Diff of the two buildlogs: -- --- b1/build.log 2024-05-20 13:58:39.752086928 +0000 +++ b2/build.log 2024-05-20 14:01:46.048161180 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Jun 22 08:19:22 -12 2025 -I: pbuilder-time-stamp: 1750623562 +I: Current time: Tue May 21 03:58:43 +14 2024 +I: pbuilder-time-stamp: 1716213523 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/experimental-reproducible-base.tgz] I: copying local configuration @@ -35,53 +35,85 @@ dpkg-source: info: applying riscv5 I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/9039/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/4418/tmp/hooks/D01_modify_environment starting +debug: Running on infom07-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 20 13:58 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/4418/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/4418/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=6 ' - DISTRIBUTION='experimental' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="i686-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=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=5 ' + DIRSTACK=() + DISTRIBUTION=experimental + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='f7767f4d031a410199e8350b90a755d2' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='9039' - PS1='# ' - PS2='> ' + INVOCATION_ID=58fcafab7fd444f8a8770f9437b3764d + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=4418 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.7za2gf8O/pbuilderrc_AEPP --distribution experimental --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.7za2gf8O/b1 --logfile b1/build.log hisat2_2.2.1-5~0exp.dsc' - SUDO_GID='111' - 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.7za2gf8O/pbuilderrc_kB69 --distribution experimental --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.7za2gf8O/b2 --logfile b2/build.log hisat2_2.2.1-5~0exp.dsc' + SUDO_GID=111 + 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 infom08-i386 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-21-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 19 21:18 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/9039/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 17 15:01 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/4418/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -179,7 +211,7 @@ Get: 53 http://deb.debian.org/debian unstable/main i386 libyaml-0-2 i386 0.2.5-1+b1 [55.2 kB] Get: 54 http://deb.debian.org/debian unstable/main i386 pandoc-data all 3.1.3-2 [445 kB] Get: 55 http://deb.debian.org/debian unstable/main i386 pandoc i386 3.1.3+ds-3 [35.7 MB] -Fetched 62.3 MB in 1s (54.5 MB/s) +Fetched 62.3 MB in 1s (93.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (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 ... 19703 files and directories currently installed.) @@ -375,8 +407,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Sun Jun 22 20:19:40 UTC 2025. -Universal Time is now: Sun Jun 22 20:19:40 UTC 2025. +Local time is now: Mon May 20 13:59:05 UTC 2024. +Universal Time is now: Mon May 20 13:59:05 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -426,7 +458,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/hisat2-2.2.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../hisat2_2.2.1-5~0exp_source.changes +I: user script /srv/workspace/pbuilder/4418/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for experimental +I: user script /srv/workspace/pbuilder/4418/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/hisat2-2.2.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../hisat2_2.2.1-5~0exp_source.changes dpkg-buildpackage: info: source package hisat2 dpkg-buildpackage: info: source version 2.2.1-5~0exp dpkg-buildpackage: info: source distribution experimental @@ -436,7 +472,7 @@ debian/rules clean dh clean dh_auto_clean - make -j6 clean + make -j5 clean make[1]: Entering directory '/build/reproducible-path/hisat2-2.2.1' rm -f hisat2-build-s hisat2-build-l hisat2-align-s hisat2-align-l hisat2-inspect-s hisat2-inspect-l hisat2-repeat hisat2-build-s-debug hisat2-build-l-debug hisat2-align-s-debug hisat2-align-l-debug hisat2-inspect-s-debug hisat2-inspect-l-debug hisat2-repeat-debug \ hisat2-build-s.exe hisat2-build-l.exe hisat2-align-s.exe hisat2-align-l.exe hisat2-inspect-s.exe hisat2-inspect-l.exe hisat2-repeat.exe hisat2-build-s-debug.exe hisat2-build-l-debug.exe hisat2-align-s-debug.exe hisat2-align-l-debug.exe hisat2-inspect-s-debug.exe hisat2-inspect-l-debug.exe hisat2-repeat-debug.exe \ @@ -455,7 +491,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/hisat2-2.2.1' dh_auto_build -- BUILD_HOST='Debian' BUILD_TIME="22 January 2023" all doc - make -j6 "INSTALL=install --strip-program=true" BUILD_HOST=Debian "BUILD_TIME=22 January 2023" all doc + make -j5 "INSTALL=install --strip-program=true" BUILD_HOST=Debian "BUILD_TIME=22 January 2023" all doc make[2]: Entering directory '/build/reproducible-path/hisat2-2.2.1' /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"22 January 2023\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-prefix-map=/build/reproducible-path/hisat2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DNDEBUG -Wall -DMASSIVE_DATA_RLCSA \ @@ -488,13 +524,6 @@ -o hisat2-inspect-s hisat2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now -/usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \ --DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ --fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"22 January 2023\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-prefix-map=/build/reproducible-path/hisat2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DHISAT2_INSPECT_MAIN -Wall \ --I. -I third_party -I . \ --o hisat2-inspect-l hisat2_inspect.cpp \ -ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \ --lpthread -Wl,-z,relro -Wl,-z,now In file included from gfm.h:43, from hisat2_build.cpp:35: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: @@ -547,8 +576,6 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ -In file included from hgfm.h:24, - from hisat2.cpp:33: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -564,6 +591,8 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ +In file included from hgfm.h:24, + from hisat2.cpp:33: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -616,17 +645,6 @@ multikey_qsort.h:1169:70: note: in expansion of macro ‘OFF_MASK’ 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ -In file included from gfm.h:43, - from hgfm.h:24, - from hisat2_inspect.cpp:27: -blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: -blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 483 | mkeyQSortSuf(t, s, slen, 4, - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ - 484 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: -blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ @@ -668,14 +686,6 @@ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ -In file included from hisat2_inspect.cpp:25: -alt.h: In member function ‘bool ALT::repOk() const’: -assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] - 227 | if(!((a) <= (b))) { \ - | ~~~~^~~~~~ -alt.h:180:13: note: in expansion of macro ‘assert_leq’ - 180 | assert_leq(fw, 1); - | ^~~~~~~~~~ gfm.h: In instantiation of ‘void GFM::initFromVector(TStr&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, EList&, EList&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, const std::string&, bool, index_t, index_t, index_t, int, EList*, EList >*, uint32_t, bool) [with TStr = SString; index_t = long long unsigned int; std::string = std::__cxx11::basic_string; std::ofstream = std::basic_ofstream; uint32_t = unsigned int]’: gfm.h:1039:23: required from ‘GFM::GFM(TStr&, bool, int, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, index_t, index_t, index_t, int, EList&, EList&, index_t, const RefReadInParams&, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ hgfm.h:1989:14: required from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’ @@ -705,16 +715,6 @@ sse_util.h:161:51: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] 161 | inline __m128i operator[](size_t i) const { | ^ -In file included from aligner_swsse.h:28, - from aligner_sw.h:85, - from aligner_sw_driver.h:86, - from hi_aligner.h:42, - from spliced_aligner.h:23, - from hisat2.cpp:46: -sse_util.h: In member function ‘__m128i EList_m128i::operator[](size_t) const’: -sse_util.h:161:51: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] - 161 | inline __m128i operator[](size_t i) const { - | ^ blockwise_sa.h: In instantiation of ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = SString]’: blockwise_sa.h:1098:15: required from ‘void KarkkainenBlockwiseSA::nextBlock(int, int) [with TStr = SString]’ blockwise_sa.h:297:17: required from ‘TIndexOffU KarkkainenBlockwiseSA::nextSuffix() [with TStr = SString; TIndexOffU = long long unsigned int]’ @@ -745,21 +745,16 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ -gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: -gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1185 | auto_ptr ss(new stringstream()); - | ^~~~~~~~ -In file included from /usr/include/c++/13/memory:78, - from gfm.h:28: -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | template class auto_ptr; - | ^~~~~~~~ -gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1189 | auto_ptr fb(new FileBuf(ss.get())); - | ^~~~~~~~ -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | template class auto_ptr; - | ^~~~~~~~ +In file included from aligner_swsse.h:28, + from aligner_sw.h:85, + from aligner_sw_driver.h:86, + from hi_aligner.h:42, + from spliced_aligner.h:23, + from hisat2.cpp:46: +sse_util.h: In member function ‘__m128i EList_m128i::operator[](size_t) const’: +sse_util.h:161:51: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] + 161 | inline __m128i operator[](size_t i) const { + | ^ diff_sample.h: In instantiation of ‘void DifferenceCoverSample::build(int) [with TStr = SString]’: blockwise_sa.h:375:20: required from ‘void KarkkainenBlockwiseSA::build() [with TStr = SString]’ blockwise_sa.h:354:4: required from ‘void KarkkainenBlockwiseSA::reset() [with TStr = SString]’ @@ -800,6 +795,13 @@ multikey_qsort.h:496:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +hisat2.cpp: In function ‘void parseOptions(int, const char**)’: +hisat2.cpp:1823:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1823 | auto_ptr presets(new PresetsV0()); + | ^~~~~~~~ +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | template class auto_ptr; + | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf2(const T&, TIndexOffU*, size_t, TIndexOffU*, int, bool, bool, size_t, EList*) [with T = SString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: diff_sample.h:772:30: required from ‘void DifferenceCoverSample::build(int) [with TStr = SString]’ blockwise_sa.h:375:20: required from ‘void KarkkainenBlockwiseSA::build() [with TStr = SString]’ @@ -833,20 +835,6 @@ multikey_qsort.h:1169:70: note: in expansion of macro ‘OFF_MASK’ 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ -hisat2.cpp: In function ‘void parseOptions(int, const char**)’: -hisat2.cpp:1823:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1823 | auto_ptr presets(new PresetsV0()); - | ^~~~~~~~ -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | template class auto_ptr; - | ^~~~~~~~ -hisat2.cpp: In function ‘void parseOptions(int, const char**)’: -hisat2.cpp:1823:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1823 | auto_ptr presets(new PresetsV0()); - | ^~~~~~~~ -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | template class auto_ptr; - | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’ @@ -911,25 +899,6 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ -hisat2.cpp: In function ‘void multiseedSearchWorker_hisat2(void*)’: -hisat2.cpp:3167:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 3167 | auto_ptr patsrcFact(createPatsrcFactory(patsrc, tid)); - | ^~~~~~~~ -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | template class auto_ptr; - | ^~~~~~~~ -hisat2.cpp:3168:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 3168 | auto_ptr ps(patsrcFact->create()); - | ^~~~~~~~ -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | template class auto_ptr; - | ^~~~~~~~ -hisat2.cpp:3189:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 3189 | auto_ptr bmapq(new_mapq(mapqv, scoreMin, sc)); - | ^~~~~~~~ -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | template class auto_ptr; - | ^~~~~~~~ hisat2.cpp: In function ‘void driver(const char*, const std::string&, const std::string&)’: hisat2.cpp:4035:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 4035 | auto_ptr refs( @@ -937,9 +906,9 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ -hisat2.cpp: In function ‘void driver(const char*, const std::string&, const std::string&)’: -hisat2.cpp:4035:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 4035 | auto_ptr refs( +hisat2.cpp: In function ‘void parseOptions(int, const char**)’: +hisat2.cpp:1823:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1823 | auto_ptr presets(new PresetsV0()); | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; @@ -995,6 +964,25 @@ hi_aligner.h:4614:55: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘const THitInt’ {aka ‘const long long int’} [-Wsign-compare] 4614 | if(sink.numBestUnp(rdi).first > rp.khits) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +hisat2.cpp: In function ‘void multiseedSearchWorker_hisat2(void*)’: +hisat2.cpp:3167:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 3167 | auto_ptr patsrcFact(createPatsrcFactory(patsrc, tid)); + | ^~~~~~~~ +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | template class auto_ptr; + | ^~~~~~~~ +hisat2.cpp:3168:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 3168 | auto_ptr ps(patsrcFact->create()); + | ^~~~~~~~ +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | template class auto_ptr; + | ^~~~~~~~ +hisat2.cpp:3189:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 3189 | auto_ptr bmapq(new_mapq(mapqv, scoreMin, sc)); + | ^~~~~~~~ +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | template class auto_ptr; + | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:477:19: required from here @@ -1031,18 +1019,19 @@ hi_aligner.h:5688:105: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘TRefOff’ {aka ‘long long int’} [-Wsign-compare] 5688 | if(coord.off() + pepol.maxFragLen() * 2 < toff || toff + pepol.maxFragLen() * 2 < coord.off()) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -gfm.h: In instantiation of ‘void GFM::checkOrigs(const EList >&, bool) const [with index_t = unsigned int]’: -hisat2.cpp:3815:17: required from ‘void driver(const char*, const std::string&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]’ -hisat2.cpp:4351:26: required from here -gfm.h:6935:13: warning: variable ‘lastorig’ set but not used [-Wunused-but-set-variable] - 6935 | int lastorig = -1; - | ^~~~~~~~ gfm.h: In instantiation of ‘void GFM::checkOrigs(const EList >&, bool) const [with index_t = long long unsigned int]’: hisat2.cpp:3815:17: required from ‘void driver(const char*, const std::string&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]’ hisat2.cpp:4351:26: required from here gfm.h:6935:13: warning: variable ‘lastorig’ set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^~~~~~~~ +hisat2.cpp: In function ‘void driver(const char*, const std::string&, const std::string&)’: +hisat2.cpp:4035:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 4035 | auto_ptr refs( + | ^~~~~~~~ +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | template class auto_ptr; + | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ @@ -1067,28 +1056,6 @@ hi_aligner.h:2267:47: warning: comparison of integer expressions of different signedness: ‘TRefOff’ {aka ‘long long int’} and ‘long long unsigned int’ [-Wsign-compare] 2267 | findSSOffs(gfm, altdb, (coord.joinedOff() >= width ? (index_t)(coord.joinedOff() - width) : 0), (index_t)(coord.joinedOff() + width), ssOffs); | ~~~~~~~~~~~~~~~~~~^~~~~~~~ -In file included from ds.h:32, - from sequence_io.h:28, - from multikey_qsort.h:24, - from diff_sample.h:26, - from blockwise_sa.h:29: -multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: -blockwise_sa.h:477:19: required from here -btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 25 | #define OFF_MASK 0xffffffffffffffff - | ^~~~~~~~~~~~~~~~~~ -multikey_qsort.h:764:70: note: in expansion of macro ‘OFF_MASK’ - 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); - | ^~~~~~~~ -multikey_qsort.h:764:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -multikey_qsort.h:764:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] -multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: -blockwise_sa.h:483:15: required from here -multikey_qsort.h:496:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1067:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ @@ -1112,29 +1079,14 @@ multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ -multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: -multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ -blockwise_sa.h:477:19: required from here -btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 25 | #define OFF_MASK 0xffffffffffffffff - | ^~~~~~~~~~~~~~~~~~ -multikey_qsort.h:1160:70: note: in expansion of macro ‘OFF_MASK’ - 1160 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); - | ^~~~~~~~ -btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 25 | #define OFF_MASK 0xffffffffffffffff - | ^~~~~~~~~~~~~~~~~~ -multikey_qsort.h:1169:70: note: in expansion of macro ‘OFF_MASK’ - 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); - | ^~~~~~~~ In file included from aligner_seed2.h:109, from aligner_driver.h:78, from hi_aligner.h:41: group_walk.h: In instantiation of ‘std::pair GWState::advance(const GFM&, const BitPairReference&, SARangeWithOffs&, GWHit&, index_t, bool, EList, 16>*, EList, S>&, GroupWalkState&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: group_walk.h:1517:14: required from ‘bool GroupWalk2S::advanceElement(index_t, const GFM&, const BitPairReference&, SARangeWithOffs&, GroupWalkState&, WalkResult&, WalkMetrics&, PerReadMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ -hi_aligner.h:5901:34: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = unsigned int; local_index_t = short unsigned int]’ -hi_aligner.h:5664:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ -hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ +hi_aligner.h:5901:34: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ +hi_aligner.h:5664:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ +hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3537:48: required from here group_walk.h:1147:60: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 1147 | if(new_node_bot - new_node_top < gws.map.size()) { @@ -1148,11 +1100,11 @@ group_walk.h:1224:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 1224 | for(index_t j = 0; j + 1 < st.back().map_.size(); j++) { | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -hi_aligner.h: In instantiation of ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’: -hi_aligner.h:717:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ -hi_aligner.h:2337:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = unsigned int]’ -hi_aligner.h:5692:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ -hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ +hi_aligner.h: In instantiation of ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = long long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’: +hi_aligner.h:717:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = long long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ +hi_aligner.h:2337:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = long long unsigned int]’ +hi_aligner.h:5692:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ +hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3537:48: required from here hi_aligner.h:2801:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2801 | if(rfoff >= contig_len) return 0; @@ -1160,32 +1112,102 @@ hi_aligner.h:2879:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2879 | if(alt_range.first >= alts.size()) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -hi_aligner.h:3044:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] +hi_aligner.h:3044:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] 3044 | for(int i = 0; i < alt.len; i++) { | ~~^~~~~~~~~ -hi_aligner.h:3085:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] +hi_aligner.h:3085:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] 3085 | if(rd_i == rdoff && prev_alt_type == ALT_SPLICESITE) { | ~~~~~^~~~~~~~ -hi_aligner.h:3161:31: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] +hi_aligner.h:3161:31: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] 3161 | if(alignedLen == next_rdlen) return rdlen; | ~~~~~~~~~~~^~~~~~~~~~~~~ -hi_aligner.h:3197:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] +hi_aligner.h:3197:32: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] 3197 | if(mm_max_rd_i + rdoff > best_rdoff) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -hi_aligner.h:3202:39: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] +hi_aligner.h:3202:39: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] 3202 | } else if(mm_max_rd_i + rdoff == best_rdoff) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -hi_aligner.h:3454:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] +hi_aligner.h:3454:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] 3454 | if(best_rdoff < rdoff + rd_i) { | ~~~~~~~~~~~^~~~~~~~~~~~~~ +gfm.h: In instantiation of ‘void GFM::checkOrigs(const EList >&, bool) const [with index_t = unsigned int]’: +hisat2.cpp:3815:17: required from ‘void driver(const char*, const std::string&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]’ +hisat2.cpp:4351:26: required from here +gfm.h:6935:13: warning: variable ‘lastorig’ set but not used [-Wunused-but-set-variable] + 6935 | int lastorig = -1; + | ^~~~~~~~ +group_walk.h: In instantiation of ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: +group_walk.h:494:14: required from ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, index_t, index_t, index_t, index_t, const EList >&, index_t, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’ +group_walk.h:1453:18: required from ‘void GroupWalk2S::init(const GFM&, const BitPairReference&, SARangeWithOffs&, RandomSource&, WalkMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ +hi_aligner.h:5896:20: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ +hi_aligner.h:5664:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ +hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ +hisat2.cpp:3537:48: required from here +group_walk.h:785:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] + 785 | if(i + 1 < tmp_zOffs.size() && new_top == tmp_zOffs[i+1]) { + | ~~~~~~^~~~~~~~~~~~~~~~~~ +group_walk.h:789:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] + 789 | if(new_top - top == tmp_gbwt_to_node.size()) { + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +group_walk.h:795:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] + 795 | if(i + 1 < tmp_zOffs.size()) { + | ~~~~~~^~~~~~~~~~~~~~~~~~ +group_walk.h:801:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] + 801 | if(new_bot - top < tmp_gbwt_to_node.size()) { + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +hi_aligner.h: In instantiation of ‘void add_haplotypes(const EList >&, const EList >&, const EList&, Haplotype&, EList >&, index_t, bool, bool) [with index_t = long long unsigned int]’: +hi_aligner.h:2915:39: required from ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = long long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ +hi_aligner.h:717:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = long long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ +hi_aligner.h:2337:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = long long unsigned int]’ +hi_aligner.h:5692:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ +hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ +hisat2.cpp:3537:48: required from here +hi_aligner.h:2660:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] + 2660 | if(ht_range.first >= haplotypes.size()) + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ +hi_aligner.h:2675:37: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] + 2675 | if(ht_list[h].first == ht_range.first) { + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +hi_aligner.h:2713:41: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] + 2713 | if(ht_list[h].first == ht_range.first) { + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +hi_aligner.h:2737:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] + 2737 | for(; ht_range.second < haplotypes.size(); ht_range.second++) { + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +hi_aligner.h:2744:41: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] + 2744 | if(ht_list[h].first == ht_range.second) { + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ +spliced_aligner.h: In instantiation of ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int; int64_t = long long int]’: +spliced_aligner.h:331:9: required from here +spliced_aligner.h:408:18: warning: variable ‘another_spliced’ set but not used [-Wunused-but-set-variable] + 408 | bool another_spliced = false; + | ^~~~~~~~~~~~~~~ +spliced_aligner.h:782:65: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int64_t’ {aka ‘long long int’} [-Wsign-compare] + 782 | tempHit.score() + sc.sc(0) * hit.rdoff() >= hit.score()) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +spliced_aligner.h:1465:105: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int64_t’ {aka ‘long long int’} [-Wsign-compare] + 1465 | combinedHit.score() + sc.sc(0) * (rdlen - hit.rdoff() - hit.len() - hit.trim5()) >= hit.score()) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +hi_aligner.h: In instantiation of ‘bool GenomeHit::combineWith(const GenomeHit&, const Read&, const GFM&, const BitPairReference&, const ALTDB&, const RepeatDB&, SpliceSiteDB&, SwAligner&, SwMetrics&, const Scoring&, TAlScore, RandomSource&, index_t, index_t, index_t, index_t, index_t, index_t, const SpliceSite*, bool) [with index_t = long long unsigned int; TAlScore = long long int]’: +spliced_aligner.h:494:60: required from ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int; int64_t = long long int]’ +spliced_aligner.h:331:9: required from here +hi_aligner.h:1926:32: warning: comparison of integer expressions of different signedness: ‘const uint64_t’ {aka ‘const long long unsigned int’} and ‘char’ [-Wsign-compare] + 1926 | if(alt.seq == rdc) { + | ~~~~~~~~^~~~~~ +hi_aligner.h: In instantiation of ‘index_t HI_Aligner::globalGFMSearch(const GFM&, const Read&, const Scoring&, const ReportingParams&, bool, index_t, index_t&, index_t&, index_t&, index_t&, index_t&, EList >&, RandomSource&, bool&, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int]’: +spliced_aligner.h:1086:53: required from ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int; int64_t = long long int]’ +spliced_aligner.h:331:9: required from here +hi_aligner.h:6719:85: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘const THitInt’ {aka ‘const long long int’} [-Wsign-compare] + 6719 | if(node_range.first < node_range.second && node_range.second - node_range.first <= rp.kseeds) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from aligner_seed2.h:109, from aligner_driver.h:78, from hi_aligner.h:41: group_walk.h: In instantiation of ‘std::pair GWState::advance(const GFM&, const BitPairReference&, SARangeWithOffs&, GWHit&, index_t, bool, EList, 16>*, EList, S>&, GroupWalkState&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: group_walk.h:1517:14: required from ‘bool GroupWalk2S::advanceElement(index_t, const GFM&, const BitPairReference&, SARangeWithOffs&, GroupWalkState&, WalkResult&, WalkMetrics&, PerReadMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ -hi_aligner.h:5901:34: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ -hi_aligner.h:5664:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ -hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ +hi_aligner.h:5901:34: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = unsigned int; local_index_t = short unsigned int]’ +hi_aligner.h:5664:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ +hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3537:48: required from here group_walk.h:1147:60: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 1147 | if(new_node_bot - new_node_top < gws.map.size()) { @@ -1199,11 +1221,11 @@ group_walk.h:1224:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 1224 | for(index_t j = 0; j + 1 < st.back().map_.size(); j++) { | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -hi_aligner.h: In instantiation of ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = long long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’: -hi_aligner.h:717:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = long long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ -hi_aligner.h:2337:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = long long unsigned int]’ -hi_aligner.h:5692:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ -hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ +hi_aligner.h: In instantiation of ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’: +hi_aligner.h:717:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ +hi_aligner.h:2337:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = unsigned int]’ +hi_aligner.h:5692:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ +hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3537:48: required from here hi_aligner.h:2801:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2801 | if(rfoff >= contig_len) return 0; @@ -1211,32 +1233,22 @@ hi_aligner.h:2879:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2879 | if(alt_range.first >= alts.size()) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -hi_aligner.h:3044:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] +hi_aligner.h:3044:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 3044 | for(int i = 0; i < alt.len; i++) { | ~~^~~~~~~~~ -hi_aligner.h:3085:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] +hi_aligner.h:3085:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 3085 | if(rd_i == rdoff && prev_alt_type == ALT_SPLICESITE) { | ~~~~~^~~~~~~~ -hi_aligner.h:3161:31: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] +hi_aligner.h:3161:31: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 3161 | if(alignedLen == next_rdlen) return rdlen; | ~~~~~~~~~~~^~~~~~~~~~~~~ -multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: -multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ -multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ -blockwise_sa.h:477:19: required from here -btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 25 | #define OFF_MASK 0xffffffffffffffff - | ^~~~~~~~~~~~~~~~~~ -multikey_qsort.h:1071:40: note: in expansion of macro ‘OFF_MASK’ - 1071 | OFF_MASK, begin, end); - | ^~~~~~~~ -hi_aligner.h:3197:32: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] +hi_aligner.h:3197:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 3197 | if(mm_max_rd_i + rdoff > best_rdoff) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -hi_aligner.h:3202:39: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] +hi_aligner.h:3202:39: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 3202 | } else if(mm_max_rd_i + rdoff == best_rdoff) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -hi_aligner.h:3454:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] +hi_aligner.h:3454:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 3454 | if(best_rdoff < rdoff + rd_i) { | ~~~~~~~~~~~^~~~~~~~~~~~~~ group_walk.h: In instantiation of ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: @@ -1280,70 +1292,6 @@ hi_aligner.h:2744:41: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2744 | if(ht_list[h].first == ht_range.second) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ -multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: -multikey_qsort.h:1067:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ -multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ -multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ -blockwise_sa.h:477:19: required from here -btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 25 | #define OFF_MASK 0xffffffffffffffff - | ^~~~~~~~~~~~~~~~~~ -multikey_qsort.h:914:31: note: in expansion of macro ‘OFF_MASK’ - 914 | off = OFF_MASK; - | ^~~~~~~~ -btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 25 | #define OFF_MASK 0xffffffffffffffff - | ^~~~~~~~~~~~~~~~~~ -multikey_qsort.h:923:64: note: in expansion of macro ‘OFF_MASK’ - 923 | OFF_MASK, begin, end); - | ^~~~~~~~ -btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 25 | #define OFF_MASK 0xffffffffffffffff - | ^~~~~~~~~~~~~~~~~~ -multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’ - 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); - | ^~~~~~~~ -group_walk.h: In instantiation of ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: -group_walk.h:494:14: required from ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, index_t, index_t, index_t, index_t, const EList >&, index_t, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’ -group_walk.h:1453:18: required from ‘void GroupWalk2S::init(const GFM&, const BitPairReference&, SARangeWithOffs&, RandomSource&, WalkMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ -hi_aligner.h:5896:20: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ -hi_aligner.h:5664:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ -hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ -hisat2.cpp:3537:48: required from here -group_walk.h:785:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] - 785 | if(i + 1 < tmp_zOffs.size() && new_top == tmp_zOffs[i+1]) { - | ~~~~~~^~~~~~~~~~~~~~~~~~ -group_walk.h:789:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] - 789 | if(new_top - top == tmp_gbwt_to_node.size()) { - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -group_walk.h:795:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] - 795 | if(i + 1 < tmp_zOffs.size()) { - | ~~~~~~^~~~~~~~~~~~~~~~~~ -group_walk.h:801:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] - 801 | if(new_bot - top < tmp_gbwt_to_node.size()) { - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -hi_aligner.h: In instantiation of ‘void add_haplotypes(const EList >&, const EList >&, const EList&, Haplotype&, EList >&, index_t, bool, bool) [with index_t = long long unsigned int]’: -hi_aligner.h:2915:39: required from ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = long long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ -hi_aligner.h:717:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = long long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ -hi_aligner.h:2337:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = long long unsigned int]’ -hi_aligner.h:5692:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ -hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ -hisat2.cpp:3537:48: required from here -hi_aligner.h:2660:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] - 2660 | if(ht_range.first >= haplotypes.size()) - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ -hi_aligner.h:2675:37: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] - 2675 | if(ht_list[h].first == ht_range.first) { - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -hi_aligner.h:2713:41: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] - 2713 | if(ht_list[h].first == ht_range.first) { - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -hi_aligner.h:2737:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] - 2737 | for(; ht_range.second < haplotypes.size(); ht_range.second++) { - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -hi_aligner.h:2744:41: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] - 2744 | if(ht_list[h].first == ht_range.second) { - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ spliced_aligner.h: In instantiation of ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = unsigned int; local_index_t = short unsigned int; int64_t = long long int]’: spliced_aligner.h:331:9: required from here spliced_aligner.h:408:18: warning: variable ‘another_spliced’ set but not used [-Wunused-but-set-variable] @@ -1355,29 +1303,6 @@ hi_aligner.h:1926:32: warning: comparison of integer expressions of different signedness: ‘const uint64_t’ {aka ‘const long long unsigned int’} and ‘char’ [-Wsign-compare] 1926 | if(alt.seq == rdc) { | ~~~~~~~~^~~~~~ -spliced_aligner.h: In instantiation of ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int; int64_t = long long int]’: -spliced_aligner.h:331:9: required from here -spliced_aligner.h:408:18: warning: variable ‘another_spliced’ set but not used [-Wunused-but-set-variable] - 408 | bool another_spliced = false; - | ^~~~~~~~~~~~~~~ -spliced_aligner.h:782:65: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int64_t’ {aka ‘long long int’} [-Wsign-compare] - 782 | tempHit.score() + sc.sc(0) * hit.rdoff() >= hit.score()) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -spliced_aligner.h:1465:105: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int64_t’ {aka ‘long long int’} [-Wsign-compare] - 1465 | combinedHit.score() + sc.sc(0) * (rdlen - hit.rdoff() - hit.len() - hit.trim5()) >= hit.score()) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -hi_aligner.h: In instantiation of ‘bool GenomeHit::combineWith(const GenomeHit&, const Read&, const GFM&, const BitPairReference&, const ALTDB&, const RepeatDB&, SpliceSiteDB&, SwAligner&, SwMetrics&, const Scoring&, TAlScore, RandomSource&, index_t, index_t, index_t, index_t, index_t, index_t, const SpliceSite*, bool) [with index_t = long long unsigned int; TAlScore = long long int]’: -spliced_aligner.h:494:60: required from ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int; int64_t = long long int]’ -spliced_aligner.h:331:9: required from here -hi_aligner.h:1926:32: warning: comparison of integer expressions of different signedness: ‘const uint64_t’ {aka ‘const long long unsigned int’} and ‘char’ [-Wsign-compare] - 1926 | if(alt.seq == rdc) { - | ~~~~~~~~^~~~~~ -hi_aligner.h: In instantiation of ‘index_t HI_Aligner::globalGFMSearch(const GFM&, const Read&, const Scoring&, const ReportingParams&, bool, index_t, index_t&, index_t&, index_t&, index_t&, index_t&, EList >&, RandomSource&, bool&, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int]’: -spliced_aligner.h:1086:53: required from ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int; int64_t = long long int]’ -spliced_aligner.h:331:9: required from here -hi_aligner.h:6719:85: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘const THitInt’ {aka ‘const long long int’} [-Wsign-compare] - 6719 | if(node_range.first < node_range.second && node_range.second - node_range.first <= rp.kseeds) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from edit.h:26, from edit.cpp:21: alt.h: In member function ‘bool ALT::repOk() const’: @@ -1387,19 +1312,26 @@ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ -In file included from gfm.h:43, - from splice_site.h:34, - from edit.h:30, - from edit.cpp:21: -blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: -blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 483 | mkeyQSortSuf(t, s, slen, 4, - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ - 484 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: -blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] -In file included from edit.h:26: +In file included from splice_site.h:34, + from edit.h:30: +gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: +gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1185 | auto_ptr ss(new stringstream()); + | ^~~~~~~~ +In file included from /usr/include/c++/13/memory:78, + from gfm.h:28: +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | template class auto_ptr; + | ^~~~~~~~ +gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1189 | auto_ptr fb(new FileBuf(ss.get())); + | ^~~~~~~~ +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | template class auto_ptr; + | ^~~~~~~~ +In file included from alphabet.h:27, + from gfm.h:40, + from gfm.cpp:21: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ @@ -1407,8 +1339,6 @@ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ -In file included from splice_site.h:34, - from edit.h:30: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -1424,6 +1354,83 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ +In file included from sequence_io.h:30, + from hisat2_build.cpp:28: +In member function ‘void SString::resize(size_t) [with T = char]’, + inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, + inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, + inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int]’ at rfm.h:768:29: +sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] + 602 | delete cs_; + | ^~~~~~~~~~ +In member function ‘void SString::resize(size_t) [with T = char]’, + inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int]’ at rfm.h:764:24: +sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ + 610 | cs_ = new T[sz+1]; + | ^~~~~~~~~~~ +In member function ‘void SString::resize(size_t) [with T = char]’, + inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, + inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, + inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int]’ at rfm.h:766:29: +sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] + 602 | delete cs_; + | ^~~~~~~~~~ +In member function ‘void SString::resize(size_t) [with T = char]’, + inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int]’ at rfm.h:764:24: +sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ + 610 | cs_ = new T[sz+1]; + | ^~~~~~~~~~~ +In file included from gfm.h:59: +In member function ‘bool RepeatCoord::operator<(const RepeatCoord&) const [with index_t = long long unsigned int]’, + inlined from ‘bool RepeatCoord::operator<(const RepeatCoord&) const [with index_t = long long unsigned int]’ at repeat.h:38:10, + inlined from ‘size_t EList::bsearchLoBound(const T&) const [with T = RepeatCoord; int S = 128]’ at ds.h:919:18, + inlined from ‘bool RepeatDB::findCoords(index_t, index_t, index_t, index_t, index_t, const EList&, const ALTDB&, EList, RepeatCoord > >&, index_t, index_t) const [with index_t = long long unsigned int]’ at repeat.h:466:45, + inlined from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ at hi_aligner.h:4391:44: +repeat.h:41:20: warning: ‘cmp.RepeatCoord::fw’ may be used uninitialized [-Wmaybe-uninitialized] + 41 | if(fw != o.fw) + | ~~^~ +repeat.h: In member function ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’: +repeat.h:464:30: note: ‘cmp’ declared here + 464 | RepeatCoord cmp; + | ^~~ +In member function ‘bool RepeatCoord::operator<(const RepeatCoord&) const [with index_t = long long unsigned int]’, + inlined from ‘bool RepeatCoord::operator<(const RepeatCoord&) const [with index_t = long long unsigned int]’ at repeat.h:38:10, + inlined from ‘size_t EList::bsearchLoBound(const T&) const [with T = RepeatCoord; int S = 128]’ at ds.h:919:18, + inlined from ‘bool RepeatDB::findCoords(index_t, index_t, index_t, index_t, index_t, const EList&, const ALTDB&, EList, RepeatCoord > >&, index_t, index_t) const [with index_t = long long unsigned int]’ at repeat.h:466:45, + inlined from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ at hi_aligner.h:4391:44: +repeat.h:43:26: warning: ‘cmp.RepeatCoord::alleleID’ may be used uninitialized [-Wmaybe-uninitialized] + 43 | if(alleleID != o.alleleID) + | ~~^~~~~~~~ +repeat.h: In member function ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’: +repeat.h:464:30: note: ‘cmp’ declared here + 464 | RepeatCoord cmp; + | ^~~ +/usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \ +-DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ +-fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"22 January 2023\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-prefix-map=/build/reproducible-path/hisat2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DHISAT2_INSPECT_MAIN -Wall \ +-I. -I third_party -I . \ +-o hisat2-inspect-l hisat2_inspect.cpp \ +ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \ +-lpthread -Wl,-z,relro -Wl,-z,now +In file included from gfm.h:43, + from hgfm.h:24, + from hisat2_inspect.cpp:27: +blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: +blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 483 | mkeyQSortSuf(t, s, slen, 4, + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ + 484 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: +blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] +In file included from hisat2_inspect.cpp:25: +alt.h: In member function ‘bool ALT::repOk() const’: +assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] + 227 | if(!((a) <= (b))) { \ + | ~~~~^~~~~~ +alt.h:180:13: note: in expansion of macro ‘assert_leq’ + 180 | assert_leq(fw, 1); + | ^~~~~~~~~~ gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -1439,8 +1446,60 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ +In file included from sequence_io.h:30: +In member function ‘void SString::resize(size_t) [with T = char]’, + inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, + inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, + inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int]’ at rfm.h:768:29: +sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] + 602 | delete cs_; + | ^~~~~~~~~~ +In member function ‘void SString::resize(size_t) [with T = char]’, + inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int]’ at rfm.h:764:24: +sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ + 610 | cs_ = new T[sz+1]; + | ^~~~~~~~~~~ +In member function ‘void SString::resize(size_t) [with T = char]’, + inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, + inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, + inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int]’ at rfm.h:766:29: +sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] + 602 | delete cs_; + | ^~~~~~~~~~ +In member function ‘void SString::resize(size_t) [with T = char]’, + inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int]’ at rfm.h:764:24: +sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ + 610 | cs_ = new T[sz+1]; + | ^~~~~~~~~~~ +In member function ‘void SString::resize(size_t) [with T = char]’, + inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, + inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, + inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2259:41: +sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] + 602 | delete cs_; + | ^~~~~~~~~~ +In member function ‘void SString::resize(size_t) [with T = char]’, + inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2255:36: +sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ + 610 | cs_ = new T[sz+1]; + | ^~~~~~~~~~~ +In member function ‘void SString::resize(size_t) [with T = char]’, + inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, + inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, + inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2257:41: +sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] + 602 | delete cs_; + | ^~~~~~~~~~ +In member function ‘void SString::resize(size_t) [with T = char]’, + inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2255:36: +sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ + 610 | cs_ = new T[sz+1]; + | ^~~~~~~~~~~ In file included from ds.h:32, - from edit.h:29: + from sequence_io.h:28, + from multikey_qsort.h:24, + from diff_sample.h:26, + from blockwise_sa.h:29: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:477:19: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] @@ -1449,8 +1508,6 @@ multikey_qsort.h:764:70: note: in expansion of macro ‘OFF_MASK’ 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ^~~~~~~~ -In file included from diff_sample.h:26, - from blockwise_sa.h:29: multikey_qsort.h:764:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1508,8 +1565,75 @@ multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ +In member function ‘void SString::resize(size_t) [with T = char]’, + inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, + inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, + inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2259:41: +sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] + 602 | delete cs_; + | ^~~~~~~~~~ +In member function ‘void SString::resize(size_t) [with T = char]’, + inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2255:36: +sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ + 610 | cs_ = new T[sz+1]; + | ^~~~~~~~~~~ +In member function ‘void SString::resize(size_t) [with T = char]’, + inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, + inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, + inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2257:41: +sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] + 602 | delete cs_; + | ^~~~~~~~~~ +In member function ‘void SString::resize(size_t) [with T = char]’, + inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2255:36: +sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ + 610 | cs_ = new T[sz+1]; + | ^~~~~~~~~~~ +In file included from splice_site.h:34, + from edit.h:30, + from edit.cpp:21: +gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: +gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1185 | auto_ptr ss(new stringstream()); + | ^~~~~~~~ +In file included from /usr/include/c++/13/memory:78, + from gfm.h:28: +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | template class auto_ptr; + | ^~~~~~~~ +gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1189 | auto_ptr fb(new FileBuf(ss.get())); + | ^~~~~~~~ +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | template class auto_ptr; + | ^~~~~~~~ +In file included from gfm.cpp:21: +gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: +gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1185 | auto_ptr ss(new stringstream()); + | ^~~~~~~~ +In file included from /usr/include/c++/13/memory:78, + from gfm.h:28: +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | template class auto_ptr; + | ^~~~~~~~ +gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1189 | auto_ptr fb(new FileBuf(ss.get())); + | ^~~~~~~~ +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | template class auto_ptr; + | ^~~~~~~~ +reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: +reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] + 522 | uint64_t origBufOff = bufOff; + | ^~~~~~~~~~ +reference.cpp:516:14: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] + 516 | bool binarySearched = false; + | ^~~~~~~~~~~~~~ In file included from gfm.h:43, - from gfm.cpp:21: + from splice_site.h:34, + from edit.h:30, + from edit.cpp:21: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 483 | mkeyQSortSuf(t, s, slen, 4, @@ -1518,25 +1642,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] -In file included from alphabet.h:27, - from gfm.h:40: -alt.h: In member function ‘bool ALT::repOk() const’: -assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] - 227 | if(!((a) <= (b))) { \ - | ~~~~^~~~~~ -alt.h:180:13: note: in expansion of macro ‘assert_leq’ - 180 | assert_leq(fw, 1); - | ^~~~~~~~~~ -In file included from alphabet.h:27, - from gfm.h:40, - from gfm.cpp:21: -alt.h: In member function ‘bool ALT::repOk() const’: -assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] - 227 | if(!((a) <= (b))) { \ - | ~~~~^~~~~~ -alt.h:180:13: note: in expansion of macro ‘assert_leq’ - 180 | assert_leq(fw, 1); - | ^~~~~~~~~~ gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -1552,6 +1657,85 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ +In file included from ds.h:32, + from edit.h:29: +multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: +blockwise_sa.h:477:19: required from here +btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 25 | #define OFF_MASK 0xffffffffffffffff + | ^~~~~~~~~~~~~~~~~~ +multikey_qsort.h:764:70: note: in expansion of macro ‘OFF_MASK’ + 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); + | ^~~~~~~~ +In file included from diff_sample.h:26, + from blockwise_sa.h:29: +multikey_qsort.h:764:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +multikey_qsort.h:764:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] +multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: +blockwise_sa.h:483:15: required from here +multikey_qsort.h:496:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: +multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ +blockwise_sa.h:477:19: required from here +btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 25 | #define OFF_MASK 0xffffffffffffffff + | ^~~~~~~~~~~~~~~~~~ +multikey_qsort.h:1160:70: note: in expansion of macro ‘OFF_MASK’ + 1160 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); + | ^~~~~~~~ +btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 25 | #define OFF_MASK 0xffffffffffffffff + | ^~~~~~~~~~~~~~~~~~ +multikey_qsort.h:1169:70: note: in expansion of macro ‘OFF_MASK’ + 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); + | ^~~~~~~~ +multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: +multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ +multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ +blockwise_sa.h:477:19: required from here +btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 25 | #define OFF_MASK 0xffffffffffffffff + | ^~~~~~~~~~~~~~~~~~ +multikey_qsort.h:1071:40: note: in expansion of macro ‘OFF_MASK’ + 1071 | OFF_MASK, begin, end); + | ^~~~~~~~ +multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: +multikey_qsort.h:1067:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ +multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ +multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ +blockwise_sa.h:477:19: required from here +btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 25 | #define OFF_MASK 0xffffffffffffffff + | ^~~~~~~~~~~~~~~~~~ +multikey_qsort.h:914:31: note: in expansion of macro ‘OFF_MASK’ + 914 | off = OFF_MASK; + | ^~~~~~~~ +btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 25 | #define OFF_MASK 0xffffffffffffffff + | ^~~~~~~~~~~~~~~~~~ +multikey_qsort.h:923:64: note: in expansion of macro ‘OFF_MASK’ + 923 | OFF_MASK, begin, end); + | ^~~~~~~~ +btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 25 | #define OFF_MASK 0xffffffffffffffff + | ^~~~~~~~~~~~~~~~~~ +multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’ + 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); + | ^~~~~~~~ +In file included from gfm.h:43, + from gfm.cpp:21: +blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: +blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 483 | mkeyQSortSuf(t, s, slen, 4, + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ + 484 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: +blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -1637,6 +1821,13 @@ multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ +reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: +reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] + 522 | uint64_t origBufOff = bufOff; + | ^~~~~~~~~~ +reference.cpp:516:14: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] + 516 | bool binarySearched = false; + | ^~~~~~~~~~~~~~ /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"22 January 2023\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-prefix-map=/build/reproducible-path/hisat2-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I. -I third_party \ @@ -1644,32 +1835,6 @@ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp mask.cpp qual.cpp aligner_bt.cpp scoring.cpp simple_func.cpp dp_framer.cpp aligner_result.cpp aligner_sw_driver.cpp aligner_sw.cpp aligner_swsse_ee_i16.cpp aligner_swsse_ee_u8.cpp aligner_swsse_loc_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse.cpp bit_packed_array.cpp repeat_builder.cpp diff_sample.cpp hisat2_repeat_main.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now make[2]: Nothing to be done for 'doc'. -In file included from sequence_io.h:30, - from hisat2_build.cpp:28: -In member function ‘void SString::resize(size_t) [with T = char]’, - inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, - inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, - inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int]’ at rfm.h:768:29: -sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] - 602 | delete cs_; - | ^~~~~~~~~~ -In member function ‘void SString::resize(size_t) [with T = char]’, - inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int]’ at rfm.h:764:24: -sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ - 610 | cs_ = new T[sz+1]; - | ^~~~~~~~~~~ -In member function ‘void SString::resize(size_t) [with T = char]’, - inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, - inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, - inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int]’ at rfm.h:766:29: -sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] - 602 | delete cs_; - | ^~~~~~~~~~ -In member function ‘void SString::resize(size_t) [with T = char]’, - inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int]’ at rfm.h:764:24: -sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ - 610 | cs_ = new T[sz+1]; - | ^~~~~~~~~~~ In file included from gfm.h:43, from hisat2_repeat.cpp:36: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: @@ -1680,31 +1845,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] -In file included from gfm.h:59: -In member function ‘bool RepeatCoord::operator<(const RepeatCoord&) const [with index_t = long long unsigned int]’, - inlined from ‘bool RepeatCoord::operator<(const RepeatCoord&) const [with index_t = long long unsigned int]’ at repeat.h:38:10, - inlined from ‘size_t EList::bsearchLoBound(const T&) const [with T = RepeatCoord; int S = 128]’ at ds.h:919:18, - inlined from ‘bool RepeatDB::findCoords(index_t, index_t, index_t, index_t, index_t, const EList&, const ALTDB&, EList, RepeatCoord > >&, index_t, index_t) const [with index_t = long long unsigned int]’ at repeat.h:466:45, - inlined from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ at hi_aligner.h:4391:44: -repeat.h:41:20: warning: ‘cmp.RepeatCoord::fw’ may be used uninitialized [-Wmaybe-uninitialized] - 41 | if(fw != o.fw) - | ~~^~ -repeat.h: In member function ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’: -repeat.h:464:30: note: ‘cmp’ declared here - 464 | RepeatCoord cmp; - | ^~~ -In member function ‘bool RepeatCoord::operator<(const RepeatCoord&) const [with index_t = long long unsigned int]’, - inlined from ‘bool RepeatCoord::operator<(const RepeatCoord&) const [with index_t = long long unsigned int]’ at repeat.h:38:10, - inlined from ‘size_t EList::bsearchLoBound(const T&) const [with T = RepeatCoord; int S = 128]’ at ds.h:919:18, - inlined from ‘bool RepeatDB::findCoords(index_t, index_t, index_t, index_t, index_t, const EList&, const ALTDB&, EList, RepeatCoord > >&, index_t, index_t) const [with index_t = long long unsigned int]’ at repeat.h:466:45, - inlined from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ at hi_aligner.h:4391:44: -repeat.h:43:26: warning: ‘cmp.RepeatCoord::alleleID’ may be used uninitialized [-Wmaybe-uninitialized] - 43 | if(alleleID != o.alleleID) - | ~~^~~~~~~~ -repeat.h: In member function ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’: -repeat.h:464:30: note: ‘cmp’ declared here - 464 | RepeatCoord cmp; - | ^~~ gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -1912,79 +2052,6 @@ multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ -In file included from sequence_io.h:30: -In member function ‘void SString::resize(size_t) [with T = char]’, - inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, - inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, - inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int]’ at rfm.h:768:29: -sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] - 602 | delete cs_; - | ^~~~~~~~~~ -In member function ‘void SString::resize(size_t) [with T = char]’, - inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int]’ at rfm.h:764:24: -sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ - 610 | cs_ = new T[sz+1]; - | ^~~~~~~~~~~ -In member function ‘void SString::resize(size_t) [with T = char]’, - inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, - inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, - inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int]’ at rfm.h:766:29: -sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] - 602 | delete cs_; - | ^~~~~~~~~~ -In member function ‘void SString::resize(size_t) [with T = char]’, - inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int]’ at rfm.h:764:24: -sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ - 610 | cs_ = new T[sz+1]; - | ^~~~~~~~~~~ -In member function ‘void SString::resize(size_t) [with T = char]’, - inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, - inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, - inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2259:41: -sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] - 602 | delete cs_; - | ^~~~~~~~~~ -In member function ‘void SString::resize(size_t) [with T = char]’, - inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2255:36: -sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ - 610 | cs_ = new T[sz+1]; - | ^~~~~~~~~~~ -In member function ‘void SString::resize(size_t) [with T = char]’, - inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, - inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, - inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2257:41: -sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] - 602 | delete cs_; - | ^~~~~~~~~~ -In member function ‘void SString::resize(size_t) [with T = char]’, - inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2255:36: -sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ - 610 | cs_ = new T[sz+1]; - | ^~~~~~~~~~~ -In member function ‘void SString::resize(size_t) [with T = char]’, - inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, - inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, - inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2259:41: -sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] - 602 | delete cs_; - | ^~~~~~~~~~ -In member function ‘void SString::resize(size_t) [with T = char]’, - inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2255:36: -sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ - 610 | cs_ = new T[sz+1]; - | ^~~~~~~~~~~ -In member function ‘void SString::resize(size_t) [with T = char]’, - inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, - inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, - inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2257:41: -sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] - 602 | delete cs_; - | ^~~~~~~~~~ -In member function ‘void SString::resize(size_t) [with T = char]’, - inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2255:36: -sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ - 610 | cs_ = new T[sz+1]; - | ^~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: @@ -2003,7 +2070,18 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ -In file included from gfm.cpp:21: +In file included from gfm.h:43, + from splice_site.h:34, + from edit.h:30, + from edit.cpp:21: +blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: +blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 483 | mkeyQSortSuf(t, s, slen, 4, + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ + 484 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: +blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -2019,10 +2097,77 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ +In file included from ds.h:32, + from edit.h:29: +multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: +blockwise_sa.h:477:19: required from here +btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 25 | #define OFF_MASK 0xffffffffffffffff + | ^~~~~~~~~~~~~~~~~~ +multikey_qsort.h:764:70: note: in expansion of macro ‘OFF_MASK’ + 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); + | ^~~~~~~~ +In file included from diff_sample.h:26, + from blockwise_sa.h:29: +multikey_qsort.h:764:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +multikey_qsort.h:764:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] +multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: +blockwise_sa.h:483:15: required from here +multikey_qsort.h:496:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: +multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ +blockwise_sa.h:477:19: required from here +btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 25 | #define OFF_MASK 0xffffffffffffffff + | ^~~~~~~~~~~~~~~~~~ +multikey_qsort.h:1160:70: note: in expansion of macro ‘OFF_MASK’ + 1160 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); + | ^~~~~~~~ +btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 25 | #define OFF_MASK 0xffffffffffffffff + | ^~~~~~~~~~~~~~~~~~ +multikey_qsort.h:1169:70: note: in expansion of macro ‘OFF_MASK’ + 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); + | ^~~~~~~~ +multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: +multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ +multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ +blockwise_sa.h:477:19: required from here +btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 25 | #define OFF_MASK 0xffffffffffffffff + | ^~~~~~~~~~~~~~~~~~ +multikey_qsort.h:1071:40: note: in expansion of macro ‘OFF_MASK’ + 1071 | OFF_MASK, begin, end); + | ^~~~~~~~ +multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: +multikey_qsort.h:1067:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ +multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ +multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ +blockwise_sa.h:477:19: required from here +btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 25 | #define OFF_MASK 0xffffffffffffffff + | ^~~~~~~~~~~~~~~~~~ +multikey_qsort.h:914:31: note: in expansion of macro ‘OFF_MASK’ + 914 | off = OFF_MASK; + | ^~~~~~~~ +btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 25 | #define OFF_MASK 0xffffffffffffffff + | ^~~~~~~~~~~~~~~~~~ +multikey_qsort.h:923:64: note: in expansion of macro ‘OFF_MASK’ + 923 | OFF_MASK, begin, end); + | ^~~~~~~~ +btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 25 | #define OFF_MASK 0xffffffffffffffff + | ^~~~~~~~~~~~~~~~~~ +multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’ + 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); + | ^~~~~~~~ In file included from gfm.h:43, - from splice_site.h:34, - from edit.h:30, - from edit.cpp:21: + from gfm.cpp:21: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 483 | mkeyQSortSuf(t, s, slen, 4, @@ -2047,7 +2192,10 @@ 65 | template class auto_ptr; | ^~~~~~~~ In file included from ds.h:32, - from edit.h:29: + from sequence_io.h:28, + from multikey_qsort.h:24, + from diff_sample.h:26, + from blockwise_sa.h:29: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:477:19: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] @@ -2056,8 +2204,6 @@ multikey_qsort.h:764:70: note: in expansion of macro ‘OFF_MASK’ 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ^~~~~~~~ -In file included from diff_sample.h:26, - from blockwise_sa.h:29: multikey_qsort.h:764:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2127,6 +2273,30 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] +In file included from edit.h:26: +alt.h: In member function ‘bool ALT::repOk() const’: +assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] + 227 | if(!((a) <= (b))) { \ + | ~~~~^~~~~~ +alt.h:180:13: note: in expansion of macro ‘assert_leq’ + 180 | assert_leq(fw, 1); + | ^~~~~~~~~~ +In file included from gfm.cpp:21: +gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: +gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1185 | auto_ptr ss(new stringstream()); + | ^~~~~~~~ +In file included from /usr/include/c++/13/memory:78, + from gfm.h:28: +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | template class auto_ptr; + | ^~~~~~~~ +gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1189 | auto_ptr fb(new FileBuf(ss.get())); + | ^~~~~~~~ +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | template class auto_ptr; + | ^~~~~~~~ gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -2218,6 +2388,13 @@ multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ +reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: +reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] + 522 | uint64_t origBufOff = bufOff; + | ^~~~~~~~~~ +reference.cpp:516:14: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] + 516 | bool binarySearched = false; + | ^~~~~~~~~~~~~~ In file included from gfm.h:43, from gfm.cpp:21: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: @@ -2228,6 +2405,15 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] +In file included from alphabet.h:27, + from gfm.h:40: +alt.h: In member function ‘bool ALT::repOk() const’: +assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] + 227 | if(!((a) <= (b))) { \ + | ~~~~^~~~~~ +alt.h:180:13: note: in expansion of macro ‘assert_leq’ + 180 | assert_leq(fw, 1); + | ^~~~~~~~~~ gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -2314,7 +2500,9 @@ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ In file included from gfm.h:43, - from gfm.cpp:21: + from splice_site.h:34, + from edit.h:30, + from edit.cpp:21: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 483 | mkeyQSortSuf(t, s, slen, 4, @@ -2339,10 +2527,7 @@ 65 | template class auto_ptr; | ^~~~~~~~ In file included from ds.h:32, - from sequence_io.h:28, - from multikey_qsort.h:24, - from diff_sample.h:26, - from blockwise_sa.h:29: + from edit.h:29: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:477:19: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] @@ -2351,6 +2536,8 @@ multikey_qsort.h:764:70: note: in expansion of macro ‘OFF_MASK’ 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ^~~~~~~~ +In file included from diff_sample.h:26, + from blockwise_sa.h:29: multikey_qsort.h:764:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2408,27 +2595,8 @@ multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ -reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: -reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] - 522 | uint64_t origBufOff = bufOff; - | ^~~~~~~~~~ -reference.cpp:516:14: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] - 516 | bool binarySearched = false; - | ^~~~~~~~~~~~~~ -reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: -reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] - 522 | uint64_t origBufOff = bufOff; - | ^~~~~~~~~~ -reference.cpp:516:14: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] - 516 | bool binarySearched = false; - | ^~~~~~~~~~~~~~ In file included from gfm.h:43, - from splice_site.h:34, - from edit.h:30, - from aligner_result.h:30, - from aligner_sw_common.h:23, - from aligner_bt.h:25, - from aligner_bt.cpp:20: + from gfm.cpp:21: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 483 | mkeyQSortSuf(t, s, slen, 4, @@ -2452,32 +2620,11 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ -In file included from aligner_bt.h:31: -sse_util.h: In member function ‘__m128i EList_m128i::operator[](size_t) const’: -sse_util.h:161:51: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] - 161 | inline __m128i operator[](size_t i) const { - | ^ -In file included from splice_site.h:34, - from edit.h:30, - from edit.cpp:21: -gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: -gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1185 | auto_ptr ss(new stringstream()); - | ^~~~~~~~ -In file included from /usr/include/c++/13/memory:78, - from gfm.h:28: -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | template class auto_ptr; - | ^~~~~~~~ -gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1189 | auto_ptr fb(new FileBuf(ss.get())); - | ^~~~~~~~ -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | template class auto_ptr; - | ^~~~~~~~ In file included from ds.h:32, - from read.h:25, - from aligner_result.h:27: + from sequence_io.h:28, + from multikey_qsort.h:24, + from diff_sample.h:26, + from blockwise_sa.h:29: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:477:19: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] @@ -2486,8 +2633,6 @@ multikey_qsort.h:764:70: note: in expansion of macro ‘OFF_MASK’ 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ^~~~~~~~ -In file included from diff_sample.h:26, - from blockwise_sa.h:29: multikey_qsort.h:764:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2545,7 +2690,30 @@ multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ -In file included from gfm.cpp:21: +reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: +reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] + 522 | uint64_t origBufOff = bufOff; + | ^~~~~~~~~~ +reference.cpp:516:14: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] + 516 | bool binarySearched = false; + | ^~~~~~~~~~~~~~ +In file included from gfm.h:43, + from splice_site.h:34, + from edit.h:30, + from aligner_seed.h:30, + from aligner_seed.cpp:21: +blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: +blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 483 | mkeyQSortSuf(t, s, slen, 4, + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ + 484 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: +blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] +In file included from splice_site.h:34, + from edit.h:30, + from aligner_seed.h:30, + from aligner_seed.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -2561,17 +2729,13 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ -reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: -reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] - 522 | uint64_t origBufOff = bufOff; - | ^~~~~~~~~~ -reference.cpp:516:14: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] - 516 | bool binarySearched = false; - | ^~~~~~~~~~~~~~ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, - from edit.cpp:21: + from aligner_result.h:30, + from aligner_sw_common.h:23, + from aligner_bt.h:25, + from aligner_bt.cpp:20: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 483 | mkeyQSortSuf(t, s, slen, 4, @@ -2595,8 +2759,24 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ +gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: +gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1185 | auto_ptr ss(new stringstream()); + | ^~~~~~~~ +In file included from /usr/include/c++/13/memory:78, + from gfm.h:28: +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | template class auto_ptr; + | ^~~~~~~~ +gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1189 | auto_ptr fb(new FileBuf(ss.get())); + | ^~~~~~~~ +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | template class auto_ptr; + | ^~~~~~~~ In file included from ds.h:32, - from edit.h:29: + from aligner_cache.h:59, + from aligner_seed.cpp:20: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:477:19: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] @@ -2664,36 +2844,14 @@ multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ -In file included from gfm.h:43, - from gfm.cpp:21: -blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: -blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 483 | mkeyQSortSuf(t, s, slen, 4, - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ - 484 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: -blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] -gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: -gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1185 | auto_ptr ss(new stringstream()); - | ^~~~~~~~ -In file included from /usr/include/c++/13/memory:78, - from gfm.h:28: -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | template class auto_ptr; - | ^~~~~~~~ -gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1189 | auto_ptr fb(new FileBuf(ss.get())); - | ^~~~~~~~ -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | template class auto_ptr; - | ^~~~~~~~ +In file included from aligner_bt.h:31: +sse_util.h: In member function ‘__m128i EList_m128i::operator[](size_t) const’: +sse_util.h:161:51: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] + 161 | inline __m128i operator[](size_t i) const { + | ^ In file included from ds.h:32, - from sequence_io.h:28, - from multikey_qsort.h:24, - from diff_sample.h:26, - from blockwise_sa.h:29: + from read.h:25, + from aligner_result.h:27: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:477:19: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] @@ -2702,6 +2860,8 @@ multikey_qsort.h:764:70: note: in expansion of macro ‘OFF_MASK’ 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ^~~~~~~~ +In file included from diff_sample.h:26, + from blockwise_sa.h:29: multikey_qsort.h:764:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2759,18 +2919,12 @@ multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ -reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: -reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] - 522 | uint64_t origBufOff = bufOff; - | ^~~~~~~~~~ -reference.cpp:516:14: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] - 516 | bool binarySearched = false; - | ^~~~~~~~~~~~~~ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, from aligner_result.h:30, - from aligner_result.cpp:22: + from aligner_seed2.h:102, + from aligner_seed2.cpp:22: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 483 | mkeyQSortSuf(t, s, slen, 4, @@ -2779,6 +2933,26 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] +In file included from splice_site.h:34, + from edit.h:30, + from aligner_result.h:30, + from aligner_seed2.h:102, + from aligner_seed2.cpp:22: +gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: +gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1185 | auto_ptr ss(new stringstream()); + | ^~~~~~~~ +In file included from /usr/include/c++/13/memory:78, + from gfm.h:28: +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | template class auto_ptr; + | ^~~~~~~~ +gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1189 | auto_ptr fb(new FileBuf(ss.get())); + | ^~~~~~~~ +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | template class auto_ptr; + | ^~~~~~~~ gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -2795,9 +2969,8 @@ 65 | template class auto_ptr; | ^~~~~~~~ In file included from ds.h:32, - from ref_read.h:33, - from reference.h:32, - from aligner_result.cpp:21: + from random_util.h:25, + from aligner_seed2.h:101: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:477:19: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] @@ -2880,6 +3053,12 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] +In file included from splice_site.h:34, + from edit.h:30, + from aligner_result.h:30, + from aligner_sw_common.h:23, + from aligner_sw.h:75, + from aligner_sw.cpp:25: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -2895,6 +3074,27 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ +gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: +gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1185 | auto_ptr ss(new stringstream()); + | ^~~~~~~~ +In file included from /usr/include/c++/13/memory:78, + from gfm.h:28: +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | template class auto_ptr; + | ^~~~~~~~ +gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1189 | auto_ptr fb(new FileBuf(ss.get())); + | ^~~~~~~~ +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | template class auto_ptr; + | ^~~~~~~~ +In file included from aligner_swsse.h:28, + from aligner_sw.h:85: +sse_util.h: In member function ‘__m128i EList_m128i::operator[](size_t) const’: +sse_util.h:161:51: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] + 161 | inline __m128i operator[](size_t i) const { + | ^ In file included from aligner_swsse.h:28, from aligner_sw.h:85: sse_util.h: In member function ‘__m128i EList_m128i::operator[](size_t) const’: @@ -2975,9 +3175,7 @@ from splice_site.h:34, from edit.h:30, from aligner_result.h:30, - from aligner_sw_common.h:23, - from aligner_sw.h:75, - from aligner_swsse_ee_i16.cpp:56: + from aligner_result.cpp:22: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 483 | mkeyQSortSuf(t, s, slen, 4, @@ -2986,6 +3184,25 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] +In file included from splice_site.h:34, + from edit.h:30, + from aligner_result.h:30, + from aligner_result.cpp:22: +gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: +gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1185 | auto_ptr ss(new stringstream()); + | ^~~~~~~~ +In file included from /usr/include/c++/13/memory:78, + from gfm.h:28: +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | template class auto_ptr; + | ^~~~~~~~ +gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1189 | auto_ptr fb(new FileBuf(ss.get())); + | ^~~~~~~~ +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | template class auto_ptr; + | ^~~~~~~~ gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -3001,15 +3218,10 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ -In file included from aligner_swsse.h:28, - from aligner_sw.h:85: -sse_util.h: In member function ‘__m128i EList_m128i::operator[](size_t) const’: -sse_util.h:161:51: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] - 161 | inline __m128i operator[](size_t i) const { - | ^ In file included from ds.h:32, - from read.h:25, - from aligner_result.h:27: + from ref_read.h:33, + from reference.h:32, + from aligner_result.cpp:21: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:477:19: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] @@ -3077,77 +3289,11 @@ multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ -In file included from splice_site.h:34, - from edit.h:30, - from aligner_seed.h:30, - from aligner_seed.cpp:21: -gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: -gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1185 | auto_ptr ss(new stringstream()); - | ^~~~~~~~ -In file included from /usr/include/c++/13/memory:78, - from gfm.h:28: -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | template class auto_ptr; - | ^~~~~~~~ -gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1189 | auto_ptr fb(new FileBuf(ss.get())); - | ^~~~~~~~ -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | template class auto_ptr; - | ^~~~~~~~ -In file included from splice_site.h:34, - from edit.h:30, - from aligner_result.h:30, - from aligner_seed2.h:102, - from aligner_seed2.cpp:22: -gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: -gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1185 | auto_ptr ss(new stringstream()); - | ^~~~~~~~ -In file included from /usr/include/c++/13/memory:78, - from gfm.h:28: -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | template class auto_ptr; - | ^~~~~~~~ -gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1189 | auto_ptr fb(new FileBuf(ss.get())); - | ^~~~~~~~ -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | template class auto_ptr; - | ^~~~~~~~ -In file included from splice_site.h:34, - from edit.h:30, - from aligner_result.h:30, - from aligner_sw_common.h:23, - from aligner_sw.h:75, - from aligner_sw.cpp:25: -gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: -gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1185 | auto_ptr ss(new stringstream()); - | ^~~~~~~~ -In file included from /usr/include/c++/13/memory:78, - from gfm.h:28: -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | template class auto_ptr; - | ^~~~~~~~ -gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1189 | auto_ptr fb(new FileBuf(ss.get())); - | ^~~~~~~~ -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | template class auto_ptr; - | ^~~~~~~~ -In file included from aligner_swsse.h:28, - from aligner_sw.h:85: -sse_util.h: In member function ‘__m128i EList_m128i::operator[](size_t) const’: -sse_util.h:161:51: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] - 161 | inline __m128i operator[](size_t i) const { - | ^ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, - from aligner_seed.h:30, - from aligner_seed.cpp:21: + from aligner_result.h:30, + from aligner_result.cpp:22: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 483 | mkeyQSortSuf(t, s, slen, 4, @@ -3171,24 +3317,10 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ -In file included from gfm.h:43, - from splice_site.h:34, - from edit.h:30, - from aligner_result.h:30, - from aligner_sw_common.h:23, - from aligner_sw.h:75, - from aligner_swsse_ee_u8.cpp:56: -blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: -blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 483 | mkeyQSortSuf(t, s, slen, 4, - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ - 484 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: -blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] In file included from ds.h:32, - from aligner_cache.h:59, - from aligner_seed.cpp:20: + from ref_read.h:33, + from reference.h:32, + from aligner_result.cpp:21: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:477:19: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] @@ -3256,6 +3388,42 @@ multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ +In file included from gfm.h:43, + from splice_site.h:34, + from edit.h:30, + from aligner_result.h:30, + from unique.h:38, + from aln_sink.h:25, + from aln_sink.cpp:22: +blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: +blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 483 | mkeyQSortSuf(t, s, slen, 4, + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ + 484 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: +blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] +In file included from splice_site.h:34, + from edit.h:30, + from aligner_result.h:30, + from unique.h:38, + from aln_sink.h:25, + from aln_sink.cpp:22: +gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: +gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1185 | auto_ptr ss(new stringstream()); + | ^~~~~~~~ +In file included from /usr/include/c++/13/memory:78, + from gfm.h:28: +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | template class auto_ptr; + | ^~~~~~~~ +gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1189 | auto_ptr fb(new FileBuf(ss.get())); + | ^~~~~~~~ +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | template class auto_ptr; + | ^~~~~~~~ gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -3271,15 +3439,9 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ -In file included from aligner_swsse.h:28, - from aligner_sw.h:85: -sse_util.h: In member function ‘__m128i EList_m128i::operator[](size_t) const’: -sse_util.h:161:51: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] - 161 | inline __m128i operator[](size_t i) const { - | ^ In file included from ds.h:32, from read.h:25, - from aligner_result.h:27: + from aln_sink.h:24: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:477:19: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] @@ -3351,8 +3513,9 @@ from splice_site.h:34, from edit.h:30, from aligner_result.h:30, - from aligner_seed2.h:102, - from aligner_seed2.cpp:22: + from aligner_sw_common.h:23, + from aligner_sw.h:75, + from aligner_sw.cpp:25: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 483 | mkeyQSortSuf(t, s, slen, 4, @@ -3376,9 +3539,15 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ +In file included from aligner_swsse.h:28, + from aligner_sw.h:85: +sse_util.h: In member function ‘__m128i EList_m128i::operator[](size_t) const’: +sse_util.h:161:51: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] + 161 | inline __m128i operator[](size_t i) const { + | ^ In file included from ds.h:32, - from random_util.h:25, - from aligner_seed2.h:101: + from read.h:25, + from aligner_result.h:27: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:477:19: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] @@ -3446,10 +3615,20 @@ multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ -In file included from splice_site.h:34, +In file included from gfm.h:43, + from splice_site.h:34, from edit.h:30, from aligner_result.h:30, - from aligner_result.cpp:22: + from unique.h:38, + from unique.cpp:20: +blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: +blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 483 | mkeyQSortSuf(t, s, slen, 4, + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ + 484 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: +blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -3465,21 +3644,11 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ -In file included from gfm.h:43, - from splice_site.h:34, +In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, - from aligner_sw_common.h:23, - from aligner_sw.h:75, - from aligner_sw.cpp:25: -blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: -blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 483 | mkeyQSortSuf(t, s, slen, 4, - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ - 484 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: -blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + from unique.h:38, + from unique.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -3495,12 +3664,6 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ -In file included from aligner_swsse.h:28, - from aligner_sw.h:85: -sse_util.h: In member function ‘__m128i EList_m128i::operator[](size_t) const’: -sse_util.h:161:51: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] - 161 | inline __m128i operator[](size_t i) const { - | ^ In file included from ds.h:32, from read.h:25, from aligner_result.h:27: @@ -3577,7 +3740,7 @@ from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, - from aligner_swsse_loc_i16.cpp:56: + from aligner_swsse_ee_i16.cpp:56: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 483 | mkeyQSortSuf(t, s, slen, 4, @@ -3681,7 +3844,9 @@ from splice_site.h:34, from edit.h:30, from aligner_result.h:30, - from aligner_result.cpp:22: + from aligner_sw_common.h:23, + from aligner_bt.h:25, + from aligner_bt.cpp:20: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 483 | mkeyQSortSuf(t, s, slen, 4, @@ -3690,6 +3855,27 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] +In file included from splice_site.h:34, + from edit.h:30, + from aligner_result.h:30, + from aligner_sw_common.h:23, + from aligner_bt.h:25, + from aligner_bt.cpp:20: +gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: +gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1185 | auto_ptr ss(new stringstream()); + | ^~~~~~~~ +In file included from /usr/include/c++/13/memory:78, + from gfm.h:28: +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | template class auto_ptr; + | ^~~~~~~~ +gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1189 | auto_ptr fb(new FileBuf(ss.get())); + | ^~~~~~~~ +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | template class auto_ptr; + | ^~~~~~~~ gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -3705,10 +3891,19 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ +In file included from aligner_bt.h:31: +sse_util.h: In member function ‘__m128i EList_m128i::operator[](size_t) const’: +sse_util.h:161:51: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] + 161 | inline __m128i operator[](size_t i) const { + | ^ +In file included from aligner_bt.h:31: +sse_util.h: In member function ‘__m128i EList_m128i::operator[](size_t) const’: +sse_util.h:161:51: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] + 161 | inline __m128i operator[](size_t i) const { + | ^ In file included from ds.h:32, - from ref_read.h:33, - from reference.h:32, - from aligner_result.cpp:21: + from read.h:25, + from aligner_result.h:27: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:477:19: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] @@ -3776,54 +3971,13 @@ multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ -In file included from splice_site.h:34, - from edit.h:30, - from aligner_result.h:30, - from unique.h:38, - from aln_sink.h:25, - from aln_sink.cpp:22: -gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: -gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1185 | auto_ptr ss(new stringstream()); - | ^~~~~~~~ -In file included from /usr/include/c++/13/memory:78, - from gfm.h:28: -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | template class auto_ptr; - | ^~~~~~~~ -gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1189 | auto_ptr fb(new FileBuf(ss.get())); - | ^~~~~~~~ -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | template class auto_ptr; - | ^~~~~~~~ -In file included from splice_site.h:34, - from edit.h:30, - from aligner_result.h:30, - from unique.h:38, - from unique.cpp:20: -gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: -gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1185 | auto_ptr ss(new stringstream()); - | ^~~~~~~~ -In file included from /usr/include/c++/13/memory:78, - from gfm.h:28: -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | template class auto_ptr; - | ^~~~~~~~ -gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1189 | auto_ptr fb(new FileBuf(ss.get())); - | ^~~~~~~~ -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | template class auto_ptr; - | ^~~~~~~~ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, from aligner_result.h:30, - from unique.h:38, - from aln_sink.h:25, - from aln_sink.cpp:22: + from aligner_sw_common.h:23, + from aligner_sw.h:75, + from aligner_swsse_ee_u8.cpp:56: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 483 | mkeyQSortSuf(t, s, slen, 4, @@ -3847,9 +4001,15 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ +In file included from aligner_swsse.h:28, + from aligner_sw.h:85: +sse_util.h: In member function ‘__m128i EList_m128i::operator[](size_t) const’: +sse_util.h:161:51: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] + 161 | inline __m128i operator[](size_t i) const { + | ^ In file included from ds.h:32, from read.h:25, - from aln_sink.h:24: + from aligner_result.h:27: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:477:19: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] @@ -3917,12 +4077,21 @@ multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ +In file included from sse_util.cpp:20: +sse_util.h: In member function ‘__m128i EList_m128i::operator[](size_t) const’: +sse_util.h:161:51: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] + 161 | inline __m128i operator[](size_t i) const { + | ^ +In file included from sse_util.cpp:20: +sse_util.h: In member function ‘__m128i EList_m128i::operator[](size_t) const’: +sse_util.h:161:51: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] + 161 | inline __m128i operator[](size_t i) const { + | ^ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, - from aligner_bt.h:25, - from aligner_bt.cpp:20: + from aligner_swsse.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -3938,7 +4107,8 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ -In file included from aligner_bt.h:31: +In file included from aligner_swsse.h:28, + from aligner_swsse.cpp:22: sse_util.h: In member function ‘__m128i EList_m128i::operator[](size_t) const’: sse_util.h:161:51: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] 161 | inline __m128i operator[](size_t i) const { @@ -3948,8 +4118,7 @@ from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, - from aligner_sw.h:75, - from aligner_swsse_loc_u8.cpp:56: + from aligner_swsse.cpp:21: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 483 | mkeyQSortSuf(t, s, slen, 4, @@ -3974,7 +4143,7 @@ 65 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_swsse.h:28, - from aligner_sw.h:85: + from aligner_swsse.cpp:22: sse_util.h: In member function ‘__m128i EList_m128i::operator[](size_t) const’: sse_util.h:161:51: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] 161 | inline __m128i operator[](size_t i) const { @@ -4049,12 +4218,40 @@ multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ +In file included from splice_site.h:34, + from edit.h:30, + from aligner_result.h:30, + from aligner_sw_common.h:23, + from aligner_sw.h:75, + from aligner_swsse_loc_i16.cpp:56: +gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: +gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1185 | auto_ptr ss(new stringstream()); + | ^~~~~~~~ +In file included from /usr/include/c++/13/memory:78, + from gfm.h:28: +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | template class auto_ptr; + | ^~~~~~~~ +gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1189 | auto_ptr fb(new FileBuf(ss.get())); + | ^~~~~~~~ +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | template class auto_ptr; + | ^~~~~~~~ +In file included from aligner_swsse.h:28, + from aligner_sw.h:85: +sse_util.h: In member function ‘__m128i EList_m128i::operator[](size_t) const’: +sse_util.h:161:51: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] + 161 | inline __m128i operator[](size_t i) const { + | ^ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, from aligner_result.h:30, - from unique.h:38, - from unique.cpp:20: + from aligner_sw_common.h:23, + from aligner_sw.h:75, + from aligner_swsse_loc_i16.cpp:56: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 483 | mkeyQSortSuf(t, s, slen, 4, @@ -4078,6 +4275,12 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ +In file included from aligner_swsse.h:28, + from aligner_sw.h:85: +sse_util.h: In member function ‘__m128i EList_m128i::operator[](size_t) const’: +sse_util.h:161:51: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] + 161 | inline __m128i operator[](size_t i) const { + | ^ In file included from ds.h:32, from read.h:25, from aligner_result.h:27: @@ -4153,8 +4356,8 @@ from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, - from aligner_bt.h:25, - from aligner_bt.cpp:20: + from aligner_sw.h:75, + from aligner_swsse_loc_i16.cpp:56: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 483 | mkeyQSortSuf(t, s, slen, 4, @@ -4178,7 +4381,8 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ -In file included from aligner_bt.h:31: +In file included from aligner_swsse.h:28, + from aligner_sw.h:85: sse_util.h: In member function ‘__m128i EList_m128i::operator[](size_t) const’: sse_util.h:161:51: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] 161 | inline __m128i operator[](size_t i) const { @@ -4253,43 +4457,12 @@ multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ -In file included from sse_util.cpp:20: -sse_util.h: In member function ‘__m128i EList_m128i::operator[](size_t) const’: -sse_util.h:161:51: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] - 161 | inline __m128i operator[](size_t i) const { - | ^ -In file included from splice_site.h:34, - from edit.h:30, - from aligner_result.h:30, - from aligner_sw_common.h:23, - from aligner_swsse.cpp:21: -gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: -gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1185 | auto_ptr ss(new stringstream()); - | ^~~~~~~~ -In file included from /usr/include/c++/13/memory:78, - from gfm.h:28: -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | template class auto_ptr; - | ^~~~~~~~ -gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1189 | auto_ptr fb(new FileBuf(ss.get())); - | ^~~~~~~~ -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | template class auto_ptr; - | ^~~~~~~~ -In file included from aligner_swsse.h:28, - from aligner_swsse.cpp:22: -sse_util.h: In member function ‘__m128i EList_m128i::operator[](size_t) const’: -sse_util.h:161:51: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] - 161 | inline __m128i operator[](size_t i) const { - | ^ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, - from aligner_swsse_loc_i16.cpp:56: + from aligner_swsse_ee_i16.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -4305,18 +4478,13 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ -In file included from aligner_swsse.h:28, - from aligner_sw.h:85: -sse_util.h: In member function ‘__m128i EList_m128i::operator[](size_t) const’: -sse_util.h:161:51: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] - 161 | inline __m128i operator[](size_t i) const { - | ^ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, - from aligner_swsse.cpp:21: + from aligner_sw.h:75, + from aligner_swsse_ee_i16.cpp:56: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 483 | mkeyQSortSuf(t, s, slen, 4, @@ -4325,6 +4493,12 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] +In file included from aligner_swsse.h:28, + from aligner_sw.h:85: +sse_util.h: In member function ‘__m128i EList_m128i::operator[](size_t) const’: +sse_util.h:161:51: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] + 161 | inline __m128i operator[](size_t i) const { + | ^ gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -4340,13 +4514,8 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ -In file included from sse_util.cpp:20: -sse_util.h: In member function ‘__m128i EList_m128i::operator[](size_t) const’: -sse_util.h:161:51: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] - 161 | inline __m128i operator[](size_t i) const { - | ^ In file included from aligner_swsse.h:28, - from aligner_swsse.cpp:22: + from aligner_sw.h:85: sse_util.h: In member function ‘__m128i EList_m128i::operator[](size_t) const’: sse_util.h:161:51: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] 161 | inline __m128i operator[](size_t i) const { @@ -4426,7 +4595,8 @@ from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, - from aligner_swsse.cpp:21: + from aligner_sw.h:75, + from aligner_swsse_loc_u8.cpp:56: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 483 | mkeyQSortSuf(t, s, slen, 4, @@ -4451,7 +4621,7 @@ 65 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_swsse.h:28, - from aligner_swsse.cpp:22: + from aligner_sw.h:85: sse_util.h: In member function ‘__m128i EList_m128i::operator[](size_t) const’: sse_util.h:161:51: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] 161 | inline __m128i operator[](size_t i) const { @@ -4532,7 +4702,7 @@ from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, - from bit_packed_array.cpp:24: + from aligner_swsse_loc_u8.cpp:56: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 483 | mkeyQSortSuf(t, s, slen, 4, @@ -4556,6 +4726,33 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ +In file included from splice_site.h:34, + from edit.h:30, + from aligner_result.h:30, + from aligner_sw_common.h:23, + from aligner_sw.h:75, + from aligner_swsse_loc_u8.cpp:56: +gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: +gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1185 | auto_ptr ss(new stringstream()); + | ^~~~~~~~ +In file included from /usr/include/c++/13/memory:78, + from gfm.h:28: +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | template class auto_ptr; + | ^~~~~~~~ +gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1189 | auto_ptr fb(new FileBuf(ss.get())); + | ^~~~~~~~ +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | template class auto_ptr; + | ^~~~~~~~ +In file included from aligner_swsse.h:28, + from aligner_sw.h:85: +sse_util.h: In member function ‘__m128i EList_m128i::operator[](size_t) const’: +sse_util.h:161:51: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] + 161 | inline __m128i operator[](size_t i) const { + | ^ In file included from aligner_swsse.h:28, from aligner_sw.h:85: sse_util.h: In member function ‘__m128i EList_m128i::operator[](size_t) const’: @@ -4637,23 +4834,7 @@ from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, - from aligner_sw.h:75, - from repeat_builder.cpp:26: -blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: -blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 483 | mkeyQSortSuf(t, s, slen, 4, - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ - 484 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: -blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] -In file included from gfm.h:43, - from splice_site.h:34, - from edit.h:30, - from aligner_result.h:30, - from aligner_sw_common.h:23, - from aligner_sw.h:75, - from aligner_swsse_loc_i16.cpp:56: + from aligner_swsse.cpp:21: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 483 | mkeyQSortSuf(t, s, slen, 4, @@ -4677,124 +4858,12 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ -gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: -gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1185 | auto_ptr ss(new stringstream()); - | ^~~~~~~~ -In file included from /usr/include/c++/13/memory:78, - from gfm.h:28: -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | template class auto_ptr; - | ^~~~~~~~ -gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1189 | auto_ptr fb(new FileBuf(ss.get())); - | ^~~~~~~~ -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | template class auto_ptr; - | ^~~~~~~~ -In file included from aligner_swsse.h:28, - from aligner_sw.h:85: -sse_util.h: In member function ‘__m128i EList_m128i::operator[](size_t) const’: -sse_util.h:161:51: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] - 161 | inline __m128i operator[](size_t i) const { - | ^ -repeat_builder.cpp: In function ‘std::string reverse_complement(const std::string&)’: -repeat_builder.cpp:88:30: warning: array subscript has type ‘char’ [-Wchar-subscripts] - 88 | rev[i] = asc2dnacomp[nt]; - | ^~ -repeat_builder.cpp: In function ‘std::string reverseComplement(const std::string&)’: -repeat_builder.cpp:200:53: warning: array subscript has type ‘char’ [-Wchar-subscripts] - 200 | rc.push_back(asc2dnacomp[str[si - 1]]); - | ^ -repeat_builder.cpp: In member function ‘int CoordHelper::mapJoinedOffToSeq(TIndexOffU)’: -repeat_builder.cpp:403:29: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] - 403 | for(size_t i = 0; i < num_cached_; i++) { - | ~~^~~~~~~~~~~~~ In file included from aligner_swsse.h:28, - from aligner_sw.h:85: + from aligner_swsse.cpp:22: sse_util.h: In member function ‘__m128i EList_m128i::operator[](size_t) const’: sse_util.h:161:51: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] 161 | inline __m128i operator[](size_t i) const { | ^ -repeat_builder.cpp: In function ‘size_t extract_kmer(const std::string&, size_t, size_t)’: -repeat_builder.cpp:1217:53: warning: array subscript has type ‘char’ [-Wchar-subscripts] - 1217 | kmer = (kmer << 2) | asc2dna[seq[offset + i]]; - | ^ -repeat_builder.cpp: In function ‘size_t next_kmer(size_t, char, size_t)’: -repeat_builder.cpp:1225:34: warning: array subscript has type ‘char’ [-Wchar-subscripts] - 1225 | kmer = (kmer << 2) | asc2dna[base]; - | ^~~~ -repeat_builder.cpp: In function ‘void find_gap_pos(const std::string&, const std::string&, EList&, EList&, bool, size_t, size_t, size_t&, size_t&, bool)’: -repeat_builder.cpp:1275:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] - 1275 | for(int i = seq_len - 1; i >= gap_len; i--) { - | ~~^~~~~~~~~~ -repeat_builder.cpp:1277:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] - 1277 | if(i == seq_len - 1) ed2[i] = add; - | ~~^~~~~~~~~~~~~~ -repeat_builder.cpp: In member function ‘void RB_SWAligner::makePadString(const std::string&, const std::string&, std::string&, size_t)’: -repeat_builder.cpp:2915:39: warning: array subscript has type ‘char’ [-Wchar-subscripts] - 2915 | pad[i] = "CGTA"[asc2dna[ref[i]]]; - | ^ -repeat_builder.cpp:2919:43: warning: array subscript has type ‘char’ [-Wchar-subscripts] - 2919 | pad[i] = "CGTA"[asc2dna[pad[i]]]; - | ^ -repeat_builder.cpp:2926:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] - 2926 | for(size_t i = 0; i < head_len; i++) { - | ~~^~~~~~~~~~ -repeat_builder.cpp:2929:67: warning: array subscript has type ‘char’ [-Wchar-subscripts] - 2929 | pad[pad_start + i] = "CGTA"[asc2dna[pad[pad_start + i]]]; - | ^ -repeat_builder.cpp: In member function ‘int RB_SWAligner::alignStrings(const std::string&, const std::string&, EList&, Coord&)’: -repeat_builder.cpp:3065:13: warning: variable ‘max_match_len’ set but not used [-Wunused-but-set-variable] - 3065 | int max_match_len = 0; - | ^~~~~~~~~~~~~ -In file included from ds.h:32, - from read.h:25, - from aligner_result.h:27: -multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: -blockwise_sa.h:477:19: required from here -btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 25 | #define OFF_MASK 0xffffffffffffffff - | ^~~~~~~~~~~~~~~~~~ -multikey_qsort.h:764:70: note: in expansion of macro ‘OFF_MASK’ - 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); - | ^~~~~~~~ -In file included from diff_sample.h:26, - from blockwise_sa.h:29: -multikey_qsort.h:764:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -multikey_qsort.h:764:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] -multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: -blockwise_sa.h:483:15: required from here -multikey_qsort.h:496:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: -multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ -blockwise_sa.h:477:19: required from here -btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 25 | #define OFF_MASK 0xffffffffffffffff - | ^~~~~~~~~~~~~~~~~~ -multikey_qsort.h:1160:70: note: in expansion of macro ‘OFF_MASK’ - 1160 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); - | ^~~~~~~~ -btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 25 | #define OFF_MASK 0xffffffffffffffff - | ^~~~~~~~~~~~~~~~~~ -multikey_qsort.h:1169:70: note: in expansion of macro ‘OFF_MASK’ - 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); - | ^~~~~~~~ -multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: -multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ -multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ -blockwise_sa.h:477:19: required from here -btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 25 | #define OFF_MASK 0xffffffffffffffff - | ^~~~~~~~~~~~~~~~~~ -multikey_qsort.h:1071:40: note: in expansion of macro ‘OFF_MASK’ - 1071 | OFF_MASK, begin, end); - | ^~~~~~~~ In file included from ds.h:32, from read.h:25, from aligner_result.h:27: @@ -4817,68 +4886,6 @@ multikey_qsort.h:496:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: -multikey_qsort.h:1067:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ -multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ -multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ -blockwise_sa.h:477:19: required from here -btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 25 | #define OFF_MASK 0xffffffffffffffff - | ^~~~~~~~~~~~~~~~~~ -multikey_qsort.h:914:31: note: in expansion of macro ‘OFF_MASK’ - 914 | off = OFF_MASK; - | ^~~~~~~~ -btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 25 | #define OFF_MASK 0xffffffffffffffff - | ^~~~~~~~~~~~~~~~~~ -multikey_qsort.h:923:64: note: in expansion of macro ‘OFF_MASK’ - 923 | OFF_MASK, begin, end); - | ^~~~~~~~ -btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 25 | #define OFF_MASK 0xffffffffffffffff - | ^~~~~~~~~~~~~~~~~~ -multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’ - 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); - | ^~~~~~~~ -In file included from repeat_builder.cpp:31: -repeat_builder.cpp: In instantiation of ‘RepeatBuilder::RepeatBuilder(TStr&, const EList&, const EList >&, bool, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]’: -repeat_builder.cpp:4753:16: required from here -repeat_builder.h:947:17: warning: ‘RepeatBuilder >::coordHelper_’ will be initialized after [-Wreorder] - 947 | CoordHelper coordHelper_; - | ^~~~~~~~~~~~ -repeat_builder.h:940:10: warning: ‘bool RepeatBuilder >::forward_only_’ [-Wreorder] - 940 | bool forward_only_; - | ^~~~~~~~~~~~~ -repeat_builder.cpp:3167:1: warning: when initialized here [-Wreorder] - 3167 | RepeatBuilder::RepeatBuilder(TStr& s, - | ^~~~~~~~~~~~~~~~~~~ -repeat_builder.cpp: In instantiation of ‘void RepeatBuilder::build(const RepeatParameter&) [with TStr = SString]’: -repeat_builder.cpp:4753:16: required from here -repeat_builder.cpp:3396:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string::size_type’ {aka ‘const unsigned int’} [-Wsign-compare] - 3396 | if(spos != string::npos) { - | ~~~~~^~~~~~~~~~~~~~~ -repeat_builder.cpp:3426:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string::size_type’ {aka ‘const unsigned int’} [-Wsign-compare] - 3426 | if(spos != string::npos) { - | ~~~~~^~~~~~~~~~~~~~~ -repeat_builder.cpp:3553:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string::size_type’ {aka ‘const unsigned int’} [-Wsign-compare] - 3553 | if(pos != string::npos) { - | ~~~~^~~~~~~~~~~~~~~ -repeat_builder.cpp:3563:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string::size_type’ {aka ‘const unsigned int’} [-Wsign-compare] - 3563 | if(pos != string::npos) { - | ~~~~^~~~~~~~~~~~~~~ -repeat_builder.cpp: In instantiation of ‘void RepeatBuilder::saveConsensus(const RepeatParameter&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]’: -repeat_builder.cpp:4753:16: required from here -repeat_builder.cpp:4114:34: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘const int’ [-Wsign-compare] - 4114 | if((oskip + out_len) == output_width) { - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ -repeat_builder.cpp: In instantiation of ‘void dump_tstr(const TStr&) [with TStr = SString]’: -repeat_builder.cpp:4754:46: required from here -repeat_builder.cpp:309:38: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] - 309 | for(size_t j = 0; (j < print_width) && (i + j < s_len); j++) { - | ~~~^~~~~~~~~~~~~~ -repeat_builder.cpp:310:46: warning: array subscript has type ‘char’ [-Wchar-subscripts] - 310 | buf.push_back("ACGTN"[s[i + j]]); - | ~~~~~~~^ multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:477:19: required from here @@ -4894,18 +4901,6 @@ multikey_qsort.h:1169:70: note: in expansion of macro ‘OFF_MASK’ 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ -repeat_builder.cpp: In instantiation of ‘std::string getString(const TStr&, TIndexOffU, size_t) [with TStr = SString; std::string = std::__cxx11::basic_string; TIndexOffU = long long unsigned int; size_t = unsigned int]’: -repeat_builder.cpp:3312:30: required from ‘void RepeatBuilder::build(const RepeatParameter&) [with TStr = SString]’ -repeat_builder.cpp:4753:16: required from here -repeat_builder.cpp:272:33: warning: array subscript has type ‘char’ [-Wchar-subscripts] - 272 | char nt = "ACGT"[ref[start + i]]; - | ~~~~~~^ -repeat_builder.cpp: In instantiation of ‘void getString(const TStr&, TIndexOffU, size_t, std::string&) [with TStr = SString; TIndexOffU = long long unsigned int; size_t = unsigned int; std::string = std::__cxx11::basic_string]’: -repeat_builder.cpp:3545:22: required from ‘void RepeatBuilder::build(const RepeatParameter&) [with TStr = SString]’ -repeat_builder.cpp:4753:16: required from here -repeat_builder.cpp:286:25: warning: array subscript has type ‘char’ [-Wchar-subscripts] - 286 | char nt = "ACGT"[ref[start + i]]; - | ~~~~~~^ multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ @@ -4939,51 +4934,13 @@ multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ -In file included from splice_site.h:34, - from edit.h:30, - from aligner_result.h:30, - from aligner_sw_common.h:23, - from aligner_sw.h:75, - from aligner_swsse_ee_i16.cpp:56: -gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: -gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1185 | auto_ptr ss(new stringstream()); - | ^~~~~~~~ -In file included from /usr/include/c++/13/memory:78, - from gfm.h:28: -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | template class auto_ptr; - | ^~~~~~~~ -gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1189 | auto_ptr fb(new FileBuf(ss.get())); - | ^~~~~~~~ -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | template class auto_ptr; - | ^~~~~~~~ -In file included from aligner_swsse.h:28, - from aligner_sw.h:85: -sse_util.h: In member function ‘__m128i EList_m128i::operator[](size_t) const’: -sse_util.h:161:51: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] - 161 | inline __m128i operator[](size_t i) const { - | ^ -In file included from /usr/include/c++/13/iostream:41, - from repeat_builder.cpp:21: -In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long long unsigned int) [with _CharT = char; _Traits = std::char_traits]’, - inlined from ‘void RepeatBuilder::writeAllele(TIndexOffU, TIndexOffU, Range, const std::string&, TIndexOffU, const EList&, std::ostream&) [with TStr = SString]’ at repeat_builder.cpp:3678:31: -/usr/include/c++/13/ostream:208:25: warning: ‘pos_in_chr’ may be used uninitialized [-Wmaybe-uninitialized] - 208 | { return _M_insert(__n); } - | ~~~~~~~~~^~~~~ -repeat_builder.cpp: In member function ‘void RepeatBuilder::writeAllele(TIndexOffU, TIndexOffU, Range, const std::string&, TIndexOffU, const EList&, std::ostream&) [with TStr = SString]’: -repeat_builder.cpp:3664:20: note: ‘pos_in_chr’ was declared here - 3664 | TIndexOffU pos_in_chr; - | ^~~~~~~~~~ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, - from aligner_swsse_ee_i16.cpp:56: + from bit_packed_array.cpp:24: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 483 | mkeyQSortSuf(t, s, slen, 4, @@ -5083,12 +5040,27 @@ multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ +In file included from gfm.h:43, + from splice_site.h:34, + from edit.h:30, + from aligner_result.h:30, + from aligner_sw_common.h:23, + from aligner_sw.h:75, + from repeat_builder.cpp:26: +blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: +blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 483 | mkeyQSortSuf(t, s, slen, 4, + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ + 484 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: +blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:75, - from aligner_swsse_loc_u8.cpp:56: + from aligner_swsse_ee_u8.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -5110,21 +5082,6 @@ sse_util.h:161:51: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] 161 | inline __m128i operator[](size_t i) const { | ^ -In file included from gfm.h:43, - from splice_site.h:34, - from edit.h:30, - from aligner_result.h:30, - from aligner_sw_common.h:23, - from aligner_sw.h:75, - from aligner_swsse_loc_u8.cpp:56: -blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: -blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 483 | mkeyQSortSuf(t, s, slen, 4, - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ - 484 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: -blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -5146,6 +5103,50 @@ sse_util.h:161:51: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] 161 | inline __m128i operator[](size_t i) const { | ^ +repeat_builder.cpp: In function ‘std::string reverse_complement(const std::string&)’: +repeat_builder.cpp:88:30: warning: array subscript has type ‘char’ [-Wchar-subscripts] + 88 | rev[i] = asc2dnacomp[nt]; + | ^~ +repeat_builder.cpp: In function ‘std::string reverseComplement(const std::string&)’: +repeat_builder.cpp:200:53: warning: array subscript has type ‘char’ [-Wchar-subscripts] + 200 | rc.push_back(asc2dnacomp[str[si - 1]]); + | ^ +repeat_builder.cpp: In member function ‘int CoordHelper::mapJoinedOffToSeq(TIndexOffU)’: +repeat_builder.cpp:403:29: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] + 403 | for(size_t i = 0; i < num_cached_; i++) { + | ~~^~~~~~~~~~~~~ +repeat_builder.cpp: In function ‘size_t extract_kmer(const std::string&, size_t, size_t)’: +repeat_builder.cpp:1217:53: warning: array subscript has type ‘char’ [-Wchar-subscripts] + 1217 | kmer = (kmer << 2) | asc2dna[seq[offset + i]]; + | ^ +repeat_builder.cpp: In function ‘size_t next_kmer(size_t, char, size_t)’: +repeat_builder.cpp:1225:34: warning: array subscript has type ‘char’ [-Wchar-subscripts] + 1225 | kmer = (kmer << 2) | asc2dna[base]; + | ^~~~ +repeat_builder.cpp: In function ‘void find_gap_pos(const std::string&, const std::string&, EList&, EList&, bool, size_t, size_t, size_t&, size_t&, bool)’: +repeat_builder.cpp:1275:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] + 1275 | for(int i = seq_len - 1; i >= gap_len; i--) { + | ~~^~~~~~~~~~ +repeat_builder.cpp:1277:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] + 1277 | if(i == seq_len - 1) ed2[i] = add; + | ~~^~~~~~~~~~~~~~ +repeat_builder.cpp: In member function ‘void RB_SWAligner::makePadString(const std::string&, const std::string&, std::string&, size_t)’: +repeat_builder.cpp:2915:39: warning: array subscript has type ‘char’ [-Wchar-subscripts] + 2915 | pad[i] = "CGTA"[asc2dna[ref[i]]]; + | ^ +repeat_builder.cpp:2919:43: warning: array subscript has type ‘char’ [-Wchar-subscripts] + 2919 | pad[i] = "CGTA"[asc2dna[pad[i]]]; + | ^ +repeat_builder.cpp:2926:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] + 2926 | for(size_t i = 0; i < head_len; i++) { + | ~~^~~~~~~~~~ +repeat_builder.cpp:2929:67: warning: array subscript has type ‘char’ [-Wchar-subscripts] + 2929 | pad[pad_start + i] = "CGTA"[asc2dna[pad[pad_start + i]]]; + | ^ +repeat_builder.cpp: In member function ‘int RB_SWAligner::alignStrings(const std::string&, const std::string&, EList&, Coord&)’: +repeat_builder.cpp:3065:13: warning: variable ‘max_match_len’ set but not used [-Wunused-but-set-variable] + 3065 | int max_match_len = 0; + | ^~~~~~~~~~~~~ In file included from ds.h:32, from read.h:25, from aligner_result.h:27: @@ -5168,6 +5169,60 @@ multikey_qsort.h:496:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from gfm.h:43, + from splice_site.h:34, + from edit.h:30, + from aligner_result.h:30, + from aligner_sw_common.h:23, + from aligner_sw.h:75, + from aligner_swsse_ee_u8.cpp:56: +blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: +blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] + 483 | mkeyQSortSuf(t, s, slen, 4, + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ + 484 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: +blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] +In file included from repeat_builder.cpp:31: +repeat_builder.cpp: In instantiation of ‘RepeatBuilder::RepeatBuilder(TStr&, const EList&, const EList >&, bool, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]’: +repeat_builder.cpp:4753:16: required from here +repeat_builder.h:947:17: warning: ‘RepeatBuilder >::coordHelper_’ will be initialized after [-Wreorder] + 947 | CoordHelper coordHelper_; + | ^~~~~~~~~~~~ +repeat_builder.h:940:10: warning: ‘bool RepeatBuilder >::forward_only_’ [-Wreorder] + 940 | bool forward_only_; + | ^~~~~~~~~~~~~ +repeat_builder.cpp:3167:1: warning: when initialized here [-Wreorder] + 3167 | RepeatBuilder::RepeatBuilder(TStr& s, + | ^~~~~~~~~~~~~~~~~~~ +repeat_builder.cpp: In instantiation of ‘void RepeatBuilder::build(const RepeatParameter&) [with TStr = SString]’: +repeat_builder.cpp:4753:16: required from here +repeat_builder.cpp:3396:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string::size_type’ {aka ‘const unsigned int’} [-Wsign-compare] + 3396 | if(spos != string::npos) { + | ~~~~~^~~~~~~~~~~~~~~ +repeat_builder.cpp:3426:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string::size_type’ {aka ‘const unsigned int’} [-Wsign-compare] + 3426 | if(spos != string::npos) { + | ~~~~~^~~~~~~~~~~~~~~ +repeat_builder.cpp:3553:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string::size_type’ {aka ‘const unsigned int’} [-Wsign-compare] + 3553 | if(pos != string::npos) { + | ~~~~^~~~~~~~~~~~~~~ +repeat_builder.cpp:3563:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string::size_type’ {aka ‘const unsigned int’} [-Wsign-compare] + 3563 | if(pos != string::npos) { + | ~~~~^~~~~~~~~~~~~~~ +repeat_builder.cpp: In instantiation of ‘void RepeatBuilder::saveConsensus(const RepeatParameter&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]’: +repeat_builder.cpp:4753:16: required from here +repeat_builder.cpp:4114:34: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘const int’ [-Wsign-compare] + 4114 | if((oskip + out_len) == output_width) { + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ +repeat_builder.cpp: In instantiation of ‘void dump_tstr(const TStr&) [with TStr = SString]’: +repeat_builder.cpp:4754:46: required from here +repeat_builder.cpp:309:38: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] + 309 | for(size_t j = 0; (j < print_width) && (i + j < s_len); j++) { + | ~~~^~~~~~~~~~~~~~ +repeat_builder.cpp:310:46: warning: array subscript has type ‘char’ [-Wchar-subscripts] + 310 | buf.push_back("ACGTN"[s[i + j]]); + | ~~~~~~~^ multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:477:19: required from here @@ -5183,6 +5238,18 @@ multikey_qsort.h:1169:70: note: in expansion of macro ‘OFF_MASK’ 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ +repeat_builder.cpp: In instantiation of ‘std::string getString(const TStr&, TIndexOffU, size_t) [with TStr = SString; std::string = std::__cxx11::basic_string; TIndexOffU = long long unsigned int; size_t = unsigned int]’: +repeat_builder.cpp:3312:30: required from ‘void RepeatBuilder::build(const RepeatParameter&) [with TStr = SString]’ +repeat_builder.cpp:4753:16: required from here +repeat_builder.cpp:272:33: warning: array subscript has type ‘char’ [-Wchar-subscripts] + 272 | char nt = "ACGT"[ref[start + i]]; + | ~~~~~~^ +repeat_builder.cpp: In instantiation of ‘void getString(const TStr&, TIndexOffU, size_t, std::string&) [with TStr = SString; TIndexOffU = long long unsigned int; size_t = unsigned int; std::string = std::__cxx11::basic_string]’: +repeat_builder.cpp:3545:22: required from ‘void RepeatBuilder::build(const RepeatParameter&) [with TStr = SString]’ +repeat_builder.cpp:4753:16: required from here +repeat_builder.cpp:286:25: warning: array subscript has type ‘char’ [-Wchar-subscripts] + 286 | char nt = "ACGT"[ref[start + i]]; + | ~~~~~~^ multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ @@ -5216,48 +5283,6 @@ multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ -In file included from splice_site.h:34, - from edit.h:30, - from aligner_result.h:30, - from aligner_sw_common.h:23, - from aligner_sw.h:75, - from aligner_swsse_ee_u8.cpp:56: -gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: -gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1185 | auto_ptr ss(new stringstream()); - | ^~~~~~~~ -In file included from /usr/include/c++/13/memory:78, - from gfm.h:28: -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | template class auto_ptr; - | ^~~~~~~~ -gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1189 | auto_ptr fb(new FileBuf(ss.get())); - | ^~~~~~~~ -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | template class auto_ptr; - | ^~~~~~~~ -In file included from aligner_swsse.h:28, - from aligner_sw.h:85: -sse_util.h: In member function ‘__m128i EList_m128i::operator[](size_t) const’: -sse_util.h:161:51: warning: SSE vector return without SSE enabled changes the ABI [-Wpsabi] - 161 | inline __m128i operator[](size_t i) const { - | ^ -In file included from gfm.h:43, - from splice_site.h:34, - from edit.h:30, - from aligner_result.h:30, - from aligner_sw_common.h:23, - from aligner_sw.h:75, - from aligner_swsse_ee_u8.cpp:56: -blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: -blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] - 483 | mkeyQSortSuf(t, s, slen, 4, - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ - 484 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: -blockwise_sa.h:483:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); @@ -5349,6 +5374,17 @@ multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ +In file included from /usr/include/c++/13/iostream:41, + from repeat_builder.cpp:21: +In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long long unsigned int) [with _CharT = char; _Traits = std::char_traits]’, + inlined from ‘void RepeatBuilder::writeAllele(TIndexOffU, TIndexOffU, Range, const std::string&, TIndexOffU, const EList&, std::ostream&) [with TStr = SString]’ at repeat_builder.cpp:3678:31: +/usr/include/c++/13/ostream:208:25: warning: ‘pos_in_chr’ may be used uninitialized [-Wmaybe-uninitialized] + 208 | { return _M_insert(__n); } + | ~~~~~~~~~^~~~~ +repeat_builder.cpp: In member function ‘void RepeatBuilder::writeAllele(TIndexOffU, TIndexOffU, Range, const std::string&, TIndexOffU, const EList&, std::ostream&) [with TStr = SString]’: +repeat_builder.cpp:3664:20: note: ‘pos_in_chr’ was declared here + 3664 | TIndexOffU pos_in_chr; + | ^~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, @@ -5370,37 +5406,6 @@ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ -In file included from splice_site.h:34, - from edit.h:30, - from splice_site.cpp:20: -gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: -gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1185 | auto_ptr ss(new stringstream()); - | ^~~~~~~~ -In file included from /usr/include/c++/13/memory:78, - from gfm.h:28: -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | template class auto_ptr; - | ^~~~~~~~ -gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 1189 | auto_ptr fb(new FileBuf(ss.get())); - | ^~~~~~~~ -/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here - 65 | template class auto_ptr; - | ^~~~~~~~ -splice_site.cpp: In member function ‘void SpliceSiteDB::read(const GFM&, const EList >&)’: -splice_site.cpp:717:59: warning: ‘?:’ using integer constants in boolean context, the expression will always evaluate to ‘true’ [-Wint-in-bool-context] - 717 | exons.back().init(ref, left, right, fw == '+' ? SPL_FW : SPL_RC); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~ -In file included from edit.h:29: -ds.h: In instantiation of ‘void EList::push_back_array(const T*, size_t) [with T = Exon; int S = 128; size_t = unsigned int]’: -splice_site.cpp:722:31: required from here -ds.h:663:28: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘class Exon’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] - 663 | std::memcpy(list_ + cur_, l, bytes); - | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -splice_site.h:377:7: note: ‘class Exon’ declared here - 377 | class Exon { - | ^~~~ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, @@ -5609,6 +5614,37 @@ multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ +In file included from splice_site.h:34, + from edit.h:30, + from splice_site.cpp:20: +gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: +gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1185 | auto_ptr ss(new stringstream()); + | ^~~~~~~~ +In file included from /usr/include/c++/13/memory:78, + from gfm.h:28: +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | template class auto_ptr; + | ^~~~~~~~ +gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1189 | auto_ptr fb(new FileBuf(ss.get())); + | ^~~~~~~~ +/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here + 65 | template class auto_ptr; + | ^~~~~~~~ +splice_site.cpp: In member function ‘void SpliceSiteDB::read(const GFM&, const EList >&)’: +splice_site.cpp:717:59: warning: ‘?:’ using integer constants in boolean context, the expression will always evaluate to ‘true’ [-Wint-in-bool-context] + 717 | exons.back().init(ref, left, right, fw == '+' ? SPL_FW : SPL_RC); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~ +In file included from edit.h:29: +ds.h: In instantiation of ‘void EList::push_back_array(const T*, size_t) [with T = Exon; int S = 128; size_t = unsigned int]’: +splice_site.cpp:722:31: required from here +ds.h:663:28: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘class Exon’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] + 663 | std::memcpy(list_ + cur_, l, bytes); + | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +splice_site.h:377:7: note: ‘class Exon’ declared here + 377 | class Exon { + | ^~~~ make[2]: Leaving directory '/build/reproducible-path/hisat2-2.2.1' help2man ./hisat2 --no-info --name \ 'graph-based alignment of short nucleotide reads to many genomes, wrapper script' \ @@ -5674,12 +5710,14 @@ 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/4418/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/4418/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/9039 and its subdirectories -I: Current time: Sun Jun 22 08:21:35 -12 2025 -I: pbuilder-time-stamp: 1750623695 +I: removing directory /srv/workspace/pbuilder/4418 and its subdirectories +I: Current time: Tue May 21 04:01:45 +14 2024 +I: pbuilder-time-stamp: 1716213705