Diff of the two buildlogs: -- --- b1/build.log 2025-11-29 23:37:35.695423037 +0000 +++ b2/build.log 2025-11-29 23:42:36.419745073 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Jan 1 17:54:45 -12 2027 -I: pbuilder-time-stamp: 1798869285 +I: Current time: Sun Nov 30 13:37:37 +14 2025 +I: pbuilder-time-stamp: 1764459457 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -29,53 +29,85 @@ dpkg-source: info: applying blhc.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2825941/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2539860/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Nov 29 23:38 /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/2539860/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2539860/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + 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]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 nocheck' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='202543dca814467bbad62c7767d729fc' - 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='2825941' - PS1='# ' - PS2='> ' + INVOCATION_ID=8fad5e8a48134145857127ec29a43a27 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2539860 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.vsNkLOy8/pbuilderrc_8JTW --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.vsNkLOy8/b1 --logfile b1/build.log salmon_1.10.3+ds1-1.dsc' - SUDO_GID='111' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.vsNkLOy8/pbuilderrc_aMDu --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.vsNkLOy8/b2 --logfile b2/build.log salmon_1.10.3+ds1-1.dsc' + SUDO_GID=111 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos15-amd64 6.12.57+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.57-1 (2025-11-05) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.57+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.57-1 (2025-11-05) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2825941/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2539860/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -409,7 +441,7 @@ Get: 234 http://deb.debian.org/debian unstable/main amd64 python3-sphinx-rtd-theme all 3.0.2+dfsg-3 [29.7 kB] Get: 235 http://deb.debian.org/debian unstable/main amd64 rapmap-dev all 0.15.0+dfsg-5 [194 kB] Get: 236 http://deb.debian.org/debian unstable/main amd64 sphinx-doc all 8.2.3-10 [3514 kB] -Fetched 164 MB in 4s (45.5 MB/s) +Fetched 164 MB in 2s (92.1 MB/s) Preconfiguring packages ... Selecting previously unselected package fonts-lato. (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 ... 19866 files and directories currently installed.) @@ -1176,8 +1208,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Sat Jan 2 05:56:56 UTC 2027. -Universal Time is now: Sat Jan 2 05:56:56 UTC 2027. +Local time is now: Sat Nov 29 23:39:00 UTC 2025. +Universal Time is now: Sat Nov 29 23:39:00 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:amd64 (1.83.0-5) ... @@ -1397,7 +1429,11 @@ Solving dependencies... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/reproducible-path/salmon-1.10.3+ds1/ && 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 > ../salmon_1.10.3+ds1-1_source.changes +I: user script /srv/workspace/pbuilder/2539860/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/2539860/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/salmon-1.10.3+ds1/ && 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 > ../salmon_1.10.3+ds1-1_source.changes dpkg-buildpackage: info: source package salmon dpkg-buildpackage: info: source version 1.10.3+ds1-1 dpkg-buildpackage: info: source distribution unstable @@ -1438,7 +1474,7 @@ '/usr/share/rapmap/src/bit_array.c' -> '/build/reproducible-path/salmon-1.10.3+ds1/external/install/src/rapmap/bit_array.c' '/usr/share/rapmap/src/rank9b.cpp' -> '/build/reproducible-path/salmon-1.10.3+ds1/external/install/src/rapmap/rank9b.cpp' dh_auto_configure -- -DCONDA_BUILD=1 -DFETCHED_RAPMAP=1 -DBZIP2_LIBRARIES=-lbz2 -DBZIP2_INCLUDE_DIR=/usr/include -DLIBLZMA_INCLUDE_DIR=/usr/include/ -DLIBLZMA_LIBRARY=lzma -DLIBLZMA_HAS_AUTO_DECODER=1 -DLIBLZMA_HAS_EASY_ENCODER=1 -DLIBLZMA_HAS_LZMA_PRESET=1 -DCMAKE_MODULE_PATH=/usr/share/cmake/Modules -DTBB_WILL_RECONFIGURE=FALSE -DBOOST_WILL_RECONFIGURE=FALSE -DCMAKE_BUILD_TYPE=Release -DUSE_SHARED_LIBS=TRUE - cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DCONDA_BUILD=1 -DFETCHED_RAPMAP=1 -DBZIP2_LIBRARIES=-lbz2 -DBZIP2_INCLUDE_DIR=/usr/include -DLIBLZMA_INCLUDE_DIR=/usr/include/ -DLIBLZMA_LIBRARY=lzma -DLIBLZMA_HAS_AUTO_DECODER=1 -DLIBLZMA_HAS_EASY_ENCODER=1 -DLIBLZMA_HAS_LZMA_PRESET=1 -DCMAKE_MODULE_PATH=/usr/share/cmake/Modules -DTBB_WILL_RECONFIGURE=FALSE -DBOOST_WILL_RECONFIGURE=FALSE -DCMAKE_BUILD_TYPE=Release -DUSE_SHARED_LIBS=TRUE .. + cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DBUILD_TESTING:BOOL=OFF -DCONDA_BUILD=1 -DFETCHED_RAPMAP=1 -DBZIP2_LIBRARIES=-lbz2 -DBZIP2_INCLUDE_DIR=/usr/include -DLIBLZMA_INCLUDE_DIR=/usr/include/ -DLIBLZMA_LIBRARY=lzma -DLIBLZMA_HAS_AUTO_DECODER=1 -DLIBLZMA_HAS_EASY_ENCODER=1 -DLIBLZMA_HAS_LZMA_PRESET=1 -DCMAKE_MODULE_PATH=/usr/share/cmake/Modules -DTBB_WILL_RECONFIGURE=FALSE -DBOOST_WILL_RECONFIGURE=FALSE -DCMAKE_BUILD_TYPE=Release -DUSE_SHARED_LIBS=TRUE .. CC: gcc -- The C compiler identification is GNU 15.2.0 -- The CXX compiler identification is GNU 15.2.0 @@ -1550,11 +1586,12 @@ TBB_LIBRARIES = TBB_LIB_INSTALL_DIR = TBBGLOBS = --- Configuring done (3.3s) +-- Configuring done (5.2s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: + BUILD_TESTING CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR @@ -1570,7 +1607,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/salmon-1.10.3+ds1' dh_auto_build - cd obj-x86_64-linux-gnu && make -j42 INSTALL="install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j40 INSTALL="install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/salmon-1.10.3+ds1 -B/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -1583,194 +1620,188 @@ make -f external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/depend make[4]: Entering directory '/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu' cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.3+ds1 /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/ntcard /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/DependInfo.cmake "--color=" -make -f external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/depend make[4]: Entering directory '/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu' cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.3+ds1 /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphdump /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/DependInfo.cmake "--color=" +make -f external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/depend +make -f external/pufferfish/src/CMakeFiles/puffer.dir/build.make external/pufferfish/src/CMakeFiles/puffer.dir/depend make[4]: Entering directory '/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu' cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.3+ds1 /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphconstructor /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/DependInfo.cmake "--color=" -make -f external/pufferfish/src/CMakeFiles/puffer.dir/build.make external/pufferfish/src/CMakeFiles/puffer.dir/depend make[4]: Entering directory '/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu' cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.3+ds1 /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/src /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/DependInfo.cmake "--color=" make -f src/CMakeFiles/salmon_core.dir/build.make src/CMakeFiles/salmon_core.dir/depend +make -f src/CMakeFiles/alevin_core.dir/build.make src/CMakeFiles/alevin_core.dir/depend make[4]: Entering directory '/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu' cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.3+ds1 /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/src /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/DependInfo.cmake "--color=" -make -f src/CMakeFiles/alevin_core.dir/build.make src/CMakeFiles/alevin_core.dir/depend +make -f src/CMakeFiles/UnitTestsMain.dir/build.make src/CMakeFiles/UnitTestsMain.dir/depend make[4]: Entering directory '/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu' cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.3+ds1 /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/src /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/DependInfo.cmake "--color=" -make -f src/CMakeFiles/UnitTestsMain.dir/build.make src/CMakeFiles/UnitTestsMain.dir/depend make[4]: Entering directory '/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu' cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.3+ds1 /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/src /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/puffer.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.3+ds1 /build/reproducible-path/salmon-1.10.3+ds1/src /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/src /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/alevin_core.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.3+ds1 /build/reproducible-path/salmon-1.10.3+ds1/src /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/src /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/salmon_core.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.3+ds1 /build/reproducible-path/salmon-1.10.3+ds1/src /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/src /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/alevin_core.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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+make -f external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/build.make external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/build +make -f external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/build.make external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/build make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu' +make -f external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/build make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu' -make -f external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/build.make external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/build -make -f external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/build.make external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/build -make -f 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-I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/alevin_core.dir/edlib.cpp.o -MF 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-I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/compressedstring.cpp.o -MF CMakeFiles/twopaco.dir/compressedstring.cpp.o.d -o CMakeFiles/twopaco.dir/compressedstring.cpp.o -c /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphconstructor/compressedstring.cpp +[ 30%] Building CXX object src/CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -msse -msse2 -mno-sse4.1 -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o -MF CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o.d -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o -c /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/ksw2pp/ksw2_extf2_sse.c +cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.3+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong 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-I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/UnitTestsMain.dir/__/tests/UnitTests.cpp.o -MF CMakeFiles/UnitTestsMain.dir/__/tests/UnitTests.cpp.o.d -o CMakeFiles/UnitTestsMain.dir/__/tests/UnitTests.cpp.o -c /build/reproducible-path/salmon-1.10.3+ds1/tests/UnitTests.cpp +cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o -c /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/ksw2pp/ksw2_extd.c +cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump && /usr/bin/c++ 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/usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -msse -msse2 -mno-sse4.1 -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o -MF CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o.d -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o -c /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/ksw2pp/ksw2_extd2_sse.c +cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration 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-I/build/reproducible-path/salmon-1.10.3+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context 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external/pufferfish/src/CMakeFiles/puffer.dir/Util.cpp.o -MF CMakeFiles/puffer.dir/Util.cpp.o.d -o CMakeFiles/puffer.dir/Util.cpp.o -c /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/Util.cpp -[ 35%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o -cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o -MF CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o.d -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o -c /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/ksw2pp/ksw2_extz2_sse.c -[ 36%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/rank9b.cpp.o -cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.3+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS 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/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphconstructor/test.cpp cc1: warning: command-line option '-Wno-reorder' is valid for C++/ObjC++ but not for C cc1: warning: command-line option '-Wno-deprecated-copy' is valid for C++/ObjC++ but not for C -[ 38%] Building CXX object src/CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o -cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.3+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.3+ds1/external -I/build/reproducible-path/salmon-1.10.3+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish 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/usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.3+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.3+ds1/external -I/build/reproducible-path/salmon-1.10.3+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC 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-Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o -MF CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o -c /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/PufferfishKmerQuery.cpp -[ 46%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/FastxParser.cpp.o +[ 43%] Building CXX object src/CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.3+ds1/include -g -O2 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-D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o -MF CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o.d -o CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o -c /build/reproducible-path/salmon-1.10.3+ds1/src/AlevinUtils.cpp +cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.3+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o -MF CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o -c /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/PufferfishTestLookup.cpp +[ 45%] Building CXX object src/CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o +cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.3+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.3+ds1/external -I/build/reproducible-path/salmon-1.10.3+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder 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-I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o -MF CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o.d -o CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o -c /build/reproducible-path/salmon-1.10.3+ds1/src/GenomicFeature.cpp [ 47%] Building CXX object src/CMakeFiles/salmon_core.dir/VersionChecker.cpp.o cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.3+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.3+ds1/external -I/build/reproducible-path/salmon-1.10.3+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/VersionChecker.cpp.o -MF CMakeFiles/salmon_core.dir/VersionChecker.cpp.o.d -o CMakeFiles/salmon_core.dir/VersionChecker.cpp.o -c /build/reproducible-path/salmon-1.10.3+ds1/src/VersionChecker.cpp [ 48%] Building CXX object src/CMakeFiles/salmon_core.dir/SBModel.cpp.o cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.3+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.3+ds1/external -I/build/reproducible-path/salmon-1.10.3+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer 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external/pufferfish/src/CMakeFiles/puffer.dir/MemCollector.cpp.o -MF CMakeFiles/puffer.dir/MemCollector.cpp.o.d -o CMakeFiles/puffer.dir/MemCollector.cpp.o -c /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/MemCollector.cpp -[ 57%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o -cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.3+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.3+ds1/external -I/build/reproducible-path/salmon-1.10.3+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o -MF CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o.d -o CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o -c /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonExceptions.cpp In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.3+ds1/include/AlevinOpts.hpp:5, @@ -1784,48 +1815,26 @@ 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' -[ 58%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o -make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu' +[ 55%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o +[ 56%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.3+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.3+ds1/external -I/build/reproducible-path/salmon-1.10.3+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o -MF CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o.d -o CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o -c /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonStringUtils.cpp -[ 58%] Built target ksw2pp_sse4 -[ 59%] Building CXX object src/CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o +[ 57%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/FixFasta.cpp.o +cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.3+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/FixFasta.cpp.o -MF CMakeFiles/puffer.dir/FixFasta.cpp.o.d -o CMakeFiles/puffer.dir/FixFasta.cpp.o -c /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/FixFasta.cpp +cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.3+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.3+ds1/external -I/build/reproducible-path/salmon-1.10.3+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o -MF CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o.d -o CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o -c /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonExceptions.cpp +[ 58%] Building CXX object src/CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.3+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.3+ds1/external -I/build/reproducible-path/salmon-1.10.3+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o -MF CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o.d -o CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o -c /build/reproducible-path/salmon-1.10.3+ds1/src/SimplePosBias.cpp -[ 60%] Building CXX object src/CMakeFiles/salmon_core.dir/SGSmooth.cpp.o -cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.3+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.3+ds1/external -I/build/reproducible-path/salmon-1.10.3+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/SGSmooth.cpp.o -MF CMakeFiles/salmon_core.dir/SGSmooth.cpp.o.d -o CMakeFiles/salmon_core.dir/SGSmooth.cpp.o -c /build/reproducible-path/salmon-1.10.3+ds1/src/SGSmooth.cpp -[ 60%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/MemChainer.cpp.o -cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.3+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/MemChainer.cpp.o -MF CMakeFiles/puffer.dir/MemChainer.cpp.o.d -o CMakeFiles/puffer.dir/MemChainer.cpp.o -c /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/MemChainer.cpp -[ 61%] Linking CXX static library libntcard.a -cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/cmake -P CMakeFiles/ntcard.dir/cmake_clean_target.cmake make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/cmake -E cmake_link_script CMakeFiles/ntcard.dir/link.txt --verbose=1 -[ 61%] Built target ksw2pp_sse2 -[ 62%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PuffAligner.cpp.o -cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.3+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PuffAligner.cpp.o -MF CMakeFiles/puffer.dir/PuffAligner.cpp.o.d -o CMakeFiles/puffer.dir/PuffAligner.cpp.o -c /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/PuffAligner.cpp -/usr/bin/ar qc libntcard.a CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o CMakeFiles/ntcard.dir/nthll.cpp.o -/usr/bin/ranlib libntcard.a make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu' -[ 62%] Building CXX object src/CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o -cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.3+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.3+ds1/external -I/build/reproducible-path/salmon-1.10.3+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o -MF CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o.d -o CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o -c /build/reproducible-path/salmon-1.10.3+ds1/external/install/src/pufferfish/metro/metrohash64.cpp -[ 62%] Built target ntcard -[ 63%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishAligner.cpp.o -cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.3+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishAligner.cpp.o -MF CMakeFiles/puffer.dir/PufferfishAligner.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishAligner.cpp.o -c /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/PufferfishAligner.cpp -In file included from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, - from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/Util.hpp:19, - from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/PufferfishSparseIndex.hpp:13, - from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/PufferfishSparseIndex.cpp:10: -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 197 | registry_t() {} - | ^ -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' -[ 64%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 198 | registry_t(const registry_t&) = delete; - | ^ -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' -cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.3+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o -MF CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o.d -o CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o -c /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/RefSeqConstructor.cpp -[ 65%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/metro/metrohash64.cpp.o -cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.3+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/metro/metrohash64.cpp.o -MF CMakeFiles/puffer.dir/metro/metrohash64.cpp.o.d -o CMakeFiles/puffer.dir/metro/metrohash64.cpp.o -c /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/metro/metrohash64.cpp +[ 58%] Built target ksw2pp_sse4 +[ 58%] Built target ksw2pp_sse2 +[ 59%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/MemCollector.cpp.o +cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.3+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/MemCollector.cpp.o -MF CMakeFiles/puffer.dir/MemCollector.cpp.o.d -o CMakeFiles/puffer.dir/MemCollector.cpp.o -c /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/MemCollector.cpp +[ 59%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/MemChainer.cpp.o +cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.3+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/MemChainer.cpp.o -MF CMakeFiles/puffer.dir/MemChainer.cpp.o.d -o CMakeFiles/puffer.dir/MemChainer.cpp.o -c /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/MemChainer.cpp +make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu' +[ 59%] Built target ksw2pp_basic +[ 60%] Building CXX object src/CMakeFiles/salmon_core.dir/SGSmooth.cpp.o +cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.3+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.3+ds1/external -I/build/reproducible-path/salmon-1.10.3+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/SGSmooth.cpp.o -MF CMakeFiles/salmon_core.dir/SGSmooth.cpp.o.d -o CMakeFiles/salmon_core.dir/SGSmooth.cpp.o -c /build/reproducible-path/salmon-1.10.3+ds1/src/SGSmooth.cpp In file included from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/Util.hpp:19, @@ -1838,36 +1847,19 @@ 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' -[ 66%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o -cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.3+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o -MF CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o.d -o CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o -c /build/reproducible-path/salmon-1.10.3+ds1/src/LibraryFormat.cpp -make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu' -[ 66%] Built target ksw2pp_basic make -f external/pufferfish/src/CMakeFiles/ksw2pp.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp.dir/depend make[4]: Entering directory '/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu' cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.3+ds1 /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/src /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu' -In file included from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, - from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/Util.hpp:19, - from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/PufferfishValidate.cpp:15: -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 197 | registry_t() {} - | ^ -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' make -f external/pufferfish/src/CMakeFiles/ksw2pp.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp.dir/build -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 198 | registry_t(const registry_t&) = delete; - | ^ -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' make[4]: Entering directory '/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu' -[ 67%] Linking CXX static library libksw2pp.a +[ 61%] Linking CXX static library libksw2pp.a cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -P CMakeFiles/ksw2pp.dir/cmake_clean_target.cmake -cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ksw2pp.dir/link.txt --verbose=1 In file included from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/Util.hpp:19, - from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/PufferfishIndex.hpp:12, - from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/PufferfishIndex.cpp:9: + from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/PufferfishBaseIndex.hpp:14, + from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/PufferfishBaseIndex.cpp:1: /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -1876,12 +1868,15 @@ 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' +cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ksw2pp.dir/link.txt --verbose=1 +[ 62%] Linking CXX static library libntcard.a +cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/cmake -P CMakeFiles/ntcard.dir/cmake_clean_target.cmake +cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/cmake -E cmake_link_script CMakeFiles/ntcard.dir/link.txt --verbose=1 In file included from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/Util.hpp:19, - from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5, - from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1, - from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/PufferfishIndexer.cpp:20: + from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/PufferfishLossyIndex.hpp:12, + from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/PufferfishLossyIndex.cpp:7: /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -1893,11 +1888,16 @@ "/usr/bin/gcc-ar-15" qc libksw2pp.a CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o "/usr/bin/gcc-ranlib-15" libksw2pp.a make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu' -[ 67%] Built target ksw2pp +[ 63%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PuffAligner.cpp.o +cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.3+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PuffAligner.cpp.o -MF CMakeFiles/puffer.dir/PuffAligner.cpp.o.d -o CMakeFiles/puffer.dir/PuffAligner.cpp.o -c /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/PuffAligner.cpp +/usr/bin/ar qc libntcard.a CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o CMakeFiles/ntcard.dir/nthll.cpp.o +/usr/bin/ranlib libntcard.a +make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu' In file included from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/Util.hpp:19, - from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/PufferfishKmerQuery.cpp:13: + from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/PufferfishSparseIndex.hpp:13, + from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/PufferfishSparseIndex.cpp:10: /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -1906,10 +1906,20 @@ 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' +[ 63%] Built target ksw2pp +[ 63%] Built target ntcard +[ 63%] Building CXX object src/CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o +cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.3+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.3+ds1/external -I/build/reproducible-path/salmon-1.10.3+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o -MF CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o.d -o CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o -c /build/reproducible-path/salmon-1.10.3+ds1/external/install/src/pufferfish/metro/metrohash64.cpp +[ 64%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishAligner.cpp.o +cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.3+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishAligner.cpp.o -MF CMakeFiles/puffer.dir/PufferfishAligner.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishAligner.cpp.o -c /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/PufferfishAligner.cpp +[ 65%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o +cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.3+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o -MF CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o.d -o CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o -c /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/RefSeqConstructor.cpp In file included from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/Util.hpp:19, - from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/PufferfishTestLookup.cpp:14: + from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5, + from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1, + from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/PufferfishIndexer.cpp:20: /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -1921,7 +1931,8 @@ In file included from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/Util.hpp:19, - from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/PufferfishStats.cpp:16: + from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/PufferfishIndex.hpp:12, + from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/PufferfishIndex.cpp:9: /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -1933,8 +1944,7 @@ In file included from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/Util.hpp:19, - from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/PufferfishBaseIndex.hpp:14, - from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/PufferfishBaseIndex.cpp:1: + from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/PufferfishValidate.cpp:15: /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -1946,8 +1956,7 @@ In file included from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/Util.hpp:19, - from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/PufferfishLossyIndex.hpp:12, - from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/PufferfishLossyIndex.cpp:7: + from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/PufferfishStats.cpp:16: /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -1956,11 +1965,14 @@ 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' +[ 66%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/metro/metrohash64.cpp.o +cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.3+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/metro/metrohash64.cpp.o -MF CMakeFiles/puffer.dir/metro/metrohash64.cpp.o.d -o CMakeFiles/puffer.dir/metro/metrohash64.cpp.o -c /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/metro/metrohash64.cpp +[ 67%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o +cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.3+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o -MF CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o.d -o CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o -c /build/reproducible-path/salmon-1.10.3+ds1/src/LibraryFormat.cpp In file included from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/Util.hpp:19, - from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5, - from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: + from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/PufferfishTestLookup.cpp:14: /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -1972,8 +1984,8 @@ In file included from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/Util.hpp:19, - from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/PuffAligner.hpp:8, - from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/PufferfishExamine.cpp:6: + from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5, + from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -1982,13 +1994,10 @@ 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/PufferfishTestLookup.cpp: In function 'std::vector get_kmers(const std::string&, uint32_t)': -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/PufferfishTestLookup.cpp:25:78: warning: unused parameter 'k' [-Wunused-parameter] - 25 | std::vector get_kmers(const std::string& fasta_file, uint32_t k) { - | ~~~~~~~~~^ In file included from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/FixFasta.cpp:5: + from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/Util.hpp:19, + from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/PufferfishKmerQuery.cpp:13: /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -2009,11 +2018,15 @@ 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/PufferfishTestLookup.cpp: In function 'std::vector get_kmers(const std::string&, uint32_t)': +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/PufferfishTestLookup.cpp:25:78: warning: unused parameter 'k' [-Wunused-parameter] + 25 | std::vector get_kmers(const std::string& fasta_file, uint32_t k) { + | ~~~~~~~~~^ In file included from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/Util.hpp:19, - from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/RefSeqConstructor.hpp:7, - from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/RefSeqConstructor.cpp:1: + from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/PuffAligner.hpp:8, + from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/PufferfishExamine.cpp:6: /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -2025,8 +2038,9 @@ In file included from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/Util.hpp:19, - from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/PuffAligner.hpp:8, - from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/PuffAligner.cpp:2: + from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/PufferfishIndex.hpp:12, + from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/MemCollector.hpp:6, + from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/MemCollector.cpp:1: /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -2049,6 +2063,17 @@ 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' +In file included from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, + from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/spdlog.h:192, + from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/FixFasta.cpp:5: +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 197 | registry_t() {} + | ^ +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 198 | registry_t(const registry_t&) = delete; + | ^ +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.3+ds1/include/AlevinUtils.hpp:27, @@ -2064,9 +2089,8 @@ In file included from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/Util.hpp:19, - from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/PufferfishIndex.hpp:12, - from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/MemCollector.hpp:6, - from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/MemCollector.cpp:1: + from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/RefSeqConstructor.hpp:7, + from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/RefSeqConstructor.cpp:1: /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -2077,7 +2101,9 @@ /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' In file included from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/PufferfishAligner.cpp:35: + from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/Util.hpp:19, + from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/PuffAligner.hpp:8, + from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/PuffAligner.cpp:2: /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -2249,97 +2275,17 @@ /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::vector; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::vector; _T2 = unsigned int]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/RefSeqConstructor.hpp:5: -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(dest_it) const [with Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; destructive_iterator = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >; dest_it = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >]': -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::destructive_begin() [with Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; destructive_iterator = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >]' - 2607 | destructive_iterator destructive_begin() { return _mk_destructive_iterator(table.destructive_begin()); } - | ^~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:2817:43: required from 'void spp::sparse_hashtable::_move_from(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; size_type = long unsigned int]' - 2817 | for (destructive_iterator it = ht.destructive_begin(); - | ~~~^~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:2948:9: required from 'spp::sparse_hashtable::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; size_type = long unsigned int]' - 2948 | _move_from(mover, ht, min_buckets_wanted); - | ^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:2745:26: required from 'bool spp::sparse_hashtable::_resize_delta(size_type) [with Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; size_type = long unsigned int]' - 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); - | ^~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:3278:21: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' - 3278 | if (_resize_delta(1)) - | ^~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = unsigned int; T = pufferfish::util::ContigBlock; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = pufferfish::util::ContigBlock]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/RefSeqConstructor.cpp:143:65: required from 'Task RefSeqConstructor::doDFS(size_t, size_t, bool, pufferfish::util::ContigBlock&, uint32_t, pufferfish::util::ContigBlock&, bool, uint32_t, bool, std::string&, bool) [with PufferfishIndexT = PufferfishIndex; size_t = long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string]' - 143 | pufferfish::util::ContigBlock& cb = (*contigSeqCache_)[c.cid]; - | ~~~~~~~~~~~~~~~~~~^ -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/RefSeqConstructor.cpp:466:16: required from here - 466 | template class RefSeqConstructor; - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:2632:78: warning: implicitly-declared 'constexpr spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >&)' is deprecated [-Wdeprecated-copy] - 2632 | destructive_iterator _mk_destructive_iterator(dest_it it) const { return it; } - | ^~ -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:946:33: note: because 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >' has user-provided 'spp::Two_d_destructive_iterator& spp::Two_d_destructive_iterator::operator=(const spp::Two_d_destructive_iterator&) [with T = std::pair; row_it = spp::sparsegroup, spp::libc_allocator > >*; col_it = std::pair*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator >]' - 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); - | ^~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' - 1440 | _set_val(&_group[offset], val); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = unsigned int; T = pufferfish::util::ContigBlock; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = pufferfish::util::ContigBlock]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/RefSeqConstructor.cpp:143:65: required from 'Task RefSeqConstructor::doDFS(size_t, size_t, bool, pufferfish::util::ContigBlock&, uint32_t, pufferfish::util::ContigBlock&, bool, uint32_t, bool, std::string&, bool) [with PufferfishIndexT = PufferfishIndex; size_t = long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string]' - 143 | pufferfish::util::ContigBlock& cb = (*contigSeqCache_)[c.cid]; - | ~~~~~~~~~~~~~~~~~~^ -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/RefSeqConstructor.cpp:466:16: required from here - 466 | template class RefSeqConstructor; - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = pufferfish::util::ContigBlock; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = pufferfish::util::ContigBlock]' [-Wcast-user-defined] - 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' - 1407 | _init_val((mutable_pointer)&_group[num_items], val); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' - 1435 | _set_aux(alloc, offset, val, check_alloc_type()); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = unsigned int; T = pufferfish::util::ContigBlock; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = pufferfish::util::ContigBlock]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/RefSeqConstructor.cpp:143:65: required from 'Task RefSeqConstructor::doDFS(size_t, size_t, bool, pufferfish::util::ContigBlock&, uint32_t, pufferfish::util::ContigBlock&, bool, uint32_t, bool, std::string&, bool) [with PufferfishIndexT = PufferfishIndex; size_t = long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string]' - 143 | pufferfish::util::ContigBlock& cb = (*contigSeqCache_)[c.cid]; - | ~~~~~~~~~~~~~~~~~~^ -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/RefSeqConstructor.cpp:466:16: required from here - 466 | template class RefSeqConstructor; - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = pufferfish::util::ContigBlock; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = pufferfish::util::ContigBlock]' [-Wcast-user-defined] - 1339 | ::new (p) value_type(std::move((mutable_reference)val)); - | ^~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, + from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/spdlog.h:192, + from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/PufferfishAligner.cpp:35: +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 197 | registry_t() {} + | ^ +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 198 | registry_t(const registry_t&) = delete; + | ^ +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' In file included from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9: /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(dest_it) const [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; destructive_iterator = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >; dest_it = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >]': /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::destructive_begin() [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; destructive_iterator = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >]' @@ -2503,6 +2449,112 @@ /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::vector; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::vector; _T2 = unsigned int]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/RefSeqConstructor.hpp:5: +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(dest_it) const [with Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; destructive_iterator = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >; dest_it = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >]': +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::destructive_begin() [with Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; destructive_iterator = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >]' + 2607 | destructive_iterator destructive_begin() { return _mk_destructive_iterator(table.destructive_begin()); } + | ^~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:2817:43: required from 'void spp::sparse_hashtable::_move_from(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; size_type = long unsigned int]' + 2817 | for (destructive_iterator it = ht.destructive_begin(); + | ~~~^~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:2948:9: required from 'spp::sparse_hashtable::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; size_type = long unsigned int]' + 2948 | _move_from(mover, ht, min_buckets_wanted); + | ^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:2745:26: required from 'bool spp::sparse_hashtable::_resize_delta(size_type) [with Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; size_type = long unsigned int]' + 2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to); + | ^~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:3278:21: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' + 3278 | if (_resize_delta(1)) + | ^~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = unsigned int; T = pufferfish::util::ContigBlock; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = pufferfish::util::ContigBlock]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/RefSeqConstructor.cpp:143:65: required from 'Task RefSeqConstructor::doDFS(size_t, size_t, bool, pufferfish::util::ContigBlock&, uint32_t, pufferfish::util::ContigBlock&, bool, uint32_t, bool, std::string&, bool) [with PufferfishIndexT = PufferfishIndex; size_t = long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string]' + 143 | pufferfish::util::ContigBlock& cb = (*contigSeqCache_)[c.cid]; + | ~~~~~~~~~~~~~~~~~~^ +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/RefSeqConstructor.cpp:466:16: required from here + 466 | template class RefSeqConstructor; + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:2632:78: warning: implicitly-declared 'constexpr spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >&)' is deprecated [-Wdeprecated-copy] + 2632 | destructive_iterator _mk_destructive_iterator(dest_it it) const { return it; } + | ^~ +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:946:33: note: because 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >' has user-provided 'spp::Two_d_destructive_iterator& spp::Two_d_destructive_iterator::operator=(const spp::Two_d_destructive_iterator&) [with T = std::pair; row_it = spp::sparsegroup, spp::libc_allocator > >*; col_it = std::pair*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator >]' + 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); + | ^~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1440 | _set_val(&_group[offset], val); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = unsigned int; T = pufferfish::util::ContigBlock; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = pufferfish::util::ContigBlock]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/RefSeqConstructor.cpp:143:65: required from 'Task RefSeqConstructor::doDFS(size_t, size_t, bool, pufferfish::util::ContigBlock&, uint32_t, pufferfish::util::ContigBlock&, bool, uint32_t, bool, std::string&, bool) [with PufferfishIndexT = PufferfishIndex; size_t = long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string]' + 143 | pufferfish::util::ContigBlock& cb = (*contigSeqCache_)[c.cid]; + | ~~~~~~~~~~~~~~~~~~^ +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/RefSeqConstructor.cpp:466:16: required from here + 466 | template class RefSeqConstructor; + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = pufferfish::util::ContigBlock; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = pufferfish::util::ContigBlock]' [-Wcast-user-defined] + 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' + 1407 | _init_val((mutable_pointer)&_group[num_items], val); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1435 | _set_aux(alloc, offset, val, check_alloc_type()); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = unsigned int; T = pufferfish::util::ContigBlock; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = pufferfish::util::ContigBlock]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/RefSeqConstructor.cpp:143:65: required from 'Task RefSeqConstructor::doDFS(size_t, size_t, bool, pufferfish::util::ContigBlock&, uint32_t, pufferfish::util::ContigBlock&, bool, uint32_t, bool, std::string&, bool) [with PufferfishIndexT = PufferfishIndex; size_t = long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string]' + 143 | pufferfish::util::ContigBlock& cb = (*contigSeqCache_)[c.cid]; + | ~~~~~~~~~~~~~~~~~~^ +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/RefSeqConstructor.cpp:466:16: required from here + 466 | template class RefSeqConstructor; + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = pufferfish::util::ContigBlock; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = pufferfish::util::ContigBlock]' [-Wcast-user-defined] + 1339 | ::new (p) value_type(std::move((mutable_reference)val)); + | ^~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/spdlog_impl.h:12, + from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/spdlog.h:192, + from /build/reproducible-path/salmon-1.10.3+ds1/include/SalmonOpts.hpp:7, + from /build/reproducible-path/salmon-1.10.3+ds1/include/SalmonUtils.hpp:30, + from /build/reproducible-path/salmon-1.10.3+ds1/include/UtilityFunctions.hpp:4, + from /build/reproducible-path/salmon-1.10.3+ds1/include/SBModel.hpp:6, + from /build/reproducible-path/salmon-1.10.3+ds1/src/SBModel.cpp:1: +/build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 197 | registry_t() {} + | ^ +/build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' +/build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 198 | registry_t(const registry_t&) = delete; + | ^ +/build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' In file included from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/FixFasta.cpp:4: /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(dest_it) const [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; destructive_iterator = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >; dest_it = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >]': /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::destructive_begin() [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; destructive_iterator = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >]' @@ -2585,21 +2637,6 @@ /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:946:33: note: because 'spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::input_iterator_tag, spp::libc_allocator > >' has user-provided 'spp::Two_d_destructive_iterator& spp::Two_d_destructive_iterator::operator=(const spp::Two_d_destructive_iterator&) [with T = std::__cxx11::basic_string; row_it = spp::sparsegroup, spp::libc_allocator > >*; col_it = std::__cxx11::basic_string*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator >]' 946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o); | ^~~~~~~~ -In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/spdlog_impl.h:12, - from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.3+ds1/include/SalmonOpts.hpp:7, - from /build/reproducible-path/salmon-1.10.3+ds1/include/SalmonUtils.hpp:30, - from /build/reproducible-path/salmon-1.10.3+ds1/include/UtilityFunctions.hpp:4, - from /build/reproducible-path/salmon-1.10.3+ds1/include/SBModel.hpp:6, - from /build/reproducible-path/salmon-1.10.3+ds1/src/SBModel.cpp:1: -/build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 197 | registry_t() {} - | ^ -/build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' -/build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 198 | registry_t(const registry_t&) = delete; - | ^ -/build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair > >; Alloc = spp::libc_allocator > > >; mutable_value_type = std::pair > >; reference = std::pair > >&]': /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; allocator_type = spp::libc_allocator > > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 1407 | _init_val((mutable_pointer)&_group[num_items], val); @@ -2628,6 +2665,10 @@ /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup > >, spp::libc_allocator > > > >::value_type' {aka 'std::pair > >'} to 'spp::sparsegroup > >, spp::libc_allocator > > > >::mutable_reference' {aka 'std::pair > >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = std::vector >; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = std::vector >]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/src/AlevinUtils.cpp: In function 'bool alevin::utils::extractBarcode(std::string&, std::string&, ProtocolT&, std::string&) [with ProtocolT = alevin::protocols::SciSeq3; std::string = std::__cxx11::basic_string]': +/build/reproducible-path/salmon-1.10.3+ds1/src/AlevinUtils.cpp:350:104: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 350 | if (pt.anchorPos != std::string::npos && ( pt.anchorPos == pt.maxHairpinIndexLen || pt.anchorPos == pt.maxHairpinIndexLen -1) // only 2 possible values of pt.anchorPos + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/Util.hpp:19, @@ -2657,10 +2698,6 @@ 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' -/build/reproducible-path/salmon-1.10.3+ds1/src/AlevinUtils.cpp: In function 'bool alevin::utils::extractBarcode(std::string&, std::string&, ProtocolT&, std::string&) [with ProtocolT = alevin::protocols::SciSeq3; std::string = std::__cxx11::basic_string]': -/build/reproducible-path/salmon-1.10.3+ds1/src/AlevinUtils.cpp:350:104: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 350 | if (pt.anchorPos != std::string::npos && ( pt.anchorPos == pt.maxHairpinIndexLen || pt.anchorPos == pt.maxHairpinIndexLen -1) // only 2 possible values of pt.anchorPos - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/AlevinUtils.hpp:47: /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair, std::vector >; Alloc = spp::libc_allocator, std::vector > >; value_type = std::pair, std::vector >; reference = std::pair, std::vector >&]': /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, std::vector >; T = std::pair, std::vector >; Alloc = spp::libc_allocator, std::vector > >; allocator_type = spp::libc_allocator, std::vector > >; size_type = unsigned char]' @@ -2936,6 +2973,13 @@ /usr/bin/ranlib libgraphdump.a make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu' [ 68%] Built target graphdump +[ 69%] Linking CXX static library libalevin_core.a +cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/alevin_core.dir/cmake_clean_target.cmake +cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/alevin_core.dir/link.txt --verbose=1 +"/usr/bin/gcc-ar-15" qc libalevin_core.a CMakeFiles/alevin_core.dir/edlib.cpp.o CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o +"/usr/bin/gcc-ranlib-15" libalevin_core.a +make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu' +[ 69%] Built target alevin_core In file included from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/digestpp/algorithm/sha2.hpp:9, from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/digestpp/digestpp.hpp:6, from /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/src/FixFasta.cpp:27: @@ -2966,16 +3010,13 @@ /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: object 'byte' of size 1 169 | unsigned char byte = *begin++; | ^~~~ -[ 69%] Linking CXX static library libalevin_core.a -cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/alevin_core.dir/cmake_clean_target.cmake -cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/alevin_core.dir/link.txt --verbose=1 -"/usr/bin/gcc-ar-15" qc libalevin_core.a CMakeFiles/alevin_core.dir/edlib.cpp.o CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o -"/usr/bin/gcc-ranlib-15" libalevin_core.a -make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu' -[ 69%] Built target alevin_core [ 70%] Linking CXX static library libsalmon_core.a cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/salmon_core.dir/cmake_clean_target.cmake cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/salmon_core.dir/link.txt --verbose=1 +"/usr/bin/gcc-ar-15" qc libsalmon_core.a CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o CMakeFiles/salmon_core.dir/backtrace.cc.o CMakeFiles/salmon_core.dir/xxhash.c.o CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o CMakeFiles/salmon_core.dir/VersionChecker.cpp.o CMakeFiles/salmon_core.dir/SBModel.cpp.o CMakeFiles/salmon_core.dir/FastxParser.cpp.o CMakeFiles/salmon_core.dir/StadenUtils.cpp.o CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o CMakeFiles/salmon_core.dir/SGSmooth.cpp.o CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o +"/usr/bin/gcc-ranlib-15" libsalmon_core.a +make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu' +[ 70%] Built target salmon_core In member function 'void digestpp::detail::sha2_provider::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]', inlined from 'digestpp::detail::sha2_provider::update(const unsigned char*, size_t)::' at /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61, inlined from 'void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider::update(const unsigned char*, size_t)::]' at /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12, @@ -2990,10 +3031,6 @@ /build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: object 'byte' of size 1 169 | unsigned char byte = *begin++; | ^~~~ -"/usr/bin/gcc-ar-15" qc libsalmon_core.a CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o CMakeFiles/salmon_core.dir/backtrace.cc.o CMakeFiles/salmon_core.dir/xxhash.c.o CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o CMakeFiles/salmon_core.dir/VersionChecker.cpp.o CMakeFiles/salmon_core.dir/SBModel.cpp.o CMakeFiles/salmon_core.dir/FastxParser.cpp.o CMakeFiles/salmon_core.dir/StadenUtils.cpp.o CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o CMakeFiles/salmon_core.dir/SGSmooth.cpp.o CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o -"/usr/bin/gcc-ranlib-15" libsalmon_core.a -make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu' -[ 70%] Built target salmon_core [ 71%] Linking CXX static library libUnitTestsMain.a cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/UnitTestsMain.dir/cmake_clean_target.cmake cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/UnitTestsMain.dir/link.txt --verbose=1 @@ -3010,19 +3047,23 @@ make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/unitTests.dir/build.make src/CMakeFiles/unitTests.dir/build make[4]: Entering directory '/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu' -[ 74%] Building CXX object src/CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o -[ 74%] Building CXX object src/CMakeFiles/unitTests.dir/__/tests/LibraryTypeTests.cpp.o [ 76%] Building CXX object src/CMakeFiles/unitTests.dir/__/tests/GCSampleTests.cpp.o +[ 76%] Building CXX object src/CMakeFiles/unitTests.dir/__/tests/LibraryTypeTests.cpp.o [ 76%] Building CXX object src/CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_TIMER_DYN_LINK -DBOOST_TIMER_NO_LIB -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.3+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.3+ds1/external -I/build/reproducible-path/salmon-1.10.3+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/unitTests.dir/__/tests/LibraryTypeTests.cpp.o -MF CMakeFiles/unitTests.dir/__/tests/LibraryTypeTests.cpp.o.d -o CMakeFiles/unitTests.dir/__/tests/LibraryTypeTests.cpp.o -c /build/reproducible-path/salmon-1.10.3+ds1/tests/LibraryTypeTests.cpp -cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_TIMER_DYN_LINK -DBOOST_TIMER_NO_LIB -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.3+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.3+ds1/external -I/build/reproducible-path/salmon-1.10.3+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o -MF CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o.d -o CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o -c /build/reproducible-path/salmon-1.10.3+ds1/external/install/src/pufferfish/rank9b.cpp +[ 76%] Building CXX object src/CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_TIMER_DYN_LINK 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-DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o -MF CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o.d -o CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o -c /build/reproducible-path/salmon-1.10.3+ds1/src/FragmentLengthDistribution.cpp cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_TIMER_DYN_LINK 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-D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o -MF CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o.d -o CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o -c /build/reproducible-path/salmon-1.10.3+ds1/external/install/src/pufferfish/rank9b.cpp +/usr/bin/ar qc libpuffer.a CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o CMakeFiles/puffer.dir/PufferfishIndex.cpp.o CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o CMakeFiles/puffer.dir/edlib.cpp.o CMakeFiles/puffer.dir/Util.cpp.o CMakeFiles/puffer.dir/rank9sel.cpp.o CMakeFiles/puffer.dir/rank9b.cpp.o CMakeFiles/puffer.dir/PufferfishValidate.cpp.o CMakeFiles/puffer.dir/PufferfishStats.cpp.o CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o CMakeFiles/puffer.dir/PufferfishExamine.cpp.o CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o CMakeFiles/puffer.dir/FastxParser.cpp.o CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o CMakeFiles/puffer.dir/PufferFS.cpp.o CMakeFiles/puffer.dir/xxhash.c.o CMakeFiles/puffer.dir/FixFasta.cpp.o CMakeFiles/puffer.dir/MemCollector.cpp.o CMakeFiles/puffer.dir/MemChainer.cpp.o CMakeFiles/puffer.dir/PuffAligner.cpp.o CMakeFiles/puffer.dir/PufferfishAligner.cpp.o CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o CMakeFiles/puffer.dir/metro/metrohash64.cpp.o CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o +/usr/bin/ranlib libpuffer.a +make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu' +[ 76%] Built target puffer In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.3+ds1/include/SalmonOpts.hpp:7, from /build/reproducible-path/salmon-1.10.3+ds1/include/SalmonUtils.hpp:30, - from /build/reproducible-path/salmon-1.10.3+ds1/src/FragmentLengthDistribution.cpp:12: + from /build/reproducible-path/salmon-1.10.3+ds1/tests/LibraryTypeTests.cpp:6: /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -3048,7 +3089,7 @@ from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.3+ds1/include/SalmonOpts.hpp:7, from /build/reproducible-path/salmon-1.10.3+ds1/include/SalmonUtils.hpp:30, - from /build/reproducible-path/salmon-1.10.3+ds1/tests/LibraryTypeTests.cpp:6: + from /build/reproducible-path/salmon-1.10.3+ds1/src/FragmentLengthDistribution.cpp:12: /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -3057,10 +3098,6 @@ 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' -/usr/bin/ar qc libpuffer.a CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o CMakeFiles/puffer.dir/PufferfishIndex.cpp.o CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o CMakeFiles/puffer.dir/edlib.cpp.o CMakeFiles/puffer.dir/Util.cpp.o CMakeFiles/puffer.dir/rank9sel.cpp.o CMakeFiles/puffer.dir/rank9b.cpp.o 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/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/unitTests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/unitTests.dir/link.d CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o CMakeFiles/unitTests.dir/__/tests/GCSampleTests.cpp.o CMakeFiles/unitTests.dir/__/tests/LibraryTypeTests.cpp.o -o unitTests -L/build/reproducible-path/salmon-1.10.3+ds1/lib -L/build/reproducible-path/salmon-1.10.3+ds1/external/install/lib -Wl,-rpath,"\$ORIGIN/../lib:\$ORIGIN/../../lib:\$ORIGIN/:\$ORIGIN/../../external/install/lib" -lboost_iostreams -lboost_filesystem -lboost_system -lboost_timer -lboost_chrono -lboost_program_options -lboost_regex libsalmon_core.a libalevin_core.a -lgff libUnitTestsMain.a /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_timer.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libstaden-read.so /usr/lib/x86_64-linux-gnu/libhtscodecs.so /usr/lib/x86_64-linux-gnu/libcurl.so -lz -lm -llzma -lbz2 -ltbb -ltbbmalloc -lgomp -lrt -ldl /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 @@ -3081,54 +3118,54 @@ make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/salmon.dir/build.make src/CMakeFiles/salmon.dir/build make[4]: Entering directory '/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu' -[ 80%] Building CXX object src/CMakeFiles/salmon.dir/FASTAParser.cpp.o -[ 80%] Building CXX object src/CMakeFiles/salmon.dir/SalmonAlevin.cpp.o +[ 80%] Building CXX object src/CMakeFiles/salmon.dir/EMUtils.cpp.o +[ 80%] Building CXX object src/CMakeFiles/salmon.dir/CollapsedEMOptimizer.cpp.o [ 80%] Building CXX object src/CMakeFiles/salmon.dir/CollapsedCellOptimizer.cpp.o -cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.3+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.3+ds1/external -I/build/reproducible-path/salmon-1.10.3+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish 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-ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/Alevin.cpp.o -MF CMakeFiles/salmon.dir/Alevin.cpp.o.d -o CMakeFiles/salmon.dir/Alevin.cpp.o -c /build/reproducible-path/salmon-1.10.3+ds1/src/Alevin.cpp cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.3+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.3+ds1/external -I/build/reproducible-path/salmon-1.10.3+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra 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-I/build/reproducible-path/salmon-1.10.3+ds1/external -I/build/reproducible-path/salmon-1.10.3+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops 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-I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy 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-Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o -MF CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o.d -o CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o -c /build/reproducible-path/salmon-1.10.3+ds1/src/FragmentStartPositionDistribution.cpp +[ 93%] Building CXX object src/CMakeFiles/salmon.dir/SalmonQuantMerge.cpp.o +[ 94%] Building CXX object src/CMakeFiles/salmon.dir/ProgramOptionsGenerator.cpp.o cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 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-I/build/reproducible-path/salmon-1.10.3+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/BAMUtils.cpp.o -MF CMakeFiles/salmon.dir/BAMUtils.cpp.o.d -o CMakeFiles/salmon.dir/BAMUtils.cpp.o -c /build/reproducible-path/salmon-1.10.3+ds1/src/BAMUtils.cpp +cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.3+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.3+ds1/external -I/build/reproducible-path/salmon-1.10.3+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.3+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/AlignmentCommon.cpp.o -MF CMakeFiles/salmon.dir/AlignmentCommon.cpp.o.d -o CMakeFiles/salmon.dir/AlignmentCommon.cpp.o -c /build/reproducible-path/salmon-1.10.3+ds1/src/AlignmentCommon.cpp In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/pcg_random.hpp:104, from /build/reproducible-path/salmon-1.10.3+ds1/src/CollapsedGibbsSampler.cpp:22: /build/reproducible-path/salmon-1.10.3+ds1/include/pcg_extras.hpp:563:51: warning: macro '__DATE__' might prevent reproducible builds [-Wdate-time] @@ -3153,9 +3190,9 @@ /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.3+ds1/include/SalmonOpts.hpp:7, - from /build/reproducible-path/salmon-1.10.3+ds1/include/ProgramOptionsGenerator.hpp:5, - from /build/reproducible-path/salmon-1.10.3+ds1/src/ProgramOptionsGenerator.cpp:4: + from /build/reproducible-path/salmon-1.10.3+ds1/include/AlignmentCommon.hpp:10, + from /build/reproducible-path/salmon-1.10.3+ds1/include/AlignmentModel.hpp:6, + from /build/reproducible-path/salmon-1.10.3+ds1/src/AlignmentModel.cpp:8: /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -3166,9 +3203,7 @@ /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.3+ds1/include/AlignmentCommon.hpp:10, - from /build/reproducible-path/salmon-1.10.3+ds1/include/AlignmentModel.hpp:6, - from /build/reproducible-path/salmon-1.10.3+ds1/src/AlignmentModel.cpp:8: + from /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonQuantMerge.cpp:29: /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -3179,7 +3214,8 @@ /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonQuantMerge.cpp:29: + from /build/reproducible-path/salmon-1.10.3+ds1/include/ONTAlignmentModel.hpp:9, + from /build/reproducible-path/salmon-1.10.3+ds1/src/ONTAlignmentModel.cpp:11: /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -3202,8 +3238,8 @@ /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.3+ds1/include/ONTAlignmentModel.hpp:9, - from /build/reproducible-path/salmon-1.10.3+ds1/src/ONTAlignmentModel.cpp:11: + from /build/reproducible-path/salmon-1.10.3+ds1/include/AlevinHash.hpp:7, + from /build/reproducible-path/salmon-1.10.3+ds1/src/AlevinHash.cpp:1: /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -3214,8 +3250,9 @@ /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.3+ds1/include/SalmonOpts.hpp:7, - from /build/reproducible-path/salmon-1.10.3+ds1/src/FASTAParser.cpp:11: + from /build/reproducible-path/salmon-1.10.3+ds1/include/AlevinUtils.hpp:27, + from /build/reproducible-path/salmon-1.10.3+ds1/include/Graph.hpp:8, + from /build/reproducible-path/salmon-1.10.3+ds1/src/Graph.cpp:1: /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -3226,8 +3263,9 @@ /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.3+ds1/include/AlevinHash.hpp:7, - from /build/reproducible-path/salmon-1.10.3+ds1/src/AlevinHash.cpp:1: + from /build/reproducible-path/salmon-1.10.3+ds1/include/SalmonOpts.hpp:7, + from /build/reproducible-path/salmon-1.10.3+ds1/include/ProgramOptionsGenerator.hpp:5, + from /build/reproducible-path/salmon-1.10.3+ds1/src/ProgramOptionsGenerator.cpp:4: /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -3238,11 +3276,7 @@ /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/Util.hpp:19, - from /build/reproducible-path/salmon-1.10.3+ds1/include/ReadPair.hpp:6, - from /build/reproducible-path/salmon-1.10.3+ds1/include/AlignmentGroup.hpp:15, - from /build/reproducible-path/salmon-1.10.3+ds1/include/AlignmentLibrary.hpp:12, - from /build/reproducible-path/salmon-1.10.3+ds1/src/GZipWriter.cpp:9: + from /build/reproducible-path/salmon-1.10.3+ds1/src/Alevin.cpp:48: /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -3253,7 +3287,8 @@ /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.3+ds1/src/Alevin.cpp:48: + from /build/reproducible-path/salmon-1.10.3+ds1/include/SalmonOpts.hpp:7, + from /build/reproducible-path/salmon-1.10.3+ds1/src/FASTAParser.cpp:11: /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -3264,8 +3299,11 @@ /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.3+ds1/include/SalmonIndex.hpp:11, - from /build/reproducible-path/salmon-1.10.3+ds1/src/Salmon.cpp:49: + from /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/Util.hpp:19, + from /build/reproducible-path/salmon-1.10.3+ds1/include/ReadPair.hpp:6, + from /build/reproducible-path/salmon-1.10.3+ds1/include/AlignmentGroup.hpp:15, + from /build/reproducible-path/salmon-1.10.3+ds1/include/AlignmentLibrary.hpp:12, + from /build/reproducible-path/salmon-1.10.3+ds1/src/CollapsedEMOptimizer.cpp:22: /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -3276,9 +3314,11 @@ /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.3+ds1/include/SalmonOpts.hpp:7, - from /build/reproducible-path/salmon-1.10.3+ds1/include/SalmonUtils.hpp:30, - from /build/reproducible-path/salmon-1.10.3+ds1/src/FragmentLengthDistribution.cpp:12: + from /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/Util.hpp:19, + from /build/reproducible-path/salmon-1.10.3+ds1/include/ReadPair.hpp:6, + from /build/reproducible-path/salmon-1.10.3+ds1/include/AlignmentGroup.hpp:15, + from /build/reproducible-path/salmon-1.10.3+ds1/include/AlignmentLibrary.hpp:12, + from /build/reproducible-path/salmon-1.10.3+ds1/src/GZipWriter.cpp:9: /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -3289,11 +3329,8 @@ /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.3+ds1/include/SalmonOpts.hpp:7, - from /build/reproducible-path/salmon-1.10.3+ds1/include/SalmonUtils.hpp:30, - from /build/reproducible-path/salmon-1.10.3+ds1/include/Transcript.hpp:8, - from /build/reproducible-path/salmon-1.10.3+ds1/include/EMUtils.hpp:6, - from /build/reproducible-path/salmon-1.10.3+ds1/src/EMUtils.cpp:1: + from /build/reproducible-path/salmon-1.10.3+ds1/include/SalmonIndex.hpp:11, + from /build/reproducible-path/salmon-1.10.3+ds1/src/BuildSalmonIndex.cpp:34: /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -3304,11 +3341,10 @@ /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/Util.hpp:19, - from /build/reproducible-path/salmon-1.10.3+ds1/include/ReadPair.hpp:6, - from /build/reproducible-path/salmon-1.10.3+ds1/include/AlignmentGroup.hpp:15, - from /build/reproducible-path/salmon-1.10.3+ds1/include/AlignmentLibrary.hpp:12, - from /build/reproducible-path/salmon-1.10.3+ds1/src/CollapsedEMOptimizer.cpp:22: + from /build/reproducible-path/salmon-1.10.3+ds1/include/AlevinUtils.hpp:27, + from /build/reproducible-path/salmon-1.10.3+ds1/include/Graph.hpp:8, + from /build/reproducible-path/salmon-1.10.3+ds1/include/DedupUMI.hpp:4, + from /build/reproducible-path/salmon-1.10.3+ds1/src/DedupUMI.cpp:1: /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -3319,9 +3355,9 @@ /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.3+ds1/include/AlevinUtils.hpp:27, - from /build/reproducible-path/salmon-1.10.3+ds1/include/Graph.hpp:8, - from /build/reproducible-path/salmon-1.10.3+ds1/src/Graph.cpp:1: + from /build/reproducible-path/salmon-1.10.3+ds1/include/SalmonOpts.hpp:7, + from /build/reproducible-path/salmon-1.10.3+ds1/include/SalmonUtils.hpp:30, + from /build/reproducible-path/salmon-1.10.3+ds1/src/FragmentLengthDistribution.cpp:12: /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -3330,22 +3366,13 @@ 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' -/build/reproducible-path/salmon-1.10.3+ds1/src/AlignmentModel.cpp: In member function 'AlignmentModel::AlnModelProb AlignmentModel::logLikelihood(bam_seq_t*, bam_seq_t*, Transcript&, std::vector >&)': -/build/reproducible-path/salmon-1.10.3+ds1/src/AlignmentModel.cpp:96:33: warning: unused parameter 'primary' [-Wunused-parameter] - 96 | bam_seq_t* read, bam_seq_t* primary, Transcript& ref, - | ~~~~~~~~~~~^~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/src/AlignmentModel.cpp: In member function 'double AlignmentModel::logLikelihood(const ReadPair&, const ReadPair&, Transcript&)': -/build/reproducible-path/salmon-1.10.3+ds1/src/AlignmentModel.cpp:230:75: warning: unused parameter 'primary' [-Wunused-parameter] - 230 | double AlignmentModel::logLikelihood(const ReadPair& hit, const ReadPair& primary, Transcript& ref) { - | ~~~~~~~~~~~~~~~~^~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/src/AlignmentModel.cpp: In member function 'void AlignmentModel::update(const ReadPair&, const ReadPair&, Transcript&, double, double)': -/build/reproducible-path/salmon-1.10.3+ds1/src/AlignmentModel.cpp:429:66: warning: unused parameter 'primary' [-Wunused-parameter] - 429 | void AlignmentModel::update(const ReadPair& hit, const ReadPair& primary, - | ~~~~~~~~~~~~~~~~^~~~~~~ In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.3+ds1/include/SalmonIndex.hpp:11, - from /build/reproducible-path/salmon-1.10.3+ds1/src/BuildSalmonIndex.cpp:34: + from /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/Util.hpp:19, + from /build/reproducible-path/salmon-1.10.3+ds1/include/ReadPair.hpp:6, + from /build/reproducible-path/salmon-1.10.3+ds1/include/AlignmentGroup.hpp:15, + from /build/reproducible-path/salmon-1.10.3+ds1/include/AlignmentLibrary.hpp:12, + from /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonQuantifyAlignments.cpp:33: /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -3367,7 +3394,8 @@ /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonQuantify.cpp:75: + from /build/reproducible-path/salmon-1.10.3+ds1/include/SalmonIndex.hpp:11, + from /build/reproducible-path/salmon-1.10.3+ds1/src/Salmon.cpp:49: /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -3393,6 +3421,18 @@ 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' +/build/reproducible-path/salmon-1.10.3+ds1/src/AlignmentModel.cpp: In member function 'AlignmentModel::AlnModelProb AlignmentModel::logLikelihood(bam_seq_t*, bam_seq_t*, Transcript&, std::vector >&)': +/build/reproducible-path/salmon-1.10.3+ds1/src/AlignmentModel.cpp:96:33: warning: unused parameter 'primary' [-Wunused-parameter] + 96 | bam_seq_t* read, bam_seq_t* primary, Transcript& ref, + | ~~~~~~~~~~~^~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/src/AlignmentModel.cpp: In member function 'double AlignmentModel::logLikelihood(const ReadPair&, const ReadPair&, Transcript&)': +/build/reproducible-path/salmon-1.10.3+ds1/src/AlignmentModel.cpp:230:75: warning: unused parameter 'primary' [-Wunused-parameter] + 230 | double AlignmentModel::logLikelihood(const ReadPair& hit, const ReadPair& primary, Transcript& ref) { + | ~~~~~~~~~~~~~~~~^~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/src/AlignmentModel.cpp: In member function 'void AlignmentModel::update(const ReadPair&, const ReadPair&, Transcript&, double, double)': +/build/reproducible-path/salmon-1.10.3+ds1/src/AlignmentModel.cpp:429:66: warning: unused parameter 'primary' [-Wunused-parameter] + 429 | void AlignmentModel::update(const ReadPair& hit, const ReadPair& primary, + | ~~~~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/salmon-1.10.3+ds1/src/ONTAlignmentModel.cpp: In constructor 'ONTAlignmentModel::ONTAlignmentModel(double, uint32_t)': /build/reproducible-path/salmon-1.10.3+ds1/src/ONTAlignmentModel.cpp:17:45: warning: unused parameter 'alpha' [-Wunused-parameter] 17 | ONTAlignmentModel::ONTAlignmentModel(double alpha, uint32_t readBins) @@ -3411,40 +3451,11 @@ | ~~~~~~~~~~~~~~^~ In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.3+ds1/include/AlevinUtils.hpp:27, - from /build/reproducible-path/salmon-1.10.3+ds1/include/Graph.hpp:8, - from /build/reproducible-path/salmon-1.10.3+ds1/include/DedupUMI.hpp:4, - from /build/reproducible-path/salmon-1.10.3+ds1/src/DedupUMI.cpp:1: -/build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 197 | registry_t() {} - | ^ -/build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' -/build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 198 | registry_t(const registry_t&) = delete; - | ^ -/build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' -In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/spdlog_impl.h:12, - from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/Util.hpp:19, - from /build/reproducible-path/salmon-1.10.3+ds1/include/ReadPair.hpp:6, - from /build/reproducible-path/salmon-1.10.3+ds1/include/AlignmentGroup.hpp:15, - from /build/reproducible-path/salmon-1.10.3+ds1/include/AlignmentLibrary.hpp:12, - from /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonQuantifyAlignments.cpp:33: -/build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 197 | registry_t() {} - | ^ -/build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' -/build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 198 | registry_t(const registry_t&) = delete; - | ^ -/build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' -In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/spdlog_impl.h:12, - from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/spdlog.h:192, - from /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/Util.hpp:19, - from /build/reproducible-path/salmon-1.10.3+ds1/include/ReadPair.hpp:6, - from /build/reproducible-path/salmon-1.10.3+ds1/include/AlignmentGroup.hpp:15, - from /build/reproducible-path/salmon-1.10.3+ds1/include/AlignmentLibrary.hpp:12, - from /build/reproducible-path/salmon-1.10.3+ds1/src/CollapsedGibbsSampler.cpp:30: + from /build/reproducible-path/salmon-1.10.3+ds1/include/SalmonOpts.hpp:7, + from /build/reproducible-path/salmon-1.10.3+ds1/include/SalmonUtils.hpp:30, + from /build/reproducible-path/salmon-1.10.3+ds1/include/Transcript.hpp:8, + from /build/reproducible-path/salmon-1.10.3+ds1/include/EMUtils.hpp:6, + from /build/reproducible-path/salmon-1.10.3+ds1/src/EMUtils.cpp:1: /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ @@ -3453,15 +3464,6 @@ 198 | registry_t(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' -In file included from /build/reproducible-path/salmon-1.10.3+ds1/src/Alevin.cpp:60: -/build/reproducible-path/salmon-1.10.3+ds1/include/BarcodeModel.hpp: In function 'void alevin::model::coinTossBarcodeModel(std::string, const std::vector >&, MapT&)': -/build/reproducible-path/salmon-1.10.3+ds1/include/BarcodeModel.hpp:168:31: warning: loop variable 'trueBarcode' creates a copy from type 'const std::string' {aka 'const std::__cxx11::basic_string'} [-Wrange-loop-construct] - 168 | for(const std::string trueBarcode: trueBarcodes){ - | ^~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/include/BarcodeModel.hpp:168:31: note: use reference type to prevent copying - 168 | for(const std::string trueBarcode: trueBarcodes){ - | ^~~~~~~~~~~ - | & In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/AlevinUtils.hpp:47: /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' @@ -3612,6 +3614,41 @@ /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::pair; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::pair; _T2 = unsigned int]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/spdlog_impl.h:12, + from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/spdlog.h:192, + from /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonQuantify.cpp:75: +/build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 197 | registry_t() {} + | ^ +/build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' +/build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 198 | registry_t(const registry_t&) = delete; + | ^ +/build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' +In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/spdlog_impl.h:12, + from /build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/spdlog.h:192, + from /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/Util.hpp:19, + from /build/reproducible-path/salmon-1.10.3+ds1/include/ReadPair.hpp:6, + from /build/reproducible-path/salmon-1.10.3+ds1/include/AlignmentGroup.hpp:15, + from /build/reproducible-path/salmon-1.10.3+ds1/include/AlignmentLibrary.hpp:12, + from /build/reproducible-path/salmon-1.10.3+ds1/src/CollapsedGibbsSampler.cpp:30: +/build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 197 | registry_t() {} + | ^ +/build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >' +/build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 198 | registry_t(const registry_t&) = delete; + | ^ +/build/reproducible-path/salmon-1.10.3+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' +In file included from /build/reproducible-path/salmon-1.10.3+ds1/src/Alevin.cpp:60: +/build/reproducible-path/salmon-1.10.3+ds1/include/BarcodeModel.hpp: In function 'void alevin::model::coinTossBarcodeModel(std::string, const std::vector >&, MapT&)': +/build/reproducible-path/salmon-1.10.3+ds1/include/BarcodeModel.hpp:168:31: warning: loop variable 'trueBarcode' creates a copy from type 'const std::string' {aka 'const std::__cxx11::basic_string'} [-Wrange-loop-construct] + 168 | for(const std::string trueBarcode: trueBarcodes){ + | ^~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/include/BarcodeModel.hpp:168:31: note: use reference type to prevent copying + 168 | for(const std::string trueBarcode: trueBarcodes){ + | ^~~~~~~~~~~ + | & In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/EquivalenceClassBuilder.hpp:18, from /build/reproducible-path/salmon-1.10.3+ds1/include/AlignmentLibrary.hpp:19: /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': @@ -4555,8 +4592,9 @@ /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, long unsigned int>, spp::libc_allocator, long unsigned int> > >::value_type' {aka 'std::pair, long unsigned int>'} to 'spp::sparsegroup, long unsigned int>, spp::libc_allocator, long unsigned int> > >::mutable_reference' {aka 'std::pair, long unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _U2 = long unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::__cxx11::basic_string; _T2 = long unsigned int]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/EquivalenceClassBuilder.hpp:18, - from /build/reproducible-path/salmon-1.10.3+ds1/include/AlignmentLibrary.hpp:19: +In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/AlevinUtils.hpp:47, + from /build/reproducible-path/salmon-1.10.3+ds1/include/AlevinHash.hpp:10, + from /build/reproducible-path/salmon-1.10.3+ds1/src/Alevin.cpp:58: /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1440 | _set_val(&_group[offset], val); @@ -4607,6 +4645,7 @@ /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/AlevinUtils.hpp:47: /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1440 | _set_val(&_group[offset], val); @@ -4632,13 +4671,10 @@ /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' - 1407 | _init_val((mutable_pointer)&_group[num_items], val); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1435 | _set_aux(alloc, offset, val, check_alloc_type()); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1440 | _set_val(&_group[offset], val); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ @@ -4657,16 +4693,13 @@ /build/reproducible-path/salmon-1.10.3+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-Wcast-user-defined] - 1339 | ::new (p) value_type(std::move((mutable_reference)val)); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' - 1390 | _init_val((mutable_pointer)(_group + offset), val); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' - 1435 | _set_aux(alloc, offset, val, check_alloc_type()); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-Wcast-user-defined] + 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1440 | _set_val(&_group[offset], val); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ @@ -4685,16 +4718,13 @@ /build/reproducible-path/salmon-1.10.3+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] - 1339 | ::new (p) value_type(std::move((mutable_reference)val)); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' - 1407 | _init_val((mutable_pointer)&_group[num_items], val); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1435 | _set_aux(alloc, offset, val, check_alloc_type()); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] + 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1440 | _set_val(&_group[offset], val); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ @@ -4713,60 +4743,32 @@ /build/reproducible-path/salmon-1.10.3+ds1/include/Graph.hpp:28:21: required from here 28 | edges[source].insert(sink); | ^ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-Wcast-user-defined] - 1339 | ::new (p) value_type(std::move((mutable_reference)val)); - | ^~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/AlevinUtils.hpp:47, - from /build/reproducible-path/salmon-1.10.3+ds1/include/AlevinHash.hpp:10, - from /build/reproducible-path/salmon-1.10.3+ds1/src/Alevin.cpp:58: -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1440 | _set_val(&_group[offset], val); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here - 51 | barcodeGroup[barcode][umi] = 1; - | ^ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-Wcast-user-defined] +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = std::vector; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = std::vector]' 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here - 51 | barcodeGroup[barcode][umi] = 1; - | ^ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] +/build/reproducible-path/salmon-1.10.3+ds1/src/DedupUMI.cpp:32:17: required from here + 32 | tidMap[txp].emplace_back(eqId); + | ^ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = std::vector; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = std::vector]' [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/EquivalenceClassBuilder.hpp:18, @@ -4821,162 +4823,104 @@ /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/EquivalenceClassBuilder.hpp:18, - from /build/reproducible-path/salmon-1.10.3+ds1/include/ReadExperiment.hpp:7: -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair, std::pair > >; Alloc = spp::libc_allocator, std::pair > > >; value_type = std::pair, std::pair > >; reference = std::pair, std::pair > >&]': +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, std::pair > >; T = std::pair, std::pair > >; Alloc = spp::libc_allocator, std::pair > > >; allocator_type = spp::libc_allocator, std::pair > > >; size_type = unsigned char]' 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, std::pair > >; T = std::pair, std::pair > >; Alloc = spp::libc_allocator, std::pair > > >; pointer = std::pair, std::pair > >*; allocator_type = spp::libc_allocator, std::pair > > >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, std::pair > >; T = std::pair, std::pair > >; Alloc = spp::libc_allocator, std::pair > > >; reference = std::pair, std::pair > >&; size_type = long unsigned int]' 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, std::pair > >; Value = std::pair, std::pair > >; Key = std::vector; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, std::pair >, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, std::pair >, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, std::pair > > >; reference = std::pair, std::pair > >&; size_type = long unsigned int]' 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, std::pair >, boost::hash > >::DefaultValue; KT = std::vector&; Value = std::pair, std::pair > >; Key = std::vector; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, std::pair >, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, std::pair >, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, std::pair > > >; value_type = std::pair, std::pair > >]' 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::vector&; Key = std::vector; T = std::pair >; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, std::pair > > >; mapped_type = std::pair >]' 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here - 51 | barcodeGroup[barcode][umi] = 1; - | ^ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-Wcast-user-defined] +/build/reproducible-path/salmon-1.10.3+ds1/src/DedupUMI.cpp:285:29: required from here + 285 | eqclassHash[genesVec].first += 1; + | ^ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, std::pair > >, spp::libc_allocator, std::pair > > > >::value_type' {aka 'std::pair, std::pair > >'} to 'spp::sparsegroup, std::pair > >, spp::libc_allocator, std::pair > > > >::mutable_reference' {aka 'std::pair, std::pair > >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::vector; _U2 = std::pair >; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::vector; _T2 = std::pair >]' [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = short unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = short unsigned int&; Value = std::pair; Key = short unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = short unsigned int&; Key = short unsigned int; T = short unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = short unsigned int]' 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here - 51 | barcodeGroup[barcode][umi] = 1; - | ^ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] +/build/reproducible-path/salmon-1.10.3+ds1/src/DedupUMI.cpp:286:47: required from here + 286 | eqclassHash[genesVec].second[readspmol] += 1; + | ^ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const short unsigned int; _U2 = short unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = short unsigned int; _T2 = short unsigned int]' [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]' 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::vector; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]' 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int, boost::hash > >::DefaultValue; KT = std::vector&; Value = std::pair, unsigned int>; Key = std::vector; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>]' 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::vector&; Key = std::vector; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/include/Graph.hpp:28:21: required from here - 28 | edges[source].insert(sink); - | ^ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-Wcast-user-defined] +/build/reproducible-path/salmon-1.10.3+ds1/src/DedupUMI.cpp:413:29: required from here + 413 | eqclassHash[genesVec] += 1; + | ^ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::vector; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::vector; _T2 = unsigned int]' [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' - 1407 | _init_val((mutable_pointer)&_group[num_items], val); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1435 | _set_aux(alloc, offset, val, check_alloc_type()); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here - 51 | barcodeGroup[barcode][umi] = 1; - | ^ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-Wcast-user-defined] - 1339 | ::new (p) value_type(std::move((mutable_reference)val)); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' - 1390 | _init_val((mutable_pointer)(_group + offset), val); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' - 1435 | _set_aux(alloc, offset, val, check_alloc_type()); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here - 51 | barcodeGroup[barcode][umi] = 1; - | ^ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] - 1339 | ::new (p) value_type(std::move((mutable_reference)val)); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = unsigned int&; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/include/Graph.hpp:28:21: required from here - 28 | edges[source].insert(sink); - | ^ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-Wcast-user-defined] +/build/reproducible-path/salmon-1.10.3+ds1/src/DedupUMI.cpp:477:29: required from here + 477 | vertexIndices[gene] = gid; + | ^ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': @@ -5035,31 +4979,6 @@ /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' - 1440 | _set_val(&_group[offset], val); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = short unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = const short unsigned int&; Value = std::pair; Key = short unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = const short unsigned int&; Key = short unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/src/CollapsedCellOptimizer.cpp:747:45: required from here - 747 | arboFragCounts[gid][it.first] += it.second; - | ^ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const short unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = short unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] - 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); - | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 1407 | _init_val((mutable_pointer)&_group[num_items], val); @@ -5172,172 +5091,6 @@ /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' - 1390 | _init_val((mutable_pointer)(_group + offset), val); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' - 1435 | _set_aux(alloc, offset, val, check_alloc_type()); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = short unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = const short unsigned int&; Value = std::pair; Key = short unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = const short unsigned int&; Key = short unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/src/CollapsedCellOptimizer.cpp:747:45: required from here - 747 | arboFragCounts[gid][it.first] += it.second; - | ^ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const short unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = short unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] - 1339 | ::new (p) value_type(std::move((mutable_reference)val)); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' - 1440 | _set_val(&_group[offset], val); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int>::DefaultValue; KT = std::__cxx11::basic_string&; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = unsigned int; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/src/CollapsedCellOptimizer.cpp:1087:29: required from 'bool CollapsedCellOptimizer::optimize(EqMapT&, spp::sparse_hash_map&, spp::sparse_hash_map, unsigned int>&, AlevinOpts&, GZipWriter&, std::vector >&, std::vector&, CFreqMapT&, size_t) [with ProtocolT = alevin::protocols::DropSeq; EqMapT = libcuckoo::cuckoohash_map, std::allocator >, 4>; CFreqMapT = tsl::array_map; size_t = long unsigned int]' - 1087 | mRnaGenes.insert(geneIdxMap[ gene ]); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/src/CollapsedCellOptimizer.cpp:1426:68: required from here - 1426 | size_t numLowConfidentBarcode); - | ^ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::__cxx11::basic_string; _T2 = unsigned int]' [-Wcast-user-defined] - 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; mutable_value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' - 1407 | _init_val((mutable_pointer)&_group[num_items], val); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' - 1435 | _set_aux(alloc, offset, val, check_alloc_type()); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int>::DefaultValue; KT = std::__cxx11::basic_string&; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = unsigned int; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/src/CollapsedCellOptimizer.cpp:1087:29: required from 'bool CollapsedCellOptimizer::optimize(EqMapT&, spp::sparse_hash_map&, spp::sparse_hash_map, unsigned int>&, AlevinOpts&, GZipWriter&, std::vector >&, std::vector&, CFreqMapT&, size_t) [with ProtocolT = alevin::protocols::DropSeq; EqMapT = libcuckoo::cuckoohash_map, std::allocator >, 4>; CFreqMapT = tsl::array_map; size_t = long unsigned int]' - 1087 | mRnaGenes.insert(geneIdxMap[ gene ]); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/src/CollapsedCellOptimizer.cpp:1426:68: required from here - 1426 | size_t numLowConfidentBarcode); - | ^ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::__cxx11::basic_string; _T2 = unsigned int]' [-Wcast-user-defined] - 1339 | ::new (p) value_type(std::move((mutable_reference)val)); - | ^~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/EquivalenceClassBuilder.hpp:18, - from /build/reproducible-path/salmon-1.10.3+ds1/include/ReadExperiment.hpp:7, - from /build/reproducible-path/salmon-1.10.3+ds1/include/SalmonMappingUtils.hpp:44, - from /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonQuantify.cpp:93: -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1440 | _set_val(&_group[offset], val); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here - 51 | barcodeGroup[barcode][umi] = 1; - | ^ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-Wcast-user-defined] - 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' - 1440 | _set_val(&_group[offset], val); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here - 51 | barcodeGroup[barcode][umi] = 1; - | ^ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] - 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1440 | _set_val(&_group[offset], val); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/include/Graph.hpp:28:21: required from here - 28 | edges[source].insert(sink); - | ^ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-Wcast-user-defined] - 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); - | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::DropSeq; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]' 1730 | process_reads_sc_sketch( @@ -5392,6 +5145,31 @@ /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1440 | _set_val(&_group[offset], val); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/include/Graph.hpp:28:21: required from here + 28 | edges[source].insert(sink); + | ^ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-Wcast-user-defined] + 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); + | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::DropSeq; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishIndex; size_t = long unsigned int]' 1730 | process_reads_sc_sketch( @@ -5446,88 +5224,144 @@ /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = std::vector; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = std::vector]' 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here - 51 | barcodeGroup[barcode][umi] = 1; - | ^ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-Wcast-user-defined] +/build/reproducible-path/salmon-1.10.3+ds1/src/DedupUMI.cpp:32:17: required from here + 32 | tidMap[txp].emplace_back(eqId); + | ^ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = std::vector; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = std::vector]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair, std::pair > >; Alloc = spp::libc_allocator, std::pair > > >; mutable_value_type = std::pair, std::pair > >; reference = std::pair, std::pair > >&]': +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair, std::pair > >; T = std::pair, std::pair > >; Alloc = spp::libc_allocator, std::pair > > >; allocator_type = spp::libc_allocator, std::pair > > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' + 1407 | _init_val((mutable_pointer)&_group[num_items], val); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, std::pair > >; T = std::pair, std::pair > >; Alloc = spp::libc_allocator, std::pair > > >; allocator_type = spp::libc_allocator, std::pair > > >; size_type = unsigned char]' + 1435 | _set_aux(alloc, offset, val, check_alloc_type()); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, std::pair > >; T = std::pair, std::pair > >; Alloc = spp::libc_allocator, std::pair > > >; pointer = std::pair, std::pair > >*; allocator_type = spp::libc_allocator, std::pair > > >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, std::pair > >; T = std::pair, std::pair > >; Alloc = spp::libc_allocator, std::pair > > >; reference = std::pair, std::pair > >&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, std::pair > >; Value = std::pair, std::pair > >; Key = std::vector; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, std::pair >, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, std::pair >, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, std::pair > > >; reference = std::pair, std::pair > >&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, std::pair >, boost::hash > >::DefaultValue; KT = std::vector&; Value = std::pair, std::pair > >; Key = std::vector; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, std::pair >, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, std::pair >, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, std::pair > > >; value_type = std::pair, std::pair > >]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::vector&; Key = std::vector; T = std::pair >; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, std::pair > > >; mapped_type = std::pair >]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/src/DedupUMI.cpp:285:29: required from here + 285 | eqclassHash[genesVec].first += 1; + | ^ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, std::pair > >, spp::libc_allocator, std::pair > > > >::value_type' {aka 'std::pair, std::pair > >'} to 'spp::sparsegroup, std::pair > >, spp::libc_allocator, std::pair > > > >::mutable_reference' {aka 'std::pair, std::pair > >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::vector; _U2 = std::pair >; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::vector; _T2 = std::pair >]' [-Wcast-user-defined] + 1339 | ::new (p) value_type(std::move((mutable_reference)val)); + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' 1390 | _init_val((mutable_pointer)(_group + offset), val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = short unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = short unsigned int&; Value = std::pair; Key = short unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = short unsigned int&; Key = short unsigned int; T = short unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = short unsigned int]' 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here - 51 | barcodeGroup[barcode][umi] = 1; - | ^ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] +/build/reproducible-path/salmon-1.10.3+ds1/src/DedupUMI.cpp:286:47: required from here + 286 | eqclassHash[genesVec].second[readspmol] += 1; + | ^ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const short unsigned int; _U2 = short unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = short unsigned int; _T2 = short unsigned int]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; mutable_value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]' 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::vector; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]' 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int, boost::hash > >::DefaultValue; KT = std::vector&; Value = std::pair, unsigned int>; Key = std::vector; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>]' 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::vector&; Key = std::vector; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/include/Graph.hpp:28:21: required from here - 28 | edges[source].insert(sink); - | ^ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-Wcast-user-defined] +/build/reproducible-path/salmon-1.10.3+ds1/src/DedupUMI.cpp:413:29: required from here + 413 | eqclassHash[genesVec] += 1; + | ^ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::vector; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::vector; _T2 = unsigned int]' [-Wcast-user-defined] + 1339 | ::new (p) value_type(std::move((mutable_reference)val)); + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' + 1390 | _init_val((mutable_pointer)(_group + offset), val); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1435 | _set_aux(alloc, offset, val, check_alloc_type()); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = unsigned int&; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/src/DedupUMI.cpp:477:29: required from here + 477 | vertexIndices[gene] = gid; + | ^ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::CITESeq; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': @@ -5746,6 +5580,114 @@ /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ +In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/EquivalenceClassBuilder.hpp:18, + from /build/reproducible-path/salmon-1.10.3+ds1/include/ReadExperiment.hpp:7: +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1440 | _set_val(&_group[offset], val); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here + 51 | barcodeGroup[barcode][umi] = 1; + | ^ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-Wcast-user-defined] + 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1440 | _set_val(&_group[offset], val); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here + 51 | barcodeGroup[barcode][umi] = 1; + | ^ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] + 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' + 1407 | _init_val((mutable_pointer)&_group[num_items], val); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1435 | _set_aux(alloc, offset, val, check_alloc_type()); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here + 51 | barcodeGroup[barcode][umi] = 1; + | ^ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-Wcast-user-defined] + 1339 | ::new (p) value_type(std::move((mutable_reference)val)); + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' + 1390 | _init_val((mutable_pointer)(_group + offset), val); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1435 | _set_aux(alloc, offset, val, check_alloc_type()); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here + 51 | barcodeGroup[barcode][umi] = 1; + | ^ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] + 1339 | ::new (p) value_type(std::move((mutable_reference)val)); + | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::ChromiumV3; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]' 1730 | process_reads_sc_sketch( @@ -5905,6 +5847,34 @@ /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp:489:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable] 489 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' + 1407 | _init_val((mutable_pointer)&_group[num_items], val); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1435 | _set_aux(alloc, offset, val, check_alloc_type()); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/include/Graph.hpp:28:21: required from here + 28 | edges[source].insert(sink); + | ^ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-Wcast-user-defined] + 1339 | ::new (p) value_type(std::move((mutable_reference)val)); + | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ @@ -5962,6 +5932,40 @@ /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' + 1440 | _set_val(&_group[offset], val); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2251:27: required from 'void spp::sparsetable::move(size_type, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int; reference = std::pair, unsigned int>&]' + 2251 | which_group(i).set(_alloc, pos_in_group(i), val); + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2830:23: required from 'void spp::sparse_hashtable::_move_from(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]' + 2830 | table.move(bucknum, *it); // moves the value to here + | ~~~~~~~~~~^~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2948:9: required from 'spp::sparse_hashtable::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]' + 2948 | _move_from(mover, ht, min_buckets_wanted); + | ^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2680:30: required from 'bool spp::sparse_hashtable::_maybe_shrink() [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >]' + 2680 | sparse_hashtable tmp(MoveDontCopy, *this, sz); + | ^~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2846:13: required from 'void spp::sparse_hashtable::resize(size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]' + 2846 | _maybe_shrink(); + | ^~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3799:51: required from 'void spp::sparse_hash_map::resize(size_type) [with Key = std::pair; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]' + 3799 | void resize(size_type cnt) { rep.resize(cnt); } + | ~~~~~~~~~~^~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3801:41: required from 'void spp::sparse_hash_map::reserve(size_type) [with Key = std::pair; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]' + 3801 | void reserve(size_type cnt) { resize(cnt); } // c++11 + | ^~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/src/DedupUMI.cpp:39:25: required from here + 39 | vertexIndexMap.reserve(numClasses); + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::pair; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::pair; _T2 = unsigned int]' [-Wcast-user-defined] + 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); + | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::Gemcode; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]' 1730 | process_reads_sc_sketch( @@ -6070,6 +6074,31 @@ /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1440 | _set_val(&_group[offset], val); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/include/Graph.hpp:28:21: required from here + 28 | edges[source].insert(sink); + | ^ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-Wcast-user-defined] + 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); + | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::CELSeq; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]' 1730 | process_reads_sc_sketch( @@ -6124,6 +6153,58 @@ /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ +In file included from /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:65: +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp_utils.h: In instantiation of 'T* spp::libc_allocator::reallocate(pointer, size_t) [with T = std::pair, unsigned int>; pointer = std::pair, unsigned int>*; size_t = long unsigned int]': +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1383:38: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' + 1383 | _group = alloc.reallocate(_group, num_alloc); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' + 1435 | _set_aux(alloc, offset, val, check_alloc_type()); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2251:27: required from 'void spp::sparsetable::move(size_type, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int; reference = std::pair, unsigned int>&]' + 2251 | which_group(i).set(_alloc, pos_in_group(i), val); + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2830:23: required from 'void spp::sparse_hashtable::_move_from(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]' + 2830 | table.move(bucknum, *it); // moves the value to here + | ~~~~~~~~~~^~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2948:9: required from 'spp::sparse_hashtable::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]' + 2948 | _move_from(mover, ht, min_buckets_wanted); + | ^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2680:30: required from 'bool spp::sparse_hashtable::_maybe_shrink() [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >]' + 2680 | sparse_hashtable tmp(MoveDontCopy, *this, sz); + | ^~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2846:13: required from 'void spp::sparse_hashtable::resize(size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]' + 2846 | _maybe_shrink(); + | ^~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3799:51: required from 'void spp::sparse_hash_map::resize(size_type) [with Key = std::pair; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]' + 3799 | void resize(size_type cnt) { rep.resize(cnt); } + | ~~~~~~~~~~^~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3801:41: required from 'void spp::sparse_hash_map::reserve(size_type) [with Key = std::pair; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]' + 3801 | void reserve(size_type cnt) { resize(cnt); } // c++11 + | ^~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/src/DedupUMI.cpp:39:25: required from here + 39 | vertexIndexMap.reserve(numClasses); + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp_utils.h:425:51: warning: 'void* realloc(void*, size_t)' moving an object of non-trivially copyable type 'struct std::pair, unsigned int>'; use 'new' and 'delete' instead [-Wclass-memaccess] + 425 | pointer res = static_cast(realloc(p, new_size * sizeof(T))); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/15/bits/stl_algobase.h:64, + from /usr/include/c++/15/string:53, + from /usr/include/c++/15/bits/locale_classes.h:42, + from /usr/include/c++/15/bits/ios_base.h:43, + from /usr/include/c++/15/streambuf:45, + from /usr/include/c++/15/bits/streambuf_iterator.h:37, + from /usr/include/c++/15/iterator:68, + from /usr/include/boost/graph/graph_traits.hpp:14, + from /usr/include/boost/graph/depth_first_search.hpp:17, + from /usr/include/boost/graph/connected_components.hpp:15, + from /build/reproducible-path/salmon-1.10.3+ds1/include/Graph.hpp:4: +/usr/include/c++/15/bits/stl_pair.h:302:12: note: 'struct std::pair, unsigned int>' declared here + 302 | struct pair + | ^~~~ /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::CELSeq; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishIndex; size_t = long unsigned int]' 1730 | process_reads_sc_sketch( @@ -6175,9 +6256,71 @@ /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp:489:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable] 489 | LibraryFormat expectedLibraryFormat = rl.format(); | ^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; mutable_value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' + 1390 | _init_val((mutable_pointer)(_group + offset), val); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' + 1435 | _set_aux(alloc, offset, val, check_alloc_type()); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2251:27: required from 'void spp::sparsetable::move(size_type, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int; reference = std::pair, unsigned int>&]' + 2251 | which_group(i).set(_alloc, pos_in_group(i), val); + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2830:23: required from 'void spp::sparse_hashtable::_move_from(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]' + 2830 | table.move(bucknum, *it); // moves the value to here + | ~~~~~~~~~~^~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2948:9: required from 'spp::sparse_hashtable::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]' + 2948 | _move_from(mover, ht, min_buckets_wanted); + | ^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2680:30: required from 'bool spp::sparse_hashtable::_maybe_shrink() [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >]' + 2680 | sparse_hashtable tmp(MoveDontCopy, *this, sz); + | ^~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2846:13: required from 'void spp::sparse_hashtable::resize(size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]' + 2846 | _maybe_shrink(); + | ^~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3799:51: required from 'void spp::sparse_hash_map::resize(size_type) [with Key = std::pair; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]' + 3799 | void resize(size_type cnt) { rep.resize(cnt); } + | ~~~~~~~~~~^~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3801:41: required from 'void spp::sparse_hash_map::reserve(size_type) [with Key = std::pair; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]' + 3801 | void reserve(size_type cnt) { resize(cnt); } // c++11 + | ^~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/src/DedupUMI.cpp:39:25: required from here + 39 | vertexIndexMap.reserve(numClasses); + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::pair; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::pair; _T2 = unsigned int]' [-Wcast-user-defined] + 1339 | ::new (p) value_type(std::move((mutable_reference)val)); + | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1440 | _set_val(&_group[offset], val); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = short unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = const short unsigned int&; Value = std::pair; Key = short unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = const short unsigned int&; Key = short unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/src/CollapsedCellOptimizer.cpp:747:45: required from here + 747 | arboFragCounts[gid][it.first] += it.second; + | ^ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const short unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = short unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] + 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); + | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::CELSeq2; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]' 1730 | process_reads_sc_sketch( @@ -6394,6 +6537,62 @@ /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' + 1407 | _init_val((mutable_pointer)&_group[num_items], val); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1435 | _set_aux(alloc, offset, val, check_alloc_type()); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here + 51 | barcodeGroup[barcode][umi] = 1; + | ^ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-Wcast-user-defined] + 1339 | ::new (p) value_type(std::move((mutable_reference)val)); + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' + 1390 | _init_val((mutable_pointer)(_group + offset), val); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1435 | _set_aux(alloc, offset, val, check_alloc_type()); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here + 51 | barcodeGroup[barcode][umi] = 1; + | ^ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] + 1339 | ::new (p) value_type(std::move((mutable_reference)val)); + | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::SplitSeqV2; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]' 1730 | process_reads_sc_sketch( @@ -6502,6 +6701,34 @@ /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' + 1407 | _init_val((mutable_pointer)&_group[num_items], val); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1435 | _set_aux(alloc, offset, val, check_alloc_type()); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/include/Graph.hpp:28:21: required from here + 28 | edges[source].insert(sink); + | ^ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-Wcast-user-defined] + 1339 | ::new (p) value_type(std::move((mutable_reference)val)); + | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::QuartzSeq2; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]' 1730 | process_reads_sc_sketch( @@ -6610,6 +6837,34 @@ /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' + 1390 | _init_val((mutable_pointer)(_group + offset), val); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1435 | _set_aux(alloc, offset, val, check_alloc_type()); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = short unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = const short unsigned int&; Value = std::pair; Key = short unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = const short unsigned int&; Key = short unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/src/CollapsedCellOptimizer.cpp:747:45: required from here + 747 | arboFragCounts[gid][it.first] += it.second; + | ^ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const short unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = short unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] + 1339 | ::new (p) value_type(std::move((mutable_reference)val)); + | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::SciSeq3; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]' 1730 | process_reads_sc_sketch( @@ -6664,6 +6919,34 @@ /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' + 1440 | _set_val(&_group[offset], val); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int>::DefaultValue; KT = std::__cxx11::basic_string&; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = unsigned int; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/src/CollapsedCellOptimizer.cpp:1087:29: required from 'bool CollapsedCellOptimizer::optimize(EqMapT&, spp::sparse_hash_map&, spp::sparse_hash_map, unsigned int>&, AlevinOpts&, GZipWriter&, std::vector >&, std::vector&, CFreqMapT&, size_t) [with ProtocolT = alevin::protocols::DropSeq; EqMapT = libcuckoo::cuckoohash_map, std::allocator >, 4>; CFreqMapT = tsl::array_map; size_t = long unsigned int]' + 1087 | mRnaGenes.insert(geneIdxMap[ gene ]); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/src/CollapsedCellOptimizer.cpp:1426:68: required from here + 1426 | size_t numLowConfidentBarcode); + | ^ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::__cxx11::basic_string; _T2 = unsigned int]' [-Wcast-user-defined] + 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); + | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::SciSeq3; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishIndex; size_t = long unsigned int]' 1730 | process_reads_sc_sketch( @@ -6718,6 +7001,58 @@ /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ +In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/EquivalenceClassBuilder.hpp:18, + from /build/reproducible-path/salmon-1.10.3+ds1/include/AlignmentLibrary.hpp:19: +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1440 | _set_val(&_group[offset], val); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here + 51 | barcodeGroup[barcode][umi] = 1; + | ^ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-Wcast-user-defined] + 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1440 | _set_val(&_group[offset], val); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here + 51 | barcodeGroup[barcode][umi] = 1; + | ^ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] + 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); + | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::Custom; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]' 1730 | process_reads_sc_sketch( @@ -6934,6 +7269,37 @@ /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; mutable_value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' + 1407 | _init_val((mutable_pointer)&_group[num_items], val); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' + 1435 | _set_aux(alloc, offset, val, check_alloc_type()); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' + 1453 | _set(alloc, i, offset, val); // may change _group pointer + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]' + 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]' + 3170 | return table.set(pos, obj); + | ~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int>::DefaultValue; KT = std::__cxx11::basic_string&; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>]' + 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = unsigned int; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]' + 3813 | return rep.template find_or_insert(std::forward(key)).second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/src/CollapsedCellOptimizer.cpp:1087:29: required from 'bool CollapsedCellOptimizer::optimize(EqMapT&, spp::sparse_hash_map&, spp::sparse_hash_map, unsigned int>&, AlevinOpts&, GZipWriter&, std::vector >&, std::vector&, CFreqMapT&, size_t) [with ProtocolT = alevin::protocols::DropSeq; EqMapT = libcuckoo::cuckoohash_map, std::allocator >, 4>; CFreqMapT = tsl::array_map; size_t = long unsigned int]' + 1087 | mRnaGenes.insert(geneIdxMap[ gene ]); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/src/CollapsedCellOptimizer.cpp:1426:68: required from here + 1426 | size_t numLowConfidentBarcode); + | ^ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::__cxx11::basic_string; _T2 = unsigned int]' [-Wcast-user-defined] + 1339 | ::new (p) value_type(std::move((mutable_reference)val)); + | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/EquivalenceClassBuilder.hpp:18, from /build/reproducible-path/salmon-1.10.3+ds1/include/AlignmentLibrary.hpp:19: /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': @@ -7011,36 +7377,13 @@ /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/AlevinUtils.hpp:47: -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1440 | _set_val(&_group[offset], val); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/include/Graph.hpp:28:21: required from here - 28 | edges[source].insert(sink); - | ^ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-Wcast-user-defined] - 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1440 | _set_val(&_group[offset], val); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' + 1407 | _init_val((mutable_pointer)&_group[num_items], val); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' + 1435 | _set_aux(alloc, offset, val, check_alloc_type()); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ @@ -7059,13 +7402,16 @@ /build/reproducible-path/salmon-1.10.3+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-Wcast-user-defined] - 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' - 1440 | _set_val(&_group[offset], val); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-Wcast-user-defined] + 1339 | ::new (p) value_type(std::move((mutable_reference)val)); + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' + 1390 | _init_val((mutable_pointer)(_group + offset), val); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' + 1435 | _set_aux(alloc, offset, val, check_alloc_type()); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ @@ -7084,9 +7430,9 @@ /build/reproducible-path/salmon-1.10.3+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here 51 | barcodeGroup[barcode][umi] = 1; | ^ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] - 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); - | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] + 1339 | ::new (p) value_type(std::move((mutable_reference)val)); + | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 1407 | _init_val((mutable_pointer)&_group[num_items], val); @@ -7143,56 +7489,6 @@ /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1440 | _set_val(&_group[offset], val); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = std::vector; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = std::vector]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/src/DedupUMI.cpp:32:17: required from here - 32 | tidMap[txp].emplace_back(eqId); - | ^ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = std::vector; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = std::vector]' [-Wcast-user-defined] - 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair, std::pair > >; Alloc = spp::libc_allocator, std::pair > > >; value_type = std::pair, std::pair > >; reference = std::pair, std::pair > >&]': -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, std::pair > >; T = std::pair, std::pair > >; Alloc = spp::libc_allocator, std::pair > > >; allocator_type = spp::libc_allocator, std::pair > > >; size_type = unsigned char]' - 1440 | _set_val(&_group[offset], val); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, std::pair > >; T = std::pair, std::pair > >; Alloc = spp::libc_allocator, std::pair > > >; pointer = std::pair, std::pair > >*; allocator_type = spp::libc_allocator, std::pair > > >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, std::pair > >; T = std::pair, std::pair > >; Alloc = spp::libc_allocator, std::pair > > >; reference = std::pair, std::pair > >&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, std::pair > >; Value = std::pair, std::pair > >; Key = std::vector; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, std::pair >, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, std::pair >, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, std::pair > > >; reference = std::pair, std::pair > >&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, std::pair >, boost::hash > >::DefaultValue; KT = std::vector&; Value = std::pair, std::pair > >; Key = std::vector; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, std::pair >, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, std::pair >, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, std::pair > > >; value_type = std::pair, std::pair > >]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::vector&; Key = std::vector; T = std::pair >; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, std::pair > > >; mapped_type = std::pair >]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/src/DedupUMI.cpp:285:29: required from here - 285 | eqclassHash[genesVec].first += 1; - | ^ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, std::pair > >, spp::libc_allocator, std::pair > > > >::value_type' {aka 'std::pair, std::pair > >'} to 'spp::sparsegroup, std::pair > >, spp::libc_allocator, std::pair > > > >::mutable_reference' {aka 'std::pair, std::pair > >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::vector; _U2 = std::pair >; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::vector; _T2 = std::pair >]' [-Wcast-user-defined] - 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); - | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 1407 | _init_val((mutable_pointer)&_group[num_items], val); @@ -7221,88 +7517,62 @@ /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' +In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/AlevinUtils.hpp:47, + from /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp:95: +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = short unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = short unsigned int&; Value = std::pair; Key = short unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = short unsigned int&; Key = short unsigned int; T = short unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = short unsigned int]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/src/DedupUMI.cpp:286:47: required from here - 286 | eqclassHash[genesVec].second[readspmol] += 1; - | ^ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const short unsigned int; _U2 = short unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = short unsigned int; _T2 = short unsigned int]' [-Wcast-user-defined] +/build/reproducible-path/salmon-1.10.3+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here + 51 | barcodeGroup[barcode][umi] = 1; + | ^ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::vector; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int, boost::hash > >::DefaultValue; KT = std::vector&; Value = std::pair, unsigned int>; Key = std::vector; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::vector&; Key = std::vector; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/src/DedupUMI.cpp:413:29: required from here - 413 | eqclassHash[genesVec] += 1; - | ^ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::vector; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::vector; _T2 = unsigned int]' [-Wcast-user-defined] +/build/reproducible-path/salmon-1.10.3+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here + 51 | barcodeGroup[barcode][umi] = 1; + | ^ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1440 | _set_val(&_group[offset], val); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = unsigned int&; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/src/DedupUMI.cpp:477:29: required from here - 477 | vertexIndices[gene] = gid; - | ^ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] - 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' - 1407 | _init_val((mutable_pointer)&_group[num_items], val); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1435 | _set_aux(alloc, offset, val, check_alloc_type()); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ @@ -7321,9 +7591,9 @@ /build/reproducible-path/salmon-1.10.3+ds1/include/Graph.hpp:28:21: required from here 28 | edges[source].insert(sink); | ^ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-Wcast-user-defined] - 1339 | ::new (p) value_type(std::move((mutable_reference)val)); - | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-Wcast-user-defined] + 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); + | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 1407 | _init_val((mutable_pointer)&_group[num_items], val); @@ -7380,271 +7650,95 @@ /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' - 1407 | _init_val((mutable_pointer)&_group[num_items], val); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1435 | _set_aux(alloc, offset, val, check_alloc_type()); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = std::vector; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = std::vector]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/src/DedupUMI.cpp:32:17: required from here - 32 | tidMap[txp].emplace_back(eqId); - | ^ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = std::vector; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = std::vector]' [-Wcast-user-defined] - 1339 | ::new (p) value_type(std::move((mutable_reference)val)); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair, std::pair > >; Alloc = spp::libc_allocator, std::pair > > >; mutable_value_type = std::pair, std::pair > >; reference = std::pair, std::pair > >&]': -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair, std::pair > >; T = std::pair, std::pair > >; Alloc = spp::libc_allocator, std::pair > > >; allocator_type = spp::libc_allocator, std::pair > > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, std::pair > >; T = std::pair, std::pair > >; Alloc = spp::libc_allocator, std::pair > > >; allocator_type = spp::libc_allocator, std::pair > > >; size_type = unsigned char]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, std::pair > >; T = std::pair, std::pair > >; Alloc = spp::libc_allocator, std::pair > > >; pointer = std::pair, std::pair > >*; allocator_type = spp::libc_allocator, std::pair > > >; size_type = unsigned char]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, std::pair > >; T = std::pair, std::pair > >; Alloc = spp::libc_allocator, std::pair > > >; reference = std::pair, std::pair > >&; size_type = long unsigned int]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, std::pair > >; Value = std::pair, std::pair > >; Key = std::vector; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, std::pair >, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, std::pair >, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, std::pair > > >; reference = std::pair, std::pair > >&; size_type = long unsigned int]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; size_type = long unsigned int]' 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, std::pair >, boost::hash > >::DefaultValue; KT = std::vector&; Value = std::pair, std::pair > >; Key = std::vector; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, std::pair >, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, std::pair >, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, std::pair > > >; value_type = std::pair, std::pair > >]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::vector&; Key = std::vector; T = std::pair >; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, std::pair > > >; mapped_type = std::pair >]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/src/DedupUMI.cpp:285:29: required from here - 285 | eqclassHash[genesVec].first += 1; - | ^ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, std::pair > >, spp::libc_allocator, std::pair > > > >::value_type' {aka 'std::pair, std::pair > >'} to 'spp::sparsegroup, std::pair > >, spp::libc_allocator, std::pair > > > >::mutable_reference' {aka 'std::pair, std::pair > >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::vector; _U2 = std::pair >; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::vector; _T2 = std::pair >]' [-Wcast-user-defined] +/build/reproducible-path/salmon-1.10.3+ds1/include/Graph.hpp:28:21: required from here + 28 | edges[source].insert(sink); + | ^ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' - 1390 | _init_val((mutable_pointer)(_group + offset), val); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' - 1435 | _set_aux(alloc, offset, val, check_alloc_type()); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' + 1440 | _set_val(&_group[offset], val); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]' 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = short unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]' 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = short unsigned int&; Value = std::pair; Key = short unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int>::DefaultValue; KT = std::__cxx11::basic_string&; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>]' 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = short unsigned int&; Key = short unsigned int; T = short unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = short unsigned int]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = unsigned int; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/src/DedupUMI.cpp:286:47: required from here - 286 | eqclassHash[genesVec].second[readspmol] += 1; - | ^ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const short unsigned int; _U2 = short unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = short unsigned int; _T2 = short unsigned int]' [-Wcast-user-defined] - 1339 | ::new (p) value_type(std::move((mutable_reference)val)); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; mutable_value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' +/build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp:2647:50: required from 'int alevinQuant(AlevinOpts&, SalmonOpts&, SoftMapT&, TrueBcsT&, spp::sparse_hash_map&, spp::sparse_hash_map, unsigned int>&, boost::program_options::parsed_options&, CFreqMapT&, size_t, std::unique_ptr&) [with ProtocolT = alevin::protocols::DropSeq; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; boost::program_options::parsed_options = boost::program_options::basic_parsed_options; CFreqMapT = tsl::array_map; size_t = long unsigned int]' + 2647 | trueBarcodesIndexMap[ trueBarcodesVec[i] ] = i; +/build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp:2786:54: required from here + 2786 | std::unique_ptr& salmonIndex); + | ^ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::__cxx11::basic_string; _T2 = unsigned int]' [-Wcast-user-defined] + 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; mutable_value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 1407 | _init_val((mutable_pointer)&_group[num_items], val); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' - 1435 | _set_aux(alloc, offset, val, check_alloc_type()); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::vector; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int, boost::hash > >::DefaultValue; KT = std::vector&; Value = std::pair, unsigned int>; Key = std::vector; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::vector&; Key = std::vector; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/src/DedupUMI.cpp:413:29: required from here - 413 | eqclassHash[genesVec] += 1; - | ^ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::vector; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::vector; _T2 = unsigned int]' [-Wcast-user-defined] - 1339 | ::new (p) value_type(std::move((mutable_reference)val)); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' - 1390 | _init_val((mutable_pointer)(_group + offset), val); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' 1435 | _set_aux(alloc, offset, val, check_alloc_type()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; size_type = unsigned char]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' 1453 | _set(alloc, i, offset, val); // may change _group pointer | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]' 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; size_type = long unsigned int]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]' 3170 | return table.set(pos, obj); | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = unsigned int&; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int>::DefaultValue; KT = std::__cxx11::basic_string&; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>]' 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = unsigned int; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/src/DedupUMI.cpp:477:29: required from here - 477 | vertexIndices[gene] = gid; - | ^ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] - 1339 | ::new (p) value_type(std::move((mutable_reference)val)); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' - 1440 | _set_val(&_group[offset], val); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2251:27: required from 'void spp::sparsetable::move(size_type, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int; reference = std::pair, unsigned int>&]' - 2251 | which_group(i).set(_alloc, pos_in_group(i), val); - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2830:23: required from 'void spp::sparse_hashtable::_move_from(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]' - 2830 | table.move(bucknum, *it); // moves the value to here - | ~~~~~~~~~~^~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2948:9: required from 'spp::sparse_hashtable::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]' - 2948 | _move_from(mover, ht, min_buckets_wanted); - | ^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2680:30: required from 'bool spp::sparse_hashtable::_maybe_shrink() [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >]' - 2680 | sparse_hashtable tmp(MoveDontCopy, *this, sz); - | ^~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2846:13: required from 'void spp::sparse_hashtable::resize(size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]' - 2846 | _maybe_shrink(); - | ^~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3799:51: required from 'void spp::sparse_hash_map::resize(size_type) [with Key = std::pair; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]' - 3799 | void resize(size_type cnt) { rep.resize(cnt); } - | ~~~~~~~~~~^~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3801:41: required from 'void spp::sparse_hash_map::reserve(size_type) [with Key = std::pair; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]' - 3801 | void reserve(size_type cnt) { resize(cnt); } // c++11 - | ^~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/src/DedupUMI.cpp:39:25: required from here - 39 | vertexIndexMap.reserve(numClasses); - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::pair; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::pair; _T2 = unsigned int]' [-Wcast-user-defined] - 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); - | ^~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:65: -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp_utils.h: In instantiation of 'T* spp::libc_allocator::reallocate(pointer, size_t) [with T = std::pair, unsigned int>; pointer = std::pair, unsigned int>*; size_t = long unsigned int]': -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1383:38: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' - 1383 | _group = alloc.reallocate(_group, num_alloc); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' - 1435 | _set_aux(alloc, offset, val, check_alloc_type()); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2251:27: required from 'void spp::sparsetable::move(size_type, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int; reference = std::pair, unsigned int>&]' - 2251 | which_group(i).set(_alloc, pos_in_group(i), val); - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2830:23: required from 'void spp::sparse_hashtable::_move_from(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]' - 2830 | table.move(bucknum, *it); // moves the value to here - | ~~~~~~~~~~^~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2948:9: required from 'spp::sparse_hashtable::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]' - 2948 | _move_from(mover, ht, min_buckets_wanted); - | ^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2680:30: required from 'bool spp::sparse_hashtable::_maybe_shrink() [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >]' - 2680 | sparse_hashtable tmp(MoveDontCopy, *this, sz); - | ^~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2846:13: required from 'void spp::sparse_hashtable::resize(size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]' - 2846 | _maybe_shrink(); - | ^~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3799:51: required from 'void spp::sparse_hash_map::resize(size_type) [with Key = std::pair; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]' - 3799 | void resize(size_type cnt) { rep.resize(cnt); } - | ~~~~~~~~~~^~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3801:41: required from 'void spp::sparse_hash_map::reserve(size_type) [with Key = std::pair; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]' - 3801 | void reserve(size_type cnt) { resize(cnt); } // c++11 - | ^~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/src/DedupUMI.cpp:39:25: required from here - 39 | vertexIndexMap.reserve(numClasses); - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp_utils.h:425:51: warning: 'void* realloc(void*, size_t)' moving an object of non-trivially copyable type 'struct std::pair, unsigned int>'; use 'new' and 'delete' instead [-Wclass-memaccess] - 425 | pointer res = static_cast(realloc(p, new_size * sizeof(T))); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/15/bits/stl_algobase.h:64, - from /usr/include/c++/15/string:53, - from /usr/include/c++/15/bits/locale_classes.h:42, - from /usr/include/c++/15/bits/ios_base.h:43, - from /usr/include/c++/15/streambuf:45, - from /usr/include/c++/15/bits/streambuf_iterator.h:37, - from /usr/include/c++/15/iterator:68, - from /usr/include/boost/graph/graph_traits.hpp:14, - from /usr/include/boost/graph/depth_first_search.hpp:17, - from /usr/include/boost/graph/connected_components.hpp:15, - from /build/reproducible-path/salmon-1.10.3+ds1/include/Graph.hpp:4: -/usr/include/c++/15/bits/stl_pair.h:302:12: note: 'struct std::pair, unsigned int>' declared here - 302 | struct pair - | ^~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; mutable_value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' - 1390 | _init_val((mutable_pointer)(_group + offset), val); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' - 1435 | _set_aux(alloc, offset, val, check_alloc_type()); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2251:27: required from 'void spp::sparsetable::move(size_type, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int; reference = std::pair, unsigned int>&]' - 2251 | which_group(i).set(_alloc, pos_in_group(i), val); - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2830:23: required from 'void spp::sparse_hashtable::_move_from(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]' - 2830 | table.move(bucknum, *it); // moves the value to here - | ~~~~~~~~~~^~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2948:9: required from 'spp::sparse_hashtable::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]' - 2948 | _move_from(mover, ht, min_buckets_wanted); - | ^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2680:30: required from 'bool spp::sparse_hashtable::_maybe_shrink() [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >]' - 2680 | sparse_hashtable tmp(MoveDontCopy, *this, sz); - | ^~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2846:13: required from 'void spp::sparse_hashtable::resize(size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]' - 2846 | _maybe_shrink(); - | ^~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3799:51: required from 'void spp::sparse_hash_map::resize(size_type) [with Key = std::pair; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]' - 3799 | void resize(size_type cnt) { rep.resize(cnt); } - | ~~~~~~~~~~^~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3801:41: required from 'void spp::sparse_hash_map::reserve(size_type) [with Key = std::pair; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int]' - 3801 | void reserve(size_type cnt) { resize(cnt); } // c++11 - | ^~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/src/DedupUMI.cpp:39:25: required from here - 39 | vertexIndexMap.reserve(numClasses); - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::pair; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::pair; _T2 = unsigned int]' [-Wcast-user-defined] +/build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp:2647:50: required from 'int alevinQuant(AlevinOpts&, SalmonOpts&, SoftMapT&, TrueBcsT&, spp::sparse_hash_map&, spp::sparse_hash_map, unsigned int>&, boost::program_options::parsed_options&, CFreqMapT&, size_t, std::unique_ptr&) [with ProtocolT = alevin::protocols::DropSeq; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; boost::program_options::parsed_options = boost::program_options::basic_parsed_options; CFreqMapT = tsl::array_map; size_t = long unsigned int]' + 2647 | trueBarcodesIndexMap[ trueBarcodesVec[i] ] = i; +/build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp:2786:54: required from here + 2786 | std::unique_ptr& salmonIndex); + | ^ +/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::__cxx11::basic_string; _T2 = unsigned int]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/AlevinUtils.hpp:47, - from /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp:95: +In file included from /build/reproducible-path/salmon-1.10.3+ds1/include/EquivalenceClassBuilder.hpp:18, + from /build/reproducible-path/salmon-1.10.3+ds1/include/ReadExperiment.hpp:7, + from /build/reproducible-path/salmon-1.10.3+ds1/include/SalmonMappingUtils.hpp:44, + from /build/reproducible-path/salmon-1.10.3+ds1/src/SalmonQuantify.cpp:93: /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char]' 1440 | _set_val(&_group[offset], val); @@ -7804,63 +7898,6 @@ /build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' - 1440 | _set_val(&_group[offset], val); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int>::DefaultValue; KT = std::__cxx11::basic_string&; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = unsigned int; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp:2647:50: required from 'int alevinQuant(AlevinOpts&, SalmonOpts&, SoftMapT&, TrueBcsT&, spp::sparse_hash_map&, spp::sparse_hash_map, unsigned int>&, boost::program_options::parsed_options&, CFreqMapT&, size_t, std::unique_ptr&) [with ProtocolT = alevin::protocols::DropSeq; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; boost::program_options::parsed_options = boost::program_options::basic_parsed_options; CFreqMapT = tsl::array_map; size_t = long unsigned int]' - 2647 | trueBarcodesIndexMap[ trueBarcodesVec[i] ] = i; -/build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp:2786:54: required from here - 2786 | std::unique_ptr& salmonIndex); - | ^ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::__cxx11::basic_string; _T2 = unsigned int]' [-Wcast-user-defined] - 1355 | *(mutable_pointer)p = std::move((mutable_reference)val); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; mutable_value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' - 1407 | _init_val((mutable_pointer)&_group[num_items], val); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' - 1435 | _set_aux(alloc, offset, val, check_alloc_type()); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char]' - 1453 | _set(alloc, i, offset, val); // may change _group pointer - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]' - 2242 | pointer p(group.set(_alloc, pos_in_group(i), val)); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, unsigned int>&; size_type = long unsigned int]' - 3170 | return table.set(pos, obj); - | ~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int>::DefaultValue; KT = std::__cxx11::basic_string&; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>]' - 3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = unsigned int; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]' - 3813 | return rep.template find_or_insert(std::forward(key)).second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp:2647:50: required from 'int alevinQuant(AlevinOpts&, SalmonOpts&, SoftMapT&, TrueBcsT&, spp::sparse_hash_map&, spp::sparse_hash_map, unsigned int>&, boost::program_options::parsed_options&, CFreqMapT&, size_t, std::unique_ptr&) [with ProtocolT = alevin::protocols::DropSeq; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; boost::program_options::parsed_options = boost::program_options::basic_parsed_options; CFreqMapT = tsl::array_map; size_t = long unsigned int]' - 2647 | trueBarcodesIndexMap[ trueBarcodesVec[i] ] = i; -/build/reproducible-path/salmon-1.10.3+ds1/src/SalmonAlevin.cpp:2786:54: required from here - 2786 | std::unique_ptr& salmonIndex); - | ^ -/build/reproducible-path/salmon-1.10.3+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type = true; _T1 = std::__cxx11::basic_string; _T2 = unsigned int]' [-Wcast-user-defined] - 1339 | ::new (p) value_type(std::move((mutable_reference)val)); - | ^~~~~~~~~~~~~~~~~~~~~~ [100%] Linking CXX executable salmon cd /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/salmon.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.3+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/salmon.dir/link.d CMakeFiles/salmon.dir/EMUtils.cpp.o CMakeFiles/salmon.dir/CollapsedEMOptimizer.cpp.o CMakeFiles/salmon.dir/CollapsedCellOptimizer.cpp.o CMakeFiles/salmon.dir/CollapsedGibbsSampler.cpp.o CMakeFiles/salmon.dir/Salmon.cpp.o CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o CMakeFiles/salmon.dir/Graph.cpp.o CMakeFiles/salmon.dir/DedupUMI.cpp.o CMakeFiles/salmon.dir/Alevin.cpp.o CMakeFiles/salmon.dir/AlevinHash.cpp.o CMakeFiles/salmon.dir/SalmonAlevin.cpp.o CMakeFiles/salmon.dir/WhiteList.cpp.o CMakeFiles/salmon.dir/SalmonQuantify.cpp.o CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o CMakeFiles/salmon.dir/GZipWriter.cpp.o CMakeFiles/salmon.dir/SalmonQuantMerge.cpp.o CMakeFiles/salmon.dir/ProgramOptionsGenerator.cpp.o CMakeFiles/salmon.dir/FASTAParser.cpp.o CMakeFiles/salmon.dir/AlignmentModel.cpp.o CMakeFiles/salmon.dir/ONTAlignmentModel.cpp.o CMakeFiles/salmon.dir/AlignmentCommon.cpp.o CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o CMakeFiles/salmon.dir/BAMUtils.cpp.o -o salmon -L/build/reproducible-path/salmon-1.10.3+ds1/lib -L/build/reproducible-path/salmon-1.10.3+ds1/external/install/lib -Wl,-rpath,"\$ORIGIN/../lib:\$ORIGIN/../../lib:\$ORIGIN/:\$ORIGIN/../../external/install/lib" ../external/pufferfish/src/libpuffer.a libsalmon_core.a ../external/pufferfish/external/twopaco/graphconstructor/libtwopaco.a ../external/pufferfish/external/twopaco/graphdump/libgraphdump.a ../external/pufferfish/external/ntcard/libntcard.a -lgff -lboost_iostreams -lboost_filesystem -lboost_system -lboost_timer -lboost_chrono -lboost_program_options -lboost_regex /usr/lib/x86_64-linux-gnu/libcurl.so -lz -lm /usr/lib/x86_64-linux-gnu/libstaden-read.so /usr/lib/x86_64-linux-gnu/libhtscodecs.so -llzma -lbz2 -lgomp ../external/pufferfish/src/libksw2pp.a libalevin_core.a -ltbb -ltbbmalloc -ljemalloc -lrt -ldl @@ -7950,11 +7987,11 @@ preparing documents... done copying assets... copying static files... -Writing evaluated template result to /build/reproducible-path/salmon-1.10.3+ds1/doc/build/html/_static/documentation_options.js Writing evaluated template result to /build/reproducible-path/salmon-1.10.3+ds1/doc/build/html/_static/language_data.js Writing evaluated template result to /build/reproducible-path/salmon-1.10.3+ds1/doc/build/html/_static/basic.css -Writing evaluated template result to /build/reproducible-path/salmon-1.10.3+ds1/doc/build/html/_static/classic.css +Writing evaluated template result to /build/reproducible-path/salmon-1.10.3+ds1/doc/build/html/_static/documentation_options.js Writing evaluated template result to /build/reproducible-path/salmon-1.10.3+ds1/doc/build/html/_static/sidebar.js +Writing evaluated template result to /build/reproducible-path/salmon-1.10.3+ds1/doc/build/html/_static/classic.css copying static files: done copying extra files... copying extra files: done @@ -7984,231 +8021,12 @@ --include=../../debian/salmon-${option}-man-include \ > ../../debian/salmon-${option}.1; done make[1]: Leaving directory '/build/reproducible-path/salmon-1.10.3+ds1' - debian/rules override_dh_auto_test -make[1]: Entering directory '/build/reproducible-path/salmon-1.10.3+ds1' -dh_auto_test --no-parallel - cd obj-x86_64-linux-gnu && make -j1 test ARGS\+=--verbose ARGS\+=-j1 -make[2]: Entering directory '/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu' -Running tests... -/usr/bin/ctest --force-new-ctest-process --verbose -j1 -UpdateCTestConfiguration from :/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/DartConfiguration.tcl -UpdateCTestConfiguration from :/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/DartConfiguration.tcl -Test project /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu -Constructing a list of tests -Done constructing a list of tests -Updating test list for fixtures -Added 0 tests to meet fixture requirements -Checking test dependency graph... -Checking test dependency graph end -test 1 - Start 1: unit_tests - -1: Test command: /usr/bin/cmake "-DTOPLEVEL_DIR=/build/reproducible-path/salmon-1.10.3+ds1" "-P" "/build/reproducible-path/salmon-1.10.3+ds1/cmake/UnitTests.cmake" -1: Working Directory: /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/src -1: Test timeout computed to be: 10000000 -1: -- For unit tests, will set working directory to /build/reproducible-path/salmon-1.10.3+ds1/tests -1: =============================================================================== -1: All tests passed (1992917 assertions in 4 test cases) -1: -1/2 Test #1: unit_tests ....................... Passed 0.21 sec -test 2 - Start 2: salmon_read_test_quasi - -2: Test command: /usr/bin/cmake "-DTOPLEVEL_DIR=/build/reproducible-path/salmon-1.10.3+ds1" "-P" "/build/reproducible-path/salmon-1.10.3+ds1/cmake/TestSalmonQuasi.cmake" -2: Working Directory: /build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu/src -2: Test timeout computed to be: 10000000 -2: sample_data/ -2: sample_data/reads_2.fastq -2: sample_data/sample_alignments.bam -2: sample_data/transcripts.fasta -2: sample_data/reads_1.fastq -2: index ["sample_salmon_quasi_index"] did not previously exist . . . creating it -2: [2027-01-01 17:59:59.541] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode. -2: [2027-01-01 17:59:59.541] [jLog] [info] building index -2: out : sample_salmon_quasi_index -2: [2027-01-01 17:59:59.541] [puff::index::jointLog] [info] Running fixFasta -2: -2: [Step 1 of 4] : counting k-mers -2: -2: [2027-01-01 17:59:59.543] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides -2: [2027-01-01 17:59:59.543] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts -2: wrote 15 cleaned references -2: [2027-01-01 17:59:59.544] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers -2: [2027-01-01 17:59:59.545] [puff::index::jointLog] [info] ntHll estimated 54811 distinct k-mers, setting filter size to 2^20 -2: Threads = 2 -2: Vertex length = 31 -2: Hash functions = 5 -2: Filter size = 1048576 -2: Capacity = 2 -2: Files: -2: sample_salmon_quasi_index/ref_k31_fixed.fa -2: -------------------------------------------------------------------------------- -2: Round 0, 0:1048576 -2: Pass Filling Filtering -2: 1 0 0 -2: 2 0 0 -2: True junctions count = 14 -2: False junctions count = 17 -2: Hash table size = 31 -2: Candidate marks count = 54 -2: -------------------------------------------------------------------------------- -2: Reallocating bifurcations time: 0 -2: True marks count: 51 -2: Edges construction time: 0 -2: -------------------------------------------------------------------------------- -2: Distinct junctions = 14 -2: -2: TwoPaCo::buildGraphMain:: allocated with scalable_malloc; freeing. -2: TwoPaCo::buildGraphMain:: Calling scalable_allocation_command(TBBMALLOC_CLEAN_ALL_BUFFERS, 0); -2: allowedIn: 12 -2: Max Junction ID: 70 -2: seen.size():569 kmerInfo.size():71 -2: approximateContigTotalLength: 17465 -2: counters for complex kmers: -2: (prec>1 & succ>1)=0 | (succ>1 & isStart)=0 | (prec>1 & isEnd)=0 | (isStart & isEnd)=0 -2: contig count: 24 element count: 19592 complex nodes: 0 -2: # of ones in rank vector: 23 -2: [2027-01-01 17:59:59.563] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file. -2: [2027-01-01 17:59:59.563] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory sample_salmon_quasi_index -2: size = 19592 -2: ----------------------------------------- -2: | Loading contigs | Time = 76.156 us -2: ----------------------------------------- -2: size = 19592 -2: ----------------------------------------- -2: | Loading contig boundaries | Time = 65.509 us -2: ----------------------------------------- -2: Number of ones: 23 -2: Number of ones per inventory item: 512 -2: Inventory entries filled: 1 -2: 23 -2: [2027-01-01 17:59:59.563] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure. -2: [2027-01-01 17:59:59.563] [puff::index::jointLog] [info] contig count for validation: 23 -2: [2027-01-01 17:59:59.563] [puff::index::jointLog] [info] Total # of Contigs : 23 -2: [2027-01-01 17:59:59.563] [puff::index::jointLog] [info] Total # of numerical Contigs : 23 -2: [2027-01-01 17:59:59.563] [puff::index::jointLog] [info] Total # of contig vec entries: 36 -2: [2027-01-01 17:59:59.563] [puff::index::jointLog] [info] bits per offset entry 6 -2: [2027-01-01 17:59:59.563] [puff::index::jointLog] [info] Done constructing the contig vector. 24 -2: [2027-01-01 17:59:59.564] [puff::index::jointLog] [info] # segments = 23 -2: [2027-01-01 17:59:59.564] [puff::index::jointLog] [info] total length = 19,592 -2: [2027-01-01 17:59:59.564] [puff::index::jointLog] [info] Reading the reference files ... -2: [2027-01-01 17:59:59.565] [puff::index::jointLog] [info] positional integer width = 15 -2: [2027-01-01 17:59:59.565] [puff::index::jointLog] [info] seqSize = 19,592 -2: [2027-01-01 17:59:59.565] [puff::index::jointLog] [info] rankSize = 19,592 -2: [2027-01-01 17:59:59.565] [puff::index::jointLog] [info] 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elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec -2: [2027-01-01 17:59:59.579] [puff::index::jointLog] [info] mphf size = 0.0125198 MB -2: [2027-01-01 17:59:59.579] [puff::index::jointLog] [info] chunk size = 9,796 -2: [2027-01-01 17:59:59.579] [puff::index::jointLog] [info] chunk 0 = [0, 9,796) -2: [2027-01-01 17:59:59.579] [puff::index::jointLog] [info] chunk 1 = [9,796, 19,562) -2: [2027-01-01 17:59:59.580] [puff::index::jointLog] [info] finished populating pos vector -2: [2027-01-01 17:59:59.580] [puff::index::jointLog] [info] writing index components -2: [2027-01-01 17:59:59.581] [puff::index::jointLog] [info] finished writing dense pufferfish index -2: [2027-01-01 17:59:59.581] [jLog] [info] done building index -2: for info, total work write each : 2.331 total work inram from level 3 : 4.322 total work raw : 25.000 -2: Bitarray 105024 bits (100.00 %) (array + ranks ) -2: final hash 0 bits (0.00 %) (nb in final hash 0) -2: ### salmon (selective-alignment-based) v1.10.3 -2: ### [ program ] => salmon -2: ### [ command ] => quant -2: ### [ index ] => { sample_salmon_quasi_index } -2: ### [ libType ] => { IU } -2: ### [ mates1 ] => { reads_1.fastq } -2: ### [ mates2 ] => { reads_2.fastq } -2: ### [ output ] => { sample_salmon_quasi_quant } -2: Logs will be written to sample_salmon_quasi_quant/logs -2: [2027-01-01 17:59:59.614] [jointLog] [info] setting maxHashResizeThreads to 42 -2: ----------------------------------------- -2: | Loading contig table | Time = 23.03 us -2: ----------------------------------------- -2: size = 24 -2: ----------------------------------------- -2: | Loading contig offsets | Time = 84.624 us -2: ----------------------------------------- -2: ----------------------------------------- -2: | Loading reference lengths | Time = 8.76 us -2: ----------------------------------------- -2: ----------------------------------------- -2: | Loading mphf table | Time = 69.756 us -2: ----------------------------------------- -2: size = 19592 -2: Number of ones: 23 -2: Number of ones per inventory item: 512 -2: Inventory entries filled: 1 -2: ----------------------------------------- -2: | Loading contig boundaries | Time = 177.63 us -2: ----------------------------------------- -2: size = 19592 -2: ----------------------------------------- -2: | Loading sequence | Time = 91.292 us -2: ----------------------------------------- -2: size = 18902 -2: ----------------------------------------- -2: | Loading positions | Time = 111.53 us -2: ----------------------------------------- -2: size = 28562 -2: ----------------------------------------- -2: | Loading reference sequence | Time = 78.303 us -2: ----------------------------------------- -2: ----------------------------------------- -2: | Loading reference accumulative lengths | Time = 7.793 us -2: ----------------------------------------- -2: [2027-01-01 17:59:59.614] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. -2: [2027-01-01 17:59:59.614] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 -2: [2027-01-01 17:59:59.614] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35. -2: [2027-01-01 17:59:59.614] [jointLog] [info] parsing read library format -2: [2027-01-01 17:59:59.614] [jointLog] [info] There is 1 library. -2: [2027-01-01 17:59:59.614] [jointLog] [info] Loading pufferfish index -2: [2027-01-01 17:59:59.614] [jointLog] [info] Loading dense pufferfish index. -2: [2027-01-01 17:59:59.615] [jointLog] [info] done -2: [2027-01-01 17:59:59.664] [jointLog] [info] Index contained 15 targets -2: [2027-01-01 17:59:59.664] [jointLog] [info] Number of decoys : 0 -2: -2: -2: -2: -2: -2: -2: -2: -2: [2027-01-01 17:59:59.875] [jointLog] [info] Computed 28 rich equivalence classes for further processing -2: [2027-01-01 17:59:59.875] [jointLog] [info] Counted 10,000 total reads in the equivalence classes -2: -2: -2: -2: -2: [2027-01-01 17:59:59.889] [jointLog] [info] Number of mappings discarded because of alignment score : 67 -2: [2027-01-01 17:59:59.889] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 0 -2: [2027-01-01 17:59:59.889] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 -2: [2027-01-01 17:59:59.889] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0 -2: [2027-01-01 17:59:59.889] [jointLog] [warning] Only 10000 fragments were mapped, but the number of burn-in fragments was set to 5000000. -2: The effective lengths have been computed using the observed mappings. -2: -2: [2027-01-01 17:59:59.889] [jointLog] [info] Mapping rate = 100% -2: -2: [2027-01-01 17:59:59.889] [jointLog] [info] finished quantifyLibrary() -2: [2027-01-01 17:59:59.968] [jointLog] [info] Starting optimizer -2: [2027-01-01 17:59:59.969] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate -2: [2027-01-01 17:59:59.969] [jointLog] [info] iteration = 0 | max rel diff. = 14.87 -2: [2027-01-01 17:59:59.971] [jointLog] [info] iteration = 100 | max rel diff. = 3.31091e-05 -2: [2027-01-01 17:59:59.971] [jointLog] [info] Finished optimizer -2: [2027-01-01 17:59:59.971] [jointLog] [info] writing output -2: -2: Salmon (read) ran successfully -2/2 Test #2: salmon_read_test_quasi ........... Passed 1.20 sec - -100% tests passed, 0 tests failed out of 2 - -Total Test time (real) = 1.44 sec -make[2]: Leaving directory '/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu' -make[1]: Leaving directory '/build/reproducible-path/salmon-1.10.3+ds1' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/salmon-1.10.3+ds1' dh_auto_install - cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/salmon-1.10.3\+ds1/debian/salmon AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j40 install DESTDIR=/build/reproducible-path/salmon-1.10.3\+ds1/debian/salmon AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/salmon-1.10.3+ds1 -B/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -8240,31 +8058,36 @@ make[2]: Leaving directory '/build/reproducible-path/salmon-1.10.3+ds1/obj-x86_64-linux-gnu' rm -Rvf /build/reproducible-path/salmon-1.10.3+ds1/debian/salmon/usr/lib removed '/build/reproducible-path/salmon-1.10.3+ds1/debian/salmon/usr/lib/libsalmon_core.a' -removed '/build/reproducible-path/salmon-1.10.3+ds1/debian/salmon/usr/lib/twopaco/twopaco-targets-release.cmake' -removed '/build/reproducible-path/salmon-1.10.3+ds1/debian/salmon/usr/lib/twopaco/twopaco-targets.cmake' -removed directory '/build/reproducible-path/salmon-1.10.3+ds1/debian/salmon/usr/lib/twopaco' -removed '/build/reproducible-path/salmon-1.10.3+ds1/debian/salmon/usr/lib/libntcard.a' removed '/build/reproducible-path/salmon-1.10.3+ds1/debian/salmon/usr/lib/libgraphdump.a' -removed '/build/reproducible-path/salmon-1.10.3+ds1/debian/salmon/usr/lib/libtwopaco.a' -removed '/build/reproducible-path/salmon-1.10.3+ds1/debian/salmon/usr/lib/ntcard/ntcard-targets-release.cmake' removed '/build/reproducible-path/salmon-1.10.3+ds1/debian/salmon/usr/lib/ntcard/ntcard-targets.cmake' +removed '/build/reproducible-path/salmon-1.10.3+ds1/debian/salmon/usr/lib/ntcard/ntcard-targets-release.cmake' removed directory '/build/reproducible-path/salmon-1.10.3+ds1/debian/salmon/usr/lib/ntcard' -removed '/build/reproducible-path/salmon-1.10.3+ds1/debian/salmon/usr/lib/graphdump/graphdump-targets-release.cmake' +removed '/build/reproducible-path/salmon-1.10.3+ds1/debian/salmon/usr/lib/libtwopaco.a' removed '/build/reproducible-path/salmon-1.10.3+ds1/debian/salmon/usr/lib/graphdump/graphdump-targets.cmake' +removed '/build/reproducible-path/salmon-1.10.3+ds1/debian/salmon/usr/lib/graphdump/graphdump-targets-release.cmake' removed directory '/build/reproducible-path/salmon-1.10.3+ds1/debian/salmon/usr/lib/graphdump' +removed '/build/reproducible-path/salmon-1.10.3+ds1/debian/salmon/usr/lib/libntcard.a' +removed '/build/reproducible-path/salmon-1.10.3+ds1/debian/salmon/usr/lib/twopaco/twopaco-targets-release.cmake' +removed '/build/reproducible-path/salmon-1.10.3+ds1/debian/salmon/usr/lib/twopaco/twopaco-targets.cmake' +removed directory '/build/reproducible-path/salmon-1.10.3+ds1/debian/salmon/usr/lib/twopaco' removed directory '/build/reproducible-path/salmon-1.10.3+ds1/debian/salmon/usr/lib' make[1]: Leaving directory '/build/reproducible-path/salmon-1.10.3+ds1' dh_install dh_installdocs dh_sphinxdoc dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/salmon/usr/share/doc/salmon/html/_static/copybutton.js -dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/salmon/usr/share/doc/salmon/html/_static/menu.js dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/salmon/usr/share/doc/salmon/html/_static/search-focus.js +dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/salmon/usr/share/doc/salmon/html/_static/menu.js dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/salmon/usr/share/doc/salmon/html/_static/themetoggle.js dh_installchangelogs debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/salmon-1.10.3+ds1' [ -d sample_data ] || tar xzvf sample_data.tgz +sample_data/ +sample_data/reads_2.fastq +sample_data/sample_alignments.bam +sample_data/transcripts.fasta +sample_data/reads_1.fastq dh_installexamples make[1]: Leaving directory '/build/reproducible-path/salmon-1.10.3+ds1' dh_installman @@ -8286,8 +8109,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'salmon' in '../salmon_1.10.3+ds1-1_amd64.deb'. dpkg-deb: building package 'salmon-dbgsym' in '../salmon-dbgsym_1.10.3+ds1-1_amd64.deb'. +dpkg-deb: building package 'salmon' in '../salmon_1.10.3+ds1-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../salmon_1.10.3+ds1-1_amd64.buildinfo dpkg-genchanges --build=binary -O../salmon_1.10.3+ds1-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -8295,12 +8118,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2539860/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2539860/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/2825941 and its subdirectories -I: Current time: Fri Jan 1 18:00:35 -12 2027 -I: pbuilder-time-stamp: 1798869635 +I: removing directory /srv/workspace/pbuilder/2539860 and its subdirectories +I: Current time: Sun Nov 30 13:42:36 +14 2025 +I: pbuilder-time-stamp: 1764459756