~~~~~ -aligner.cpp:1502:40: warning: unused variable 'unfile' [-Wunused-variable] - 1502 | FILE * file = NULL, *alfile = NULL, *unfile = NULL; - | ^~~~~~ -aligner.cpp:1505:7: warning: unused variable 'strand' [-Wunused-variable] - 1505 | int strand; - | ^~~~~~ -aligner.cpp:1508:9: warning: unused variable 'ratio' [-Wunused-variable] - 1508 | float ratio; - | ^~~~~ -aligner.cpp:1514:31: warning: unused variable 'strata' [-Wunused-variable] - 1514 | bool sorted = info->sorted, strata = info->strata; - | ^~~~~~ -aligner.cpp: In member function 'AlignRes Aligner::alignPairEnd(AlignInfo*, char*)': -aligner.cpp:1685:17: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 1685 | for (i = 0; i < res.nRead; i++) { - | ~~^~~~~~~~~~~ -aligner.cpp:1754:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] - 1754 | delete writer; - | ^~~~~~~~~~~~~ -aligner.cpp:1637:8: warning: unused variable 'success' [-Wunused-variable] - 1637 | bool success; - | ^~~~~~~ -aligner.cpp:1638:16: warning: unused variable 'nSuccessRead' [-Wunused-variable] - 1638 | unsigned int nSuccessRead = 0; - | ^~~~~~~~~~~~ -aligner.cpp:1639:10: warning: unused variable 'file' [-Wunused-variable] - 1639 | FILE * file = NULL; - | ^~~~ -aligner.cpp:1646:8: warning: unused variable 'mateFilename' [-Wunused-variable] - 1646 | char mateFilename[256]; - | ^~~~~~~~~~~~ -aligner.cpp:1652:31: warning: unused variable 'strata' [-Wunused-variable] - 1652 | bool sorted = info->sorted, strata = info->strata; - | ^~~~~~ -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; - | ^ -main.cpp:350:10: warning: unused variable 'j' [-Wunused-variable] - 350 | int i, j, ret; - | ^ -aligner.cpp: In member function 'AlignRes Aligner::mergeSingleEnd(AlignInfo*, int, char*)': -aligner.cpp:1851:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] - 1851 | delete writer; - | ^~~~~~~~~~~~~ -aligner.cpp:1775:10: warning: unused variable 'ret' [-Wunused-variable] - 1775 | int i, ret; - | ^~~ -aligner.cpp: In member function 'AlignRes Aligner::mergePairEnd(AlignInfo*, int, char*)': -aligner.cpp:1989:3: warning: deleting object of abstract class type 'Writer' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor] - 1989 | delete writer; - | ^~~~~~~~~~~~~ -aligner.cpp:1874:10: warning: unused variable 'ret' [-Wunused-variable] - 1874 | int i, ret; - | ^~~ -main.cpp: In function 'int main(int, char**)': -main.cpp:523:7: warning: unused variable 'numKeys' [-Wunused-variable] - 523 | int numKeys; - | ^~~~~~~ -main.cpp:526:7: warning: unused variable 'nSeq' [-Wunused-variable] - 526 | int nSeq = 1; - | ^~~~ -main.cpp:532:21: warning: unused variable 'sequence' [-Wunused-variable] - 532 | CompactSequence * sequence; - | ^~~~~~~~ -main.cpp:534:15: warning: unused variable 'threadpool' [-Wunused-variable] - 534 | pthread_t * threadpool; - | ^~~~~~~~~~ -main.cpp:536:9: warning: unused variable 'threadid' [-Wunused-variable] - 536 | int * threadid; - | ^~~~~~~~ -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) - | ~~^~~~~~~~~~~~~ -hash.cpp:285:33: warning: comparison of integer expressions of different signedness: 'uint32' {aka 'unsigned int'} and 'int' [-Wsign-compare] - 285 | if (useEmbedTables() && tmp > embedShreshold) { - | ~~~~^~~~~~~~~~~~~~~~ -hash.cpp: In member function 'void HashTable::setScanThreshold(double)': -hash.cpp:343:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] - 343 | for (int i = 0; i < nHistogram - 1; i++) { - | ~~^~~~~~~~~~~~~~~~ -hash.cpp: In member function 'void HashTable::insert(int64*, unsigned int)': -hash.cpp:460:38: warning: operation on '*(((HashTable*)this)->HashTable::overflowPool + ((sizetype)(((long unsigned int)curOverflowEntry) * 4)))' may be undefined [-Wsequence-point] - 460 | overflowPool[curOverflowEntry] = -hash.cpp:411:10: warning: unused variable 'seqOffset' [-Wunused-variable] - 411 | uint32 seqOffset; - | ^~~~~~~~~ -hash.cpp:413:10: warning: unused variable 'counter' [-Wunused-variable] - 413 | uint32 counter = 0; - | ^~~~~~~ -hash.cpp:414:11: warning: variable 'seqVector' set but not used [-Wunused-but-set-variable] - 414 | int64 * seqVector; - | ^~~~~~~~~ -hash.cpp:416:11: warning: unused variable 'target' [-Wunused-variable] - 416 | int64 * target = &tspace[8]; - | ^~~~~~ -hash.cpp:417:8: warning: unused variable 'isBloomFilter' [-Wunused-variable] - 417 | bool isBloomFilter; - | ^~~~~~~~~~~~~ -hash.cpp:418:12: warning: unused variable 'bloomFilter' [-Wunused-variable] - 418 | uint32 * bloomFilter; - | ^~~~~~~~~~~ -hash.cpp:419:10: warning: unused variable 'bloomFilterNum' [-Wunused-variable] - 419 | uint32 bloomFilterNum; - | ^~~~~~~~~~~~~~ -hash.cpp: In member function 'int HashTable::buildEmbedTable()': -hash.cpp:469:33: warning: unused variable 'rest' [-Wunused-variable] - 469 | int64 * query = &ttspace[8], *rest = &ttspace[24], *rest1 = &ttspace[40], - | ^~~~ -hash.cpp:469:55: warning: unused variable 'rest1' [-Wunused-variable] - 469 | int64 * query = &ttspace[8], *rest = &ttspace[24], *rest1 = &ttspace[40], - | ^~~~~ -hash.cpp:470:8: warning: unused variable 'rest2' [-Wunused-variable] - 470 | *rest2 = &ttspace[56], *noheadkey = &ttspace[72]; - | ^~~~~ -hash.cpp:470:31: warning: unused variable 'noheadkey' [-Wunused-variable] - 470 | *rest2 = &ttspace[56], *noheadkey = &ttspace[72]; - | ^~~~~~~~~ -hash.cpp:472:34: warning: variable 'startOffset' set but not used [-Wunused-but-set-variable] - 472 | uint32 seqOffset, entryOffset, startOffset; - | ^~~~~~~~~~~ -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]; - | ^~~~~~~~~ -hash.cpp:590:8: warning: unused variable 'subkey4' [-Wunused-variable] - 590 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; - | ^~~~~~~ -hash.cpp:590:32: warning: unused variable 'subkey5' [-Wunused-variable] - 590 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; - | ^~~~~~~ -hash.cpp: In member function 'void HashTable::insertEmbedTableEntry(int64*, uint32, int, int)': -hash.cpp:662:11: warning: unused variable 'noheadkey' [-Wunused-variable] - 662 | int64 * noheadkey = &tspace[8], *rest = &tspace[24]; - | ^~~~~~~~~ -hash.cpp:665:8: warning: unused variable 'subkey4' [-Wunused-variable] - 665 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; - | ^~~~~~~ -hash.cpp:665:32: warning: unused variable 'subkey5' [-Wunused-variable] - 665 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; - | ^~~~~~~ -hash.cpp: In member function 'unsigned int HashTable::lookup(int64*, int64*, int, char*, strand, int, HitSet*, bool)': -hash.cpp:746:7: warning: unused variable 'num' [-Wunused-variable] - 746 | int num; - | ^~~ -hash.cpp:750:11: warning: unused variable 'diff' [-Wunused-variable] - 750 | int64 * diff = &tspace1[8], *target = &tspace2[8]; - | ^~~~ -hash.cpp:753:10: warning: unused variable 'sid' [-Wunused-variable] - 753 | uint32 sid, soffset; - | ^~~ -hash.cpp:753:15: warning: unused variable 'soffset' [-Wunused-variable] - 753 | uint32 sid, soffset; - | ^~~~~~~ -hash.cpp: In member function 'unsigned int HashTable::lookupEmbedTable(int64*, uint32, int, char*, strand, int, HitSet*, bool)': -hash.cpp:962:11: warning: unused variable 'noheadkey' [-Wunused-variable] - 962 | int64 * noheadkey = &tspace[8], *rest = &tspace[24]; - | ^~~~~~~~~ -hash.cpp:965:8: warning: unused variable 'subkey4' [-Wunused-variable] - 965 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; - | ^~~~~~~ -hash.cpp:965:32: warning: unused variable 'subkey5' [-Wunused-variable] - 965 | *subkey4 = &tspace[88], *subkey5 = &tspace[104]; - | ^~~~~~~ -hash.cpp:973:11: warning: unused variable 'seqVector' [-Wunused-variable] - 973 | int64 * seqVector = sequence->getSequence(); - | ^~~~~~~~~ -hash.cpp: In member function 'bool HashTable::lookup(int64*, uint32)': -hash.cpp:1052:7: warning: unused variable 'num' [-Wunused-variable] - 1052 | int num; - | ^~~ -hash.cpp:1056:11: warning: unused variable 'diff' [-Wunused-variable] - 1056 | int64 * diff = &tspace1[8], *target = &tspace2[8]; - | ^~~~ -hash.cpp:1056:32: warning: unused variable 'target' [-Wunused-variable] - 1056 | int64 * diff = &tspace1[8], *target = &tspace2[8]; - | ^~~~~~ -hash.cpp:1057:11: warning: variable 'seqVector' set but not used [-Wunused-but-set-variable] - 1057 | int64 * seqVector; - | ^~~~~~~~~ -hash.cpp:1059:10: warning: unused variable 'sid' [-Wunused-variable] - 1059 | uint32 sid, soffset; - | ^~~ -hash.cpp:1059:15: warning: unused variable 'soffset' [-Wunused-variable] - 1059 | uint32 sid, soffset; - | ^~~~~~~ -hash.cpp: In member function 'uint32 HashTable::printOverflowList(uint32, uint32, int64*)': -hash.cpp:1184:23: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] - 1184 | for (int i = 0; i < keyOffset / BITS_PER_BASE; i++) -hash.cpp:1188:23: warning: comparison of integer expressions of different signedness: 'int' and 'uint32' {aka 'unsigned int'} [-Wsign-compare] - 1188 | for (int i = 0; i < (lenSeq - keyOffset - lenKey) / BITS_PER_BASE; i++) -hash.cpp:1247:27: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] - 1247 | for (int j = 0; j < strlen(set[i].str); j++) - | ~~^~~~~~~~~~~~~~~~~~~~ -hash.cpp:1254:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] - 1254 | for (int j = 0; j < strlen(set[i].str); j++) - | ~~^~~~~~~~~~~~~~~~~~~~ -hash.cpp:1137:11: warning: unused variable 'diff' [-Wunused-variable] - 1137 | int64 * diff = &tspace1[8], *target = &tspace2[8]; - | ^~~~ -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; - | ^~~~ -hash.cpp:1321:34: warning: variable 'offset' set but not used [-Wunused-but-set-variable] - 1321 | uint32 entryOffset, seqOffset, offset; - | ^~~~~~ -hash.cpp: In member function 'void HashTable::checkRepeat(uint32)': -hash.cpp:1673:34: warning: variable 'offset' set but not used [-Wunused-but-set-variable] - 1673 | uint32 entryOffset, seqOffset, offset; - | ^~~~~~ -hash.cpp:1690:5: warning: label 'restart' defined but not used [-Wunused-label] - 1690 | restart: if (buckets[bucketId] == HASH_EMPTY - | ^~~~~~~ +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) { + | ~~~~^~~~~~~ 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 '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: +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 }; @@ -1513,7 +1549,7 @@ 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-8F2QESlL + rm -fr -- /tmp/dh-xdg-rundir-zkb7cXX5 create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/wham-align.substvars @@ -1628,12 +1664,14 @@ 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/3958280/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3958280/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/56488 and its subdirectories -I: Current time: Thu Jun 26 00:11:30 -12 2025 -I: pbuilder-time-stamp: 1750939890 +I: removing directory /srv/workspace/pbuilder/3958280 and its subdirectories +I: Current time: Fri May 24 19:50:09 +14 2024 +I: pbuilder-time-stamp: 1716529809