Diff of the two buildlogs: -- --- b1/build.log 2025-03-15 21:07:58.049323208 +0000 +++ b2/build.log 2025-03-15 21:11:17.280379987 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Mar 15 09:01:46 -12 2025 -I: pbuilder-time-stamp: 1742072506 +I: Current time: Sat Apr 18 17:31:01 +14 2026 +I: pbuilder-time-stamp: 1776483061 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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/1109181/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3802134/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +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 Apr 18 03:31 /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/3802134/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3802134/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='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + 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=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='99294e4a618b4f4588d7df325e3a8b1e' - 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='1109181' - PS1='# ' - PS2='> ' + INVOCATION_ID=c0c8802a1ae9474fbf37547f76cae900 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3802134 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.dXA6VozD/pbuilderrc_JBKW --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.dXA6VozD/b1 --logfile b1/build.log hisat2_2.2.1-5.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + 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.dXA6VozD/pbuilderrc_p9W8 --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.dXA6VozD/b2 --logfile b2/build.log hisat2_2.2.1-5.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.1.0-32-cloud-arm64 #1 SMP Debian 6.1.129-1 (2025-03-06) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-32-cloud-arm64 #1 SMP Debian 6.1.129-1 (2025-03-06) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1109181/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3802134/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 trixie/main arm64 libyaml-0-2 arm64 0.2.5-2 [49.2 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 pandoc-data all 3.1.11.1-3 [459 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 pandoc arm64 3.1.11.1+ds-2 [26.2 MB] -Fetched 53.9 MB in 1s (102 MB/s) +Fetched 53.9 MB in 0s (188 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 ... 19917 files and directories currently installed.) @@ -358,8 +390,8 @@ Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' -Local time is now: Sat Mar 15 21:02:21 UTC 2025. -Universal Time is now: Sat Mar 15 21:02:21 UTC 2025. +Local time is now: Sat Apr 18 03:31:18 UTC 2026. +Universal Time is now: Sat Apr 18 03:31:18 UTC 2026. 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/3802134/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/3802134/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 @@ -499,8 +535,82 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -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_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 hisat2_repeat.cpp:36: +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.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()); + | ^~~~~~~~ +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.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()); + | ^~~~~~~~ +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 hisat2_inspect.cpp:25: +alt.h: In member function ‘bool ALT::repOk() const’: +assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] + 227 | if(!((a) <= (b))) { \ + | ~~~~^~~~~~ +alt.h:180:13: note: in expansion of macro ‘assert_leq’ + 180 | assert_leq(fw, 1); + | ^~~~~~~~~~ +gfm.h: In instantiation of ‘void GFM::initFromVector(TStr&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, EList&, EList&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, const std::string&, bool, index_t, index_t, index_t, int, EList*, EList >*, uint32_t, bool) [with TStr = SString; index_t = long 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 unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ 1039 | initFromVector( | ~~~~~~~~~~~~~~~~~~~~^ 1040 | s, @@ -549,7 +659,7 @@ | ~~~~~ 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 unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = 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]’ @@ -667,126 +777,8 @@ 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.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()); - | ^~~~~~~~ -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 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; - | ^~~~~~~~ -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 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()); - | ^~~~~~~~ -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 hisat2_repeat.cpp:36: -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, - 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 ‘< >’ -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 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 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, @@ -835,7 +827,7 @@ | ~~~~~ 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 unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = 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]’ @@ -945,6 +937,67 @@ gfm.h:2167:33: warning: variable ‘template_len’ set but not used [-Wunused-but-set-variable] 2167 | index_t template_len = 0; | ^~~~~~~~~~~~ +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 aligner_sw.h:76, + from hisat2_repeat.cpp:37: +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 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 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 ‘< >’ +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()); @@ -971,6 +1024,39 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ +hisat2.cpp: In function ‘void parseOptions(int, const char**)’: +hisat2.cpp:1823:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 1823 | auto_ptr presets(new PresetsV0()); + | ^~~~~~~~ +/usr/include/c++/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; + | ^~~~~~~~ +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( @@ -978,23 +1064,6 @@ /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, - from hisat2_repeat.cpp:37: -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 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 ‘< >’ 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 = unsigned int; local_index_t = short unsigned int]’: hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ 4107 | mate_found |= alignMate( @@ -1053,6 +1122,309 @@ 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 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 unsigned int’ and ‘const THitInt’ {aka ‘const 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 unsigned int’ and ‘TRefId’ {aka ‘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 unsigned int’ and ‘TRefOff’ {aka ‘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 int’} and ‘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 unsigned int’ and ‘const THitInt’ {aka ‘const 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 unsigned int’ and ‘const THitInt’ {aka ‘const 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 unsigned int’ and ‘const THitInt’ {aka ‘const 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 unsigned int’ and ‘const THitInt’ {aka ‘const 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 unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] + 4614 | if(sink.numBestUnp(rdi).first > rp.khits) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +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 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 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 unsigned int’ and ‘TRefOff’ {aka ‘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 unsigned int’ and ‘TRefOff’ {aka ‘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 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 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 unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] + 5661 | if(nelt > 0 && nelt <= rp.kseeds && hitlen > max_hitlen) { + | ~~~~~^~~~~~~~~~~~ +hi_aligner.h:5688:105: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefOff’ {aka ‘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 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; + | ^~~~~~~~ +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 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 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 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 int’} and ‘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 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 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 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 int’} and ‘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: @@ -1354,13 +1726,6 @@ 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) { | ~~~~~~~~~~~^~~~~~~~~~~~~~ -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; - | ^~~~~~~~ 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); @@ -1658,342 +2023,6 @@ 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) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ -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; - | ^~~~~~~~ -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 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 unsigned int’ and ‘const THitInt’ {aka ‘const 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 unsigned int’ and ‘TRefId’ {aka ‘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 unsigned int’ and ‘TRefOff’ {aka ‘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 int’} and ‘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 unsigned int’ and ‘const THitInt’ {aka ‘const 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 unsigned int’ and ‘const THitInt’ {aka ‘const 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 unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] - 4578 | align2repeat = (numBestPair == 0 || numBestPair > rp.khits); - | ~~~~~~~~~~~~^~~~~~~~~~ -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 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; - | ^~~~~~~~~~~~~~~ -hi_aligner.h:4584:83: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const 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 unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] - 4614 | if(sink.numBestUnp(rdi).first > rp.khits) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -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 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 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 unsigned int’ and ‘TRefOff’ {aka ‘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 unsigned int’ and ‘TRefOff’ {aka ‘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 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 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 unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] - 5661 | if(nelt > 0 && nelt <= rp.kseeds && hitlen > max_hitlen) { - | ~~~~~^~~~~~~~~~~~ -hi_aligner.h:5688:105: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefOff’ {aka ‘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 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; - | ^~~~~~~~ -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 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 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 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 int’} and ‘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 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 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 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 int’} and ‘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: @@ -2592,6 +2621,13 @@ hi_aligner.h:2744:41: warning: comparison of integer expressions of different signedness: ‘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 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 unsigned int; local_index_t = short unsigned int; int64_t = long int]’: spliced_aligner.h:331:9: required from here 331 | int64_t SplicedAligner::hybridSearch_recur( @@ -2685,17 +2721,7 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -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: +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()); @@ -2711,6 +2737,13 @@ /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’: @@ -2720,7 +2753,17 @@ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ -In file included from gfm.cpp:21: +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()); @@ -2753,13 +2796,6 @@ /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 alphabet.h:27, from gfm.h:40, from gfm.cpp:21: @@ -2903,6 +2939,30 @@ 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 splice_site.h:34, from edit.h:30, from aligner_result.h:30, @@ -2930,30 +2990,6 @@ 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ -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, from hisat2_build.cpp:28: In member function ‘void SString::resize(size_t) [with T = char]’, @@ -3004,6 +3040,14 @@ sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ +ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: +ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 367 | if(i + 1 >= recs.size() || recs[i+1].first) { + | ~~~~~~^~~~~~~~~~~~~~ +ref_read.cpp: In function ‘std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)’: +ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] + 440 | if(i + 1 >= recs.size() || recs[i+1].first) { + | ~~~~~~^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, @@ -3039,14 +3083,6 @@ ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ -ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: -ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 367 | if(i + 1 >= recs.size() || recs[i+1].first) { - | ~~~~~~^~~~~~~~~~~~~~ -ref_read.cpp: In function ‘std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)’: -ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] - 440 | if(i + 1 >= recs.size() || recs[i+1].first) { - | ~~~~~~^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: @@ -3099,6 +3135,13 @@ /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 splice_site.h:34, from edit.h:30, from aligner_result.h:30, @@ -3126,13 +3169,6 @@ 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; - | ^~~~~~~~~~~~~~ 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] @@ -3498,8 +3534,9 @@ | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, - from aligner_seed.h:30, - from aligner_seed.cpp:21: + from aligner_result.h:30, + from aligner_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()); @@ -3517,9 +3554,8 @@ | ^~~~~~~~ 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: + 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()); @@ -3712,8 +3748,9 @@ 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: + 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()); @@ -3732,9 +3769,8 @@ 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 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()); @@ -3795,7 +3831,8 @@ from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, - from aligner_swsse.cpp:21: + from aligner_sw.h:75, + from aligner_swsse_loc_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()); @@ -3815,8 +3852,7 @@ from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, - from aligner_sw.h:75, - from aligner_swsse_loc_i16.cpp:56: + 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()); @@ -4050,10 +4086,7 @@ | ^~~~~~~~ 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 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()); @@ -4069,9 +4102,27 @@ /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 = long 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 { + | ^~~~ In file included from splice_site.h:34, from edit.h:30, - from splice_site.cpp:20: + 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()); @@ -4087,21 +4138,6 @@ /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 = long 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 { - | ^~~~ In file included from splice_site.h:34, from edit.h:30, from splice_site.cpp:20: @@ -4194,9 +4230,9 @@ make[1]: Leaving directory '/build/reproducible-path/hisat2-2.2.1' dh_md5sums dh_builddeb -dpkg-deb: building package 'hisat2-dbgsym' in '../hisat2-dbgsym_2.2.1-5_arm64.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_arm64.deb'. +dpkg-deb: building package 'hisat2-dbgsym' in '../hisat2-dbgsym_2.2.1-5_arm64.deb'. dpkg-genbuildinfo --build=binary -O../hisat2_2.2.1-5_arm64.buildinfo dpkg-genchanges --build=binary -O../hisat2_2.2.1-5_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -4204,12 +4240,14 @@ 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/3802134/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3802134/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/1109181 and its subdirectories -I: Current time: Sat Mar 15 09:07:57 -12 2025 -I: pbuilder-time-stamp: 1742072877 +I: removing directory /srv/workspace/pbuilder/3802134 and its subdirectories +I: Current time: Sat Apr 18 17:34:16 +14 2026 +I: pbuilder-time-stamp: 1776483256