Diff of the two buildlogs: -- --- b1/build.log 2025-01-31 01:52:01.640770628 +0000 +++ b2/build.log 2025-01-31 02:22:19.390848028 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jan 30 13:35:55 -12 2025 -I: pbuilder-time-stamp: 1738287355 +I: Current time: Fri Jan 31 15:53:00 +14 2025 +I: pbuilder-time-stamp: 1738288380 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -32,52 +32,84 @@ dpkg-source: info: applying riscv5 I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/11631/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/13600/tmp/hooks/D01_modify_environment starting +debug: Running on ff64a. +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 Jan 31 01:53 /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/13600/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/13600/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=6 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='4093641fad3c458e8191349a3abd9bc0' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='11631' - PS1='# ' - PS2='> ' + INVOCATION_ID=cfa7c7a3dcf74fcfac1197fd98918a83 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=13600 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.F5XIMsLX/pbuilderrc_pcZF --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.F5XIMsLX/b1 --logfile b1/build.log hisat2_2.2.1-5.dsc' - SUDO_GID='110' - SUDO_UID='103' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.F5XIMsLX/pbuilderrc_4mYa --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.F5XIMsLX/b2 --logfile b2/build.log hisat2_2.2.1-5.dsc' + SUDO_GID=114 + SUDO_UID=109 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux virt32z 6.1.0-30-armmp-lpae #1 SMP Debian 6.1.124-1 (2025-01-12) armv7l GNU/Linux + Linux i-capture-the-hostname 6.1.0-30-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/11631/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/13600/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -172,7 +204,7 @@ Get: 50 http://deb.debian.org/debian unstable/main armhf libyaml-0-2 armhf 0.2.5-2 [45.4 kB] Get: 51 http://deb.debian.org/debian unstable/main armhf pandoc-data all 3.1.11.1-3 [459 kB] Get: 52 http://deb.debian.org/debian unstable/main armhf pandoc armhf 3.1.11.1+ds-2 [32.7 MB] -Fetched 59.8 MB in 13s (4687 kB/s) +Fetched 59.8 MB in 4s (15.0 MB/s) Preconfiguring packages ... 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 ... 19567 files and directories currently installed.) @@ -358,8 +390,8 @@ Setting up tzdata (2025a-1) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Jan 31 01:37:13 UTC 2025. -Universal Time is now: Fri Jan 31 01:37:13 UTC 2025. +Local time is now: Fri Jan 31 01:56:31 UTC 2025. +Universal Time is now: Fri Jan 31 01:56:31 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -407,7 +439,11 @@ 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_source.changes +I: user script /srv/workspace/pbuilder/13600/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/13600/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_source.changes dpkg-buildpackage: info: source package hisat2 dpkg-buildpackage: info: source version 2.2.1-5 dpkg-buildpackage: info: source distribution unstable @@ -417,7 +453,7 @@ debian/rules clean dh clean dh_auto_clean - make -j3 clean + make -j6 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 \ @@ -436,7 +472,7 @@ 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="09 July 2024" all doc - make -j3 "INSTALL=install --strip-program=true" BUILD_HOST=Debian "BUILD_TIME=09 July 2024" all doc + make -j6 "INSTALL=install --strip-program=true" BUILD_HOST=Debian "BUILD_TIME=09 July 2024" all doc make[2]: Entering directory '/build/reproducible-path/hisat2-2.2.1' /usr/bin/g++ -O3 -funroll-loops -g3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"09 July 2024\"" -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 -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DNDEBUG -Wall -DMASSIVE_DATA_RLCSA \ @@ -456,6 +492,26 @@ -o hisat2-align-s hisat2.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 qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat2_main.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now +/usr/bin/g++ -O3 -funroll-loops -g3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ +-fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"09 July 2024\"" -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 -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ +-I. -I third_party \ +-o hisat2-align-l hisat2.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 qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat2_main.cpp \ +-lpthread -Wl,-z,relro -Wl,-z,now +/usr/bin/g++ -O3 -funroll-loops -g3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 \ +-DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ +-fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"09 July 2024\"" -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 -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DHISAT2_INSPECT_MAIN -Wall \ +-I. -I third_party -I . \ +-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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 \ +-DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ +-fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"09 July 2024\"" -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 -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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]’: @@ -466,8 +522,33 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 hgfm.h:24, +In file included from hisat2_build.cpp:35: +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++/14/memory:78, + from gfm.h:28: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +In file included from gfm.h:43, + from hgfm.h:24, from hisat2.cpp:33: +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()); @@ -483,6 +564,8 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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()); @@ -498,7 +581,6 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -In file included from hisat2_build.cpp:35: 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()); @@ -565,65 +647,8 @@ 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]’ - 1166 | bucketSortSufDcU8(host1, host, hlen, s, slen, dc, - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1167 | (uint8_t)hi, begin, end, depth, sanityCheck); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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]’ - 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -blockwise_sa.h:477:19: required from here - 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 478 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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]’ - 1067 | selectionSortSufDcU8(host1, host, hlen, s, slen, dc, hi, - | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1068 | begin, end, depth, sanityCheck); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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]’ - 1166 | bucketSortSufDcU8(host1, host, hlen, s, slen, dc, - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1167 | (uint8_t)hi, begin, end, depth, sanityCheck); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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]’ - 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -blockwise_sa.h:477:19: required from here - 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 478 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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); - | ^~~~~~~~ -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]’ +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 = 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 = unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ 1039 | initFromVector( | ~~~~~~~~~~~~~~~~~~~~^ 1040 | s, @@ -672,7 +697,7 @@ | ~~~~~ 1062 | verbose); | ~~~~~~~~ -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]’ +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 = unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = unsigned int; uint32_t = unsigned int]’ 1989 | _in6(NULL) | ^ hisat2_build.cpp:535:15: required from ‘void driver(const std::string&, EList >&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, int, bool, EList*, EList >*, EList*, EList >*) [with TStr = SString; std::string = std::__cxx11::basic_string]’ @@ -782,8 +807,73 @@ gfm.h:2167:33: warning: variable ‘template_len’ set but not used [-Wunused-but-set-variable] 2167 | index_t template_len = 0; | ^~~~~~~~~~~~ -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 = 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 = unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ +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); + | ^~~~~~~~~~ +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]’ + 1166 | bucketSortSufDcU8(host1, host, hlen, s, slen, dc, + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1167 | (uint8_t)hi, begin, end, depth, sanityCheck); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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]’ + 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +blockwise_sa.h:477:19: required from here + 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 478 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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]’ + 1067 | selectionSortSufDcU8(host1, host, hlen, s, slen, dc, hi, + | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1068 | begin, end, depth, sanityCheck); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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]’ + 1166 | bucketSortSufDcU8(host1, host, hlen, s, slen, dc, + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1167 | (uint8_t)hi, begin, end, depth, sanityCheck); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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]’ + 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +blockwise_sa.h:477:19: required from here + 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 478 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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); + | ^~~~~~~~ +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]’ 1039 | initFromVector( | ~~~~~~~~~~~~~~~~~~~~^ 1040 | s, @@ -832,7 +922,7 @@ | ~~~~~ 1062 | verbose); | ~~~~~~~~ -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 = unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = unsigned int; 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]’ 1989 | _in6(NULL) | ^ hisat2_build.cpp:535:15: required from ‘void driver(const std::string&, EList >&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, int, bool, EList*, EList >*, EList*, EList >*) [with TStr = SString; std::string = std::__cxx11::basic_string]’ @@ -945,6 +1035,17 @@ gfm.h:2342:106: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 2342 | std::numeric_limits::max(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +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 aligner_sw.h:76, from aligner_sw_driver.h:86, from hi_aligner.h:42, @@ -955,6 +1056,31 @@ 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ +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); + | ^~~~~~~~~~ +In file included from hgfm.h:24, + from hisat2_inspect.cpp:27: +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++/14/memory:78, + from gfm.h:28: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ 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]’ 1098 | this->qsort(bucket); @@ -1202,6 +1328,16 @@ 813 | sanityCheckOrderedSufs(t, t.length(), sPrimeArr, sPrimeSz, v); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff_sample.h:813:43: 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_sw.h:76, + from aligner_sw_driver.h:86, + from hi_aligner.h:42, + from spliced_aligner.h:23, + from hisat2.cpp:46: +aligner_sw_nuc.h: At global scope: +aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 191 | NBest() { nelt_ = nbest_ = n_ = 0; } + | ^ +aligner_sw_nuc.h:191:17: note: remove the ‘< >’ multikey_qsort.h: In instantiation of ‘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]’: blockwise_sa.h:447:19: required from ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = SString]’ 447 | mkeyQSortSufDcU8(t, host, len, s, slen, *_dc.get(), 4, @@ -1458,13 +1594,6 @@ 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); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -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++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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]’ 772 | mkeyQSortSuf2(t, sPrimeArr, sPrimeSz, sPrimeOrderArr, 4, @@ -1866,21 +1995,9 @@ multikey_qsort.h:1071:40: note: in expansion of macro ‘OFF_MASK’ 1071 | OFF_MASK, begin, end); | ^~~~~~~~ -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++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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)); +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++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; @@ -2038,6 +2155,73 @@ multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’ 1007 | 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++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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( + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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++/14/memory:78, + from gfm.h:28: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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( @@ -2045,6 +2229,36 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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: +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 + 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 478 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 + 483 | mkeyQSortSuf(t, s, slen, 4, + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ + 484 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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); + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 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]’ 3815 | gfm.checkOrigs(os, false); @@ -2055,6 +2269,353 @@ gfm.h:6935:13: warning: variable ‘lastorig’ set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^~~~~~~~ +hi_aligner.h: In instantiation of ‘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 + 3537 | int ret = splicedAligner.go( + | ~~~~~~~~~~~~~~~~~^ + 3538 | sc, + | ~~~ + 3539 | pepol, + | ~~~~~~ + 3540 | *multiseed_tpol, + | ~~~~~~~~~~~~~~~~ + 3541 | *gpol, + | ~~~~~~ + 3542 | gfm, + | ~~~~ + 3543 | rgfm, + | ~~~~~ + 3544 | *altdb, + | ~~~~~~~ + 3545 | *repeatdb, + | ~~~~~~~~~~ + 3546 | *raltdb, + | ~~~~~~~~ + 3547 | ref, + | ~~~~ + 3548 | rref, + | ~~~~~ + 3549 | sw, + | ~~~ + 3550 | *ssdb, + | ~~~~~~ + 3551 | wlm, + | ~~~~ + 3552 | prm, + | ~~~~ + 3553 | swmSeed, + | ~~~~~~~~ + 3554 | him, + | ~~~~ + 3555 | rnd, + | ~~~~ + 3556 | msinkwrap); + | ~~~~~~~~~~ +hi_aligner.h:4385:84: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘const THitInt’ {aka ‘const long long int’} [-Wsign-compare] + 4385 | if(sink.bestPair() >= estScore && sink.numBestPair().first > rp.khits) + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +hi_aligner.h:4404:55: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘TRefId’ {aka ‘long long int’} [-Wsign-compare] + 4404 | if(positions[p].first.tid != res.refid()) continue; + | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +hi_aligner.h:4405:63: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘TRefOff’ {aka ‘long long int’} [-Wsign-compare] + 4405 | if(positions[p].first.toff + 1000 < res.refoff() || + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +hi_aligner.h:4406:52: warning: comparison of integer expressions of different signedness: ‘TRefOff’ {aka ‘long long int’} and ‘long long unsigned int’ [-Wsign-compare] + 4406 | res.refoff() + 1000 < positions[p].first.toff) continue; + | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +hi_aligner.h:4407:88: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘const THitInt’ {aka ‘const long long int’} [-Wsign-compare] + 4407 | if(sink.bestPair() >= estScore && sink.numBestPair().first > rp.khits) + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +hi_aligner.h:4489:92: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘const THitInt’ {aka ‘const long long int’} [-Wsign-compare] + 4489 | if(sink.bestPair() >= estScore && sink.numBestPair().first > rp.khits) + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +hi_aligner.h:4578:69: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘const THitInt’ {aka ‘const long long int’} [-Wsign-compare] + 4578 | align2repeat = (numBestPair == 0 || numBestPair > rp.khits); + | ~~~~~~~~~~~~^~~~~~~~~~ +hi_aligner.h:4584:83: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘const THitInt’ {aka ‘const long long int’} [-Wsign-compare] + 4584 | align2repeat = (rs->size() == 0 || sink.numBestUnp(rdi).first > rp.khits); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +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) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +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]’ + 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +blockwise_sa.h:477:19: required from here + 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 478 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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); + | ^~~~~~~~ +hi_aligner.h: In instantiation of ‘bool HI_Aligner::pairReads(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, WalkMetrics&, PerReadMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’: +hi_aligner.h:4088:17: 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]’ + 4088 | pairReads(sc, pepol, tpol, gpol, gfm, altdb, repeatdb, ref, wlm, prm, him, rnd, sink); + | ^~~~~~~~~ +hisat2.cpp:3537:48: required from here + 3537 | int ret = splicedAligner.go( + | ~~~~~~~~~~~~~~~~~^ + 3538 | sc, + | ~~~ + 3539 | pepol, + | ~~~~~~ + 3540 | *multiseed_tpol, + | ~~~~~~~~~~~~~~~~ + 3541 | *gpol, + | ~~~~~~ + 3542 | gfm, + | ~~~~ + 3543 | rgfm, + | ~~~~~ + 3544 | *altdb, + | ~~~~~~~ + 3545 | *repeatdb, + | ~~~~~~~~~~ + 3546 | *raltdb, + | ~~~~~~~~ + 3547 | ref, + | ~~~~ + 3548 | rref, + | ~~~~~ + 3549 | sw, + | ~~~ + 3550 | *ssdb, + | ~~~~~~ + 3551 | wlm, + | ~~~~ + 3552 | prm, + | ~~~~ + 3553 | swmSeed, + | ~~~~~~~~ + 3554 | him, + | ~~~~ + 3555 | rnd, + | ~~~~ + 3556 | msinkwrap); + | ~~~~~~~~~~ +hi_aligner.h:5990:51: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘TRefOff’ {aka ‘long long int’} [-Wsign-compare] + 5990 | if(_repeatConcordant[r].first == left.off() && + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +hi_aligner.h:5991:52: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘TRefOff’ {aka ‘long long int’} [-Wsign-compare] + 5991 | _repeatConcordant[r].second == left2.off()) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +hi_aligner.h: In instantiation of ‘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]’ + 4107 | mate_found |= alignMate( + | ^~~~~~~~~ +hisat2.cpp:3537:48: required from here + 3537 | int ret = splicedAligner.go( + | ~~~~~~~~~~~~~~~~~^ + 3538 | sc, + | ~~~ + 3539 | pepol, + | ~~~~~~ + 3540 | *multiseed_tpol, + | ~~~~~~~~~~~~~~~~ + 3541 | *gpol, + | ~~~~~~ + 3542 | gfm, + | ~~~~ + 3543 | rgfm, + | ~~~~~ + 3544 | *altdb, + | ~~~~~~~ + 3545 | *repeatdb, + | ~~~~~~~~~~ + 3546 | *raltdb, + | ~~~~~~~~ + 3547 | ref, + | ~~~~ + 3548 | rref, + | ~~~~~ + 3549 | sw, + | ~~~ + 3550 | *ssdb, + | ~~~~~~ + 3551 | wlm, + | ~~~~ + 3552 | prm, + | ~~~~ + 3553 | swmSeed, + | ~~~~~~~~ + 3554 | him, + | ~~~~ + 3555 | rnd, + | ~~~~ + 3556 | msinkwrap); + | ~~~~~~~~~~ +hi_aligner.h:5661:33: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘const THitInt’ {aka ‘const long long int’} [-Wsign-compare] + 5661 | if(nelt > 0 && nelt <= rp.kseeds && hitlen > max_hitlen) { + | ~~~~~^~~~~~~~~~~~ +hi_aligner.h:5688:65: warning: comparison of integer expressions of different signedness: ‘TRefOff’ {aka ‘long long int’} and ‘long long unsigned int’ [-Wsign-compare] + 5688 | if(coord.off() + pepol.maxFragLen() * 2 < toff || toff + pepol.maxFragLen() * 2 < coord.off()) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ +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 = 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]’ + 3815 | gfm.checkOrigs(os, false); + | ~~~~~~~~~~~~~~^~~~~~~~~~~ +hisat2.cpp:4351:26: required from here + 4351 | driver >("DNA", bt2index, outfile); + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +gfm.h:6935:13: warning: variable ‘lastorig’ set but not used [-Wunused-but-set-variable] + 6935 | int lastorig = -1; + | ^~~~~~~~ +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]’ + 1166 | bucketSortSufDcU8(host1, host, hlen, s, slen, dc, + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1167 | (uint8_t)hi, begin, end, depth, sanityCheck); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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]’ + 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +blockwise_sa.h:477:19: required from here + 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 478 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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: In instantiation of ‘index_t HI_Aligner::getAnchorHits(const GFM&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const ALTDB&, const RepeatDB&, const BitPairReference&, RandomSource&, index_t, bool, EList >&, index_t, SharedTempVars&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool) [with index_t = long long unsigned int; local_index_t = short unsigned int]’: +hi_aligner.h:5525:23: required from ‘bool HI_Aligner::align(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&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ + 5525 | index_t numHits = getAnchorHits(gfm, + | ^~~~~~~~~~~~~ +hi_aligner.h:4080:31: 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]’ + 4080 | found[rdi][fwi] = align(sc, pepol, tpol, gpol, gfm, altdb, repeatdb, ref, swa, ssdb, rdi, fw, wlm, prm, swm, him, rnd, sink); + | ^~~~~ +hisat2.cpp:3537:48: required from here + 3537 | int ret = splicedAligner.go( + | ~~~~~~~~~~~~~~~~~^ + 3538 | sc, + | ~~~ + 3539 | pepol, + | ~~~~~~ + 3540 | *multiseed_tpol, + | ~~~~~~~~~~~~~~~~ + 3541 | *gpol, + | ~~~~~~ + 3542 | gfm, + | ~~~~ + 3543 | rgfm, + | ~~~~~ + 3544 | *altdb, + | ~~~~~~~ + 3545 | *repeatdb, + | ~~~~~~~~~~ + 3546 | *raltdb, + | ~~~~~~~~ + 3547 | ref, + | ~~~~ + 3548 | rref, + | ~~~~~ + 3549 | sw, + | ~~~ + 3550 | *ssdb, + | ~~~~~~ + 3551 | wlm, + | ~~~~ + 3552 | prm, + | ~~~~ + 3553 | swmSeed, + | ~~~~~~~~ + 3554 | him, + | ~~~~ + 3555 | rnd, + | ~~~~ + 3556 | msinkwrap); + | ~~~~~~~~~~ +hi_aligner.h:5150:32: warning: comparison of integer expressions of different signedness: ‘TRefId’ {aka ‘long long int’} and ‘long long unsigned int’ [-Wsign-compare] + 5150 | if(coord.ref() == numeric_limits::max()) + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +hi_aligner.h: In instantiation of ‘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]’ + 5692 | GenomeHit::adjustWithALT( + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ + 5693 | hitoff - hitlen + 1, + | ~~~~~~~~~~~~~~~~~~~~ + 5694 | hitlen, + | ~~~~~~~ + 5695 | coord, + | ~~~~~~ + 5696 | _sharedVars, + | ~~~~~~~~~~~~ + 5697 | _genomeHits, + | ~~~~~~~~~~~~ + 5698 | *this->_rds[ordi], + | ~~~~~~~~~~~~~~~~~~ + 5699 | gfm, + | ~~~~ + 5700 | altdb, + | ~~~~~~ + 5701 | ref, + | ~~~~ + 5702 | gpol); + | ~~~~~ +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]’ + 4107 | mate_found |= alignMate( + | ^~~~~~~~~ +hisat2.cpp:3537:48: required from here + 3537 | int ret = splicedAligner.go( + | ~~~~~~~~~~~~~~~~~^ + 3538 | sc, + | ~~~ + 3539 | pepol, + | ~~~~~~ + 3540 | *multiseed_tpol, + | ~~~~~~~~~~~~~~~~ + 3541 | *gpol, + | ~~~~~~ + 3542 | gfm, + | ~~~~ + 3543 | rgfm, + | ~~~~~ + 3544 | *altdb, + | ~~~~~~~ + 3545 | *repeatdb, + | ~~~~~~~~~~ + 3546 | *raltdb, + | ~~~~~~~~ + 3547 | ref, + | ~~~~ + 3548 | rref, + | ~~~~~ + 3549 | sw, + | ~~~ + 3550 | *ssdb, + | ~~~~~~ + 3551 | wlm, + | ~~~~ + 3552 | prm, + | ~~~~ + 3553 | swmSeed, + | ~~~~~~~~ + 3554 | him, + | ~~~~ + 3555 | rnd, + | ~~~~ + 3556 | msinkwrap); + | ~~~~~~~~~~ +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 aligner_seed2.h:109, from aligner_driver.h:78, from hi_aligner.h:41: @@ -2356,6 +2917,43 @@ 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) { | ~~~~~~~~~~~^~~~~~~~~~~~~~ +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]’ + 1067 | selectionSortSufDcU8(host1, host, hlen, s, slen, dc, hi, + | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1068 | begin, end, depth, sanityCheck); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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]’ + 1166 | bucketSortSufDcU8(host1, host, hlen, s, slen, dc, + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1167 | (uint8_t)hi, begin, end, depth, sanityCheck); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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]’ + 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +blockwise_sa.h:477:19: required from here + 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 478 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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]’ 494 | return init(gfm, ref, sa, sts, hit, range, reportList, res, met); @@ -2653,980 +3251,6 @@ 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) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ -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 - 331 | int64_t SplicedAligner::hybridSearch_recur( - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -spliced_aligner.h:408:18: warning: variable ‘another_spliced’ set but not used [-Wunused-but-set-variable] - 408 | bool another_spliced = false; - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/set:62, - from gfm.h:32: -/usr/include/c++/14/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long long unsigned int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: -/usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 - 2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/map:63, - from repeat.h:26, - from gfm.h:59: -/usr/include/c++/14/bits/stl_map.h: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long unsigned int; _Tp = long long unsigned int; _Compare = std::less; _Alloc = std::allocator >]’: -/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 - 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 514 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 515 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple::CompositeNodeIDs&>, std::tuple<>}; _Key = RefGraph::CompositeNodeIDs; _Val = std::pair::CompositeNodeIDs, long long unsigned int>; _KeyOfValue = std::_Select1st::CompositeNodeIDs, long long unsigned int> >; _Compare = std::less::CompositeNodeIDs>; _Alloc = std::allocator::CompositeNodeIDs, long long unsigned int> >]’: -/usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type ‘std::_Rb_tree::CompositeNodeIDs, std::pair::CompositeNodeIDs, long long unsigned int>, std::_Select1st::CompositeNodeIDs, long long unsigned int> >, std::less::CompositeNodeIDs>, std::allocator::CompositeNodeIDs, long long unsigned int> > >::const_iterator’ changed in GCC 7.1 - 2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = RefGraph::CompositeNodeIDs; _Tp = long long unsigned int; _Compare = std::less::CompositeNodeIDs>; _Alloc = std::allocator::CompositeNodeIDs, long long unsigned int> >]’, - inlined from ‘static void RefGraph::reverseDeterminize(EList&, EList&, index_t&, index_t) [with index_t = long long unsigned int]’ at gbwt_graph.h:1321:14: -/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree::CompositeNodeIDs, std::pair::CompositeNodeIDs, long long unsigned int>, std::_Select1st::CompositeNodeIDs, long long unsigned int> >, std::less::CompositeNodeIDs>, std::allocator::CompositeNodeIDs, long long unsigned int> > >::const_iterator’ changed in GCC 7.1 - 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 514 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 515 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = RefGraph::CompositeNodeIDs; _Tp = long long unsigned int; _Compare = std::less::CompositeNodeIDs>; _Alloc = std::allocator::CompositeNodeIDs, long long unsigned int> >]’, - inlined from ‘static void RefGraph::reverseDeterminize(EList&, EList&, index_t&, index_t) [with index_t = long long unsigned int]’ at gbwt_graph.h:1387:26: -/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree::CompositeNodeIDs, std::pair::CompositeNodeIDs, long long unsigned int>, std::_Select1st::CompositeNodeIDs, long long unsigned int> >, std::less::CompositeNodeIDs>, std::allocator::CompositeNodeIDs, long long unsigned int> > >::const_iterator’ changed in GCC 7.1 - 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 514 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 515 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -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 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 member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long unsigned int; _Tp = long long unsigned int; _Compare = std::less; _Alloc = std::allocator >]’, - 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:2280:40: -/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 - 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 514 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 515 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long unsigned int; _Tp = long long unsigned int; _Compare = std::less; _Alloc = std::allocator >]’, - 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:2316:75: -/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 - 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 514 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 515 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -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++/14/memory:78, - from gfm.h:28: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -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()); - | ^~~~~~~~ -In file included from /usr/include/c++/14/memory:78, - from gfm.h:28: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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 - 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 478 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 - 483 | mkeyQSortSuf(t, s, slen, 4, - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ - 484 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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]’ - 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -blockwise_sa.h:477:19: required from here - 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 478 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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]’ - 1166 | bucketSortSufDcU8(host1, host, hlen, s, slen, dc, - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1167 | (uint8_t)hi, begin, end, depth, sanityCheck); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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]’ - 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -blockwise_sa.h:477:19: required from here - 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 478 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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]’ - 1067 | selectionSortSufDcU8(host1, host, hlen, s, slen, dc, hi, - | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1068 | begin, end, depth, sanityCheck); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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]’ - 1166 | bucketSortSufDcU8(host1, host, hlen, s, slen, dc, - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1167 | (uint8_t)hi, begin, end, depth, sanityCheck); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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]’ - 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -blockwise_sa.h:477:19: required from here - 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 478 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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.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++/14/memory:78, - from gfm.h:28: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -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] -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; - | ^~~~~~~~~~~~~~ -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++/14/memory:78, - from gfm.h:28: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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: -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 - 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 478 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 - 483 | mkeyQSortSuf(t, s, slen, 4, - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ - 484 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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]’ - 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -blockwise_sa.h:477:19: required from here - 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 478 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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]’ - 1166 | bucketSortSufDcU8(host1, host, hlen, s, slen, dc, - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1167 | (uint8_t)hi, begin, end, depth, sanityCheck); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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]’ - 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -blockwise_sa.h:477:19: required from here - 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 478 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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]’ - 1067 | selectionSortSufDcU8(host1, host, hlen, s, slen, dc, hi, - | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1068 | begin, end, depth, sanityCheck); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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]’ - 1166 | bucketSortSufDcU8(host1, host, hlen, s, slen, dc, - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1167 | (uint8_t)hi, begin, end, depth, sanityCheck); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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]’ - 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -blockwise_sa.h:477:19: required from here - 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 478 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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); - | ^~~~~~~~ -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ --fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"09 July 2024\"" -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 -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ --I. -I third_party \ --o hisat2-align-l hisat2.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 qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat2_main.cpp \ --lpthread -Wl,-z,relro -Wl,-z,now -In file included from gfm.h:43, - from hgfm.h:24, - from hisat2.cpp:33: -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++/14/memory:78, - from gfm.h:28: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -/usr/bin/g++ -O3 -funroll-loops -g3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 \ --DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ --fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"09 July 2024\"" -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 -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DHISAT2_INSPECT_MAIN -Wall \ --I. -I third_party -I . \ --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 -In file included from aligner_sw.h:76, - from aligner_sw_driver.h:86, - from hi_aligner.h:42, - from spliced_aligner.h:23, - from hisat2.cpp:46: -aligner_sw_nuc.h: At global scope: -aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 191 | NBest() { nelt_ = nbest_ = n_ = 0; } - | ^ -aligner_sw_nuc.h:191:17: note: remove the ‘< >’ -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++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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( - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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: -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 - 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 478 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 - 483 | mkeyQSortSuf(t, s, slen, 4, - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ - 484 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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); - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -hi_aligner.h: In instantiation of ‘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 - 3537 | int ret = splicedAligner.go( - | ~~~~~~~~~~~~~~~~~^ - 3538 | sc, - | ~~~ - 3539 | pepol, - | ~~~~~~ - 3540 | *multiseed_tpol, - | ~~~~~~~~~~~~~~~~ - 3541 | *gpol, - | ~~~~~~ - 3542 | gfm, - | ~~~~ - 3543 | rgfm, - | ~~~~~ - 3544 | *altdb, - | ~~~~~~~ - 3545 | *repeatdb, - | ~~~~~~~~~~ - 3546 | *raltdb, - | ~~~~~~~~ - 3547 | ref, - | ~~~~ - 3548 | rref, - | ~~~~~ - 3549 | sw, - | ~~~ - 3550 | *ssdb, - | ~~~~~~ - 3551 | wlm, - | ~~~~ - 3552 | prm, - | ~~~~ - 3553 | swmSeed, - | ~~~~~~~~ - 3554 | him, - | ~~~~ - 3555 | rnd, - | ~~~~ - 3556 | msinkwrap); - | ~~~~~~~~~~ -hi_aligner.h:4385:84: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘const THitInt’ {aka ‘const long long int’} [-Wsign-compare] - 4385 | if(sink.bestPair() >= estScore && sink.numBestPair().first > rp.khits) - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -hi_aligner.h:4404:55: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘TRefId’ {aka ‘long long int’} [-Wsign-compare] - 4404 | if(positions[p].first.tid != res.refid()) continue; - | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -hi_aligner.h:4405:63: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘TRefOff’ {aka ‘long long int’} [-Wsign-compare] - 4405 | if(positions[p].first.toff + 1000 < res.refoff() || - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -hi_aligner.h:4406:52: warning: comparison of integer expressions of different signedness: ‘TRefOff’ {aka ‘long long int’} and ‘long long unsigned int’ [-Wsign-compare] - 4406 | res.refoff() + 1000 < positions[p].first.toff) continue; - | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -hi_aligner.h:4407:88: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘const THitInt’ {aka ‘const long long int’} [-Wsign-compare] - 4407 | if(sink.bestPair() >= estScore && sink.numBestPair().first > rp.khits) - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -hi_aligner.h:4489:92: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘const THitInt’ {aka ‘const long long int’} [-Wsign-compare] - 4489 | if(sink.bestPair() >= estScore && sink.numBestPair().first > rp.khits) - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -hi_aligner.h:4578:69: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘const THitInt’ {aka ‘const long long int’} [-Wsign-compare] - 4578 | align2repeat = (numBestPair == 0 || numBestPair > rp.khits); - | ~~~~~~~~~~~~^~~~~~~~~~ -hi_aligner.h:4584:83: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘const THitInt’ {aka ‘const long long int’} [-Wsign-compare] - 4584 | align2repeat = (rs->size() == 0 || sink.numBestUnp(rdi).first > rp.khits); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -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) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -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]’ - 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -blockwise_sa.h:477:19: required from here - 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 478 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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); - | ^~~~~~~~ -hi_aligner.h: In instantiation of ‘bool HI_Aligner::pairReads(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, WalkMetrics&, PerReadMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’: -hi_aligner.h:4088:17: 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]’ - 4088 | pairReads(sc, pepol, tpol, gpol, gfm, altdb, repeatdb, ref, wlm, prm, him, rnd, sink); - | ^~~~~~~~~ -hisat2.cpp:3537:48: required from here - 3537 | int ret = splicedAligner.go( - | ~~~~~~~~~~~~~~~~~^ - 3538 | sc, - | ~~~ - 3539 | pepol, - | ~~~~~~ - 3540 | *multiseed_tpol, - | ~~~~~~~~~~~~~~~~ - 3541 | *gpol, - | ~~~~~~ - 3542 | gfm, - | ~~~~ - 3543 | rgfm, - | ~~~~~ - 3544 | *altdb, - | ~~~~~~~ - 3545 | *repeatdb, - | ~~~~~~~~~~ - 3546 | *raltdb, - | ~~~~~~~~ - 3547 | ref, - | ~~~~ - 3548 | rref, - | ~~~~~ - 3549 | sw, - | ~~~ - 3550 | *ssdb, - | ~~~~~~ - 3551 | wlm, - | ~~~~ - 3552 | prm, - | ~~~~ - 3553 | swmSeed, - | ~~~~~~~~ - 3554 | him, - | ~~~~ - 3555 | rnd, - | ~~~~ - 3556 | msinkwrap); - | ~~~~~~~~~~ -hi_aligner.h:5990:51: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘TRefOff’ {aka ‘long long int’} [-Wsign-compare] - 5990 | if(_repeatConcordant[r].first == left.off() && - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -hi_aligner.h:5991:52: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘TRefOff’ {aka ‘long long int’} [-Wsign-compare] - 5991 | _repeatConcordant[r].second == left2.off()) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -hi_aligner.h: In instantiation of ‘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]’ - 4107 | mate_found |= alignMate( - | ^~~~~~~~~ -hisat2.cpp:3537:48: required from here - 3537 | int ret = splicedAligner.go( - | ~~~~~~~~~~~~~~~~~^ - 3538 | sc, - | ~~~ - 3539 | pepol, - | ~~~~~~ - 3540 | *multiseed_tpol, - | ~~~~~~~~~~~~~~~~ - 3541 | *gpol, - | ~~~~~~ - 3542 | gfm, - | ~~~~ - 3543 | rgfm, - | ~~~~~ - 3544 | *altdb, - | ~~~~~~~ - 3545 | *repeatdb, - | ~~~~~~~~~~ - 3546 | *raltdb, - | ~~~~~~~~ - 3547 | ref, - | ~~~~ - 3548 | rref, - | ~~~~~ - 3549 | sw, - | ~~~ - 3550 | *ssdb, - | ~~~~~~ - 3551 | wlm, - | ~~~~ - 3552 | prm, - | ~~~~ - 3553 | swmSeed, - | ~~~~~~~~ - 3554 | him, - | ~~~~ - 3555 | rnd, - | ~~~~ - 3556 | msinkwrap); - | ~~~~~~~~~~ -hi_aligner.h:5661:33: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘const THitInt’ {aka ‘const long long int’} [-Wsign-compare] - 5661 | if(nelt > 0 && nelt <= rp.kseeds && hitlen > max_hitlen) { - | ~~~~~^~~~~~~~~~~~ -hi_aligner.h:5688:65: warning: comparison of integer expressions of different signedness: ‘TRefOff’ {aka ‘long long int’} and ‘long long unsigned int’ [-Wsign-compare] - 5688 | if(coord.off() + pepol.maxFragLen() * 2 < toff || toff + pepol.maxFragLen() * 2 < coord.off()) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ -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 = 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]’ - 3815 | gfm.checkOrigs(os, false); - | ~~~~~~~~~~~~~~^~~~~~~~~~~ -hisat2.cpp:4351:26: required from here - 4351 | driver >("DNA", bt2index, outfile); - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -gfm.h:6935:13: warning: variable ‘lastorig’ set but not used [-Wunused-but-set-variable] - 6935 | int lastorig = -1; - | ^~~~~~~~ -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]’ - 1166 | bucketSortSufDcU8(host1, host, hlen, s, slen, dc, - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1167 | (uint8_t)hi, begin, end, depth, sanityCheck); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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]’ - 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -blockwise_sa.h:477:19: required from here - 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 478 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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: In instantiation of ‘index_t HI_Aligner::getAnchorHits(const GFM&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const ALTDB&, const RepeatDB&, const BitPairReference&, RandomSource&, index_t, bool, EList >&, index_t, SharedTempVars&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool) [with index_t = long long unsigned int; local_index_t = short unsigned int]’: -hi_aligner.h:5525:23: required from ‘bool HI_Aligner::align(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&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ - 5525 | index_t numHits = getAnchorHits(gfm, - | ^~~~~~~~~~~~~ -hi_aligner.h:4080:31: 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]’ - 4080 | found[rdi][fwi] = align(sc, pepol, tpol, gpol, gfm, altdb, repeatdb, ref, swa, ssdb, rdi, fw, wlm, prm, swm, him, rnd, sink); - | ^~~~~ -hisat2.cpp:3537:48: required from here - 3537 | int ret = splicedAligner.go( - | ~~~~~~~~~~~~~~~~~^ - 3538 | sc, - | ~~~ - 3539 | pepol, - | ~~~~~~ - 3540 | *multiseed_tpol, - | ~~~~~~~~~~~~~~~~ - 3541 | *gpol, - | ~~~~~~ - 3542 | gfm, - | ~~~~ - 3543 | rgfm, - | ~~~~~ - 3544 | *altdb, - | ~~~~~~~ - 3545 | *repeatdb, - | ~~~~~~~~~~ - 3546 | *raltdb, - | ~~~~~~~~ - 3547 | ref, - | ~~~~ - 3548 | rref, - | ~~~~~ - 3549 | sw, - | ~~~ - 3550 | *ssdb, - | ~~~~~~ - 3551 | wlm, - | ~~~~ - 3552 | prm, - | ~~~~ - 3553 | swmSeed, - | ~~~~~~~~ - 3554 | him, - | ~~~~ - 3555 | rnd, - | ~~~~ - 3556 | msinkwrap); - | ~~~~~~~~~~ -hi_aligner.h:5150:32: warning: comparison of integer expressions of different signedness: ‘TRefId’ {aka ‘long long int’} and ‘long long unsigned int’ [-Wsign-compare] - 5150 | if(coord.ref() == numeric_limits::max()) - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -hi_aligner.h: In instantiation of ‘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]’ - 5692 | GenomeHit::adjustWithALT( - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ - 5693 | hitoff - hitlen + 1, - | ~~~~~~~~~~~~~~~~~~~~ - 5694 | hitlen, - | ~~~~~~~ - 5695 | coord, - | ~~~~~~ - 5696 | _sharedVars, - | ~~~~~~~~~~~~ - 5697 | _genomeHits, - | ~~~~~~~~~~~~ - 5698 | *this->_rds[ordi], - | ~~~~~~~~~~~~~~~~~~ - 5699 | gfm, - | ~~~~ - 5700 | altdb, - | ~~~~~~ - 5701 | ref, - | ~~~~ - 5702 | gpol); - | ~~~~~ -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]’ - 4107 | mate_found |= alignMate( - | ^~~~~~~~~ -hisat2.cpp:3537:48: required from here - 3537 | int ret = splicedAligner.go( - | ~~~~~~~~~~~~~~~~~^ - 3538 | sc, - | ~~~ - 3539 | pepol, - | ~~~~~~ - 3540 | *multiseed_tpol, - | ~~~~~~~~~~~~~~~~ - 3541 | *gpol, - | ~~~~~~ - 3542 | gfm, - | ~~~~ - 3543 | rgfm, - | ~~~~~ - 3544 | *altdb, - | ~~~~~~~ - 3545 | *repeatdb, - | ~~~~~~~~~~ - 3546 | *raltdb, - | ~~~~~~~~ - 3547 | ref, - | ~~~~ - 3548 | rref, - | ~~~~~ - 3549 | sw, - | ~~~ - 3550 | *ssdb, - | ~~~~~~ - 3551 | wlm, - | ~~~~ - 3552 | prm, - | ~~~~ - 3553 | swmSeed, - | ~~~~~~~~ - 3554 | him, - | ~~~~ - 3555 | rnd, - | ~~~~ - 3556 | msinkwrap); - | ~~~~~~~~~~ -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); - | ~~~~~~~~~~~~~~~~~~^~~~~~~~ -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]’ - 1067 | selectionSortSufDcU8(host1, host, hlen, s, slen, dc, hi, - | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1068 | begin, end, depth, sanityCheck); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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]’ - 1166 | bucketSortSufDcU8(host1, host, hlen, s, slen, dc, - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1167 | (uint8_t)hi, begin, end, depth, sanityCheck); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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]’ - 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -blockwise_sa.h:477:19: required from here - 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 478 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 aligner_seed2.h:109, from aligner_driver.h:78, from hi_aligner.h:41: @@ -4225,6 +3849,13 @@ 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 + 331 | int64_t SplicedAligner::hybridSearch_recur( + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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: 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 331 | int64_t SplicedAligner::hybridSearch_recur( @@ -4276,295 +3907,6 @@ 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 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); - | ^~~~~~~~~~ -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++/14/memory:78, - from gfm.h:28: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -In file included from hgfm.h:24, - from hisat2_inspect.cpp:27: -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++/14/memory:78, - from gfm.h:28: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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++/14/memory:78, - from gfm.h:28: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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 edit.h:26, - from edit.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); - | ^~~~~~~~~~ -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++/14/memory:78, - from gfm.h:28: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -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++/14/memory:78, - from gfm.h:28: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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++/14/memory:78, - from gfm.h:28: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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))) { \ - | ~~~~^~~~~~ -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, - 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++/14/memory:78, - from gfm.h:28: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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++/14/memory:78, - from gfm.h:28: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -In file included from aligner_sw.h:76: -aligner_sw_nuc.h: At global scope: -aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 191 | NBest() { nelt_ = nbest_ = n_ = 0; } - | ^ -aligner_sw_nuc.h:191:17: note: remove the ‘< >’ -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++/14/memory:78, - from gfm.h:28: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 \ --DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ --fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"09 July 2024\"" -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 -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 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++/14/memory:78, - from gfm.h:28: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -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()); - | ^~~~~~~~ -In file included from /usr/include/c++/14/memory:78, - from gfm.h:28: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ In file included from ds.h:32, from sequence_io.h:28, from multikey_qsort.h:24, @@ -4673,94 +4015,23 @@ 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 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++/14/memory:78, - from gfm.h:28: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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_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++/14/memory:78, - from gfm.h:28: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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_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++/14/memory:78, - from gfm.h:28: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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_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++/14/memory:78, - from gfm.h:28: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -In file included from aligner_sw.h:76: -aligner_sw_nuc.h: At global scope: -aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 191 | NBest() { nelt_ = nbest_ = n_ = 0; } - | ^ -aligner_sw_nuc.h:191:17: note: remove the ‘< >’ +In file included from /usr/include/c++/14/set:62, + from gfm.h:32: +/usr/include/c++/14/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long long unsigned int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: +/usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 + 2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/map:63, + from repeat.h:26, + from gfm.h:59: +/usr/include/c++/14/bits/stl_map.h: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long unsigned int; _Tp = long long unsigned int; _Compare = std::less; _Alloc = std::allocator >]’: +/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 + 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 514 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 515 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, @@ -4913,6 +4184,15 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 edit.h:26, + from edit.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); + | ^~~~~~~~~~ In file included from alphabet.h:27, from gfm.h:40: alt.h: In member function ‘bool ALT::repOk() const’: @@ -4922,168 +4202,8 @@ 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()); - | ^~~~~~~~ -In file included from /usr/include/c++/14/memory:78, - from gfm.h:28: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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_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++/14/memory:78, - from gfm.h:28: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -In file included from aligner_sw.h:76: -aligner_sw_nuc.h: At global scope: -aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 191 | NBest() { nelt_ = nbest_ = n_ = 0; } - | ^ -aligner_sw_nuc.h:191:17: note: remove the ‘< >’ -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 - 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 478 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 - 483 | mkeyQSortSuf(t, s, slen, 4, - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ - 484 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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]’ - 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -blockwise_sa.h:477:19: required from here - 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 478 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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]’ - 1166 | bucketSortSufDcU8(host1, host, hlen, s, slen, dc, - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1167 | (uint8_t)hi, begin, end, depth, sanityCheck); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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]’ - 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -blockwise_sa.h:477:19: required from here - 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 478 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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]’ - 1067 | selectionSortSufDcU8(host1, host, hlen, s, slen, dc, hi, - | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1068 | begin, end, depth, sanityCheck); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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]’ - 1166 | bucketSortSufDcU8(host1, host, hlen, s, slen, dc, - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1167 | (uint8_t)hi, begin, end, depth, sanityCheck); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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]’ - 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -blockwise_sa.h:477:19: required from here - 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 478 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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: -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 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()); @@ -5099,123 +4219,6 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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 - 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 478 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 - 483 | mkeyQSortSuf(t, s, slen, 4, - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ - 484 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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]’ - 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -blockwise_sa.h:477:19: required from here - 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 478 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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]’ - 1166 | bucketSortSufDcU8(host1, host, hlen, s, slen, dc, - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1167 | (uint8_t)hi, begin, end, depth, sanityCheck); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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]’ - 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -blockwise_sa.h:477:19: required from here - 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 478 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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]’ - 1067 | selectionSortSufDcU8(host1, host, hlen, s, slen, dc, hi, - | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1068 | begin, end, depth, sanityCheck); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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]’ - 1166 | bucketSortSufDcU8(host1, host, hlen, s, slen, dc, - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1167 | (uint8_t)hi, begin, end, depth, sanityCheck); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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]’ - 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -blockwise_sa.h:477:19: required from here - 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 478 | this->verbose(), this->sanityCheck()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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()); @@ -5339,12 +4342,20 @@ 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, - 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: +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); + | ^~~~~~~~~~ +/usr/include/c++/14/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple::CompositeNodeIDs&>, std::tuple<>}; _Key = RefGraph::CompositeNodeIDs; _Val = std::pair::CompositeNodeIDs, long long unsigned int>; _KeyOfValue = std::_Select1st::CompositeNodeIDs, long long unsigned int> >; _Compare = std::less::CompositeNodeIDs>; _Alloc = std::allocator::CompositeNodeIDs, long long unsigned int> >]’: +/usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type ‘std::_Rb_tree::CompositeNodeIDs, std::pair::CompositeNodeIDs, long long unsigned int>, std::_Select1st::CompositeNodeIDs, long long unsigned int> >, std::less::CompositeNodeIDs>, std::allocator::CompositeNodeIDs, long long unsigned int> > >::const_iterator’ changed in GCC 7.1 + 2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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()); @@ -5360,19 +4371,6 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -In file included from aligner_sw.h:76: -aligner_sw_nuc.h: At global scope: -aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 191 | NBest() { nelt_ = nbest_ = n_ = 0; } - | ^ -aligner_sw_nuc.h:191:17: note: remove the ‘< >’ -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 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"09 July 2024\"" -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 -fstack-clash-protection -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I. -I third_party \ @@ -5520,6 +4518,31 @@ 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: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; + | ^~~ 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]’ 1098 | this->qsort(bucket); @@ -5745,39 +4768,102 @@ 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 ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = RefGraph::CompositeNodeIDs; _Tp = long long unsigned int; _Compare = std::less::CompositeNodeIDs>; _Alloc = std::allocator::CompositeNodeIDs, long long unsigned int> >]’, + inlined from ‘static void RefGraph::reverseDeterminize(EList&, EList&, index_t&, index_t) [with index_t = long long unsigned int]’ at gbwt_graph.h:1321:14: +/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree::CompositeNodeIDs, std::pair::CompositeNodeIDs, long long unsigned int>, std::_Select1st::CompositeNodeIDs, long long unsigned int> >, std::less::CompositeNodeIDs>, std::allocator::CompositeNodeIDs, long long unsigned int> > >::const_iterator’ changed in GCC 7.1 + 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 514 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 515 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = RefGraph::CompositeNodeIDs; _Tp = long long unsigned int; _Compare = std::less::CompositeNodeIDs>; _Alloc = std::allocator::CompositeNodeIDs, long long unsigned int> >]’, + inlined from ‘static void RefGraph::reverseDeterminize(EList&, EList&, index_t&, index_t) [with index_t = long long unsigned int]’ at gbwt_graph.h:1387:26: +/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree::CompositeNodeIDs, std::pair::CompositeNodeIDs, long long unsigned int>, std::_Select1st::CompositeNodeIDs, long long unsigned int> >, std::less::CompositeNodeIDs>, std::allocator::CompositeNodeIDs, long long unsigned int> > >::const_iterator’ changed in GCC 7.1 + 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 514 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 515 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +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 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 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 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++/14/memory:78, - from gfm.h:28: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -In file included from aligner_sw.h:76: -aligner_sw_nuc.h: At global scope: -aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 191 | NBest() { nelt_ = nbest_ = n_ = 0; } - | ^ -aligner_sw_nuc.h:191:17: note: remove the ‘< >’ -In file included from splice_site.h:34, - from edit.h:30, - from aligner_result.h:30, - from aligner_seed2.h:102, - from aligner_driver.h:78, - from aligner_driver.cpp:20: + 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()); @@ -5793,9 +4879,49 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -In file included from splice_site.h:34, - from edit.h:30, - from splice_site.cpp:20: +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 member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long unsigned int; _Tp = long long unsigned int; _Compare = std::less; _Alloc = std::allocator >]’, + 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:2280:40: +/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 + 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 514 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 515 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long unsigned int; _Tp = long long unsigned int; _Compare = std::less; _Alloc = std::allocator >]’, + 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:2316:75: +/usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 + 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 514 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 515 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +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()); @@ -5811,21 +4937,13 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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 - 722 | _exons.push_back_array(exons.begin(), exons.size()); - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 { - | ^~~~ +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, @@ -5838,19 +4956,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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: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] 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()); @@ -5895,21 +5000,6 @@ 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); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -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++/14/memory:78, - from gfm.h:28: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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]’ 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); @@ -5988,9 +5078,36 @@ 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++/14/memory:78, + from gfm.h:28: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ In file included from ds.h:32, - from aligner_cache.h:59, - from aligner_seed.cpp:20: + 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 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, @@ -6003,8 +5120,6 @@ 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); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -6097,21 +5212,9 @@ 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] -In file included from gfm.h:43, 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 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, @@ -6135,26 +5238,8 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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++/14/memory:78, - from gfm.h:28: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | 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 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, @@ -6167,6 +5252,8 @@ 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); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -6258,9 +5345,43 @@ 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]’: +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++/14/memory:78, + from gfm.h:28: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ In file included from ds.h:32, - from random_util.h:25, - from aligner_seed2.h:101: + 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 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, @@ -6273,8 +5394,6 @@ 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); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -6376,10 +5495,7 @@ 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_sw.cpp:25: + 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, @@ -6403,15 +5519,8 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -In file included from aligner_sw.h:76: -aligner_sw_nuc.h: At global scope: -aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 191 | NBest() { nelt_ = nbest_ = n_ = 0; } - | ^ -aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from ds.h:32, - from read.h:25, - from aligner_result.h:27: + 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 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, @@ -6521,7 +5630,9 @@ 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, @@ -6546,9 +5657,8 @@ 59 | 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 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 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, @@ -6654,13 +5764,26 @@ 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, +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 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++/14/memory:78, + from gfm.h:28: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +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, @@ -6685,8 +5808,10 @@ 59 | 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 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, @@ -6699,8 +5824,6 @@ 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); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -6792,13 +5915,41 @@ 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.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++/14/memory:78, + from gfm.h:28: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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 aligner_result.h:30, - from unique.h:38, - from aln_sink.h:25, - from aln_sink.cpp:22: + 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, @@ -6823,8 +5974,9 @@ 59 | template class auto_ptr; | ^~~~~~~~ In file included from ds.h:32, - from read.h:25, - from aln_sink.h:24: + 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 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, @@ -6934,8 +6086,9 @@ 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_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, @@ -6959,6 +6112,12 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ +In file included from aligner_sw.h:76: +aligner_sw_nuc.h: At global scope: +aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 191 | NBest() { nelt_ = nbest_ = n_ = 0; } + | ^ +aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from ds.h:32, from read.h:25, from aligner_result.h:27: @@ -7071,7 +6230,9 @@ 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_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, @@ -7095,10 +6256,28 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ +In file included from aligner_sw.h:76: +aligner_sw_nuc.h: At global scope: +aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 191 | NBest() { nelt_ = nbest_ = n_ = 0; } + | ^ +aligner_sw_nuc.h:191:17: note: remove the ‘< >’ +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 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 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, @@ -7204,21 +6383,6 @@ 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 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: -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()); @@ -7235,8 +6399,8 @@ 59 | template class auto_ptr; | ^~~~~~~~ In file included from ds.h:32, - from read.h:25, - from aligner_result.h:27: + 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 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, @@ -7346,9 +6510,8 @@ 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: + 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, @@ -7372,15 +6535,9 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -In file included from aligner_sw.h:76: -aligner_sw_nuc.h: At global scope: -aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 191 | NBest() { nelt_ = nbest_ = n_ = 0; } - | ^ -aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from ds.h:32, - from read.h:25, - from aligner_result.h:27: + 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 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, @@ -7429,6 +6586,25 @@ 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 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++/14/memory:78, + from gfm.h:28: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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]’ 1166 | bucketSortSufDcU8(host1, host, hlen, s, slen, dc, @@ -7492,7 +6668,7 @@ 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_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, @@ -7630,12 +6806,73 @@ 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_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++/14/memory:78, + from gfm.h:28: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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++/14/memory:78, + from gfm.h:28: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +In file included from aligner_sw.h:76: +aligner_sw_nuc.h: At global scope: +aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 191 | NBest() { nelt_ = nbest_ = n_ = 0; } + | ^ +aligner_sw_nuc.h:191:17: note: remove the ‘< >’ +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: +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_swsse.cpp:21: + 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, @@ -7660,8 +6897,9 @@ 59 | template class auto_ptr; | ^~~~~~~~ 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 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, @@ -7767,21 +7005,6 @@ 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 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: -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()); @@ -7911,13 +7134,32 @@ 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_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++/14/memory:78, + from gfm.h:28: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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: + 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, @@ -8059,9 +7301,9 @@ 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 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, @@ -8085,15 +7327,9 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -In file included from aligner_sw.h:76: -aligner_sw_nuc.h: At global scope: -aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 191 | NBest() { nelt_ = nbest_ = n_ = 0; } - | ^ -aligner_sw_nuc.h:191:17: note: remove the ‘< >’ 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 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, @@ -8121,21 +7357,6 @@ 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); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -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: -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 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]’ 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); @@ -8214,6 +7435,41 @@ 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++/14/memory:78, + from gfm.h:28: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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 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()); @@ -8229,12 +7485,6 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -In file included from aligner_sw.h:76: -aligner_sw_nuc.h: At global scope: -aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 191 | NBest() { nelt_ = nbest_ = n_ = 0; } - | ^ -aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from ds.h:32, from read.h:25, from aligner_result.h:27: @@ -8343,13 +7593,33 @@ 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 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++/14/memory:78, + from gfm.h:28: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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_loc_u8.cpp:56: + 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, @@ -8373,12 +7643,6 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -In file included from aligner_sw.h:76: -aligner_sw_nuc.h: At global scope: -aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 191 | NBest() { nelt_ = nbest_ = n_ = 0; } - | ^ -aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from ds.h:32, from read.h:25, from aligner_result.h:27: @@ -8487,6 +7751,27 @@ 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 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++/14/memory:78, + from gfm.h:28: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, @@ -8631,13 +7916,32 @@ 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_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++/14/memory:78, + from gfm.h:28: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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: + 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, @@ -8661,12 +7965,6 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -In file included from aligner_sw.h:76: -aligner_sw_nuc.h: At global scope: -aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 191 | NBest() { nelt_ = nbest_ = n_ = 0; } - | ^ -aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from ds.h:32, from read.h:25, from aligner_result.h:27: @@ -8912,13 +8210,40 @@ 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++/14/memory:78, + from gfm.h:28: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +In file included from aligner_sw.h:76: +aligner_sw_nuc.h: At global scope: +aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 191 | NBest() { nelt_ = nbest_ = n_ = 0; } + | ^ +aligner_sw_nuc.h:191:17: note: remove the ‘< >’ 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 bit_packed_array.cpp:24: + 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, @@ -9060,9 +8385,9 @@ from splice_site.h:34, from edit.h:30, from aligner_result.h:30, - from aligner_seed2.h:102, - from aligner_driver.h:78, - from aligner_driver.cpp:20: + from aligner_sw_common.h:23, + from aligner_sw.h:75, + 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, @@ -9086,24 +8411,15 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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 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 aligner_sw.h:76: +aligner_sw_nuc.h: At global scope: +aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 191 | NBest() { nelt_ = nbest_ = n_ = 0; } + | ^ +aligner_sw_nuc.h:191:17: note: remove the ‘< >’ 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 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, @@ -9209,6 +8525,21 @@ 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 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] 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()); @@ -9449,6 +8780,668 @@ 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++/14/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++/14/ostream:216:25: warning: ‘pos_in_chr’ may be used uninitialized [-Wmaybe-uninitialized] + 216 | { 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: +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++/14/memory:78, + from gfm.h:28: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +In file included from aligner_sw.h:76: +aligner_sw_nuc.h: At global scope: +aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 191 | NBest() { nelt_ = nbest_ = n_ = 0; } + | ^ +aligner_sw_nuc.h:191:17: note: remove the ‘< >’ +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 + 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 478 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 + 483 | mkeyQSortSuf(t, s, slen, 4, + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ + 484 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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]’ + 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +blockwise_sa.h:477:19: required from here + 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 478 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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]’ + 1166 | bucketSortSufDcU8(host1, host, hlen, s, slen, dc, + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1167 | (uint8_t)hi, begin, end, depth, sanityCheck); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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]’ + 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +blockwise_sa.h:477:19: required from here + 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 478 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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]’ + 1067 | selectionSortSufDcU8(host1, host, hlen, s, slen, dc, hi, + | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1068 | begin, end, depth, sanityCheck); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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]’ + 1166 | bucketSortSufDcU8(host1, host, hlen, s, slen, dc, + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1167 | (uint8_t)hi, begin, end, depth, sanityCheck); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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]’ + 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +blockwise_sa.h:477:19: required from here + 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 478 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 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++/14/memory:78, + from gfm.h:28: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +In file included from aligner_sw.h:76: +aligner_sw_nuc.h: At global scope: +aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 191 | NBest() { nelt_ = nbest_ = n_ = 0; } + | ^ +aligner_sw_nuc.h:191:17: note: remove the ‘< >’ +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()); + | ^~~~~~~~ +In file included from /usr/include/c++/14/memory:78, + from gfm.h:28: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +In file included from aligner_sw.h:76: +aligner_sw_nuc.h: At global scope: +aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 191 | NBest() { nelt_ = nbest_ = n_ = 0; } + | ^ +aligner_sw_nuc.h:191:17: note: remove the ‘< >’ +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 + 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 478 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 + 483 | mkeyQSortSuf(t, s, slen, 4, + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ + 484 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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]’ + 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +blockwise_sa.h:477:19: required from here + 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 478 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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]’ + 1166 | bucketSortSufDcU8(host1, host, hlen, s, slen, dc, + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1167 | (uint8_t)hi, begin, end, depth, sanityCheck); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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]’ + 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +blockwise_sa.h:477:19: required from here + 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 478 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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]’ + 1067 | selectionSortSufDcU8(host1, host, hlen, s, slen, dc, hi, + | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1068 | begin, end, depth, sanityCheck); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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]’ + 1166 | bucketSortSufDcU8(host1, host, hlen, s, slen, dc, + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1167 | (uint8_t)hi, begin, end, depth, sanityCheck); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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]’ + 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +blockwise_sa.h:477:19: required from here + 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 478 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 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++/14/memory:78, + from gfm.h:28: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +In file included from aligner_sw.h:76: +aligner_sw_nuc.h: At global scope: +aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 191 | NBest() { nelt_ = nbest_ = n_ = 0; } + | ^ +aligner_sw_nuc.h:191:17: note: remove the ‘< >’ +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()); + | ^~~~~~~~ +In file included from /usr/include/c++/14/memory:78, + from gfm.h:28: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +In file included from aligner_sw.h:76: +aligner_sw_nuc.h: At global scope: +aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 191 | NBest() { nelt_ = nbest_ = n_ = 0; } + | ^ +aligner_sw_nuc.h:191:17: note: remove the ‘< >’ +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 + 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 478 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 + 483 | mkeyQSortSuf(t, s, slen, 4, + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ + 484 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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]’ + 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +blockwise_sa.h:477:19: required from here + 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 478 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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]’ + 1166 | bucketSortSufDcU8(host1, host, hlen, s, slen, dc, + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1167 | (uint8_t)hi, begin, end, depth, sanityCheck); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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]’ + 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +blockwise_sa.h:477:19: required from here + 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 478 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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]’ + 1067 | selectionSortSufDcU8(host1, host, hlen, s, slen, dc, hi, + | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1068 | begin, end, depth, sanityCheck); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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]’ + 1166 | bucketSortSufDcU8(host1, host, hlen, s, slen, dc, + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1167 | (uint8_t)hi, begin, end, depth, sanityCheck); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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]’ + 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +blockwise_sa.h:477:19: required from here + 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 478 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 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++/14/memory:78, + from gfm.h:28: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +In file included from aligner_sw.h:76: +aligner_sw_nuc.h: At global scope: +aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 191 | NBest() { nelt_ = nbest_ = n_ = 0; } + | ^ +aligner_sw_nuc.h:191:17: note: remove the ‘< >’ +In file included from gfm.h:43, + from splice_site.h:34, + from edit.h:30, + from aligner_result.h:30, + from aligner_seed2.h:102, + from aligner_driver.h:78, + from aligner_driver.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()); + | ^~~~~~~~ +In file included from /usr/include/c++/14/memory:78, + from gfm.h:28: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +In file included from ds.h:32, + 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 + 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 478 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 + 483 | mkeyQSortSuf(t, s, slen, 4, + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ + 484 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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]’ + 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +blockwise_sa.h:477:19: required from here + 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 478 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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]’ + 1166 | bucketSortSufDcU8(host1, host, hlen, s, slen, dc, + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1167 | (uint8_t)hi, begin, end, depth, sanityCheck); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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]’ + 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +blockwise_sa.h:477:19: required from here + 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 478 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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]’ + 1067 | selectionSortSufDcU8(host1, host, hlen, s, slen, dc, hi, + | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1068 | begin, end, depth, sanityCheck); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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]’ + 1166 | bucketSortSufDcU8(host1, host, hlen, s, slen, dc, + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1167 | (uint8_t)hi, begin, end, depth, sanityCheck); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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]’ + 763 | mkeyQSortSufDcU8(host1, host, hlen, s, slen, dc, hi, 0, slen, 0, sanityCheck); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +blockwise_sa.h:477:19: required from here + 477 | mkeyQSortSufDcU8(t, t, len, s, slen, *_dc.get(), 4, + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 478 | this->verbose(), this->sanityCheck()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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, @@ -9461,6 +9454,27 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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_seed2.h:102, + from aligner_driver.h:78, + from aligner_driver.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++/14/memory:78, + from gfm.h:28: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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()); @@ -9597,17 +9611,39 @@ 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++/14/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++/14/ostream:216:25: warning: ‘pos_in_chr’ may be used uninitialized [-Wmaybe-uninitialized] - 216 | { 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 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++/14/memory:78, + from gfm.h:28: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | 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 + 722 | _exons.push_back_array(exons.begin(), exons.size()); + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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' \ @@ -9660,12 +9696,12 @@ diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged -dpkg-shlibdeps: warning: debian/hisat2/usr/bin/hisat2-align-l contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/hisat2/usr/bin/hisat2-align-s contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/hisat2/usr/bin/hisat2-build-s contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/hisat2/usr/bin/hisat2-inspect-l contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/hisat2/usr/bin/hisat2-inspect-s contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/hisat2/usr/bin/hisat2-align-l contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/hisat2/usr/bin/hisat2-build-l contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/hisat2/usr/bin/hisat2-build-s contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/hisat2/usr/bin/hisat2-align-s contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb debian/rules override_dh_gencontrol make[1]: Entering directory '/build/reproducible-path/hisat2-2.2.1' @@ -9674,8 +9710,8 @@ dh_md5sums dh_builddeb dpkg-deb: building package 'hisat2-dbgsym' in '../hisat2-dbgsym_2.2.1-5_armhf.deb'. -dpkg-deb: building package 'python3-hisat2' in '../python3-hisat2_2.2.1-5_all.deb'. dpkg-deb: building package 'hisat2' in '../hisat2_2.2.1-5_armhf.deb'. +dpkg-deb: building package 'python3-hisat2' in '../python3-hisat2_2.2.1-5_all.deb'. dpkg-genbuildinfo --build=binary -O../hisat2_2.2.1-5_armhf.buildinfo dpkg-genchanges --build=binary -O../hisat2_2.2.1-5_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -9683,12 +9719,14 @@ 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/13600/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/13600/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/11631 and its subdirectories -I: Current time: Thu Jan 30 13:51:52 -12 2025 -I: pbuilder-time-stamp: 1738288312 +I: removing directory /srv/workspace/pbuilder/13600 and its subdirectories +I: Current time: Fri Jan 31 16:22:13 +14 2025 +I: pbuilder-time-stamp: 1738290133