Diff of the two buildlogs: -- --- b1/build.log 2024-11-18 11:57:41.347970386 +0000 +++ b2/build.log 2024-11-18 12:00:56.055141820 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Dec 21 06:18:22 -12 2025 -I: pbuilder-time-stamp: 1766341102 +I: Current time: Tue Nov 19 01:57:44 +14 2024 +I: pbuilder-time-stamp: 1731931064 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -25,52 +25,84 @@ dpkg-source: info: unpacking libpwizlite_3.0.8-1.debian.tar.xz I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/393612/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1194285/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 18 11:57 /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/1194285/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1194285/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='trixie' - 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]="2" [2]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.32(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=20 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='c8a9de4a8feb45d19f4002dd9fa26770' - 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='393612' - PS1='# ' - PS2='> ' + INVOCATION_ID=a49931d5457d4002968f8055351f55ea + 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=1194285 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.fVtBeMvY/pbuilderrc_36kG --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.fVtBeMvY/b1 --logfile b1/build.log libpwizlite_3.0.8-1.dsc' - SUDO_GID='111' - 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.fVtBeMvY/pbuilderrc_KHMa --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.fVtBeMvY/b2 --logfile b2/build.log libpwizlite_3.0.8-1.dsc' + SUDO_GID=111 + 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 6.10.11+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.10.11-1~bpo12+1 (2024-10-03) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-27-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/393612/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1194285/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -271,7 +303,7 @@ Get: 143 http://deb.debian.org/debian trixie/main amd64 libhdf5-dev amd64 1.10.10+repack-4 [2652 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 python3-roman all 4.2-1 [10.4 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB] -Fetched 87.7 MB in 10s (8869 kB/s) +Fetched 87.7 MB in 5s (17.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. (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 ... 19969 files and directories currently installed.) @@ -757,8 +789,8 @@ Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Sun Dec 21 18:19:21 UTC 2025. -Universal Time is now: Sun Dec 21 18:19:21 UTC 2025. +Local time is now: Mon Nov 18 11:58:38 UTC 2024. +Universal Time is now: Mon Nov 18 11:58:38 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:amd64 (1.83.0-3.2) ... @@ -888,7 +920,11 @@ fakeroot is already the newest version (1.36-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/reproducible-path/libpwizlite-3.0.8/ && 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 > ../libpwizlite_3.0.8-1_source.changes +I: user script /srv/workspace/pbuilder/1194285/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/1194285/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/libpwizlite-3.0.8/ && 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 > ../libpwizlite_3.0.8-1_source.changes dpkg-buildpackage: info: source package libpwizlite dpkg-buildpackage: info: source version 3.0.8-1 dpkg-buildpackage: info: source distribution unstable @@ -974,7 +1010,7 @@ -- Boost_INCLUDES: /usr/include -- Boost_LIB_DIRS: /usr/lib/x86_64-linux-gnu STATUS: Now managing the CPack process --- Configuring done (2.8s) +-- Configuring done (2.5s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -987,483 +1023,483 @@ -- Build files have been written to: /build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu rst2man debian/libpwizlite.3.rst > debian/libpwizlite.3 sh debian/make-included-headers-hierarchy.sh -baseName: arbitrary_positional_facade.hpp -dirName: boost/iostreams -'boost/iostreams/arbitrary_positional_facade.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/iostreams/arbitrary_positional_facade.hpp' -baseName: base64.hpp -dirName: boost/iostreams/filter -'boost/iostreams/filter/base64.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/iostreams/filter/base64.hpp' -baseName: iterator.hpp -dirName: boost/enum -'boost/enum/iterator.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/enum/iterator.hpp' -baseName: base.hpp -dirName: boost/enum -'boost/enum/base.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/enum/base.hpp' -baseName: bitfield.hpp -dirName: boost/enum -'boost/enum/bitfield.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/enum/bitfield.hpp' -baseName: macros.hpp -dirName: boost/enum -'boost/enum/macros.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/enum/macros.hpp' -baseName: foreach_field.hpp -dirName: boost -'boost/foreach_field.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/foreach_field.hpp' -baseName: thread_specific_singleton.hpp -dirName: boost/utility -'boost/utility/thread_specific_singleton.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/utility/thread_specific_singleton.hpp' -baseName: mutexed_singleton.hpp -dirName: boost/utility -'boost/utility/mutexed_singleton.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/utility/mutexed_singleton.hpp' -baseName: singleton_manager.hpp -dirName: boost/utility/detail -'boost/utility/detail/singleton_manager.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/utility/detail/singleton_manager.hpp' -baseName: restricted.hpp -dirName: boost/utility/detail -'boost/utility/detail/restricted.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/utility/detail/restricted.hpp' -baseName: member_dereference.hpp -dirName: boost/utility/detail -'boost/utility/detail/member_dereference.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/utility/detail/member_dereference.hpp' -baseName: singleton.hpp -dirName: boost/utility -'boost/utility/singleton.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/utility/singleton.hpp' -baseName: cstdio.hpp +baseName: convert.hpp dirName: boost/nowide -'boost/nowide/cstdio.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/nowide/cstdio.hpp' -baseName: cenv.hpp +'boost/nowide/convert.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/nowide/convert.hpp' +baseName: args.hpp dirName: boost/nowide -'boost/nowide/cenv.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/nowide/cenv.hpp' +'boost/nowide/args.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/nowide/args.hpp' +baseName: windows.hpp +dirName: boost/nowide +'boost/nowide/windows.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/nowide/windows.hpp' +baseName: config.hpp +dirName: boost/nowide +'boost/nowide/config.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/nowide/config.hpp' baseName: iostream.hpp dirName: boost/nowide 'boost/nowide/iostream.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/nowide/iostream.hpp' -baseName: filebuf.hpp +baseName: cenv.hpp dirName: boost/nowide -'boost/nowide/filebuf.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/nowide/filebuf.hpp' -baseName: convert.hpp +'boost/nowide/cenv.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/nowide/cenv.hpp' +baseName: cstdlib.hpp dirName: boost/nowide -'boost/nowide/convert.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/nowide/convert.hpp' -baseName: args.hpp +'boost/nowide/cstdlib.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/nowide/cstdlib.hpp' +baseName: cstdio.hpp dirName: boost/nowide -'boost/nowide/args.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/nowide/args.hpp' +'boost/nowide/cstdio.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/nowide/cstdio.hpp' baseName: system.hpp dirName: boost/nowide 'boost/nowide/system.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/nowide/system.hpp' baseName: stackstring.hpp dirName: boost/nowide 'boost/nowide/stackstring.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/nowide/stackstring.hpp' -baseName: cstdlib.hpp +baseName: filebuf.hpp dirName: boost/nowide -'boost/nowide/cstdlib.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/nowide/cstdlib.hpp' +'boost/nowide/filebuf.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/nowide/filebuf.hpp' baseName: fstream.hpp dirName: boost/nowide 'boost/nowide/fstream.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/nowide/fstream.hpp' -baseName: windows.hpp -dirName: boost/nowide -'boost/nowide/windows.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/nowide/windows.hpp' -baseName: config.hpp -dirName: boost/nowide -'boost/nowide/config.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/nowide/config.hpp' +baseName: macros.hpp +dirName: boost/enum +'boost/enum/macros.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/enum/macros.hpp' +baseName: bitfield.hpp +dirName: boost/enum +'boost/enum/bitfield.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/enum/bitfield.hpp' +baseName: base.hpp +dirName: boost/enum +'boost/enum/base.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/enum/base.hpp' +baseName: iterator.hpp +dirName: boost/enum +'boost/enum/iterator.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/enum/iterator.hpp' +baseName: singleton.hpp +dirName: boost/utility +'boost/utility/singleton.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/utility/singleton.hpp' +baseName: singleton_manager.hpp +dirName: boost/utility/detail +'boost/utility/detail/singleton_manager.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/utility/detail/singleton_manager.hpp' +baseName: member_dereference.hpp +dirName: boost/utility/detail +'boost/utility/detail/member_dereference.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/utility/detail/member_dereference.hpp' +baseName: restricted.hpp +dirName: boost/utility/detail +'boost/utility/detail/restricted.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/utility/detail/restricted.hpp' +baseName: thread_specific_singleton.hpp +dirName: boost/utility +'boost/utility/thread_specific_singleton.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/utility/thread_specific_singleton.hpp' +baseName: mutexed_singleton.hpp +dirName: boost/utility +'boost/utility/mutexed_singleton.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/utility/mutexed_singleton.hpp' baseName: enum.hpp dirName: boost 'boost/enum.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/enum.hpp' +baseName: foreach_field.hpp +dirName: boost +'boost/foreach_field.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/foreach_field.hpp' +baseName: base64.hpp +dirName: boost/iostreams/filter +'boost/iostreams/filter/base64.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/iostreams/filter/base64.hpp' +baseName: arbitrary_positional_facade.hpp +dirName: boost/iostreams +'boost/iostreams/arbitrary_positional_facade.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/boost/iostreams/arbitrary_positional_facade.hpp' baseName: Version.hpp dirName: pwiz 'pwiz/Version.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/Version.hpp' -baseName: BinaryIndexStream.hpp -dirName: pwiz/data/common -'pwiz/data/common/BinaryIndexStream.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/common/BinaryIndexStream.hpp' -baseName: Index.hpp -dirName: pwiz/data/common -'pwiz/data/common/Index.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/common/Index.hpp' -baseName: cv.hpp -dirName: pwiz/data/common -'pwiz/data/common/cv.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/common/cv.hpp' -baseName: obo.hpp -dirName: pwiz/data/common -'pwiz/data/common/obo.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/common/obo.hpp' -baseName: MemoryIndex.hpp -dirName: pwiz/data/common -'pwiz/data/common/MemoryIndex.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/common/MemoryIndex.hpp' -baseName: ParamTypes.hpp -dirName: pwiz/data/common -'pwiz/data/common/ParamTypes.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/common/ParamTypes.hpp' -baseName: diff_std.hpp -dirName: pwiz/data/common -'pwiz/data/common/diff_std.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/common/diff_std.hpp' -baseName: CVTranslator.hpp -dirName: pwiz/data/common -'pwiz/data/common/CVTranslator.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/common/CVTranslator.hpp' -baseName: Unimod.hpp -dirName: pwiz/data/common -'pwiz/data/common/Unimod.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/common/Unimod.hpp' -baseName: SpectrumIterator.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/SpectrumIterator.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/SpectrumIterator.hpp' -baseName: Serializer_MSn.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/Serializer_MSn.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/Serializer_MSn.hpp' -baseName: Version.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/Version.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/Version.hpp' -baseName: Serializer_MGF.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/Serializer_MGF.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/Serializer_MGF.hpp' -baseName: SpectrumList_MGF.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/SpectrumList_MGF.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/SpectrumList_MGF.hpp' -baseName: Connection_mzMLb.hpp -dirName: pwiz/data/msdata/mzmlb -'pwiz/data/msdata/mzmlb/Connection_mzMLb.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/mzmlb/Connection_mzMLb.hpp' -baseName: RAMPAdapter.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/RAMPAdapter.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/RAMPAdapter.hpp' -baseName: ChromatogramListBase.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/ChromatogramListBase.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/ChromatogramListBase.hpp' -baseName: Serializer_mzXML.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/Serializer_mzXML.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/Serializer_mzXML.hpp' -baseName: BinaryDataEncoder.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/BinaryDataEncoder.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/BinaryDataEncoder.hpp' -baseName: MemoryMRUCache.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/MemoryMRUCache.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/MemoryMRUCache.hpp' -baseName: SpectrumInfo.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/SpectrumInfo.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/SpectrumInfo.hpp' -baseName: SpectrumList_mzML.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/SpectrumList_mzML.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/SpectrumList_mzML.hpp' -baseName: examples.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/examples.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/examples.hpp' -baseName: ChromatogramList_mzML.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/ChromatogramList_mzML.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/ChromatogramList_mzML.hpp' -baseName: IO.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/IO.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/IO.hpp' -baseName: SpectrumList_BTDX.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/SpectrumList_BTDX.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/SpectrumList_BTDX.hpp' -baseName: Index_mzML.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/Index_mzML.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/Index_mzML.hpp' -baseName: Reader.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/Reader.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/Reader.hpp' -baseName: SpectrumList_mzXML.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/SpectrumList_mzXML.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/SpectrumList_mzXML.hpp' -baseName: Diff.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/Diff.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/Diff.hpp' -baseName: Serializer_mzML.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/Serializer_mzML.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/Serializer_mzML.hpp' -baseName: SpectrumListCache.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/SpectrumListCache.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/SpectrumListCache.hpp' -baseName: SpectrumWorkerThreads.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/SpectrumWorkerThreads.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/SpectrumWorkerThreads.hpp' -baseName: DefaultReaderList.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/DefaultReaderList.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/DefaultReaderList.hpp' -baseName: MSData.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/MSData.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/MSData.hpp' -baseName: TextWriter.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/TextWriter.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/TextWriter.hpp' -baseName: MSDataMerger.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/MSDataMerger.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/MSDataMerger.hpp' -baseName: SpectrumList_MSn.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/SpectrumList_MSn.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/SpectrumList_MSn.hpp' -baseName: MSDataFile.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/MSDataFile.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/MSDataFile.hpp' -baseName: SHA1OutputObserver.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/SHA1OutputObserver.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/SHA1OutputObserver.hpp' -baseName: LegacyAdapter.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/LegacyAdapter.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/LegacyAdapter.hpp' -baseName: SpectrumList_mz5.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/SpectrumList_mz5.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/SpectrumList_mz5.hpp' -baseName: References.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/References.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/References.hpp' -baseName: SpectrumListBase.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/SpectrumListBase.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/SpectrumListBase.hpp' -baseName: Serializer_mz5.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/Serializer_mz5.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/Serializer_mz5.hpp' -baseName: MSNumpress.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/MSNumpress.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/MSNumpress.hpp' -baseName: ChromatogramList_mz5.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/ChromatogramList_mz5.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/ChromatogramList_mz5.hpp' -baseName: SpectrumListWrapper.hpp -dirName: pwiz/data/msdata -'pwiz/data/msdata/SpectrumListWrapper.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/SpectrumListWrapper.hpp' -baseName: FrequencyData.hpp -dirName: pwiz/data/misc -'pwiz/data/misc/FrequencyData.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/misc/FrequencyData.hpp' -baseName: FrequencyDataTestData.hpp -dirName: pwiz/data/misc -'pwiz/data/misc/FrequencyDataTestData.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/misc/FrequencyDataTestData.hpp' -baseName: PeakData.hpp -dirName: pwiz/data/misc -'pwiz/data/misc/PeakData.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/misc/PeakData.hpp' -baseName: MinimumPepXML.hpp -dirName: pwiz/data/misc -'pwiz/data/misc/MinimumPepXML.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/misc/MinimumPepXML.hpp' -baseName: CalibrationParameters.hpp -dirName: pwiz/data/misc -'pwiz/data/misc/CalibrationParameters.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/misc/CalibrationParameters.hpp' -baseName: SampleDatum.hpp -dirName: pwiz/data/misc -'pwiz/data/misc/SampleDatum.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/misc/SampleDatum.hpp' -baseName: bin1d.hpp -dirName: pwiz/utility/findmf/base/resample -'pwiz/utility/findmf/base/resample/bin1d.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/findmf/base/resample/bin1d.hpp' -baseName: determinebinwidth.hpp -dirName: pwiz/utility/findmf/base/resample/utilities -'pwiz/utility/findmf/base/resample/utilities/determinebinwidth.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/findmf/base/resample/utilities/determinebinwidth.hpp' -baseName: masscomparefunctors.hpp -dirName: pwiz/utility/findmf/base/resample -'pwiz/utility/findmf/base/resample/masscomparefunctors.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/findmf/base/resample/masscomparefunctors.hpp' -baseName: breakspec.hpp -dirName: pwiz/utility/findmf/base/resample -'pwiz/utility/findmf/base/resample/breakspec.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/findmf/base/resample/breakspec.hpp' -baseName: determinebinwidth.hpp -dirName: pwiz/utility/findmf/base/resample -'pwiz/utility/findmf/base/resample/determinebinwidth.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/findmf/base/resample/determinebinwidth.hpp' +baseName: IsotopeCalculator.hpp +dirName: pwiz/utility/chemistry +'pwiz/utility/chemistry/IsotopeCalculator.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/chemistry/IsotopeCalculator.hpp' +baseName: Chemistry.hpp +dirName: pwiz/utility/chemistry +'pwiz/utility/chemistry/Chemistry.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/chemistry/Chemistry.hpp' +baseName: MzMobilityWindow.hpp +dirName: pwiz/utility/chemistry +'pwiz/utility/chemistry/MzMobilityWindow.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/chemistry/MzMobilityWindow.hpp' +baseName: ChemistryData.hpp +dirName: pwiz/utility/chemistry +'pwiz/utility/chemistry/ChemistryData.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/chemistry/ChemistryData.hpp' +baseName: Ion.hpp +dirName: pwiz/utility/chemistry +'pwiz/utility/chemistry/Ion.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/chemistry/Ion.hpp' +baseName: MZTolerance.hpp +dirName: pwiz/utility/chemistry +'pwiz/utility/chemistry/MZTolerance.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/chemistry/MZTolerance.hpp' +baseName: IsotopeEnvelopeEstimator.hpp +dirName: pwiz/utility/chemistry +'pwiz/utility/chemistry/IsotopeEnvelopeEstimator.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/chemistry/IsotopeEnvelopeEstimator.hpp' +baseName: IsotopeTable.hpp +dirName: pwiz/utility/chemistry +'pwiz/utility/chemistry/IsotopeTable.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/chemistry/IsotopeTable.hpp' +baseName: XMLWriter.hpp +dirName: pwiz/utility/minimxml +'pwiz/utility/minimxml/XMLWriter.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/minimxml/XMLWriter.hpp' +baseName: SAXParser.hpp +dirName: pwiz/utility/minimxml +'pwiz/utility/minimxml/SAXParser.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/minimxml/SAXParser.hpp' +baseName: Stats.hpp +dirName: pwiz/utility/math +'pwiz/utility/math/Stats.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/math/Stats.hpp' +baseName: OrderedPair.hpp +dirName: pwiz/utility/math +'pwiz/utility/math/OrderedPair.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/math/OrderedPair.hpp' +baseName: qr.hpp +dirName: pwiz/utility/math +'pwiz/utility/math/qr.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/math/qr.hpp' +baseName: MatrixInverse.hpp +dirName: pwiz/utility/math +'pwiz/utility/math/MatrixInverse.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/math/MatrixInverse.hpp' +baseName: Types.hpp +dirName: pwiz/utility/math +'pwiz/utility/math/Types.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/math/Types.hpp' +baseName: HouseholderQR.hpp +dirName: pwiz/utility/math +'pwiz/utility/math/HouseholderQR.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/math/HouseholderQR.hpp' +baseName: LinearLeastSquares.hpp +dirName: pwiz/utility/math +'pwiz/utility/math/LinearLeastSquares.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/math/LinearLeastSquares.hpp' +baseName: LinearSolver.hpp +dirName: pwiz/utility/math +'pwiz/utility/math/LinearSolver.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/math/LinearSolver.hpp' +baseName: erf.hpp +dirName: pwiz/utility/math +'pwiz/utility/math/erf.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/math/erf.hpp' +baseName: MatchedFilter.hpp +dirName: pwiz/utility/math +'pwiz/utility/math/MatchedFilter.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/math/MatchedFilter.hpp' +baseName: round.hpp +dirName: pwiz/utility/math +'pwiz/utility/math/round.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/math/round.hpp' +baseName: Parabola.hpp +dirName: pwiz/utility/math +'pwiz/utility/math/Parabola.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/math/Parabola.hpp' baseName: scale.hpp dirName: pwiz/utility/findmf/base/base 'pwiz/utility/findmf/base/base/scale.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/findmf/base/base/scale.hpp' -baseName: diff.hpp -dirName: pwiz/utility/findmf/base/base -'pwiz/utility/findmf/base/base/diff.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/findmf/base/base/diff.hpp' -baseName: copyif.hpp -dirName: pwiz/utility/findmf/base/base -'pwiz/utility/findmf/base/base/copyif.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/findmf/base/base/copyif.hpp' baseName: interpolation.hpp dirName: pwiz/utility/findmf/base/base/utilities 'pwiz/utility/findmf/base/base/utilities/interpolation.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/findmf/base/base/utilities/interpolation.hpp' baseName: base.hpp dirName: pwiz/utility/findmf/base/base/utilities 'pwiz/utility/findmf/base/base/utilities/base.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/findmf/base/base/utilities/base.hpp' -baseName: interpolate.hpp +baseName: copyif.hpp dirName: pwiz/utility/findmf/base/base -'pwiz/utility/findmf/base/base/interpolate.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/findmf/base/base/interpolate.hpp' +'pwiz/utility/findmf/base/base/copyif.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/findmf/base/base/copyif.hpp' +baseName: constants.hpp +dirName: pwiz/utility/findmf/base/base +'pwiz/utility/findmf/base/base/constants.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/findmf/base/base/constants.hpp' +baseName: diff.hpp +dirName: pwiz/utility/findmf/base/base +'pwiz/utility/findmf/base/base/diff.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/findmf/base/base/diff.hpp' baseName: base.hpp dirName: pwiz/utility/findmf/base/base 'pwiz/utility/findmf/base/base/base.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/findmf/base/base/base.hpp' -baseName: constants.hpp +baseName: interpolate.hpp dirName: pwiz/utility/findmf/base/base -'pwiz/utility/findmf/base/base/constants.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/findmf/base/base/constants.hpp' -baseName: preparedata.hpp -dirName: pwiz/utility/findmf/base/filter/utilities -'pwiz/utility/findmf/base/filter/utilities/preparedata.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/findmf/base/filter/utilities/preparedata.hpp' -baseName: gauss.hpp -dirName: pwiz/utility/findmf/base/filter/utilities -'pwiz/utility/findmf/base/filter/utilities/gauss.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/findmf/base/filter/utilities/gauss.hpp' +'pwiz/utility/findmf/base/base/interpolate.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/findmf/base/base/interpolate.hpp' baseName: filter.hpp dirName: pwiz/utility/findmf/base/filter 'pwiz/utility/findmf/base/filter/filter.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/findmf/base/filter/filter.hpp' +baseName: gauss.hpp +dirName: pwiz/utility/findmf/base/filter/utilities +'pwiz/utility/findmf/base/filter/utilities/gauss.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/findmf/base/filter/utilities/gauss.hpp' +baseName: preparedata.hpp +dirName: pwiz/utility/findmf/base/filter/utilities +'pwiz/utility/findmf/base/filter/utilities/preparedata.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/findmf/base/filter/utilities/preparedata.hpp' baseName: gaussfilter.hpp dirName: pwiz/utility/findmf/base/filter 'pwiz/utility/findmf/base/filter/gaussfilter.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/findmf/base/filter/gaussfilter.hpp' -baseName: LinearLeastSquares.hpp -dirName: pwiz/utility/math -'pwiz/utility/math/LinearLeastSquares.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/math/LinearLeastSquares.hpp' -baseName: erf.hpp -dirName: pwiz/utility/math -'pwiz/utility/math/erf.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/math/erf.hpp' -baseName: LinearSolver.hpp -dirName: pwiz/utility/math -'pwiz/utility/math/LinearSolver.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/math/LinearSolver.hpp' -baseName: OrderedPair.hpp -dirName: pwiz/utility/math -'pwiz/utility/math/OrderedPair.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/math/OrderedPair.hpp' -baseName: MatrixInverse.hpp -dirName: pwiz/utility/math -'pwiz/utility/math/MatrixInverse.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/math/MatrixInverse.hpp' -baseName: MatchedFilter.hpp -dirName: pwiz/utility/math -'pwiz/utility/math/MatchedFilter.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/math/MatchedFilter.hpp' -baseName: qr.hpp -dirName: pwiz/utility/math -'pwiz/utility/math/qr.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/math/qr.hpp' -baseName: Parabola.hpp -dirName: pwiz/utility/math -'pwiz/utility/math/Parabola.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/math/Parabola.hpp' -baseName: HouseholderQR.hpp -dirName: pwiz/utility/math -'pwiz/utility/math/HouseholderQR.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/math/HouseholderQR.hpp' -baseName: Stats.hpp -dirName: pwiz/utility/math -'pwiz/utility/math/Stats.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/math/Stats.hpp' -baseName: Types.hpp -dirName: pwiz/utility/math -'pwiz/utility/math/Types.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/math/Types.hpp' -baseName: round.hpp -dirName: pwiz/utility/math -'pwiz/utility/math/round.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/math/round.hpp' -baseName: XMLWriter.hpp -dirName: pwiz/utility/minimxml -'pwiz/utility/minimxml/XMLWriter.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/minimxml/XMLWriter.hpp' -baseName: SAXParser.hpp -dirName: pwiz/utility/minimxml -'pwiz/utility/minimxml/SAXParser.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/minimxml/SAXParser.hpp' +baseName: bin1d.hpp +dirName: pwiz/utility/findmf/base/resample +'pwiz/utility/findmf/base/resample/bin1d.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/findmf/base/resample/bin1d.hpp' +baseName: determinebinwidth.hpp +dirName: pwiz/utility/findmf/base/resample/utilities +'pwiz/utility/findmf/base/resample/utilities/determinebinwidth.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/findmf/base/resample/utilities/determinebinwidth.hpp' +baseName: breakspec.hpp +dirName: pwiz/utility/findmf/base/resample +'pwiz/utility/findmf/base/resample/breakspec.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/findmf/base/resample/breakspec.hpp' +baseName: determinebinwidth.hpp +dirName: pwiz/utility/findmf/base/resample +'pwiz/utility/findmf/base/resample/determinebinwidth.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/findmf/base/resample/determinebinwidth.hpp' +baseName: masscomparefunctors.hpp +dirName: pwiz/utility/findmf/base/resample +'pwiz/utility/findmf/base/resample/masscomparefunctors.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/findmf/base/resample/masscomparefunctors.hpp' +baseName: unit.hpp +dirName: pwiz/utility/misc +'pwiz/utility/misc/unit.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/unit.hpp' +baseName: TabReader.hpp +dirName: pwiz/utility/misc +'pwiz/utility/misc/TabReader.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/TabReader.hpp' +baseName: Stream.hpp +dirName: pwiz/utility/misc +'pwiz/utility/misc/Stream.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/Stream.hpp' +baseName: Environment.hpp +dirName: pwiz/utility/misc +'pwiz/utility/misc/Environment.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/Environment.hpp' +baseName: Base64.hpp +dirName: pwiz/utility/misc +'pwiz/utility/misc/Base64.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/Base64.hpp' baseName: Singleton.hpp dirName: pwiz/utility/misc 'pwiz/utility/misc/Singleton.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/Singleton.hpp' -baseName: SHA1Calculator.hpp +baseName: optimized_lexical_cast.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/SHA1Calculator.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/SHA1Calculator.hpp' -baseName: Timer.hpp +'pwiz/utility/misc/optimized_lexical_cast.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/optimized_lexical_cast.hpp' +baseName: Std.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/Timer.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/Timer.hpp' -baseName: ClickwrapPrompter.hpp +'pwiz/utility/misc/Std.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/Std.hpp' +baseName: Image.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/ClickwrapPrompter.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/ClickwrapPrompter.hpp' -baseName: Environment.hpp +'pwiz/utility/misc/Image.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/Image.hpp' +baseName: MSIHandler.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/Environment.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/Environment.hpp' -baseName: endian.hpp +'pwiz/utility/misc/MSIHandler.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/MSIHandler.hpp' +baseName: Filesystem.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/endian.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/endian.hpp' +'pwiz/utility/misc/Filesystem.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/Filesystem.hpp' baseName: IntegerSet.hpp dirName: pwiz/utility/misc 'pwiz/utility/misc/IntegerSet.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/IntegerSet.hpp' baseName: Container.hpp dirName: pwiz/utility/misc 'pwiz/utility/misc/Container.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/Container.hpp' -baseName: virtual_map.hpp +baseName: CharIndexedVector.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/virtual_map.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/virtual_map.hpp' -baseName: COMInitializer.hpp +'pwiz/utility/misc/CharIndexedVector.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/CharIndexedVector.hpp' +baseName: VendorReaderTestHarness.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/COMInitializer.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/COMInitializer.hpp' +'pwiz/utility/misc/VendorReaderTestHarness.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/VendorReaderTestHarness.hpp' baseName: Once.hpp dirName: pwiz/utility/misc 'pwiz/utility/misc/Once.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/Once.hpp' -baseName: SHA1.h -dirName: pwiz/utility/misc -'pwiz/utility/misc/SHA1.h' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/SHA1.h' baseName: IterationListener.hpp dirName: pwiz/utility/misc 'pwiz/utility/misc/IterationListener.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/IterationListener.hpp' -baseName: Export.hpp +baseName: Exception.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/Export.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/Export.hpp' -baseName: almost_equal.hpp +'pwiz/utility/misc/Exception.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/Exception.hpp' +baseName: BinaryData.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/almost_equal.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/almost_equal.hpp' -baseName: MSIHandler.hpp +'pwiz/utility/misc/BinaryData.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/BinaryData.hpp' +baseName: SHA1Calculator.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/MSIHandler.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/MSIHandler.hpp' -baseName: TabReader.hpp +'pwiz/utility/misc/SHA1Calculator.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/SHA1Calculator.hpp' +baseName: Timer.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/TabReader.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/TabReader.hpp' -baseName: Stream.hpp +'pwiz/utility/misc/Timer.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/Timer.hpp' +baseName: virtual_map.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/Stream.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/Stream.hpp' -baseName: random_access_compressed_ifstream.hpp +'pwiz/utility/misc/virtual_map.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/virtual_map.hpp' +baseName: shared_map.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/random_access_compressed_ifstream.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/random_access_compressed_ifstream.hpp' -baseName: Base64.hpp +'pwiz/utility/misc/shared_map.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/shared_map.hpp' +baseName: SHA1.h dirName: pwiz/utility/misc -'pwiz/utility/misc/Base64.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/Base64.hpp' +'pwiz/utility/misc/SHA1.h' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/SHA1.h' baseName: SHA1_ostream.hpp dirName: pwiz/utility/misc 'pwiz/utility/misc/SHA1_ostream.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/SHA1_ostream.hpp' -baseName: Std.hpp -dirName: pwiz/utility/misc -'pwiz/utility/misc/Std.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/Std.hpp' -baseName: automation_vector.h -dirName: pwiz/utility/misc -'pwiz/utility/misc/automation_vector.h' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/automation_vector.h' -baseName: Image.hpp -dirName: pwiz/utility/misc -'pwiz/utility/misc/Image.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/Image.hpp' -baseName: CharIndexedVector.hpp -dirName: pwiz/utility/misc -'pwiz/utility/misc/CharIndexedVector.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/CharIndexedVector.hpp' -baseName: optimized_lexical_cast.hpp +baseName: random_access_compressed_ifstream.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/optimized_lexical_cast.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/optimized_lexical_cast.hpp' -baseName: shared_map.hpp +'pwiz/utility/misc/random_access_compressed_ifstream.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/random_access_compressed_ifstream.hpp' +baseName: String.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/shared_map.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/shared_map.hpp' -baseName: Filesystem.hpp +'pwiz/utility/misc/String.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/String.hpp' +baseName: endian.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/Filesystem.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/Filesystem.hpp' -baseName: unit.hpp +'pwiz/utility/misc/endian.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/endian.hpp' +baseName: automation_vector.h dirName: pwiz/utility/misc -'pwiz/utility/misc/unit.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/unit.hpp' +'pwiz/utility/misc/automation_vector.h' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/automation_vector.h' baseName: cpp_cli_utilities.hpp dirName: pwiz/utility/misc 'pwiz/utility/misc/cpp_cli_utilities.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/cpp_cli_utilities.hpp' -baseName: DateTime.hpp +baseName: ClickwrapPrompter.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/DateTime.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/DateTime.hpp' -baseName: VendorReaderTestHarness.hpp +'pwiz/utility/misc/ClickwrapPrompter.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/ClickwrapPrompter.hpp' +baseName: mru_list.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/VendorReaderTestHarness.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/VendorReaderTestHarness.hpp' -baseName: String.hpp +'pwiz/utility/misc/mru_list.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/mru_list.hpp' +baseName: almost_equal.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/String.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/String.hpp' -baseName: Exception.hpp +'pwiz/utility/misc/almost_equal.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/almost_equal.hpp' +baseName: Export.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/Exception.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/Exception.hpp' -baseName: BinaryData.hpp +'pwiz/utility/misc/Export.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/Export.hpp' +baseName: COMInitializer.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/BinaryData.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/BinaryData.hpp' -baseName: mru_list.hpp +'pwiz/utility/misc/COMInitializer.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/COMInitializer.hpp' +baseName: DateTime.hpp dirName: pwiz/utility/misc -'pwiz/utility/misc/mru_list.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/mru_list.hpp' -baseName: IsotopeCalculator.hpp -dirName: pwiz/utility/chemistry -'pwiz/utility/chemistry/IsotopeCalculator.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/chemistry/IsotopeCalculator.hpp' -baseName: MzMobilityWindow.hpp -dirName: pwiz/utility/chemistry -'pwiz/utility/chemistry/MzMobilityWindow.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/chemistry/MzMobilityWindow.hpp' -baseName: IsotopeEnvelopeEstimator.hpp -dirName: pwiz/utility/chemistry -'pwiz/utility/chemistry/IsotopeEnvelopeEstimator.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/chemistry/IsotopeEnvelopeEstimator.hpp' -baseName: Ion.hpp -dirName: pwiz/utility/chemistry -'pwiz/utility/chemistry/Ion.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/chemistry/Ion.hpp' -baseName: MZTolerance.hpp -dirName: pwiz/utility/chemistry -'pwiz/utility/chemistry/MZTolerance.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/chemistry/MZTolerance.hpp' -baseName: Chemistry.hpp -dirName: pwiz/utility/chemistry -'pwiz/utility/chemistry/Chemistry.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/chemistry/Chemistry.hpp' -baseName: IsotopeTable.hpp -dirName: pwiz/utility/chemistry -'pwiz/utility/chemistry/IsotopeTable.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/chemistry/IsotopeTable.hpp' -baseName: ChemistryData.hpp -dirName: pwiz/utility/chemistry -'pwiz/utility/chemistry/ChemistryData.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/chemistry/ChemistryData.hpp' -baseName: SpectrumList_Demux.hpp -dirName: pwiz/analysis/spectrum_processing -'pwiz/analysis/spectrum_processing/SpectrumList_Demux.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/analysis/spectrum_processing/SpectrumList_Demux.hpp' +'pwiz/utility/misc/DateTime.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/utility/misc/DateTime.hpp' +baseName: Version.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/Version.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/Version.hpp' +baseName: Serializer_MGF.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/Serializer_MGF.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/Serializer_MGF.hpp' +baseName: SpectrumWorkerThreads.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/SpectrumWorkerThreads.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/SpectrumWorkerThreads.hpp' +baseName: Connection_mzMLb.hpp +dirName: pwiz/data/msdata/mzmlb +'pwiz/data/msdata/mzmlb/Connection_mzMLb.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/mzmlb/Connection_mzMLb.hpp' +baseName: SpectrumListCache.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/SpectrumListCache.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/SpectrumListCache.hpp' +baseName: SpectrumListBase.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/SpectrumListBase.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/SpectrumListBase.hpp' +baseName: Serializer_mzXML.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/Serializer_mzXML.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/Serializer_mzXML.hpp' +baseName: Diff.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/Diff.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/Diff.hpp' +baseName: RAMPAdapter.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/RAMPAdapter.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/RAMPAdapter.hpp' +baseName: ChromatogramList_mz5.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/ChromatogramList_mz5.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/ChromatogramList_mz5.hpp' +baseName: SpectrumList_MSn.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/SpectrumList_MSn.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/SpectrumList_MSn.hpp' +baseName: MSDataFile.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/MSDataFile.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/MSDataFile.hpp' +baseName: MSData.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/MSData.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/MSData.hpp' +baseName: SpectrumList_MGF.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/SpectrumList_MGF.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/SpectrumList_MGF.hpp' +baseName: ChromatogramListBase.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/ChromatogramListBase.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/ChromatogramListBase.hpp' +baseName: References.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/References.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/References.hpp' +baseName: SpectrumInfo.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/SpectrumInfo.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/SpectrumInfo.hpp' +baseName: MSNumpress.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/MSNumpress.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/MSNumpress.hpp' +baseName: LegacyAdapter.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/LegacyAdapter.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/LegacyAdapter.hpp' +baseName: Reader.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/Reader.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/Reader.hpp' +baseName: DefaultReaderList.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/DefaultReaderList.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/DefaultReaderList.hpp' +baseName: Serializer_mz5.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/Serializer_mz5.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/Serializer_mz5.hpp' +baseName: SpectrumList_mzXML.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/SpectrumList_mzXML.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/SpectrumList_mzXML.hpp' +baseName: SpectrumListWrapper.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/SpectrumListWrapper.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/SpectrumListWrapper.hpp' +baseName: IO.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/IO.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/IO.hpp' +baseName: SpectrumList_BTDX.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/SpectrumList_BTDX.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/SpectrumList_BTDX.hpp' +baseName: Serializer_MSn.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/Serializer_MSn.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/Serializer_MSn.hpp' +baseName: SpectrumList_mz5.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/SpectrumList_mz5.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/SpectrumList_mz5.hpp' +baseName: SpectrumIterator.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/SpectrumIterator.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/SpectrumIterator.hpp' +baseName: Serializer_mzML.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/Serializer_mzML.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/Serializer_mzML.hpp' +baseName: SpectrumList_mzML.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/SpectrumList_mzML.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/SpectrumList_mzML.hpp' +baseName: examples.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/examples.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/examples.hpp' +baseName: SHA1OutputObserver.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/SHA1OutputObserver.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/SHA1OutputObserver.hpp' +baseName: MemoryMRUCache.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/MemoryMRUCache.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/MemoryMRUCache.hpp' +baseName: Index_mzML.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/Index_mzML.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/Index_mzML.hpp' +baseName: MSDataMerger.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/MSDataMerger.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/MSDataMerger.hpp' +baseName: BinaryDataEncoder.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/BinaryDataEncoder.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/BinaryDataEncoder.hpp' +baseName: ChromatogramList_mzML.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/ChromatogramList_mzML.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/ChromatogramList_mzML.hpp' +baseName: TextWriter.hpp +dirName: pwiz/data/msdata +'pwiz/data/msdata/TextWriter.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/msdata/TextWriter.hpp' +baseName: Index.hpp +dirName: pwiz/data/common +'pwiz/data/common/Index.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/common/Index.hpp' +baseName: MemoryIndex.hpp +dirName: pwiz/data/common +'pwiz/data/common/MemoryIndex.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/common/MemoryIndex.hpp' +baseName: BinaryIndexStream.hpp +dirName: pwiz/data/common +'pwiz/data/common/BinaryIndexStream.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/common/BinaryIndexStream.hpp' +baseName: obo.hpp +dirName: pwiz/data/common +'pwiz/data/common/obo.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/common/obo.hpp' +baseName: diff_std.hpp +dirName: pwiz/data/common +'pwiz/data/common/diff_std.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/common/diff_std.hpp' +baseName: Unimod.hpp +dirName: pwiz/data/common +'pwiz/data/common/Unimod.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/common/Unimod.hpp' +baseName: cv.hpp +dirName: pwiz/data/common +'pwiz/data/common/cv.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/common/cv.hpp' +baseName: ParamTypes.hpp +dirName: pwiz/data/common +'pwiz/data/common/ParamTypes.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/common/ParamTypes.hpp' +baseName: CVTranslator.hpp +dirName: pwiz/data/common +'pwiz/data/common/CVTranslator.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/common/CVTranslator.hpp' +baseName: FrequencyData.hpp +dirName: pwiz/data/misc +'pwiz/data/misc/FrequencyData.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/misc/FrequencyData.hpp' +baseName: MinimumPepXML.hpp +dirName: pwiz/data/misc +'pwiz/data/misc/MinimumPepXML.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/misc/MinimumPepXML.hpp' +baseName: PeakData.hpp +dirName: pwiz/data/misc +'pwiz/data/misc/PeakData.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/misc/PeakData.hpp' +baseName: FrequencyDataTestData.hpp +dirName: pwiz/data/misc +'pwiz/data/misc/FrequencyDataTestData.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/misc/FrequencyDataTestData.hpp' +baseName: SampleDatum.hpp +dirName: pwiz/data/misc +'pwiz/data/misc/SampleDatum.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/misc/SampleDatum.hpp' +baseName: CalibrationParameters.hpp +dirName: pwiz/data/misc +'pwiz/data/misc/CalibrationParameters.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/data/misc/CalibrationParameters.hpp' baseName: DemuxDataProcessingStrings.hpp dirName: pwiz/analysis/demux 'pwiz/analysis/demux/DemuxDataProcessingStrings.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/analysis/demux/DemuxDataProcessingStrings.hpp' +baseName: SpectrumList_Demux.hpp +dirName: pwiz/analysis/spectrum_processing +'pwiz/analysis/spectrum_processing/SpectrumList_Demux.hpp' -> '/build/reproducible-path/libpwizlite-3.0.8/debian/includes/pwizlite/pwiz/analysis/spectrum_processing/SpectrumList_Demux.hpp' make[1]: Leaving directory '/build/reproducible-path/libpwizlite-3.0.8' dh_auto_build -O--build-system=cmake - cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/libpwizlite-3.0.8 -B/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -1472,111 +1508,61 @@ make -f src/CMakeFiles/pwizlite-static.dir/build.make src/CMakeFiles/pwizlite-static.dir/depend make -f src/CMakeFiles/pwizlite-shared.dir/build.make src/CMakeFiles/pwizlite-shared.dir/depend make[3]: Entering directory '/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu' -cd /build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libpwizlite-3.0.8 /build/reproducible-path/libpwizlite-3.0.8/src /build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu /build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src /build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src/CMakeFiles/pwizlite-static.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu' cd /build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libpwizlite-3.0.8 /build/reproducible-path/libpwizlite-3.0.8/src /build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu /build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src /build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src/CMakeFiles/pwizlite-shared.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libpwizlite-3.0.8 /build/reproducible-path/libpwizlite-3.0.8/src /build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu /build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src /build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src/CMakeFiles/pwizlite-static.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu' -make -f src/CMakeFiles/pwizlite-static.dir/build.make src/CMakeFiles/pwizlite-static.dir/build make -f src/CMakeFiles/pwizlite-shared.dir/build.make src/CMakeFiles/pwizlite-shared.dir/build make[3]: Entering directory '/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu' +make -f src/CMakeFiles/pwizlite-static.dir/build.make src/CMakeFiles/pwizlite-static.dir/build make[3]: Entering directory '/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu' -[ 4%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/common/cv.cpp.o -[ 4%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/common/CVTranslator.cpp.o -[ 4%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/common/ParamTypes.cpp.o -[ 4%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/common/ParamTypes.cpp.o -[ 6%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/common/diff_std.cpp.o -[ 7%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/ChromatogramList_mzML.cpp.o -[ 10%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/ChromatogramList_mzML.cpp.o -[ 10%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/common/diff_std.cpp.o -[ 12%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/common/CVTranslator.cpp.o -[ 12%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/LegacyAdapter.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/common/ParamTypes.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/common/ParamTypes.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/common/ParamTypes.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.cpp -cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. 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/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzML.cpp -[ 50%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSDataFile.cpp.o -[ 51%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_MGF.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_MGF.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_MGF.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_MGF.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MGF.cpp -cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSDataFile.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSDataFile.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSDataFile.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSDataFile.cpp -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSNumpress.cpp: In function 'void pwiz::msdata::MSNumpress::encodeInt(int, unsigned char*, size_t*)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSNumpress.cpp:114:21: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 114 | } else if (init == mask) { - | ~~~~~^~~~~~~ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSNumpress.cpp: In function 'void pwiz::msdata::MSNumpress::encodeInt(int, unsigned char*, size_t*)': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSNumpress.cpp:114:21: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 114 | } else if (init == mask) { | ~~~~~^~~~~~~ -[ 52%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Reader.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Reader.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Reader.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Reader.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Reader.cpp -[ 53%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_mzXML.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_mzXML.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_mzXML.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_mzXML.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp In file included from /usr/include/c++/14/iostream:41, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSNumpress.cpp:27: In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long long int) [with _CharT = char; _Traits = std::char_traits]', @@ -1597,180 +1583,12 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSNumpress.cpp:347:15: note: 'y' was declared here 347 | long long y; | ^ -In file included from /usr/include/c++/14/iostream:41, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSNumpress.cpp:27: -In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long long int) [with _CharT = char; _Traits = std::char_traits]', - inlined from 'size_t pwiz::msdata::MSNumpress::decodeLinear(const unsigned char*, size_t, double*)' at /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSNumpress.cpp:403:33: -/usr/include/c++/14/ostream:210:25: warning: 'extrapol' may be used uninitialized [-Wmaybe-uninitialized] - 210 | { return _M_insert(__n); } - | ~~~~~~~~~^~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSNumpress.cpp: In function 'size_t pwiz::msdata::MSNumpress::decodeLinear(const unsigned char*, size_t, double*)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSNumpress.cpp:346:15: note: 'extrapol' was declared here - 346 | long long extrapol; - | ^~~~~~~~ -In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long long int) [with _CharT = char; _Traits = std::char_traits]', - inlined from 'size_t pwiz::msdata::MSNumpress::decodeLinear(const unsigned char*, size_t, double*)' at /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSNumpress.cpp:404:26: -/usr/include/c++/14/ostream:210:25: warning: 'y' may be used uninitialized [-Wmaybe-uninitialized] - 210 | { return _M_insert(__n); } - | ~~~~~~~~~^~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSNumpress.cpp: In function 'size_t pwiz::msdata::MSNumpress::decodeLinear(const unsigned char*, size_t, double*)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSNumpress.cpp:347:15: note: 'y' was declared here - 347 | long long y; - | ^ -[ 54%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_MGF.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_MGF.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_MGF.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_MGF.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MGF.cpp -[ 56%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumListBase.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumListBase.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumListBase.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumListBase.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumListBase.cpp -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/LegacyAdapter.hpp:30, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/LegacyAdapter.cpp:27: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/algorithm:60, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/LegacyAdapter.hpp:30, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/LegacyAdapter.cpp:27: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/algorithm:60, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/ChromatogramListBase.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/ChromatogramList_mzML.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/ChromatogramList_mzML.cpp:26: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/algorithm:60, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/References.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/References.cpp:25: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/algorithm:60, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/References.hpp:29, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/References.cpp:25: /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 54 | class PWIZ_API_DECL const_iterator : public std::iterator | ^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumInfo.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumInfo.cpp:27: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/algorithm:60, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/algorithm:60, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.cpp:25: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/algorithm:60, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp:24: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/algorithm:60, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzML.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzML.cpp:26: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/algorithm:60, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: @@ -1783,6 +1601,8 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 26%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSData.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSData.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSData.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSData.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.cpp In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumInfo.hpp:29, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumInfo.cpp:27: @@ -1802,101 +1622,6 @@ 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.cpp:25: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/algorithm:60, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp:24: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/algorithm:60, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MSn.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MSn.cpp:25: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/algorithm:60, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:26: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/algorithm:60, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Reader.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Reader.cpp:26: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] - 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSDataFile.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSDataFile.cpp:26: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/algorithm:60, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/ChromatogramListBase.hpp:28, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/ChromatogramList_mzML.hpp:29, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/ChromatogramList_mzML.cpp:26: @@ -1915,89 +1640,9 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/BinaryDataEncoder.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/BinaryDataEncoder.cpp:26: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/algorithm:60, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSDataFile.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSDataFile.cpp:26: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/algorithm:60, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Reader.hpp:29: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/BinaryDataEncoder.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/BinaryDataEncoder.cpp:26: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/algorithm:60, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Reader.hpp:30: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp: At global scope: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_construct.h:61, - from /usr/include/c++/14/bits/stl_tempbuf.h:61, - from /usr/include/c++/14/memory:66, - from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, - from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, - from /usr/include/boost/shared_ptr.hpp:17, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:29: -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:26: + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/LegacyAdapter.hpp:30, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/LegacyAdapter.cpp:27: /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 54 | class PWIZ_API_DECL const_iterator : public std::iterator | ^~~~~~~~ @@ -2013,6 +1658,22 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] + 769 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] + 853 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/iterator.hpp: At global scope: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumListBase.hpp:28, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.hpp:29, @@ -2034,25 +1695,6 @@ | ^~~~~~~~ In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumListBase.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzML.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzML.cpp:26: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/algorithm:60, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumListBase.hpp:28, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_BTDX.hpp:30, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:26: /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] @@ -2071,9 +1713,8 @@ 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumListBase.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:25: + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:26: /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 54 | class PWIZ_API_DECL const_iterator : public std::iterator | ^~~~~~~~ @@ -2091,8 +1732,8 @@ | ^~~~~~~~ In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumListBase.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_BTDX.hpp:30, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:26: + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzML.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzML.cpp:26: /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 54 | class PWIZ_API_DECL const_iterator : public std::iterator | ^~~~~~~~ @@ -2108,10 +1749,23 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumListBase.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzML.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzML.cpp:26: +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.cpp:26: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] + 769 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] + 853 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/BinaryDataEncoder.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/BinaryDataEncoder.cpp:26: /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 54 | class PWIZ_API_DECL const_iterator : public std::iterator | ^~~~~~~~ @@ -2127,45 +1781,11 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] - 769 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] - 853 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ -In file included from /usr/include/boost/smart_ptr/detail/requires_cxx11.hpp:9, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, - from /usr/include/boost/shared_ptr.hpp:17, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/CVTranslator.hpp:31, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/CVTranslator.cpp:27: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] - 769 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] - 853 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.cpp:26: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] - 769 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.cpp:26: + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/iterator.hpp: At global scope: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ @@ -2173,85 +1793,13 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] 769 | virtual void warn_once(const char* msg) const {} | ~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] - 769 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] - 853 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] - 769 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] - 853 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] - 853 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] - 853 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/diff_std.cpp: In function 'void pwiz::data::diff_impl::diff(const std::string&, const std::string&, std::string&, std::string&, const pwiz::data::BaseDiffConfig&)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/diff_std.cpp:40:33: warning: unused parameter 'config' [-Wunused-parameter] - 40 | const BaseDiffConfig& config) - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/diff_std.cpp: In function 'void pwiz::data::diff_impl::diff(const boost::logic::tribool&, const boost::logic::tribool&, boost::logic::tribool&, boost::logic::tribool&, const pwiz::data::BaseDiffConfig&)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/diff_std.cpp:88:33: warning: unused parameter 'config' [-Wunused-parameter] - 88 | const BaseDiffConfig& config) - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/diff_std.cpp: In function 'void pwiz::data::diff_impl::diff(pwiz::cv::CVID, pwiz::cv::CVID, pwiz::cv::CVID&, pwiz::cv::CVID&, const pwiz::data::BaseDiffConfig&)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/diff_std.cpp:124:33: warning: unused parameter 'config' [-Wunused-parameter] - 124 | const BaseDiffConfig& config) - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] - 769 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] - 769 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] - 853 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] - 853 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] - 769 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] 853 | virtual void warn_once(const char* msg) const {} | ~~~~~~~~~~~~^~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Environment.hpp:24, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Std.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:26: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Environment.hpp:24, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Std.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:26: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:25: + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.hpp:28, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp:24: /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 54 | class PWIZ_API_DECL const_iterator : public std::iterator | ^~~~~~~~ @@ -2267,77 +1815,21 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp: At global scope: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp: At global scope: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] 769 | virtual void warn_once(const char* msg) const {} | ~~~~~~~~~~~~^~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzML.hpp:31: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] - 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Reader.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Reader.cpp:26: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] - 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp: At global scope: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] 853 | virtual void warn_once(const char* msg) const {} | ~~~~~~~~~~~~^~~ -In file included from /usr/include/boost/smart_ptr/detail/requires_cxx11.hpp:9, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, - from /usr/include/boost/shared_ptr.hpp:17, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/CVTranslator.hpp:31, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/CVTranslator.cpp:27: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp: At global scope: + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.cpp:26: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/diff_std.cpp: In function 'void pwiz::data::diff_impl::diff(const std::string&, const std::string&, std::string&, std::string&, const pwiz::data::BaseDiffConfig&)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/diff_std.cpp:40:33: warning: unused parameter 'config' [-Wunused-parameter] - 40 | const BaseDiffConfig& config) - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/diff_std.cpp: In function 'void pwiz::data::diff_impl::diff(const boost::logic::tribool&, const boost::logic::tribool&, boost::logic::tribool&, boost::logic::tribool&, const pwiz::data::BaseDiffConfig&)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/diff_std.cpp:88:33: warning: unused parameter 'config' [-Wunused-parameter] - 88 | const BaseDiffConfig& config) - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/diff_std.cpp: In function 'void pwiz::data::diff_impl::diff(pwiz::cv::CVID, pwiz::cv::CVID, pwiz::cv::CVID&, pwiz::cv::CVID&, const pwiz::data::BaseDiffConfig&)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/diff_std.cpp:124:33: warning: unused parameter 'config' [-Wunused-parameter] - 124 | const BaseDiffConfig& config) - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~ In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, @@ -2346,28 +1838,22 @@ /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.hpp:32, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/ChromatogramList_mzML.cpp:27: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] - 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] - 769 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp: At global scope: +In file included from /usr/include/boost/smart_ptr/detail/requires_cxx11.hpp:9, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, + from /usr/include/boost/shared_ptr.hpp:17, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/CVTranslator.hpp:31, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/CVTranslator.cpp:27: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/requires_cxx11.hpp:9, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, + from /usr/include/boost/shared_ptr.hpp:17, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/CVTranslator.hpp:31, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/CVTranslator.cpp:27: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] - 853 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] 769 | virtual void warn_once(const char* msg) const {} @@ -2376,10 +1862,12 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] 853 | virtual void warn_once(const char* msg) const {} | ~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] - 769 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.hpp:32, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/ChromatogramList_mzML.cpp:27: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] + 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/ChromatogramList_mzML.cpp:29: /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] @@ -2415,15 +1903,22 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] 597 | stream_offset position) {return Status::Ok;} | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] + 769 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/iterator.hpp: At global scope: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] 853 | virtual void warn_once(const char* msg) const {} | ~~~~~~~~~~~~^~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Reader.hpp:29: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] 769 | virtual void warn_once(const char* msg) const {} @@ -2440,31 +1935,12 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] 853 | virtual void warn_once(const char* msg) const {} | ~~~~~~~~~~~~^~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp: At global scope: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp: At global scope: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp: At global scope: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzML.cpp:32: +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.hpp:32: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] + 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:28: /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] 585 | virtual Status processingInstruction(const std::string& name, @@ -2499,42 +1975,14 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] 597 | stream_offset position) {return Status::Ok;} | ~~~~~~~~~~~~~~^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Reader.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSDataFile.hpp:30: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] - 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp: At global scope: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] - 769 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] - 853 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Reader.hpp:30: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp: At global scope: + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.cpp:25: /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 54 | class PWIZ_API_DECL const_iterator : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_construct.h:61, - from /usr/include/c++/14/bits/stl_tempbuf.h:61, - from /usr/include/c++/14/memory:66, - from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, - from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, - from /usr/include/boost/shared_ptr.hpp:17, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:29: +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/algorithm:60, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -2544,41 +1992,7 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp: At global scope: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp: At global scope: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] - 769 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Reader.hpp:29: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] - 853 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.hpp:32: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] - 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:28: +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:28: /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] 585 | virtual Status processingInstruction(const std::string& name, @@ -2613,57 +2027,24 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] 597 | stream_offset position) {return Status::Ok;} | ~~~~~~~~~~~~~~^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MSn.hpp:28: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] - 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] - 769 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] - 769 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] - 853 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] - 853 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Reader.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSDataFile.hpp:30: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] - 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.hpp:32, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/ChromatogramList_mzML.cpp:27: + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:26: /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/CVTranslator.cpp: In function 'bool pwiz::data::shouldIgnore(const std::string&, pwiz::cv::CVID, pwiz::cv::CVID)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/CVTranslator.cpp:145:53: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 145 | return (key=="unit_" && value==MS_unit_OBSOLETE && cvid==UO_unit || - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/CVTranslator.cpp:147:40: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 147 | key=="pi_" && value==MS_PI && cvid==MS_pI || // MS_pI==isoelectric point - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/ChromatogramList_mzML.cpp:29: +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:28: /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] 585 | virtual Status processingInstruction(const std::string& name, | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/diff_std.cpp: In function 'void pwiz::data::diff_impl::diff(const std::string&, const std::string&, std::string&, std::string&, const pwiz::data::BaseDiffConfig&)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/diff_std.cpp:40:33: warning: unused parameter 'config' [-Wunused-parameter] + 40 | const BaseDiffConfig& config) + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:586:61: warning: unused parameter 'data' [-Wunused-parameter] 586 | const std::string& data, | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/CVTranslator.cpp:148:40: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 148 | key=="de_" && value==MS_DE && cvid==1001274 || // conflict between 1000246 and 1001274 - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:587:56: warning: unused parameter 'position' [-Wunused-parameter] 587 | stream_offset position) {return Status::Ok;} | ~~~~~~~~~~~~~~^~~~~~~~ @@ -2674,19 +2055,9 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:590:51: warning: unused parameter 'attributes' [-Wunused-parameter] 590 | const Attributes& attributes, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/CVTranslator.cpp: In function 'bool pwiz::data::shouldReplace(const std::string&, pwiz::cv::CVID, pwiz::cv::CVID)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/CVTranslator.cpp:153:34: warning: unused parameter 'key' [-Wunused-parameter] - 153 | bool shouldReplace(const string& key, CVID value, CVID cvid) - | ~~~~~~~~~~~~~~^~~ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:591:47: warning: unused parameter 'position' [-Wunused-parameter] 591 | stream_offset position) {return Status::Ok;} | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/CVTranslator.cpp:153:44: warning: unused parameter 'value' [-Wunused-parameter] - 153 | bool shouldReplace(const string& key, CVID value, CVID cvid) - | ~~~~~^~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/CVTranslator.cpp:153:56: warning: unused parameter 'cvid' [-Wunused-parameter] - 153 | bool shouldReplace(const string& key, CVID value, CVID cvid) - | ~~~~~^~~~ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::endElement(const std::string&, stream_offset)': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:593:50: warning: unused parameter 'name' [-Wunused-parameter] 593 | virtual Status endElement(const std::string& name, @@ -2701,23 +2072,14 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] 597 | stream_offset position) {return Status::Ok;} | ~~~~~~~~~~~~~~^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Reader.hpp:29: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] - 769 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] - 853 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] - 769 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/diff_std.cpp: In function 'void pwiz::data::diff_impl::diff(const boost::logic::tribool&, const boost::logic::tribool&, boost::logic::tribool&, boost::logic::tribool&, const pwiz::data::BaseDiffConfig&)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/diff_std.cpp:88:33: warning: unused parameter 'config' [-Wunused-parameter] + 88 | const BaseDiffConfig& config) + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/diff_std.cpp: In function 'void pwiz::data::diff_impl::diff(pwiz::cv::CVID, pwiz::cv::CVID, pwiz::cv::CVID&, pwiz::cv::CVID&, const pwiz::data::BaseDiffConfig&)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/diff_std.cpp:124:33: warning: unused parameter 'config' [-Wunused-parameter] + 124 | const BaseDiffConfig& config) + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~ In file included from /usr/include/boost/smart_ptr/detail/requires_cxx11.hpp:9, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, @@ -2725,16 +2087,6 @@ /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/requires_cxx11.hpp:9, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:17: -/usr/include/boost/iterator.hpp: At global scope: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] - 853 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, @@ -2743,12 +2095,13 @@ /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.hpp:32: +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.hpp:32, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzML.cpp:27: /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:28: +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzML.cpp:29: /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] 585 | virtual Status processingInstruction(const std::string& name, @@ -2783,13 +2136,62 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] 597 | stream_offset position) {return Status::Ok;} | ~~~~~~~~~~~~~~^~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/requires_cxx11.hpp:9, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, - from /usr/include/boost/shared_ptr.hpp:17, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/BinaryDataEncoder.hpp:30: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/CVTranslator.cpp: In function 'bool pwiz::data::shouldIgnore(const std::string&, pwiz::cv::CVID, pwiz::cv::CVID)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/CVTranslator.cpp:145:53: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 145 | return (key=="unit_" && value==MS_unit_OBSOLETE && cvid==UO_unit || + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/CVTranslator.cpp:147:40: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 147 | key=="pi_" && value==MS_PI && cvid==MS_pI || // MS_pI==isoelectric point + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/CVTranslator.cpp:148:40: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 148 | key=="de_" && value==MS_DE && cvid==1001274 || // conflict between 1000246 and 1001274 + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/CVTranslator.cpp: In function 'bool pwiz::data::shouldReplace(const std::string&, pwiz::cv::CVID, pwiz::cv::CVID)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/CVTranslator.cpp:153:34: warning: unused parameter 'key' [-Wunused-parameter] + 153 | bool shouldReplace(const string& key, CVID value, CVID cvid) + | ~~~~~~~~~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/CVTranslator.cpp:153:44: warning: unused parameter 'value' [-Wunused-parameter] + 153 | bool shouldReplace(const string& key, CVID value, CVID cvid) + | ~~~~~^~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/CVTranslator.cpp:153:56: warning: unused parameter 'cvid' [-Wunused-parameter] + 153 | bool shouldReplace(const string& key, CVID value, CVID cvid) + | ~~~~~^~~~ +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/iterator.hpp: At global scope: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Environment.hpp:24, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Std.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:26: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/iterator.hpp: At global scope: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/diff_std.cpp: In function 'void pwiz::data::diff_impl::diff(const std::string&, const std::string&, std::string&, std::string&, const pwiz::data::BaseDiffConfig&)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/diff_std.cpp:40:33: warning: unused parameter 'config' [-Wunused-parameter] + 40 | const BaseDiffConfig& config) + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/diff_std.cpp: In function 'void pwiz::data::diff_impl::diff(const boost::logic::tribool&, const boost::logic::tribool&, boost::logic::tribool&, boost::logic::tribool&, const pwiz::data::BaseDiffConfig&)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/diff_std.cpp:88:33: warning: unused parameter 'config' [-Wunused-parameter] + 88 | const BaseDiffConfig& config) + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/diff_std.cpp: In function 'void pwiz::data::diff_impl::diff(pwiz::cv::CVID, pwiz::cv::CVID, pwiz::cv::CVID&, pwiz::cv::CVID&, const pwiz::data::BaseDiffConfig&)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/diff_std.cpp:124:33: warning: unused parameter 'config' [-Wunused-parameter] + 124 | const BaseDiffConfig& config) + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] 769 | virtual void warn_once(const char* msg) const {} @@ -2798,14 +2200,32 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] 853 | virtual void warn_once(const char* msg) const {} | ~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] - 769 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] - 853 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/iterator.hpp: At global scope: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Environment.hpp:24, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Std.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/cv.cpp:34: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/iterator.hpp: At global scope: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 28%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSDataFile.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSDataFile.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSDataFile.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSDataFile.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSDataFile.cpp /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/CVTranslator.cpp: In function 'bool pwiz::data::shouldIgnore(const std::string&, pwiz::cv::CVID, pwiz::cv::CVID)': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/CVTranslator.cpp:145:53: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 145 | return (key=="unit_" && value==MS_unit_OBSOLETE && cvid==UO_unit || @@ -2826,7 +2246,83 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/CVTranslator.cpp:153:56: warning: unused parameter 'cvid' [-Wunused-parameter] 153 | bool shouldReplace(const string& key, CVID value, CVID cvid) | ~~~~~^~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:28: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerCV::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:85:47: warning: unused parameter 'position' [-Wunused-parameter] + 85 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerUserParam::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:136:47: warning: unused parameter 'position' [-Wunused-parameter] + 136 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerCVParam::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:195:47: warning: unused parameter 'position' [-Wunused-parameter] + 195 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerParamContainer::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:267:47: warning: unused parameter 'position' [-Wunused-parameter] + 267 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerFileDescription::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:504:51: warning: unused parameter 'attributes' [-Wunused-parameter] + 504 | const Attributes& attributes, + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:505:47: warning: unused parameter 'position' [-Wunused-parameter] + 505 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerComponentList::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:697:51: warning: unused parameter 'attributes' [-Wunused-parameter] + 697 | const Attributes& attributes, + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:698:47: warning: unused parameter 'position' [-Wunused-parameter] + 698 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerDataProcessing::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:970:47: warning: unused parameter 'position' [-Wunused-parameter] + 970 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerScanSettings::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:1083:47: warning: unused parameter 'position' [-Wunused-parameter] + 1083 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerProduct::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:1359:51: warning: unused parameter 'attributes' [-Wunused-parameter] + 1359 | const Attributes& attributes, + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:1360:47: warning: unused parameter 'position' [-Wunused-parameter] + 1360 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] + 769 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] + 853 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp: In function 'void pwiz::msdata::IO::writeMzMLbExtra(boost::iostreams::stream*, std::string&, size_t&, const std::string&, pwiz::minimxml::XMLWriter&, const BinaryDataArrayType&, const pwiz::msdata::BinaryDataEncoder::Config&) [with BinaryDataArrayType = pwiz::msdata::BinaryDataArray; std::string = std::__cxx11::basic_string; size_t = long unsigned int]': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:1693:47: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1693 | for (int i = 1; i < float_data.size(); i++) + | ~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:1712:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1712 | for (int i = 2; i < float_data.size(); i++) + | ~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:1774:43: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1774 | for (int i = 1; i < double_data.size(); i++) + | ~~^~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:1793:47: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1793 | for (int i = 2; i < double_data.size(); i++) + | ~~^~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:1627:142: warning: unused parameter 'writer' [-Wunused-parameter] + 1627 | void writeMzMLbExtra(stream* mzMLb_os, string& dataset, size_t& offset, const string& encoded, XMLWriter& writer, const BinaryDataArray& binaryDataArray, const BinaryDataEncoder::Config& usedConfig) + | ~~~~~~~~~~~^~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp: In function 'void pwiz::msdata::IO::writeMzMLbExtra(boost::iostreams::stream*, std::string&, size_t&, const std::string&, pwiz::minimxml::XMLWriter&, const BinaryDataArrayType&, const pwiz::msdata::BinaryDataEncoder::Config&) [with BinaryDataArrayType = pwiz::msdata::IntegerDataArray; std::string = std::__cxx11::basic_string; size_t = long unsigned int]': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:1820:143: warning: unused parameter 'writer' [-Wunused-parameter] + 1820 | void writeMzMLbExtra(stream* mzMLb_os, string& dataset, size_t& offset, const string& encoded, XMLWriter& writer, const IntegerDataArray& binaryDataArray, const BinaryDataEncoder::Config& usedConfig) + | ~~~~~~~~~~~^~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp:26: /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] 585 | virtual Status processingInstruction(const std::string& name, @@ -2861,22 +2357,62 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] 597 | stream_offset position) {return Status::Ok;} | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] - 769 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] - 853 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] - 769 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] - 853 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerSpectrum::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:2639:35: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 2639 | else if (version == 1 && name == "acquisitionList" /* mzML 1.0 */ || name == "scanList") + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerSpectrumListSimple::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:2955:47: warning: unused parameter 'position' [-Wunused-parameter] + 2955 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerChromatogramListSimple::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:3085:47: warning: unused parameter 'position' [-Wunused-parameter] + 3085 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerMSData::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:3415:31: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 3415 | else if (version == 1 && name == "acquisitionSettings" /* mzML 1.0 */ || + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:3333:47: warning: unused parameter 'position' [-Wunused-parameter] + 3333 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.hpp:32, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp:28: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] + 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/iterator.hpp: At global scope: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexListOffset::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp:86:51: warning: unused parameter 'attributes' [-Wunused-parameter] + 86 | const Attributes& attributes, + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp:87:47: warning: unused parameter 'position' [-Wunused-parameter] + 87 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexListOffset::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp:95:45: warning: unused parameter 'position' [-Wunused-parameter] + 95 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerOffset::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp:120:47: warning: unused parameter 'position' [-Wunused-parameter] + 120 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerOffset::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp:165:45: warning: unused parameter 'position' [-Wunused-parameter] + 165 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexList::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp:201:47: warning: unused parameter 'position' [-Wunused-parameter] + 201 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Environment.hpp:24, @@ -2885,7 +2421,9 @@ /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp:26: +[ 29%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Reader.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Reader.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Reader.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Reader.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Reader.cpp +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:28: /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] 585 | virtual Status processingInstruction(const std::string& name, @@ -2920,6 +2458,99 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] 597 | stream_offset position) {return Status::Ok;} | ~~~~~~~~~~~~~~^~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Reader.hpp:28, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:29: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] + 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Reader.hpp:29: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Reader.hpp:30: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp: At global scope: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /usr/include/c++/14/stdexcept:39, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Exception.hpp:28, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Std.hpp:28: +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In constructor 'pwiz::msdata::{anonymous}::SpectrumList_mzXMLImpl::SpectrumList_mzXMLImpl(boost::shared_ptr >, const pwiz::msdata::MSData&, bool)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:84:30: warning: catching polymorphic type 'struct pwiz::msdata::SpectrumList_mzXML::index_not_found' by value [-Wcatch-value=] + 84 | } catch (index_not_found e){ + | ^ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerPrecursor::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:128:47: warning: unused parameter 'position' [-Wunused-parameter] + 128 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerPrecursor::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:212:45: warning: unused parameter 'position' [-Wunused-parameter] + 212 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerPeaks::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:239:47: warning: unused parameter 'position' [-Wunused-parameter] + 239 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerPeaks::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:282:45: warning: unused parameter 'position' [-Wunused-parameter] + 282 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerPeaks::endElement(const std::string&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:302:70: warning: unused parameter 'position' [-Wunused-parameter] + 302 | virtual Status endElement(const std::string& name, stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexOffset::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:701:51: warning: unused parameter 'attributes' [-Wunused-parameter] + 701 | const Attributes& attributes, + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:702:47: warning: unused parameter 'position' [-Wunused-parameter] + 702 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexOffset::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:710:45: warning: unused parameter 'position' [-Wunused-parameter] + 710 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerOffset::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:736:47: warning: unused parameter 'position' [-Wunused-parameter] + 736 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerOffset::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:754:45: warning: unused parameter 'position' [-Wunused-parameter] + 754 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndex::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:778:51: warning: unused parameter 'attributes' [-Wunused-parameter] + 778 | const Attributes& attributes, + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:779:47: warning: unused parameter 'position' [-Wunused-parameter] + 779 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndex::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:796:59: warning: unused parameter 'text' [-Wunused-parameter] + 796 | virtual Status characters(const SAXParser::saxstring& text, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:797:45: warning: unused parameter 'position' [-Wunused-parameter] + 797 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexCreator::endElement(const std::string&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:885:45: warning: unused parameter 'position' [-Wunused-parameter] + 885 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] 769 | virtual void warn_once(const char* msg) const {} @@ -2928,7 +2559,467 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] 853 | virtual void warn_once(const char* msg) const {} | ~~~~~~~~~~~~^~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:28: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.hpp: In member function 'virtual std::string pwiz::msdata::Reader_MS2::identify(const std::string&, const std::string&) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.hpp:98:53: warning: unused parameter 'filename' [-Wunused-parameter] + 98 | virtual std::string identify(const std::string& filename, const std::string& head) const { return ""; } + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.hpp:98:82: warning: unused parameter 'head' [-Wunused-parameter] + 98 | virtual std::string identify(const std::string& filename, const std::string& head) const { return ""; } + | ~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:27: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In function 'void pwiz::msdata::{anonymous}::appendSourceFile(const std::string&, pwiz::msdata::MSData&)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:65:58: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] + 65 | sourceFile->id = sourceFile->name = BFS_STRING(p.leaf()); + | ~~~~~~^~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.hpp:64:24: note: in definition of macro 'BFS_STRING' + 64 | #define BFS_STRING(p) (p).string() + | ^ +In file included from /usr/include/boost/filesystem/operations.hpp:20, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.hpp:36: +/usr/include/boost/filesystem/path.hpp:1127:10: note: declared here + 1127 | path leaf() const { return filename(); } + | ^~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:66:67: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] + 66 | sourceFile->location = "file:///" + BFS_COMPLETE(p.branch_path()).string(); + | ~~~~~~~~~~~~~^~ +/usr/include/boost/filesystem/path.hpp:1129:10: note: declared here + 1129 | path branch_path() const { return parent_path(); } + | ^~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In function 'void pwiz::msdata::{anonymous}::fillInCommonMetadata(const std::string&, pwiz::msdata::MSData&)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:107:44: warning: 'std::string boost::filesystem::basename(const path&)' is deprecated: Use path::stem() instead [-Wdeprecated-declarations] + 107 | msd.id = msd.run.id = bfs::basename(filename); + | ~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.hpp:37: +/usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here + 35 | inline std::string basename(const path& p) + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual std::string pwiz::msdata::Reader_mzML::identify(const std::string&, const std::string&) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:126:68: warning: unused parameter 'filename' [-Wunused-parameter] + 126 | PWIZ_API_DECL std::string Reader_mzML::identify(const std::string& filename, const std::string& head) const + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_mzML::read(const std::string&, const std::string&, pwiz::msdata::MSData&, int, const pwiz::msdata::Reader::Config&) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:133:57: warning: unused parameter 'head' [-Wunused-parameter] + 133 | const std::string& head, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:136:52: warning: unused parameter 'config' [-Wunused-parameter] + 136 | const Config& config) const + | ~~~~~~~~~~~~~~^~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual std::string pwiz::msdata::Reader_mzXML::identify(const std::string&, const std::string&) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:201:69: warning: unused parameter 'filename' [-Wunused-parameter] + 201 | PWIZ_API_DECL std::string Reader_mzXML::identify(const std::string& filename, const std::string& head) const + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_mzXML::read(const std::string&, const std::string&, pwiz::msdata::MSData&, int, const pwiz::msdata::Reader::Config&) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:216:58: warning: unused parameter 'head' [-Wunused-parameter] + 216 | const std::string& head, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:219:53: warning: unused parameter 'config' [-Wunused-parameter] + 219 | const Config& config) const + | ~~~~~~~~~~~~~~^~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual std::string pwiz::msdata::Reader_MGF::identify(const std::string&, const std::string&) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:269:59: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] + 269 | return std::string(((bal::to_lower_copy(bfs::extension(filename)) == ".mgf"))?getType():""); + | ~~~~~~~~~~~~~~^~~~~~~~~~ +/usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here + 29 | inline std::string extension(const path& p) + | ^~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:267:86: warning: unused parameter 'head' [-Wunused-parameter] + 267 | PWIZ_API_DECL std::string Reader_MGF::identify(const string& filename, const string& head) const + | ~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_MGF::read(const std::string&, const std::string&, pwiz::msdata::MSData&, int, const pwiz::msdata::Reader::Config&) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:273:51: warning: unused parameter 'head' [-Wunused-parameter] + 273 | const string& head, + | ~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:276:51: warning: unused parameter 'config' [-Wunused-parameter] + 276 | const Config& config) const + | ~~~~~~~~~~~~~~^~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_MGF::read(const std::string&, const std::string&, std::vector >&, const pwiz::msdata::Reader::Config&) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:296:51: warning: unused parameter 'config' [-Wunused-parameter] + 296 | const Config& config) const + | ~~~~~~~~~~~~~~^~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual std::string pwiz::msdata::Reader_MSn::identify(const std::string&, const std::string&) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:307:86: warning: unused parameter 'head' [-Wunused-parameter] + 307 | PWIZ_API_DECL std::string Reader_MSn::identify(const string& filename, const string& head) const + | ~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_MSn::read(const std::string&, const std::string&, pwiz::msdata::MSData&, int, const pwiz::msdata::Reader::Config&) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:317:51: warning: unused parameter 'head' [-Wunused-parameter] + 317 | const string& head, + | ~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:320:51: warning: unused parameter 'config' [-Wunused-parameter] + 320 | const Config& config) const + | ~~~~~~~~~~~~~~^~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_MSn::read(const std::string&, const std::string&, std::vector >&, const pwiz::msdata::Reader::Config&) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:353:51: warning: unused parameter 'config' [-Wunused-parameter] + 353 | const Config& config) const + | ~~~~~~~~~~~~~~^~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual std::string pwiz::msdata::Reader_BTDX::identify(const std::string&, const std::string&) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:364:63: warning: unused parameter 'filename' [-Wunused-parameter] + 364 | PWIZ_API_DECL std::string Reader_BTDX::identify(const string& filename, const string& head) const + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_BTDX::read(const std::string&, const std::string&, pwiz::msdata::MSData&, int, const pwiz::msdata::Reader::Config&) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:397:41: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] + 397 | sourceFile->name = BFS_STRING(p.leaf()); + | ~~~~~~^~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.hpp:64:24: note: in definition of macro 'BFS_STRING' + 64 | #define BFS_STRING(p) (p).string() + | ^ +/usr/include/boost/filesystem/path.hpp:1127:10: note: declared here + 1127 | path leaf() const { return filename(); } + | ^~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:398:67: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] + 398 | sourceFile->location = "file:///" + BFS_COMPLETE(p.branch_path()).string(); + | ~~~~~~~~~~~~~^~ +/usr/include/boost/filesystem/path.hpp:1129:10: note: declared here + 1129 | path branch_path() const { return parent_path(); } + | ^~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:401:46: warning: 'std::string boost::filesystem::basename(const path&)' is deprecated: Use path::stem() instead [-Wdeprecated-declarations] + 401 | result.id = result.run.id = bfs::basename(filename); + | ~~~~~~~~~~~~~^~~~~~~~~~ +/usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here + 35 | inline std::string basename(const path& p) + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:380:52: warning: unused parameter 'head' [-Wunused-parameter] + 380 | const string& head, + | ~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:383:52: warning: unused parameter 'config' [-Wunused-parameter] + 383 | const Config& config) const + | ~~~~~~~~~~~~~~^~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_BTDX::read(const std::string&, const std::string&, std::vector >&, const pwiz::msdata::Reader::Config&) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:410:52: warning: unused parameter 'config' [-Wunused-parameter] + 410 | const Config& config) const + | ~~~~~~~~~~~~~~^~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual std::string pwiz::msdata::Reader_mz5::identify(const std::string&, const std::string&) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:429:62: warning: unused parameter 'filename' [-Wunused-parameter] + 429 | PWIZ_API_DECL std::string Reader_mz5::identify(const string& filename, const string& head) const + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_mz5::read(const std::string&, const std::string&, pwiz::msdata::MSData&, int, const pwiz::msdata::Reader::Config&) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:462:51: warning: unused parameter 'filename' [-Wunused-parameter] + 462 | PWIZ_API_DECL void Reader_mz5::read(const string& filename, + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:463:51: warning: unused parameter 'head' [-Wunused-parameter] + 463 | const string& head, + | ~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:464:45: warning: unused parameter 'result' [-Wunused-parameter] + 464 | MSData& result, + | ~~~~~~~~^~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:465:41: warning: unused parameter 'runIndex' [-Wunused-parameter] + 465 | int runIndex, + | ~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:466:51: warning: unused parameter 'config' [-Wunused-parameter] + 466 | const Config& config) const + | ~~~~~~~~~~~~~~^~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_mz5::read(const std::string&, const std::string&, std::vector >&, const pwiz::msdata::Reader::Config&) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:488:51: warning: unused parameter 'config' [-Wunused-parameter] + 488 | const Config& config) const + | ~~~~~~~~~~~~~~^~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_mzMLb::read(const std::string&, const std::string&, pwiz::msdata::MSData&, int, const pwiz::msdata::Reader::Config&) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:533:24: warning: unused parameter 'head' [-Wunused-parameter] + 533 | const std::string& head, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:536:19: warning: unused parameter 'config' [-Wunused-parameter] + 536 | const Config& config) const + | ~~~~~~~~~~~~~~^~~~~~ +[ 30%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_MGF.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_MGF.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_MGF.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_MGF.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MGF.cpp +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/cv.cpp:26735: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/cv.inl: In function 'const pwiz::cv::CVTermInfo& pwiz::cv::cvTermInfo(const char*)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/cv.inl:103:23: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] + 103 | for (int o=0;o= 0' is always true [-Wtype-limits] + 1121 | if ((result >= 0 && result < size()) || s == 0) + | ~~~~~~~^~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSDataFile.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSDataFile.cpp:26: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/algorithm:60, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual pwiz::msdata::SpectrumPtr pwiz::msdata::SpectrumListSimple::spectrum(size_t, bool) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.cpp:1232:75: warning: unused parameter 'getBinaryData' [-Wunused-parameter] + 1232 | PWIZ_API_DECL SpectrumPtr SpectrumListSimple::spectrum(size_t index, bool getBinaryData) const + | ~~~~~^~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual pwiz::msdata::ChromatogramPtr pwiz::msdata::ChromatogramListSimple::chromatogram(size_t, bool) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.cpp:1299:87: warning: unused parameter 'getBinaryData' [-Wunused-parameter] + 1299 | PWIZ_API_DECL ChromatogramPtr ChromatogramListSimple::chromatogram(size_t index, bool getBinaryData) const + | ~~~~~^~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_BTDX.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerPeaks::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:121:47: warning: unused parameter 'position' [-Wunused-parameter] + 121 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_BTDX.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerPeaks::endElement(const std::string&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:162:45: warning: unused parameter 'position' [-Wunused-parameter] + 162 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_BTDX.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexCreator::endElement(const std::string&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:356:45: warning: unused parameter 'position' [-Wunused-parameter] + 356 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/cv.cpp:26735: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/cv.inl: In function 'const pwiz::cv::CVTermInfo& pwiz::cv::cvTermInfo(const char*)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/cv.inl:103:23: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] + 103 | for (int o=0;o struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/iterator.hpp: At global scope: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_construct.h:61, + from /usr/include/c++/14/bits/stl_tempbuf.h:61, + from /usr/include/c++/14/memory:66, + from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, + from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, + from /usr/include/boost/shared_ptr.hpp:17, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:29: +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 39%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumListBase.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumListBase.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumListBase.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumListBase.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumListBase.cpp +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] + 769 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] + 853 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MSn.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MSn.cpp:25: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/algorithm:60, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSNumpress.cpp: In function 'void pwiz::msdata::MSNumpress::encodeInt(int, unsigned char*, size_t*)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSNumpress.cpp:114:21: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 114 | } else if (init == mask) { + | ~~~~~^~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/requires_cxx11.hpp:9, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:17: +/usr/include/boost/iterator.hpp: At global scope: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/ChromatogramListBase.hpp:28, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/ChromatogramList_mzML.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/ChromatogramList_mzML.cpp:26: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/algorithm:60, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /usr/include/c++/14/iostream:41, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSNumpress.cpp:27: +In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long long int) [with _CharT = char; _Traits = std::char_traits]', + inlined from 'size_t pwiz::msdata::MSNumpress::decodeLinear(const unsigned char*, size_t, double*)' at /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSNumpress.cpp:403:33: +/usr/include/c++/14/ostream:210:25: warning: 'extrapol' may be used uninitialized [-Wmaybe-uninitialized] + 210 | { return _M_insert(__n); } + | ~~~~~~~~~^~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSNumpress.cpp: In function 'size_t pwiz::msdata::MSNumpress::decodeLinear(const unsigned char*, size_t, double*)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSNumpress.cpp:346:15: note: 'extrapol' was declared here + 346 | long long extrapol; + | ^~~~~~~~ +In member function 'std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long long int) [with _CharT = char; _Traits = std::char_traits]', + inlined from 'size_t pwiz::msdata::MSNumpress::decodeLinear(const unsigned char*, size_t, double*)' at /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSNumpress.cpp:404:26: +/usr/include/c++/14/ostream:210:25: warning: 'y' may be used uninitialized [-Wmaybe-uninitialized] + 210 | { return _M_insert(__n); } + | ~~~~~~~~~^~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSNumpress.cpp: In function 'size_t pwiz::msdata::MSNumpress::decodeLinear(const unsigned char*, size_t, double*)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSNumpress.cpp:347:15: note: 'y' was declared here + 347 | long long y; + | ^ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/LegacyAdapter.hpp:30, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/LegacyAdapter.cpp:27: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/algorithm:60, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Reader.cpp: In member function 'virtual void pwiz::msdata::Reader::readIds(const std::string&, const std::string&, std::vector >&, const Config&) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Reader.cpp:80:119: warning: unused parameter 'config' [-Wunused-parameter] + 80 | PWIZ_API_DECL void Reader::readIds(const string& filename, const string& head, vector& results, const Config& config) const + | ~~~~~~~~~~~~~~^~~~~~ +[ 40%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/References.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/References.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/References.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/References.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/References.cpp +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:25: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/algorithm:60, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] + 769 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] + 853 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/BinaryDataEncoder.cpp: In member function 'void pwiz::msdata::BinaryDataEncoder::Impl::encode(const double*, size_t, std::string&, size_t*)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/BinaryDataEncoder.cpp:305:37: warning: 'byteCount' may be used uninitialized [-Wmaybe-uninitialized] + 305 | filterArray(byteBuffer, byteCount,compressed); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/BinaryDataEncoder.cpp:131:12: note: 'byteCount' was declared here + 131 | size_t byteCount; + | ^~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/BinaryDataEncoder.cpp:305:37: warning: 'byteBuffer' may be used uninitialized [-Wmaybe-uninitialized] + 305 | filterArray(byteBuffer, byteCount,compressed); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/BinaryDataEncoder.cpp:132:17: note: 'byteBuffer' was declared here + 132 | const void* byteBuffer; + | ^~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] + 769 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] + 853 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MSn.hpp:28: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] + 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.hpp:32, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/ChromatogramList_mzML.cpp:27: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] + 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/ChromatogramList_mzML.cpp:29: /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] 585 | virtual Status processingInstruction(const std::string& name, @@ -2963,6 +3054,14 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] 597 | stream_offset position) {return Status::Ok;} | ~~~~~~~~~~~~~~^~~~~~~~ +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/iterator.hpp: At global scope: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] 769 | virtual void warn_once(const char* msg) const {} @@ -2971,53 +3070,52 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] 853 | virtual void warn_once(const char* msg) const {} | ~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual size_t pwiz::msdata::SpectrumList::findAbbreviated(const std::string&, char) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.cpp:1121:21: warning: comparison of unsigned expression in '>= 0' is always true [-Wtype-limits] - 1121 | if ((result >= 0 && result < size()) || s == 0) - | ~~~~~~~^~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.hpp:32, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp:28: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] - 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.hpp:31: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] - 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.hpp:32, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzML.cpp:27: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] - 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +[ 41%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_MGF.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_MGF.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_MGF.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_MGF.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_MGF.cpp +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MGF.hpp:27, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MGF.cpp:25: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/algorithm:60, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Environment.hpp:24, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Std.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/cv.cpp:34: + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/iterator.hpp: At global scope: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.hpp:32, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:26: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] - 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual size_t pwiz::msdata::SpectrumList::findAbbreviated(const std::string&, char) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.cpp:1121:21: warning: comparison of unsigned expression in '>= 0' is always true [-Wtype-limits] - 1121 | if ((result >= 0 && result < size()) || s == 0) - | ~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual pwiz::msdata::SpectrumPtr pwiz::msdata::SpectrumListSimple::spectrum(size_t, bool) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.cpp:1232:75: warning: unused parameter 'getBinaryData' [-Wunused-parameter] - 1232 | PWIZ_API_DECL SpectrumPtr SpectrumListSimple::spectrum(size_t index, bool getBinaryData) const - | ~~~~~^~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual pwiz::msdata::ChromatogramPtr pwiz::msdata::ChromatogramListSimple::chromatogram(size_t, bool) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.cpp:1299:87: warning: unused parameter 'getBinaryData' [-Wunused-parameter] - 1299 | PWIZ_API_DECL ChromatogramPtr ChromatogramListSimple::chromatogram(size_t index, bool getBinaryData) const - | ~~~~~^~~~~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumListBase.hpp:28, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumListBase.cpp:25: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/algorithm:60, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, @@ -3026,7 +3124,47 @@ /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzML.cpp:29: +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzML.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzML.cpp:26: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/algorithm:60, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] + 769 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] + 853 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +[ 42%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_MSn.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_MSn.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_MSn.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_MSn.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_MSn.cpp +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MSn.cpp: In member function 'void pwiz::msdata::Serializer_MSn::write(std::ostream&, const pwiz::msdata::MSData&, const pwiz::util::IterationListenerRegistry*, bool, bool) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MSn.cpp:552:10: warning: unused parameter 'useWorkerThreads' [-Wunused-parameter] + 552 | bool useWorkerThreads, bool continueOnError) const + | ~~~~~^~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MSn.cpp:552:33: warning: unused parameter 'continueOnError' [-Wunused-parameter] + 552 | bool useWorkerThreads, bool continueOnError) const + | ~~~~~^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.hpp:31: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] + 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:32: /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] 585 | virtual Status processingInstruction(const std::string& name, @@ -3061,15 +3199,59 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] 597 | stream_offset position) {return Status::Ok;} | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual pwiz::msdata::SpectrumPtr pwiz::msdata::SpectrumListSimple::spectrum(size_t, bool) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.cpp:1232:75: warning: unused parameter 'getBinaryData' [-Wunused-parameter] - 1232 | PWIZ_API_DECL SpectrumPtr SpectrumListSimple::spectrum(size_t index, bool getBinaryData) const - | ~~~~~^~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual pwiz::msdata::ChromatogramPtr pwiz::msdata::ChromatogramListSimple::chromatogram(size_t, bool) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.cpp:1299:87: warning: unused parameter 'getBinaryData' [-Wunused-parameter] - 1299 | PWIZ_API_DECL ChromatogramPtr ChromatogramListSimple::chromatogram(size_t index, bool getBinaryData) const - | ~~~~~^~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:28: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] + 769 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] + 853 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] + 769 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] + 853 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/References.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/References.cpp:25: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/algorithm:60, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MGF.hpp:29: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] + 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] + 769 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] + 853 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzML.hpp:31: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] + 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzML.cpp:32: /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] 585 | virtual Status processingInstruction(const std::string& name, @@ -3101,6 +3283,9 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:596:59: warning: unused parameter 'text' [-Wunused-parameter] 596 | virtual Status characters(const SAXParser::saxstring& text, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] + 597 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, @@ -3109,9 +3294,219 @@ /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] - 597 | stream_offset position) {return Status::Ok;} +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/iterator.hpp: At global scope: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/iterator.hpp: At global scope: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 43%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumInfo.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumInfo.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumInfo.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumInfo.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumInfo.cpp +[ 45%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumWorkerThreads.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumWorkerThreads.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumWorkerThreads.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumWorkerThreads.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumWorkerThreads.cpp +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp: In function 'std::string pwiz::msdata::{anonymous}::translate_SourceFileTypeToRunID(const pwiz::msdata::SourceFile&, pwiz::cv::CVID)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:149:61: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] + 149 | string nameExtension = bal::to_lower_copy(bfs::extension(sf.name)); + | ~~~~~~~~~~~~~~^~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.hpp:37, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:33: +/usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here + 29 | inline std::string extension(const path& p) + | ^~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:150:65: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] + 150 | string locationExtension = bal::to_lower_copy(bfs::extension(sf.location)); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ +/usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here + 29 | inline std::string extension(const path& p) + | ^~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:157:37: warning: 'std::string boost::filesystem::basename(const path&)' is deprecated: Use path::stem() instead [-Wdeprecated-declarations] + 157 | return bfs::basename(sf.name); + | ~~~~~~~~~~~~~^~~~~~~~~ +/usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here + 35 | inline std::string basename(const path& p) + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:164:65: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] + 164 | return bfs::basename(bfs::path(sf.location).leaf()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +In file included from /usr/include/boost/filesystem/operations.hpp:20, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.hpp:36: +/usr/include/boost/filesystem/path.hpp:1127:10: note: declared here + 1127 | path leaf() const { return filename(); } + | ^~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:164:37: warning: 'std::string boost::filesystem::basename(const path&)' is deprecated: Use path::stem() instead [-Wdeprecated-declarations] + 164 | return bfs::basename(bfs::path(sf.location).leaf()); + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here + 35 | inline std::string basename(const path& p) + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:166:37: warning: 'std::string boost::filesystem::basename(const path&)' is deprecated: Use path::stem() instead [-Wdeprecated-declarations] + 166 | return bfs::basename(sf.name); + | ~~~~~~~~~~~~~^~~~~~~~~ +/usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here + 35 | inline std::string basename(const path& p) + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:172:65: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] + 172 | return bfs::basename(bfs::path(sf.location).leaf()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +/usr/include/boost/filesystem/path.hpp:1127:10: note: declared here + 1127 | path leaf() const { return filename(); } + | ^~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:172:37: warning: 'std::string boost::filesystem::basename(const path&)' is deprecated: Use path::stem() instead [-Wdeprecated-declarations] + 172 | return bfs::basename(bfs::path(sf.location).leaf()); + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here + 35 | inline std::string basename(const path& p) + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:178:65: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] + 178 | return bfs::basename(bfs::path(sf.location).leaf()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +/usr/include/boost/filesystem/path.hpp:1127:10: note: declared here + 1127 | path leaf() const { return filename(); } + | ^~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:178:37: warning: 'std::string boost::filesystem::basename(const path&)' is deprecated: Use path::stem() instead [-Wdeprecated-declarations] + 178 | return bfs::basename(bfs::path(sf.location).leaf()); + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here + 35 | inline std::string basename(const path& p) + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:184:65: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] + 184 | return bfs::basename(bfs::path(sf.location).leaf()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +/usr/include/boost/filesystem/path.hpp:1127:10: note: declared here + 1127 | path leaf() const { return filename(); } + | ^~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:184:37: warning: 'std::string boost::filesystem::basename(const path&)' is deprecated: Use path::stem() instead [-Wdeprecated-declarations] + 184 | return bfs::basename(bfs::path(sf.location).leaf()); + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here + 35 | inline std::string basename(const path& p) + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:190:65: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] + 190 | return bfs::basename(bfs::path(sf.location).leaf()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +/usr/include/boost/filesystem/path.hpp:1127:10: note: declared here + 1127 | path leaf() const { return filename(); } + | ^~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:190:37: warning: 'std::string boost::filesystem::basename(const path&)' is deprecated: Use path::stem() instead [-Wdeprecated-declarations] + 190 | return bfs::basename(bfs::path(sf.location).leaf()); + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here + 35 | inline std::string basename(const path& p) + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:195:44: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] + 195 | if (bfs::path(sf.location).leaf() == "AcqData" && + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +/usr/include/boost/filesystem/path.hpp:1127:10: note: declared here + 1127 | path leaf() const { return filename(); } + | ^~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:199:79: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] + 199 | return bfs::basename(bfs::path(sf.location).parent_path().leaf()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +/usr/include/boost/filesystem/path.hpp:1127:10: note: declared here + 1127 | path leaf() const { return filename(); } + | ^~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:199:37: warning: 'std::string boost::filesystem::basename(const path&)' is deprecated: Use path::stem() instead [-Wdeprecated-declarations] + 199 | return bfs::basename(bfs::path(sf.location).parent_path().leaf()); + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here + 35 | inline std::string basename(const path& p) + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:207:37: warning: 'std::string boost::filesystem::basename(const path&)' is deprecated: Use path::stem() instead [-Wdeprecated-declarations] + 207 | return bfs::basename(sf.name); + | ~~~~~~~~~~~~~^~~~~~~~~ +/usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here + 35 | inline std::string basename(const path& p) + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:216:37: warning: 'std::string boost::filesystem::basename(const path&)' is deprecated: Use path::stem() instead [-Wdeprecated-declarations] + 216 | return bfs::basename(sf.name); + | ~~~~~~~~~~~~~^~~~~~~~~ +/usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here + 35 | inline std::string basename(const path& p) + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:222:37: warning: 'std::string boost::filesystem::basename(const path&)' is deprecated: Use path::stem() instead [-Wdeprecated-declarations] + 222 | return bfs::basename(sf.name); + | ~~~~~~~~~~~~~^~~~~~~~~ +/usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here + 35 | inline std::string basename(const path& p) + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:228:37: warning: 'std::string boost::filesystem::basename(const path&)' is deprecated: Use path::stem() instead [-Wdeprecated-declarations] + 228 | return bfs::basename(sf.name); + | ~~~~~~~~~~~~~^~~~~~~~~ +/usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here + 35 | inline std::string basename(const path& p) + | ^~~~~~~~ +[ 46%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/mzmlb/Connection_mzMLb.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/mzmlb/Connection_mzMLb.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/mzmlb/Connection_mzMLb.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/mzmlb/Connection_mzMLb.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/mzmlb/Connection_mzMLb.cpp +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp: In function 'std::vector pwiz::msdata::{anonymous}::getPrecursorInfo(const pwiz::msdata::Spectrum&, pwiz::msdata::SpectrumListPtr, pwiz::cv::CVID)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:454:62: warning: unused parameter 'spectrumListPtr' [-Wunused-parameter] + 454 | const SpectrumListPtr spectrumListPtr, + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp: In function 'pwiz::cv::CVID pwiz::msdata::{anonymous}::translate_parentFilenameToSourceFileType(const std::string&)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:878:61: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] + 878 | string fileExtension = bal::to_lower_copy(bfs::extension(name)); + | ~~~~~~~~~~~~~~^~~~~~ +/usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here + 29 | inline std::string extension(const path& p) + | ^~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerScanFileContent::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:1027:47: warning: unused parameter 'position' [-Wunused-parameter] + 1027 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp: In function 'void pwiz::msdata::{anonymous}::fillInMetadata(pwiz::msdata::MSData&)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:1139:65: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] + 1139 | msd.id = msd.run.id = BFS_STRING(bfs::path(lcp).leaf()); + | ~~~~~~~~~~~~~~~~~~~^~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.hpp:64:24: note: in definition of macro 'BFS_STRING' + 64 | #define BFS_STRING(p) (p).string() + | ^ +/usr/include/boost/filesystem/path.hpp:1127:10: note: declared here + 1127 | path leaf() const { return filename(); } + | ^~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:1141:79: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] + 1141 | msd.id = msd.run.id = BFS_STRING(bfs::path(lcp).parent_path().leaf()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.hpp:64:24: note: in definition of macro 'BFS_STRING' + 64 | #define BFS_STRING(p) (p).string() + | ^ +/usr/include/boost/filesystem/path.hpp:1127:10: note: declared here + 1127 | path leaf() const { return filename(); } + | ^~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::Handler_msInstrument::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:1156:47: warning: unused parameter 'position' [-Wunused-parameter] + 1156 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::Handler_msInstrument::endElement(const std::string&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:1237:45: warning: unused parameter 'position' [-Wunused-parameter] + 1237 | stream_offset position) | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::Handler_dataProcessing::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:1285:47: warning: unused parameter 'position' [-Wunused-parameter] + 1285 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::Handler_mzXML::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:1353:47: warning: unused parameter 'position' [-Wunused-parameter] + 1353 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] + 769 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] + 853 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +[ 47%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/minimxml/SAXParser.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/minimxml/SAXParser.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/utility/minimxml/SAXParser.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/utility/minimxml/SAXParser.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.cpp In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, @@ -3120,20 +3515,6 @@ /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.hpp:32, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:26: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] - 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSDataFile.cpp:39: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.hpp: In member function 'virtual std::string pwiz::msdata::Reader_MS2::identify(const std::string&, const std::string&) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.hpp:98:53: warning: unused parameter 'filename' [-Wunused-parameter] - 98 | virtual std::string identify(const std::string& filename, const std::string& head) const { return ""; } - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.hpp:98:82: warning: unused parameter 'head' [-Wunused-parameter] - 98 | virtual std::string identify(const std::string& filename, const std::string& head) const { return ""; } - | ~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::HandlerIndexedMZML::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzML.cpp:278:51: warning: unused parameter 'attributes' [-Wunused-parameter] 278 | const Attributes& attributes, @@ -3141,30 +3522,146 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzML.cpp:279:47: warning: unused parameter 'position' [-Wunused-parameter] 279 | stream_offset position) | ~~~~~~~~~~~~~~^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSDataFile.cpp:39: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.hpp: In member function 'virtual std::string pwiz::msdata::Reader_MS2::identify(const std::string&, const std::string&) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.hpp:98:53: warning: unused parameter 'filename' [-Wunused-parameter] - 98 | virtual std::string identify(const std::string& filename, const std::string& head) const { return ""; } - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.hpp:98:82: warning: unused parameter 'head' [-Wunused-parameter] - 98 | virtual std::string identify(const std::string& filename, const std::string& head) const { return ""; } - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexListOffset::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp:86:51: warning: unused parameter 'attributes' [-Wunused-parameter] - 86 | const Attributes& attributes, - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp:87:47: warning: unused parameter 'position' [-Wunused-parameter] - 87 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexListOffset::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp:95:45: warning: unused parameter 'position' [-Wunused-parameter] - 95 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerOffset::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp:120:47: warning: unused parameter 'position' [-Wunused-parameter] - 120 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:28: +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumListBase.hpp:28, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_MGF.hpp:30, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_MGF.cpp:26: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/algorithm:60, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 48%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/minimxml/XMLWriter.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/minimxml/XMLWriter.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/utility/minimxml/XMLWriter.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/utility/minimxml/XMLWriter.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/XMLWriter.cpp +[ 50%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_BTDX.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_BTDX.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_BTDX.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_BTDX.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_BTDX.cpp +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumListBase.hpp:28, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_MSn.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_MSn.cpp:26: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/algorithm:60, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumInfo.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumInfo.cpp:27: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/algorithm:60, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 51%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_mzML.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_mzML.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_mzML.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_mzML.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzML.cpp +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] + 769 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] + 853 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/mzmlb/Connection_mzMLb.cpp: In constructor 'pwiz::msdata::mzmlb::Connection_mzMLb::Connection_mzMLb(const std::string&, int, int)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/mzmlb/Connection_mzMLb.cpp:142:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 142 | nbytes = (nbytes > chunk_size) ? nbytes : chunk_size; // Set per dataset cache to twice the chunk size please + | ~~~~~~~^~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] + 769 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] + 853 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/iterator.hpp: At global scope: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/iterator.hpp: At global scope: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 52%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/Base64.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/Base64.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/Base64.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/Base64.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Base64.cpp +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] + 769 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] + 853 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +[ 53%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_mzXML.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_mzXML.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_mzXML.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_mzXML.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MGF.cpp: In member function 'void pwiz::msdata::Serializer_MGF::Impl::write(std::ostream&, const pwiz::msdata::MSData&, const pwiz::util::IterationListenerRegistry*, bool, bool) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MGF.cpp:73:61: warning: 'std::string boost::filesystem::basename(const path&)' is deprecated: Use path::stem() instead [-Wdeprecated-declarations] + 73 | string thermoBasename = titleIsThermoDTA ? bfs::basename(thermoFilename) : ""; + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.hpp:37, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MGF.cpp:27: +/usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here + 35 | inline std::string basename(const path& p) + | ^~~~~~~~ +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/iterator.hpp: At global scope: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 54%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/IterationListener.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/IterationListener.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/IterationListener.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/IterationListener.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.cpp +[ 56%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/SHA1.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/SHA1.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/SHA1.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/SHA1.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/SHA1.cpp +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Environment.hpp:24, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Std.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.cpp:28: /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] 585 | virtual Status processingInstruction(const std::string& name, @@ -3185,10 +3682,6 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:591:47: warning: unused parameter 'position' [-Wunused-parameter] 591 | stream_offset position) {return Status::Ok;} | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerOffset::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp:165:45: warning: unused parameter 'position' [-Wunused-parameter] - 165 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::endElement(const std::string&, stream_offset)': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:593:50: warning: unused parameter 'name' [-Wunused-parameter] 593 | virtual Status endElement(const std::string& name, @@ -3203,19 +3696,83 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] 597 | stream_offset position) {return Status::Ok;} | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexList::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp:201:47: warning: unused parameter 'position' [-Wunused-parameter] - 201 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:31: /usr/include/boost/iterator.hpp: At global scope: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp:26: +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumListBase.hpp:28, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_BTDX.hpp:30, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:26: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/algorithm:60, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 57%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/SHA1Calculator.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/SHA1Calculator.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/SHA1Calculator.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/SHA1Calculator.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/SHA1Calculator.cpp +[ 58%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/random_access_compressed_ifstream.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/random_access_compressed_ifstream.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/random_access_compressed_ifstream.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/random_access_compressed_ifstream.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/random_access_compressed_ifstream.cpp +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] + 769 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] + 853 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumListBase.hpp:28, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:25: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/algorithm:60, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumListBase.hpp:28, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzML.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzML.cpp:26: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/algorithm:60, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:28: /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] 585 | virtual Status processingInstruction(const std::string& name, @@ -3258,29 +3815,74 @@ /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] + 769 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] + 853 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumWorkerThreads.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumWorkerThreads.cpp:26: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /usr/include/c++/14/stdexcept:39, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Exception.hpp:28, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Std.hpp:28: +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp: At global scope: + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Environment.hpp:24, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Std.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Base64.cpp:26: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 59%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/BinaryData.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/BinaryData.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/BinaryData.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/BinaryData.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] + 769 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] + 853 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] + 769 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] + 853 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp: At global scope: + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/XMLWriter.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/XMLWriter.cpp:25: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.hpp:32, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp:28: + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:26: /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:32: +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:28: /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] 585 | virtual Status processingInstruction(const std::string& name, @@ -3315,6 +3917,24 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] 597 | stream_offset position) {return Status::Ok;} | ~~~~~~~~~~~~~~^~~~~~~~ +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/iterator.hpp: At global scope: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 60%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Version.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Version.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Version.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Version.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Version.cpp +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Environment.hpp:24, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Std.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.cpp:26: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.hpp:32, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzML.cpp:27: /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': @@ -3356,90 +3976,382 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] 597 | stream_offset position) {return Status::Ok;} | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Reader.cpp: In member function 'virtual void pwiz::msdata::Reader::readIds(const std::string&, const std::string&, std::vector >&, const Config&) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Reader.cpp:80:119: warning: unused parameter 'config' [-Wunused-parameter] - 80 | PWIZ_API_DECL void Reader::readIds(const string& filename, const string& head, vector& results, const Config& config) const - | ~~~~~~~~~~~~~~^~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/requires_cxx11.hpp:9, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:17: +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: /usr/include/boost/iterator.hpp: At global scope: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:28: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] - 585 | virtual Status processingInstruction(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:586:61: warning: unused parameter 'data' [-Wunused-parameter] - 586 | const std::string& data, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:587:56: warning: unused parameter 'position' [-Wunused-parameter] - 587 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::startElement(const std::string&, const Attributes&, stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:589:52: warning: unused parameter 'name' [-Wunused-parameter] - 589 | virtual Status startElement(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:590:51: warning: unused parameter 'attributes' [-Wunused-parameter] - 590 | const Attributes& attributes, +[ 62%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/IntegerSet.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/IntegerSet.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/IntegerSet.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/IntegerSet.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IntegerSet.cpp +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.cpp:27: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] + 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +[ 63%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/String.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/String.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/String.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/String.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/String.cpp +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_BTDX.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerPeaks::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:121:47: warning: unused parameter 'position' [-Wunused-parameter] + 121 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_BTDX.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerPeaks::endElement(const std::string&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:162:45: warning: unused parameter 'position' [-Wunused-parameter] + 162 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_BTDX.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexCreator::endElement(const std::string&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:356:45: warning: unused parameter 'position' [-Wunused-parameter] + 356 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +[ 64%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/BinaryDataEncoder.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/BinaryDataEncoder.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/BinaryDataEncoder.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/BinaryDataEncoder.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/BinaryDataEncoder.cpp +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumWorkerThreads.cpp: In constructor 'pwiz::msdata::SpectrumWorkerThreads::Impl::Impl(const pwiz::msdata::SpectrumList&, bool, bool)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumWorkerThreads.cpp:337:22: warning: 'pwiz::msdata::SpectrumWorkerThreads::Impl::taskMRU_' will be initialized after [-Wreorder] + 337 | mru_list taskMRU_; + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumWorkerThreads.cpp:334:10: warning: 'bool pwiz::msdata::SpectrumWorkerThreads::Impl::continueOnError_' [-Wreorder] + 334 | bool continueOnError_; + | ^~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumWorkerThreads.cpp:60:5: warning: when initialized here [-Wreorder] + 60 | Impl(const SpectrumList& sl, bool useWorkerThreads, bool continueOnError) + | ^~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In constructor 'pwiz::msdata::{anonymous}::SpectrumList_mzXMLImpl::SpectrumList_mzXMLImpl(boost::shared_ptr >, const pwiz::msdata::MSData&, bool)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:84:30: warning: catching polymorphic type 'struct pwiz::msdata::SpectrumList_mzXML::index_not_found' by value [-Wcatch-value=] + 84 | } catch (index_not_found e){ + | ^ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerPrecursor::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:128:47: warning: unused parameter 'position' [-Wunused-parameter] + 128 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerPrecursor::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:212:45: warning: unused parameter 'position' [-Wunused-parameter] + 212 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerPeaks::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:239:47: warning: unused parameter 'position' [-Wunused-parameter] + 239 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerPeaks::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:282:45: warning: unused parameter 'position' [-Wunused-parameter] + 282 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerPeaks::endElement(const std::string&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:302:70: warning: unused parameter 'position' [-Wunused-parameter] + 302 | virtual Status endElement(const std::string& name, stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +[ 65%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/Filesystem.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/Filesystem.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/Filesystem.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/Filesystem.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.cpp +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexOffset::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:701:51: warning: unused parameter 'attributes' [-Wunused-parameter] + 701 | const Attributes& attributes, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:591:47: warning: unused parameter 'position' [-Wunused-parameter] - 591 | stream_offset position) {return Status::Ok;} +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:702:47: warning: unused parameter 'position' [-Wunused-parameter] + 702 | stream_offset position) | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::endElement(const std::string&, stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:593:50: warning: unused parameter 'name' [-Wunused-parameter] - 593 | virtual Status endElement(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:594:45: warning: unused parameter 'position' [-Wunused-parameter] - 594 | stream_offset position) {return Status::Ok;} +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexOffset::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:710:45: warning: unused parameter 'position' [-Wunused-parameter] + 710 | stream_offset position) | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::characters(const pwiz::minimxml::SAXParser::saxstring&, stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:596:59: warning: unused parameter 'text' [-Wunused-parameter] - 596 | virtual Status characters(const SAXParser::saxstring& text, +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerOffset::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:736:47: warning: unused parameter 'position' [-Wunused-parameter] + 736 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerOffset::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:754:45: warning: unused parameter 'position' [-Wunused-parameter] + 754 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndex::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:778:51: warning: unused parameter 'attributes' [-Wunused-parameter] + 778 | const Attributes& attributes, + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:779:47: warning: unused parameter 'position' [-Wunused-parameter] + 779 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndex::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:796:59: warning: unused parameter 'text' [-Wunused-parameter] + 796 | virtual Status characters(const SAXParser::saxstring& text, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] - 597 | stream_offset position) {return Status::Ok;} +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:797:45: warning: unused parameter 'position' [-Wunused-parameter] + 797 | stream_offset position) | ~~~~~~~~~~~~~~^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Reader.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:29: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] - 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexCreator::endElement(const std::string&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:885:45: warning: unused parameter 'position' [-Wunused-parameter] + 885 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/requires_cxx11.hpp:9, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, + from /usr/include/boost/shared_ptr.hpp:17, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/SHA1Calculator.hpp:28, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/SHA1Calculator.cpp:32: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:24: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/algorithm:60, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 67%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/DefaultReaderList.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/DefaultReaderList.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/DefaultReaderList.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/DefaultReaderList.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp: In instantiation of 'const T& pwiz::util::BinaryData::at(size_type) const [with T = double; const_reference = const double&; size_type = long unsigned int]': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:498:30: required from here + 498 | PWIZ_API_DECL template class BinaryData; + | ^~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:256:19: warning: comparison of unsigned expression in '< 0' is always false [-Wtype-limits] + 256 | if (index < 0 || index >= size()) + | ~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp: In instantiation of 'T& pwiz::util::BinaryData::at(size_type) [with T = double; reference = double&; size_type = long unsigned int]': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:498:30: required from here + 498 | PWIZ_API_DECL template class BinaryData; + | ^~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:263:19: warning: comparison of unsigned expression in '< 0' is always false [-Wtype-limits] + 263 | if (index < 0 || index >= size()) + | ~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp: In instantiation of 'pwiz::util::BinaryData::Impl::Impl(void*) [with T = double]': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:498:30: required from here + 498 | PWIZ_API_DECL template class BinaryData; + | ^~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:58:16: warning: unused parameter 'cliNumericArray' [-Wunused-parameter] + 58 | Impl(void* cliNumericArray) + | ~~~~~~^~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp: In instantiation of 'pwiz::util::BinaryData::Impl& pwiz::util::BinaryData::Impl::operator=(void*) [with T = double]': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:498:30: required from here + 498 | PWIZ_API_DECL template class BinaryData; + | ^~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:72:27: warning: unused parameter 'cliNumericArray' [-Wunused-parameter] + 72 | Impl& operator=(void* cliNumericArray) + | ~~~~~~^~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp: In instantiation of 'void pwiz::util::BinaryData::Impl::cacheIterators(pwiz::util::BinaryData&) [with T = double]': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:498:30: required from here + 498 | PWIZ_API_DECL template class BinaryData; + | ^~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:313:16: warning: implicitly-declared 'constexpr pwiz::util::BinaryData::iterator& pwiz::util::BinaryData::iterator::operator=(const pwiz::util::BinaryData::iterator&)' is deprecated [-Wdeprecated-copy] + 313 | begin_ = iterator(binaryData, true); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:113:9: note: because 'pwiz::util::BinaryData::iterator' has user-provided 'pwiz::util::BinaryData::iterator::iterator(const pwiz::util::BinaryData::iterator&) [with T = double]' + 113 | iterator(const iterator& rhs) : current_(rhs.current_) {} + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:314:14: warning: implicitly-declared 'constexpr pwiz::util::BinaryData::iterator& pwiz::util::BinaryData::iterator::operator=(const pwiz::util::BinaryData::iterator&)' is deprecated [-Wdeprecated-copy] + 314 | end_ = iterator(binaryData, false); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:113:9: note: because 'pwiz::util::BinaryData::iterator' has user-provided 'pwiz::util::BinaryData::iterator::iterator(const pwiz::util::BinaryData::iterator&) [with T = double]' + 113 | iterator(const iterator& rhs) : current_(rhs.current_) {} + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:315:17: warning: implicitly-declared 'constexpr pwiz::util::BinaryData::const_iterator& pwiz::util::BinaryData::const_iterator::operator=(const pwiz::util::BinaryData::const_iterator&)' is deprecated [-Wdeprecated-copy] + 315 | cbegin_ = const_iterator(binaryData, true); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:79:9: note: because 'pwiz::util::BinaryData::const_iterator' has user-provided 'pwiz::util::BinaryData::const_iterator::const_iterator(const pwiz::util::BinaryData::const_iterator&) [with T = double]' + 79 | const_iterator(const const_iterator& rhs) : current_(rhs.current_) {} + | ^~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:316:15: warning: implicitly-declared 'constexpr pwiz::util::BinaryData::const_iterator& pwiz::util::BinaryData::const_iterator::operator=(const pwiz::util::BinaryData::const_iterator&)' is deprecated [-Wdeprecated-copy] + 316 | cend_ = const_iterator(binaryData, false); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:79:9: note: because 'pwiz::util::BinaryData::const_iterator' has user-provided 'pwiz::util::BinaryData::const_iterator::const_iterator(const pwiz::util::BinaryData::const_iterator&) [with T = double]' + 79 | const_iterator(const const_iterator& rhs) : current_(rhs.current_) {} + | ^~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp: In instantiation of 'const T& pwiz::util::BinaryData::at(size_type) const [with T = float; const_reference = const float&; size_type = long unsigned int]': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:499:30: required from here + 499 | PWIZ_API_DECL template class BinaryData; + | ^~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:256:19: warning: comparison of unsigned expression in '< 0' is always false [-Wtype-limits] + 256 | if (index < 0 || index >= size()) + | ~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp: In instantiation of 'T& pwiz::util::BinaryData::at(size_type) [with T = float; reference = float&; size_type = long unsigned int]': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:499:30: required from here + 499 | PWIZ_API_DECL template class BinaryData; + | ^~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:263:19: warning: comparison of unsigned expression in '< 0' is always false [-Wtype-limits] + 263 | if (index < 0 || index >= size()) + | ~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp: In instantiation of 'pwiz::util::BinaryData::Impl::Impl(void*) [with T = float]': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:499:30: required from here + 499 | PWIZ_API_DECL template class BinaryData; + | ^~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:58:16: warning: unused parameter 'cliNumericArray' [-Wunused-parameter] + 58 | Impl(void* cliNumericArray) + | ~~~~~~^~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp: In instantiation of 'pwiz::util::BinaryData::Impl& pwiz::util::BinaryData::Impl::operator=(void*) [with T = float]': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:499:30: required from here + 499 | PWIZ_API_DECL template class BinaryData; + | ^~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:72:27: warning: unused parameter 'cliNumericArray' [-Wunused-parameter] + 72 | Impl& operator=(void* cliNumericArray) + | ~~~~~~^~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp: In instantiation of 'void pwiz::util::BinaryData::Impl::cacheIterators(pwiz::util::BinaryData&) [with T = float]': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:499:30: required from here + 499 | PWIZ_API_DECL template class BinaryData; + | ^~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:313:16: warning: implicitly-declared 'constexpr pwiz::util::BinaryData::iterator& pwiz::util::BinaryData::iterator::operator=(const pwiz::util::BinaryData::iterator&)' is deprecated [-Wdeprecated-copy] + 313 | begin_ = iterator(binaryData, true); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:113:9: note: because 'pwiz::util::BinaryData::iterator' has user-provided 'pwiz::util::BinaryData::iterator::iterator(const pwiz::util::BinaryData::iterator&) [with T = float]' + 113 | iterator(const iterator& rhs) : current_(rhs.current_) {} + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:314:14: warning: implicitly-declared 'constexpr pwiz::util::BinaryData::iterator& pwiz::util::BinaryData::iterator::operator=(const pwiz::util::BinaryData::iterator&)' is deprecated [-Wdeprecated-copy] + 314 | end_ = iterator(binaryData, false); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:113:9: note: because 'pwiz::util::BinaryData::iterator' has user-provided 'pwiz::util::BinaryData::iterator::iterator(const pwiz::util::BinaryData::iterator&) [with T = float]' + 113 | iterator(const iterator& rhs) : current_(rhs.current_) {} + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:315:17: warning: implicitly-declared 'constexpr pwiz::util::BinaryData::const_iterator& pwiz::util::BinaryData::const_iterator::operator=(const pwiz::util::BinaryData::const_iterator&)' is deprecated [-Wdeprecated-copy] + 315 | cbegin_ = const_iterator(binaryData, true); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:79:9: note: because 'pwiz::util::BinaryData::const_iterator' has user-provided 'pwiz::util::BinaryData::const_iterator::const_iterator(const pwiz::util::BinaryData::const_iterator&) [with T = float]' + 79 | const_iterator(const const_iterator& rhs) : current_(rhs.current_) {} + | ^~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:316:15: warning: implicitly-declared 'constexpr pwiz::util::BinaryData::const_iterator& pwiz::util::BinaryData::const_iterator::operator=(const pwiz::util::BinaryData::const_iterator&)' is deprecated [-Wdeprecated-copy] + 316 | cend_ = const_iterator(binaryData, false); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:79:9: note: because 'pwiz::util::BinaryData::const_iterator' has user-provided 'pwiz::util::BinaryData::const_iterator::const_iterator(const pwiz::util::BinaryData::const_iterator&) [with T = float]' + 79 | const_iterator(const const_iterator& rhs) : current_(rhs.current_) {} + | ^~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp: In instantiation of 'const T& pwiz::util::BinaryData::at(size_type) const [with T = long int; const_reference = const long int&; size_type = long unsigned int]': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:500:30: required from here + 500 | PWIZ_API_DECL template class BinaryData; + | ^~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:256:19: warning: comparison of unsigned expression in '< 0' is always false [-Wtype-limits] + 256 | if (index < 0 || index >= size()) + | ~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp: In instantiation of 'T& pwiz::util::BinaryData::at(size_type) [with T = long int; reference = long int&; size_type = long unsigned int]': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:500:30: required from here + 500 | PWIZ_API_DECL template class BinaryData; + | ^~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:263:19: warning: comparison of unsigned expression in '< 0' is always false [-Wtype-limits] + 263 | if (index < 0 || index >= size()) + | ~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp: In instantiation of 'pwiz::util::BinaryData::Impl::Impl(void*) [with T = long int]': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:500:30: required from here + 500 | PWIZ_API_DECL template class BinaryData; + | ^~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:58:16: warning: unused parameter 'cliNumericArray' [-Wunused-parameter] + 58 | Impl(void* cliNumericArray) + | ~~~~~~^~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp: In instantiation of 'pwiz::util::BinaryData::Impl& pwiz::util::BinaryData::Impl::operator=(void*) [with T = long int]': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:500:30: required from here + 500 | PWIZ_API_DECL template class BinaryData; + | ^~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:72:27: warning: unused parameter 'cliNumericArray' [-Wunused-parameter] + 72 | Impl& operator=(void* cliNumericArray) + | ~~~~~~^~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp: In instantiation of 'void pwiz::util::BinaryData::Impl::cacheIterators(pwiz::util::BinaryData&) [with T = long int]': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:500:30: required from here + 500 | PWIZ_API_DECL template class BinaryData; + | ^~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:313:16: warning: implicitly-declared 'constexpr pwiz::util::BinaryData::iterator& pwiz::util::BinaryData::iterator::operator=(const pwiz::util::BinaryData::iterator&)' is deprecated [-Wdeprecated-copy] + 313 | begin_ = iterator(binaryData, true); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:113:9: note: because 'pwiz::util::BinaryData::iterator' has user-provided 'pwiz::util::BinaryData::iterator::iterator(const pwiz::util::BinaryData::iterator&) [with T = long int]' + 113 | iterator(const iterator& rhs) : current_(rhs.current_) {} + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:314:14: warning: implicitly-declared 'constexpr pwiz::util::BinaryData::iterator& pwiz::util::BinaryData::iterator::operator=(const pwiz::util::BinaryData::iterator&)' is deprecated [-Wdeprecated-copy] + 314 | end_ = iterator(binaryData, false); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:113:9: note: because 'pwiz::util::BinaryData::iterator' has user-provided 'pwiz::util::BinaryData::iterator::iterator(const pwiz::util::BinaryData::iterator&) [with T = long int]' + 113 | iterator(const iterator& rhs) : current_(rhs.current_) {} + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:315:17: warning: implicitly-declared 'constexpr pwiz::util::BinaryData::const_iterator& pwiz::util::BinaryData::const_iterator::operator=(const pwiz::util::BinaryData::const_iterator&)' is deprecated [-Wdeprecated-copy] + 315 | cbegin_ = const_iterator(binaryData, true); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:79:9: note: because 'pwiz::util::BinaryData::const_iterator' has user-provided 'pwiz::util::BinaryData::const_iterator::const_iterator(const pwiz::util::BinaryData::const_iterator&) [with T = long int]' + 79 | const_iterator(const const_iterator& rhs) : current_(rhs.current_) {} + | ^~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:316:15: warning: implicitly-declared 'constexpr pwiz::util::BinaryData::const_iterator& pwiz::util::BinaryData::const_iterator::operator=(const pwiz::util::BinaryData::const_iterator&)' is deprecated [-Wdeprecated-copy] + 316 | cend_ = const_iterator(binaryData, false); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:79:9: note: because 'pwiz::util::BinaryData::const_iterator' has user-provided 'pwiz::util::BinaryData::const_iterator::const_iterator(const pwiz::util::BinaryData::const_iterator&) [with T = long int]' + 79 | const_iterator(const const_iterator& rhs) : current_(rhs.current_) {} + | ^~~~~~~~~~~~~~ +[ 68%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/IO.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/IO.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/IO.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/IO.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp +[ 69%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Index_mzML.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Index_mzML.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Index_mzML.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Index_mzML.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.cpp:54:21: warning: WIN32 is NOT defined + 54 | #pragma GCC warning "WIN32 is NOT defined" + | ^~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/requires_cxx11.hpp:9, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/iostreams/device/file_descriptor.hpp:28, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/random_access_compressed_ifstream.cpp:69: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp: At global scope: + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Environment.hpp:24, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Std.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IntegerSet.cpp:26: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Reader.hpp:29: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/BinaryDataEncoder.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/BinaryDataEncoder.cpp:26: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/algorithm:60, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 70%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSData.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSData.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSData.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSData.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.cpp +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IntegerSet.cpp: In member function 'void pwiz::util::IntegerSet::insert(Interval)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IntegerSet.cpp:138:79: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 138 | if (eraseBegin != intervals_.end() && eraseBegin->begin <= interval.begin && eraseBegin->end >= interval.end || + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IntegerSet.cpp: In member function 'bool pwiz::util::IntegerSet::Iterator::operator==(const pwiz::util::IntegerSet::Iterator&) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IntegerSet.cpp:325:63: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 325 | return (it_!=end_ && that.it_!=that.end_ && it_==that.it_ && value_==that.value_ || + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/random_access_compressed_ifstream.cpp: In member function 'std::streampos pwiz::util::random_access_compressed_streambuf::my_seekg(std::streampos, std::ios_base::seekdir, std::ios_base::openmode)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/random_access_compressed_ifstream.cpp:824:138: warning: unused parameter 'Mode' [-Wunused-parameter] + 824 | std::streampos random_access_compressed_streambuf::my_seekg(std::streampos offset, std::ios_base::seekdir whence,std::ios_base::openmode Mode) { + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/random_access_compressed_ifstream.cpp: In member function 'std::streampos pwiz::util::chunky_streambuf::my_seekg(boost::iostreams::stream_offset, std::ios_base::seekdir, std::ios_base::openmode)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/random_access_compressed_ifstream.cpp:1199:137: warning: unused parameter 'Mode' [-Wunused-parameter] + 1199 | std::streampos chunky_streambuf::my_seekg(boost::iostreams::stream_offset offset, std::ios_base::seekdir whence,std::ios_base::openmode Mode) { + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp: At global scope: + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Environment.hpp:24, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Std.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:26: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Reader.hpp:30: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp: At global scope: + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:26: /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 54 | class PWIZ_API_DECL const_iterator : public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /usr/include/c++/14/stdexcept:39, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Exception.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Std.hpp:28: +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/algorithm:60, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -3449,45 +4361,89 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp: At global scope: +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.hpp:28, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp:24: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/algorithm:60, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/requires_cxx11.hpp:9, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, + from /usr/include/boost/shared_ptr.hpp:17, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/BinaryDataEncoder.hpp:30: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexListOffset::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp:86:51: warning: unused parameter 'attributes' [-Wunused-parameter] - 86 | const Attributes& attributes, +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] + 769 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] + 853 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +[ 71%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSDataFile.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSDataFile.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSDataFile.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSDataFile.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSDataFile.cpp +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.hpp:32: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] + 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:28: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] + 585 | virtual Status processingInstruction(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:586:61: warning: unused parameter 'data' [-Wunused-parameter] + 586 | const std::string& data, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:587:56: warning: unused parameter 'position' [-Wunused-parameter] + 587 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::startElement(const std::string&, const Attributes&, stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:589:52: warning: unused parameter 'name' [-Wunused-parameter] + 589 | virtual Status startElement(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:590:51: warning: unused parameter 'attributes' [-Wunused-parameter] + 590 | const Attributes& attributes, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp:87:47: warning: unused parameter 'position' [-Wunused-parameter] - 87 | stream_offset position) +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:591:47: warning: unused parameter 'position' [-Wunused-parameter] + 591 | stream_offset position) {return Status::Ok;} | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexListOffset::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp:95:45: warning: unused parameter 'position' [-Wunused-parameter] - 95 | stream_offset position) +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::endElement(const std::string&, stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:593:50: warning: unused parameter 'name' [-Wunused-parameter] + 593 | virtual Status endElement(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:594:45: warning: unused parameter 'position' [-Wunused-parameter] + 594 | stream_offset position) {return Status::Ok;} | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerOffset::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp:120:47: warning: unused parameter 'position' [-Wunused-parameter] - 120 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerOffset::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp:165:45: warning: unused parameter 'position' [-Wunused-parameter] - 165 | stream_offset position) +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::characters(const pwiz::minimxml::SAXParser::saxstring&, stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:596:59: warning: unused parameter 'text' [-Wunused-parameter] + 596 | virtual Status characters(const SAXParser::saxstring& text, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] + 597 | stream_offset position) {return Status::Ok;} | ~~~~~~~~~~~~~~^~~~~~~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp: At global scope: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexList::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp:201:47: warning: unused parameter 'position' [-Wunused-parameter] - 201 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] + 769 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] + 853 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:28: /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] @@ -3530,6 +4486,14 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/iterator.hpp: At global scope: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Reader.hpp:29: /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses] @@ -3555,9 +4519,25 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 73%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Reader.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Reader.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Reader.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Reader.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Reader.cpp +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] + 769 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] + 853 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.hpp: In member function 'virtual std::string pwiz::msdata::Reader_MS2::identify(const std::string&, const std::string&) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.hpp:98:53: warning: unused parameter 'filename' [-Wunused-parameter] + 98 | virtual std::string identify(const std::string& filename, const std::string& head) const { return ""; } + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.hpp:98:82: warning: unused parameter 'head' [-Wunused-parameter] + 98 | virtual std::string identify(const std::string& filename, const std::string& head) const { return ""; } + | ~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumListBase.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumListBase.cpp:25: + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.cpp:25: /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 54 | class PWIZ_API_DECL const_iterator : public std::iterator | ^~~~~~~~ @@ -3573,46 +4553,6 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] - 769 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] - 853 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.hpp: In member function 'virtual std::string pwiz::msdata::Reader_MS2::identify(const std::string&, const std::string&) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.hpp:98:53: warning: unused parameter 'filename' [-Wunused-parameter] - 98 | virtual std::string identify(const std::string& filename, const std::string& head) const { return ""; } - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.hpp:98:82: warning: unused parameter 'head' [-Wunused-parameter] - 98 | virtual std::string identify(const std::string& filename, const std::string& head) const { return ""; } - | ~~~~~~~~~~~~~~~~~~~^~~~ -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] - 769 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] - 853 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.hpp: In member function 'virtual std::string pwiz::msdata::Reader_MS2::identify(const std::string&, const std::string&) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.hpp:98:53: warning: unused parameter 'filename' [-Wunused-parameter] - 98 | virtual std::string identify(const std::string& filename, const std::string& head) const { return ""; } - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.hpp:98:82: warning: unused parameter 'head' [-Wunused-parameter] - 98 | virtual std::string identify(const std::string& filename, const std::string& head) const { return ""; } - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MSn.cpp: In member function 'void pwiz::msdata::Serializer_MSn::write(std::ostream&, const pwiz::msdata::MSData&, const pwiz::util::IterationListenerRegistry*, bool, bool) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MSn.cpp:552:10: warning: unused parameter 'useWorkerThreads' [-Wunused-parameter] - 552 | bool useWorkerThreads, bool continueOnError) const - | ~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MSn.cpp:552:33: warning: unused parameter 'continueOnError' [-Wunused-parameter] - 552 | bool useWorkerThreads, bool continueOnError) const - | ~~~~~^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:27: /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In function 'void pwiz::msdata::{anonymous}::appendSourceFile(const std::string&, pwiz::msdata::MSData&)': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:65:58: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] @@ -3651,181 +4591,6 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:136:52: warning: unused parameter 'config' [-Wunused-parameter] 136 | const Config& config) const | ~~~~~~~~~~~~~~^~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerCV::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:85:47: warning: unused parameter 'position' [-Wunused-parameter] - 85 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerUserParam::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:136:47: warning: unused parameter 'position' [-Wunused-parameter] - 136 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerCVParam::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:195:47: warning: unused parameter 'position' [-Wunused-parameter] - 195 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual std::string pwiz::msdata::Reader_mzXML::identify(const std::string&, const std::string&) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:201:69: warning: unused parameter 'filename' [-Wunused-parameter] - 201 | PWIZ_API_DECL std::string Reader_mzXML::identify(const std::string& filename, const std::string& head) const - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_mzXML::read(const std::string&, const std::string&, pwiz::msdata::MSData&, int, const pwiz::msdata::Reader::Config&) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:216:58: warning: unused parameter 'head' [-Wunused-parameter] - 216 | const std::string& head, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:219:53: warning: unused parameter 'config' [-Wunused-parameter] - 219 | const Config& config) const - | ~~~~~~~~~~~~~~^~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual std::string pwiz::msdata::Reader_MGF::identify(const std::string&, const std::string&) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:269:59: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] - 269 | return std::string(((bal::to_lower_copy(bfs::extension(filename)) == ".mgf"))?getType():""); - | ~~~~~~~~~~~~~~^~~~~~~~~~ -/usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here - 29 | inline std::string extension(const path& p) - | ^~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:267:86: warning: unused parameter 'head' [-Wunused-parameter] - 267 | PWIZ_API_DECL std::string Reader_MGF::identify(const string& filename, const string& head) const - | ~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_MGF::read(const std::string&, const std::string&, pwiz::msdata::MSData&, int, const pwiz::msdata::Reader::Config&) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:273:51: warning: unused parameter 'head' [-Wunused-parameter] - 273 | const string& head, - | ~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:276:51: warning: unused parameter 'config' [-Wunused-parameter] - 276 | const Config& config) const - | ~~~~~~~~~~~~~~^~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_MGF::read(const std::string&, const std::string&, std::vector >&, const pwiz::msdata::Reader::Config&) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:296:51: warning: unused parameter 'config' [-Wunused-parameter] - 296 | const Config& config) const - | ~~~~~~~~~~~~~~^~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual std::string pwiz::msdata::Reader_MSn::identify(const std::string&, const std::string&) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:307:86: warning: unused parameter 'head' [-Wunused-parameter] - 307 | PWIZ_API_DECL std::string Reader_MSn::identify(const string& filename, const string& head) const - | ~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerParamContainer::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:267:47: warning: unused parameter 'position' [-Wunused-parameter] - 267 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_MSn::read(const std::string&, const std::string&, pwiz::msdata::MSData&, int, const pwiz::msdata::Reader::Config&) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:317:51: warning: unused parameter 'head' [-Wunused-parameter] - 317 | const string& head, - | ~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:320:51: warning: unused parameter 'config' [-Wunused-parameter] - 320 | const Config& config) const - | ~~~~~~~~~~~~~~^~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_MSn::read(const std::string&, const std::string&, std::vector >&, const pwiz::msdata::Reader::Config&) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:353:51: warning: unused parameter 'config' [-Wunused-parameter] - 353 | const Config& config) const - | ~~~~~~~~~~~~~~^~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual std::string pwiz::msdata::Reader_BTDX::identify(const std::string&, const std::string&) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:364:63: warning: unused parameter 'filename' [-Wunused-parameter] - 364 | PWIZ_API_DECL std::string Reader_BTDX::identify(const string& filename, const string& head) const - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_BTDX::read(const std::string&, const std::string&, pwiz::msdata::MSData&, int, const pwiz::msdata::Reader::Config&) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:397:41: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] - 397 | sourceFile->name = BFS_STRING(p.leaf()); - | ~~~~~~^~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.hpp:64:24: note: in definition of macro 'BFS_STRING' - 64 | #define BFS_STRING(p) (p).string() - | ^ -/usr/include/boost/filesystem/path.hpp:1127:10: note: declared here - 1127 | path leaf() const { return filename(); } - | ^~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:398:67: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] - 398 | sourceFile->location = "file:///" + BFS_COMPLETE(p.branch_path()).string(); - | ~~~~~~~~~~~~~^~ -/usr/include/boost/filesystem/path.hpp:1129:10: note: declared here - 1129 | path branch_path() const { return parent_path(); } - | ^~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:401:46: warning: 'std::string boost::filesystem::basename(const path&)' is deprecated: Use path::stem() instead [-Wdeprecated-declarations] - 401 | result.id = result.run.id = bfs::basename(filename); - | ~~~~~~~~~~~~~^~~~~~~~~~ -/usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here - 35 | inline std::string basename(const path& p) - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:380:52: warning: unused parameter 'head' [-Wunused-parameter] - 380 | const string& head, - | ~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:383:52: warning: unused parameter 'config' [-Wunused-parameter] - 383 | const Config& config) const - | ~~~~~~~~~~~~~~^~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_BTDX::read(const std::string&, const std::string&, std::vector >&, const pwiz::msdata::Reader::Config&) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:410:52: warning: unused parameter 'config' [-Wunused-parameter] - 410 | const Config& config) const - | ~~~~~~~~~~~~~~^~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual std::string pwiz::msdata::Reader_mz5::identify(const std::string&, const std::string&) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:429:62: warning: unused parameter 'filename' [-Wunused-parameter] - 429 | PWIZ_API_DECL std::string Reader_mz5::identify(const string& filename, const string& head) const - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_mz5::read(const std::string&, const std::string&, pwiz::msdata::MSData&, int, const pwiz::msdata::Reader::Config&) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:462:51: warning: unused parameter 'filename' [-Wunused-parameter] - 462 | PWIZ_API_DECL void Reader_mz5::read(const string& filename, - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:463:51: warning: unused parameter 'head' [-Wunused-parameter] - 463 | const string& head, - | ~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:464:45: warning: unused parameter 'result' [-Wunused-parameter] - 464 | MSData& result, - | ~~~~~~~~^~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:465:41: warning: unused parameter 'runIndex' [-Wunused-parameter] - 465 | int runIndex, - | ~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:466:51: warning: unused parameter 'config' [-Wunused-parameter] - 466 | const Config& config) const - | ~~~~~~~~~~~~~~^~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_mz5::read(const std::string&, const std::string&, std::vector >&, const pwiz::msdata::Reader::Config&) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:488:51: warning: unused parameter 'config' [-Wunused-parameter] - 488 | const Config& config) const - | ~~~~~~~~~~~~~~^~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerFileDescription::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:504:51: warning: unused parameter 'attributes' [-Wunused-parameter] - 504 | const Attributes& attributes, - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:505:47: warning: unused parameter 'position' [-Wunused-parameter] - 505 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerComponentList::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:697:51: warning: unused parameter 'attributes' [-Wunused-parameter] - 697 | const Attributes& attributes, - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:698:47: warning: unused parameter 'position' [-Wunused-parameter] - 698 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:27: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In function 'void pwiz::msdata::{anonymous}::appendSourceFile(const std::string&, pwiz::msdata::MSData&)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:65:58: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] - 65 | sourceFile->id = sourceFile->name = BFS_STRING(p.leaf()); - | ~~~~~~^~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.hpp:64:24: note: in definition of macro 'BFS_STRING' - 64 | #define BFS_STRING(p) (p).string() - | ^ -In file included from /usr/include/boost/filesystem/operations.hpp:20, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.hpp:36: -/usr/include/boost/filesystem/path.hpp:1127:10: note: declared here - 1127 | path leaf() const { return filename(); } - | ^~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:66:67: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] - 66 | sourceFile->location = "file:///" + BFS_COMPLETE(p.branch_path()).string(); - | ~~~~~~~~~~~~~^~ -/usr/include/boost/filesystem/path.hpp:1129:10: note: declared here - 1129 | path branch_path() const { return parent_path(); } - | ^~~~~~~~~~~ -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In function 'void pwiz::msdata::{anonymous}::fillInCommonMetadata(const std::string&, pwiz::msdata::MSData&)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:107:44: warning: 'std::string boost::filesystem::basename(const path&)' is deprecated: Use path::stem() instead [-Wdeprecated-declarations] - 107 | msd.id = msd.run.id = bfs::basename(filename); - | ~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.hpp:37: -/usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here - 35 | inline std::string basename(const path& p) - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual std::string pwiz::msdata::Reader_mzML::identify(const std::string&, const std::string&) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:126:68: warning: unused parameter 'filename' [-Wunused-parameter] - 126 | PWIZ_API_DECL std::string Reader_mzML::identify(const std::string& filename, const std::string& head) const - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerDataProcessing::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:970:47: warning: unused parameter 'position' [-Wunused-parameter] - 970 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, @@ -3834,24 +4599,6 @@ /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_mzML::read(const std::string&, const std::string&, pwiz::msdata::MSData&, int, const pwiz::msdata::Reader::Config&) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:133:57: warning: unused parameter 'head' [-Wunused-parameter] - 133 | const std::string& head, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:136:52: warning: unused parameter 'config' [-Wunused-parameter] - 136 | const Config& config) const - | ~~~~~~~~~~~~~~^~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_mzMLb::read(const std::string&, const std::string&, pwiz::msdata::MSData&, int, const pwiz::msdata::Reader::Config&) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:533:24: warning: unused parameter 'head' [-Wunused-parameter] - 533 | const std::string& head, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:536:19: warning: unused parameter 'config' [-Wunused-parameter] - 536 | const Config& config) const - | ~~~~~~~~~~~~~~^~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerScanSettings::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:1083:47: warning: unused parameter 'position' [-Wunused-parameter] - 1083 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual std::string pwiz::msdata::Reader_mzXML::identify(const std::string&, const std::string&) const': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:201:69: warning: unused parameter 'filename' [-Wunused-parameter] 201 | PWIZ_API_DECL std::string Reader_mzXML::identify(const std::string& filename, const std::string& head) const @@ -3899,13 +4646,6 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:353:51: warning: unused parameter 'config' [-Wunused-parameter] 353 | const Config& config) const | ~~~~~~~~~~~~~~^~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerProduct::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:1359:51: warning: unused parameter 'attributes' [-Wunused-parameter] - 1359 | const Attributes& attributes, - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:1360:47: warning: unused parameter 'position' [-Wunused-parameter] - 1360 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual std::string pwiz::msdata::Reader_BTDX::identify(const std::string&, const std::string&) const': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:364:63: warning: unused parameter 'filename' [-Wunused-parameter] 364 | PWIZ_API_DECL std::string Reader_BTDX::identify(const string& filename, const string& head) const @@ -3966,24 +4706,6 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:488:51: warning: unused parameter 'config' [-Wunused-parameter] 488 | const Config& config) const | ~~~~~~~~~~~~~~^~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MGF.hpp:27, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MGF.cpp:25: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/algorithm:60, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp: In member function 'virtual void pwiz::msdata::Reader_mzMLb::read(const std::string&, const std::string&, pwiz::msdata::MSData&, int, const pwiz::msdata::Reader::Config&) const': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:533:24: warning: unused parameter 'head' [-Wunused-parameter] 533 | const std::string& head, @@ -3991,26 +4713,70 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.cpp:536:19: warning: unused parameter 'config' [-Wunused-parameter] 536 | const Config& config) const | ~~~~~~~~~~~~~~^~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp: In function 'void pwiz::msdata::IO::writeMzMLbExtra(boost::iostreams::stream*, std::string&, size_t&, const std::string&, pwiz::minimxml::XMLWriter&, const BinaryDataArrayType&, const pwiz::msdata::BinaryDataEncoder::Config&) [with BinaryDataArrayType = pwiz::msdata::BinaryDataArray; std::string = std::__cxx11::basic_string; size_t = long unsigned int]': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:1693:47: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1693 | for (int i = 1; i < float_data.size(); i++) - | ~~^~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:1712:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1712 | for (int i = 2; i < float_data.size(); i++) - | ~~^~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:1774:43: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1774 | for (int i = 1; i < double_data.size(); i++) - | ~~^~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:1793:47: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1793 | for (int i = 2; i < double_data.size(); i++) - | ~~^~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:1627:142: warning: unused parameter 'writer' [-Wunused-parameter] - 1627 | void writeMzMLbExtra(stream* mzMLb_os, string& dataset, size_t& offset, const string& encoded, XMLWriter& writer, const BinaryDataArray& binaryDataArray, const BinaryDataEncoder::Config& usedConfig) - | ~~~~~~~~~~~^~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp: In function 'void pwiz::msdata::IO::writeMzMLbExtra(boost::iostreams::stream*, std::string&, size_t&, const std::string&, pwiz::minimxml::XMLWriter&, const BinaryDataArrayType&, const pwiz::msdata::BinaryDataEncoder::Config&) [with BinaryDataArrayType = pwiz::msdata::IntegerDataArray; std::string = std::__cxx11::basic_string; size_t = long unsigned int]': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:1820:143: warning: unused parameter 'writer' [-Wunused-parameter] - 1820 | void writeMzMLbExtra(stream* mzMLb_os, string& dataset, size_t& offset, const string& encoded, XMLWriter& writer, const IntegerDataArray& binaryDataArray, const BinaryDataEncoder::Config& usedConfig) - | ~~~~~~~~~~~^~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp:26: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] + 585 | virtual Status processingInstruction(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:586:61: warning: unused parameter 'data' [-Wunused-parameter] + 586 | const std::string& data, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:587:56: warning: unused parameter 'position' [-Wunused-parameter] + 587 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::startElement(const std::string&, const Attributes&, stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:589:52: warning: unused parameter 'name' [-Wunused-parameter] + 589 | virtual Status startElement(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:590:51: warning: unused parameter 'attributes' [-Wunused-parameter] + 590 | const Attributes& attributes, + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:591:47: warning: unused parameter 'position' [-Wunused-parameter] + 591 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::endElement(const std::string&, stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:593:50: warning: unused parameter 'name' [-Wunused-parameter] + 593 | virtual Status endElement(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:594:45: warning: unused parameter 'position' [-Wunused-parameter] + 594 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::characters(const pwiz::minimxml::SAXParser::saxstring&, stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:596:59: warning: unused parameter 'text' [-Wunused-parameter] + 596 | virtual Status characters(const SAXParser::saxstring& text, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] + 597 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.hpp:32, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp:28: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] + 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexListOffset::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp:86:51: warning: unused parameter 'attributes' [-Wunused-parameter] + 86 | const Attributes& attributes, + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp:87:47: warning: unused parameter 'position' [-Wunused-parameter] + 87 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexListOffset::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp:95:45: warning: unused parameter 'position' [-Wunused-parameter] + 95 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerOffset::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp:120:47: warning: unused parameter 'position' [-Wunused-parameter] + 120 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerOffset::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp:165:45: warning: unused parameter 'position' [-Wunused-parameter] + 165 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexList::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Index_mzML.cpp:201:47: warning: unused parameter 'position' [-Wunused-parameter] + 201 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerCV::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:85:47: warning: unused parameter 'position' [-Wunused-parameter] 85 | stream_offset position) @@ -4034,6 +4800,14 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:505:47: warning: unused parameter 'position' [-Wunused-parameter] 505 | stream_offset position) | ~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] + 769 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] + 853 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerComponentList::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:697:51: warning: unused parameter 'attributes' [-Wunused-parameter] 697 | const Attributes& attributes, @@ -4049,10 +4823,6 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:1083:47: warning: unused parameter 'position' [-Wunused-parameter] 1083 | stream_offset position) | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerSpectrum::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:2639:35: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 2639 | else if (version == 1 && name == "acquisitionList" /* mzML 1.0 */ || name == "scanList") - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerProduct::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:1359:51: warning: unused parameter 'attributes' [-Wunused-parameter] 1359 | const Attributes& attributes, @@ -4060,25 +4830,14 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:1360:47: warning: unused parameter 'position' [-Wunused-parameter] 1360 | stream_offset position) | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.cpp: In function 'std::string pwiz::msdata::id::translateNativeIDToScanNumber(pwiz::cv::CVID, const std::string&)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.cpp:582:13: warning: this statement may fall through [-Wimplicit-fallthrough=] - 582 | if (id.find("controllerType=0 controllerNumber=1") != 0) - | ^~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.cpp:587:9: note: here - 587 | case MS_Bruker_Agilent_YEP_nativeID_format: - | ^~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerSpectrumListSimple::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:2955:47: warning: unused parameter 'position' [-Wunused-parameter] - 2955 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Reader.cpp: In member function 'virtual void pwiz::msdata::Reader::readIds(const std::string&, const std::string&, std::vector >&, const Config&) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Reader.cpp:80:119: warning: unused parameter 'config' [-Wunused-parameter] - 80 | PWIZ_API_DECL void Reader::readIds(const string& filename, const string& head, vector& results, const Config& config) const - | ~~~~~~~~~~~~~~^~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerChromatogramListSimple::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:3085:47: warning: unused parameter 'position' [-Wunused-parameter] - 3085 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/iterator.hpp: At global scope: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp: In function 'void pwiz::msdata::IO::writeMzMLbExtra(boost::iostreams::stream*, std::string&, size_t&, const std::string&, pwiz::minimxml::XMLWriter&, const BinaryDataArrayType&, const pwiz::msdata::BinaryDataEncoder::Config&) [with BinaryDataArrayType = pwiz::msdata::BinaryDataArray; std::string = std::__cxx11::basic_string; size_t = long unsigned int]': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:1693:47: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1693 | for (int i = 1; i < float_data.size(); i++) @@ -4092,435 +4851,175 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:1793:47: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1793 | for (int i = 2; i < double_data.size(); i++) | ~~^~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerMSData::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:3415:31: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 3415 | else if (version == 1 && name == "acquisitionSettings" /* mzML 1.0 */ || - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:1627:142: warning: unused parameter 'writer' [-Wunused-parameter] 1627 | void writeMzMLbExtra(stream* mzMLb_os, string& dataset, size_t& offset, const string& encoded, XMLWriter& writer, const BinaryDataArray& binaryDataArray, const BinaryDataEncoder::Config& usedConfig) | ~~~~~~~~~~~^~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:3333:47: warning: unused parameter 'position' [-Wunused-parameter] - 3333 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp: In function 'void pwiz::msdata::IO::writeMzMLbExtra(boost::iostreams::stream*, std::string&, size_t&, const std::string&, pwiz::minimxml::XMLWriter&, const BinaryDataArrayType&, const pwiz::msdata::BinaryDataEncoder::Config&) [with BinaryDataArrayType = pwiz::msdata::IntegerDataArray; std::string = std::__cxx11::basic_string; size_t = long unsigned int]': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:1820:143: warning: unused parameter 'writer' [-Wunused-parameter] 1820 | void writeMzMLbExtra(stream* mzMLb_os, string& dataset, size_t& offset, const string& encoded, XMLWriter& writer, const IntegerDataArray& binaryDataArray, const BinaryDataEncoder::Config& usedConfig) | ~~~~~~~~~~~^~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.cpp: In function 'std::string pwiz::msdata::id::translateNativeIDToScanNumber(pwiz::cv::CVID, const std::string&)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.cpp:582:13: warning: this statement may fall through [-Wimplicit-fallthrough=] - 582 | if (id.find("controllerType=0 controllerNumber=1") != 0) - | ^~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.cpp:587:9: note: here - 587 | case MS_Bruker_Agilent_YEP_nativeID_format: - | ^~~~ +[ 74%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_MGF.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_MGF.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_MGF.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_MGF.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MGF.cpp /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerSpectrum::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:2639:35: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 2639 | else if (version == 1 && name == "acquisitionList" /* mzML 1.0 */ || name == "scanList") | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/function/detail/requires_cxx11.hpp:9, + from /usr/include/boost/function/detail/prologue.hpp:12, + from /usr/include/boost/function.hpp:30, + from /usr/include/boost/algorithm/string/detail/find_iterator.hpp:18, + from /usr/include/boost/algorithm/string/find_iterator.hpp:24, + from /usr/include/boost/algorithm/string/iter_find.hpp:27, + from /usr/include/boost/algorithm/string/split.hpp:16, + from /usr/include/boost/algorithm/string.hpp:23, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/String.hpp:31, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.hpp:34, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.cpp:26: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerSpectrumListSimple::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:2955:47: warning: unused parameter 'position' [-Wunused-parameter] 2955 | stream_offset position) | ~~~~~~~~~~~~~~^~~~~~~~ +[ 75%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_MSn.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_MSn.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_MSn.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_MSn.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MSn.cpp /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerChromatogramListSimple::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:3085:47: warning: unused parameter 'position' [-Wunused-parameter] 3085 | stream_offset position) | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] - 769 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp: In function 'std::string pwiz::msdata::{anonymous}::translate_SourceFileTypeToRunID(const pwiz::msdata::SourceFile&, pwiz::cv::CVID)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:149:61: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] - 149 | string nameExtension = bal::to_lower_copy(bfs::extension(sf.name)); - | ~~~~~~~~~~~~~~^~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.hpp:37, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:33: -/usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here - 29 | inline std::string extension(const path& p) - | ^~~~~~~~~ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::IO::HandlerMSData::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:3415:31: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 3415 | else if (version == 1 && name == "acquisitionSettings" /* mzML 1.0 */ || | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:150:65: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] - 150 | string locationExtension = bal::to_lower_copy(bfs::extension(sf.location)); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ -/usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here - 29 | inline std::string extension(const path& p) - | ^~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:157:37: warning: 'std::string boost::filesystem::basename(const path&)' is deprecated: Use path::stem() instead [-Wdeprecated-declarations] - 157 | return bfs::basename(sf.name); - | ~~~~~~~~~~~~~^~~~~~~~~ -/usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here - 35 | inline std::string basename(const path& p) - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:164:65: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] - 164 | return bfs::basename(bfs::path(sf.location).leaf()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -In file included from /usr/include/boost/filesystem/operations.hpp:20, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.hpp:36: -/usr/include/boost/filesystem/path.hpp:1127:10: note: declared here - 1127 | path leaf() const { return filename(); } - | ^~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:164:37: warning: 'std::string boost::filesystem::basename(const path&)' is deprecated: Use path::stem() instead [-Wdeprecated-declarations] - 164 | return bfs::basename(bfs::path(sf.location).leaf()); - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/IO.cpp:3333:47: warning: unused parameter 'position' [-Wunused-parameter] 3333 | stream_offset position) | ~~~~~~~~~~~~~~^~~~~~~~ -/usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here - 35 | inline std::string basename(const path& p) - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:166:37: warning: 'std::string boost::filesystem::basename(const path&)' is deprecated: Use path::stem() instead [-Wdeprecated-declarations] - 166 | return bfs::basename(sf.name); - | ~~~~~~~~~~~~~^~~~~~~~~ -/usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here - 35 | inline std::string basename(const path& p) - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:172:65: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] - 172 | return bfs::basename(bfs::path(sf.location).leaf()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/usr/include/boost/filesystem/path.hpp:1127:10: note: declared here - 1127 | path leaf() const { return filename(); } - | ^~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:172:37: warning: 'std::string boost::filesystem::basename(const path&)' is deprecated: Use path::stem() instead [-Wdeprecated-declarations] - 172 | return bfs::basename(bfs::path(sf.location).leaf()); - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here - 35 | inline std::string basename(const path& p) - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:178:65: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] - 178 | return bfs::basename(bfs::path(sf.location).leaf()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/usr/include/boost/filesystem/path.hpp:1127:10: note: declared here - 1127 | path leaf() const { return filename(); } - | ^~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:178:37: warning: 'std::string boost::filesystem::basename(const path&)' is deprecated: Use path::stem() instead [-Wdeprecated-declarations] - 178 | return bfs::basename(bfs::path(sf.location).leaf()); - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here - 35 | inline std::string basename(const path& p) - | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual size_t pwiz::msdata::SpectrumList::findAbbreviated(const std::string&, char) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.cpp:1121:21: warning: comparison of unsigned expression in '>= 0' is always true [-Wtype-limits] + 1121 | if ((result >= 0 && result < size()) || s == 0) + | ~~~~~~~^~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual pwiz::msdata::SpectrumPtr pwiz::msdata::SpectrumListSimple::spectrum(size_t, bool) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.cpp:1232:75: warning: unused parameter 'getBinaryData' [-Wunused-parameter] + 1232 | PWIZ_API_DECL SpectrumPtr SpectrumListSimple::spectrum(size_t index, bool getBinaryData) const + | ~~~~~^~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual pwiz::msdata::ChromatogramPtr pwiz::msdata::ChromatogramListSimple::chromatogram(size_t, bool) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.cpp:1299:87: warning: unused parameter 'getBinaryData' [-Wunused-parameter] + 1299 | PWIZ_API_DECL ChromatogramPtr ChromatogramListSimple::chromatogram(size_t index, bool getBinaryData) const + | ~~~~~^~~~~~~~~~~~~ +[ 76%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_mzML.cpp.o +[ 78%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_mzXML.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_mzML.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_mzML.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_mzML.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzML.cpp +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_mzXML.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_mzXML.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_mzXML.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSDataFile.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSDataFile.cpp:26: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/algorithm:60, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Reader.hpp:28, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Reader.cpp:26: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] + 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Reader.hpp:29: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Reader.hpp:30: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp: At global scope: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | class PWIZ_API_DECL const_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_construct.h:61, + from /usr/include/c++/14/bits/stl_tempbuf.h:61, + from /usr/include/c++/14/memory:66, + from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, + from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, + from /usr/include/boost/shared_ptr.hpp:17, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:29: +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 88 | class PWIZ_API_DECL iterator : public std::iterator + | ^~~~~~~~ +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.cpp: In function 'std::string pwiz::msdata::id::translateNativeIDToScanNumber(pwiz::cv::CVID, const std::string&)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.cpp:582:13: warning: this statement may fall through [-Wimplicit-fallthrough=] + 582 | if (id.find("controllerType=0 controllerNumber=1") != 0) + | ^~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.cpp:587:9: note: here + 587 | case MS_Bruker_Agilent_YEP_nativeID_format: + | ^~~~ +[ 79%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumListBase.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumListBase.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumListBase.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumListBase.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumListBase.cpp +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] + 769 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] 853 | virtual void warn_once(const char* msg) const {} | ~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:184:65: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] - 184 | return bfs::basename(bfs::path(sf.location).leaf()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/usr/include/boost/filesystem/path.hpp:1127:10: note: declared here - 1127 | path leaf() const { return filename(); } - | ^~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:184:37: warning: 'std::string boost::filesystem::basename(const path&)' is deprecated: Use path::stem() instead [-Wdeprecated-declarations] - 184 | return bfs::basename(bfs::path(sf.location).leaf()); - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here - 35 | inline std::string basename(const path& p) - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:190:65: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] - 190 | return bfs::basename(bfs::path(sf.location).leaf()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/usr/include/boost/filesystem/path.hpp:1127:10: note: declared here - 1127 | path leaf() const { return filename(); } - | ^~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:190:37: warning: 'std::string boost::filesystem::basename(const path&)' is deprecated: Use path::stem() instead [-Wdeprecated-declarations] - 190 | return bfs::basename(bfs::path(sf.location).leaf()); - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here - 35 | inline std::string basename(const path& p) - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:195:44: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] - 195 | if (bfs::path(sf.location).leaf() == "AcqData" && - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/usr/include/boost/filesystem/path.hpp:1127:10: note: declared here - 1127 | path leaf() const { return filename(); } - | ^~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:199:79: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] - 199 | return bfs::basename(bfs::path(sf.location).parent_path().leaf()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/usr/include/boost/filesystem/path.hpp:1127:10: note: declared here - 1127 | path leaf() const { return filename(); } - | ^~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:199:37: warning: 'std::string boost::filesystem::basename(const path&)' is deprecated: Use path::stem() instead [-Wdeprecated-declarations] - 199 | return bfs::basename(bfs::path(sf.location).parent_path().leaf()); - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here - 35 | inline std::string basename(const path& p) - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:207:37: warning: 'std::string boost::filesystem::basename(const path&)' is deprecated: Use path::stem() instead [-Wdeprecated-declarations] - 207 | return bfs::basename(sf.name); - | ~~~~~~~~~~~~~^~~~~~~~~ -/usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here - 35 | inline std::string basename(const path& p) - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:216:37: warning: 'std::string boost::filesystem::basename(const path&)' is deprecated: Use path::stem() instead [-Wdeprecated-declarations] - 216 | return bfs::basename(sf.name); - | ~~~~~~~~~~~~~^~~~~~~~~ -/usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here - 35 | inline std::string basename(const path& p) - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:222:37: warning: 'std::string boost::filesystem::basename(const path&)' is deprecated: Use path::stem() instead [-Wdeprecated-declarations] - 222 | return bfs::basename(sf.name); - | ~~~~~~~~~~~~~^~~~~~~~~ -/usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here - 35 | inline std::string basename(const path& p) - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:228:37: warning: 'std::string boost::filesystem::basename(const path&)' is deprecated: Use path::stem() instead [-Wdeprecated-declarations] - 228 | return bfs::basename(sf.name); - | ~~~~~~~~~~~~~^~~~~~~~~ -/usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here - 35 | inline std::string basename(const path& p) - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp: In function 'std::vector pwiz::msdata::{anonymous}::getPrecursorInfo(const pwiz::msdata::Spectrum&, pwiz::msdata::SpectrumListPtr, pwiz::cv::CVID)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:454:62: warning: unused parameter 'spectrumListPtr' [-Wunused-parameter] - 454 | const SpectrumListPtr spectrumListPtr, - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp: In function 'pwiz::cv::CVID pwiz::msdata::{anonymous}::translate_parentFilenameToSourceFileType(const std::string&)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:878:61: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] - 878 | string fileExtension = bal::to_lower_copy(bfs::extension(name)); - | ~~~~~~~~~~~~~~^~~~~~ -/usr/include/boost/filesystem/convenience.hpp:29:20: note: declared here - 29 | inline std::string extension(const path& p) - | ^~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerScanFileContent::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:1027:47: warning: unused parameter 'position' [-Wunused-parameter] - 1027 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp: In function 'void pwiz::msdata::{anonymous}::fillInMetadata(pwiz::msdata::MSData&)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:1139:65: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] - 1139 | msd.id = msd.run.id = BFS_STRING(bfs::path(lcp).leaf()); - | ~~~~~~~~~~~~~~~~~~~^~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.hpp:64:24: note: in definition of macro 'BFS_STRING' - 64 | #define BFS_STRING(p) (p).string() - | ^ -/usr/include/boost/filesystem/path.hpp:1127:10: note: declared here - 1127 | path leaf() const { return filename(); } - | ^~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:1141:79: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] - 1141 | msd.id = msd.run.id = BFS_STRING(bfs::path(lcp).parent_path().leaf()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.hpp:64:24: note: in definition of macro 'BFS_STRING' - 64 | #define BFS_STRING(p) (p).string() - | ^ -/usr/include/boost/filesystem/path.hpp:1127:10: note: declared here - 1127 | path leaf() const { return filename(); } - | ^~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_BTDX.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerPeaks::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:121:47: warning: unused parameter 'position' [-Wunused-parameter] - 121 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_BTDX.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerPeaks::endElement(const std::string&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:162:45: warning: unused parameter 'position' [-Wunused-parameter] - 162 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::Handler_msInstrument::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:1156:47: warning: unused parameter 'position' [-Wunused-parameter] - 1156 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::Handler_msInstrument::endElement(const std::string&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:1237:45: warning: unused parameter 'position' [-Wunused-parameter] - 1237 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::Handler_dataProcessing::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:1285:47: warning: unused parameter 'position' [-Wunused-parameter] - 1285 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::Handler_mzXML::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:1353:47: warning: unused parameter 'position' [-Wunused-parameter] - 1353 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_BTDX.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexCreator::endElement(const std::string&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:356:45: warning: unused parameter 'position' [-Wunused-parameter] - 356 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In constructor 'pwiz::msdata::{anonymous}::SpectrumList_mzXMLImpl::SpectrumList_mzXMLImpl(boost::shared_ptr >, const pwiz::msdata::MSData&, bool)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:84:30: warning: catching polymorphic type 'struct pwiz::msdata::SpectrumList_mzXML::index_not_found' by value [-Wcatch-value=] - 84 | } catch (index_not_found e){ - | ^ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerPrecursor::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:128:47: warning: unused parameter 'position' [-Wunused-parameter] - 128 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerPrecursor::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:212:45: warning: unused parameter 'position' [-Wunused-parameter] - 212 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerPeaks::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:239:47: warning: unused parameter 'position' [-Wunused-parameter] - 239 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerPeaks::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:282:45: warning: unused parameter 'position' [-Wunused-parameter] - 282 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerPeaks::endElement(const std::string&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:302:70: warning: unused parameter 'position' [-Wunused-parameter] - 302 | virtual Status endElement(const std::string& name, stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/cv.cpp:26735: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/cv.inl: In function 'const pwiz::cv::CVTermInfo& pwiz::cv::cvTermInfo(const char*)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/cv.inl:103:23: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] - 103 | for (int o=0;o >, const pwiz::msdata::MSData&, bool)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:84:30: warning: catching polymorphic type 'struct pwiz::msdata::SpectrumList_mzXML::index_not_found' by value [-Wcatch-value=] - 84 | } catch (index_not_found e){ - | ^ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerPrecursor::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:128:47: warning: unused parameter 'position' [-Wunused-parameter] - 128 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerPrecursor::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:212:45: warning: unused parameter 'position' [-Wunused-parameter] - 212 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerPeaks::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:239:47: warning: unused parameter 'position' [-Wunused-parameter] - 239 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] 769 | virtual void warn_once(const char* msg) const {} | ~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerPeaks::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:282:45: warning: unused parameter 'position' [-Wunused-parameter] - 282 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerPeaks::endElement(const std::string&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:302:70: warning: unused parameter 'position' [-Wunused-parameter] - 302 | virtual Status endElement(const std::string& name, stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] 853 | virtual void warn_once(const char* msg) const {} | ~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexOffset::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:701:51: warning: unused parameter 'attributes' [-Wunused-parameter] - 701 | const Attributes& attributes, - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:702:47: warning: unused parameter 'position' [-Wunused-parameter] - 702 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexOffset::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:710:45: warning: unused parameter 'position' [-Wunused-parameter] - 710 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerOffset::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:736:47: warning: unused parameter 'position' [-Wunused-parameter] - 736 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerOffset::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:754:45: warning: unused parameter 'position' [-Wunused-parameter] - 754 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndex::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:778:51: warning: unused parameter 'attributes' [-Wunused-parameter] - 778 | const Attributes& attributes, - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:779:47: warning: unused parameter 'position' [-Wunused-parameter] - 779 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndex::characters(const pwiz::minimxml::SAXParser::saxstring&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:796:59: warning: unused parameter 'text' [-Wunused-parameter] - 796 | virtual Status characters(const SAXParser::saxstring& text, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:797:45: warning: unused parameter 'position' [-Wunused-parameter] - 797 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::{anonymous}::HandlerIndexCreator::endElement(const std::string&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:885:45: warning: unused parameter 'position' [-Wunused-parameter] - 885 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -[ 57%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_MSn.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_MSn.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_MSn.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_MSn.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MSn.cpp -[ 58%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_MGF.cpp.o +[ 80%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_MGF.cpp.o cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_MGF.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_MGF.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_MGF.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_MGF.cpp -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/cv.cpp:26735: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/cv.inl: In function 'const pwiz::cv::CVTermInfo& pwiz::cv::cvTermInfo(const char*)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/cv.inl:103:23: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] - 103 | for (int o=0;o instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 65%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/utility/minimxml/XMLWriter.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/utility/minimxml/XMLWriter.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/utility/minimxml/XMLWriter.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/utility/minimxml/XMLWriter.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/XMLWriter.cpp -[ 67%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_mzXML.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_mzXML.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_mzXML.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_mzXML.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp -[ 68%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumListBase.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumListBase.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumListBase.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumListBase.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumListBase.cpp +[ 81%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_MSn.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_MSn.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_MSn.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_MSn.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_MSn.cpp +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSDataFile.cpp:39: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.hpp: In member function 'virtual std::string pwiz::msdata::Reader_MS2::identify(const std::string&, const std::string&) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.hpp:98:53: warning: unused parameter 'filename' [-Wunused-parameter] + 98 | virtual std::string identify(const std::string& filename, const std::string& head) const { return ""; } + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/DefaultReaderList.hpp:98:82: warning: unused parameter 'head' [-Wunused-parameter] + 98 | virtual std::string identify(const std::string& filename, const std::string& head) const { return ""; } + | ~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MGF.hpp:27, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MGF.cpp:25: + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MSn.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MSn.cpp:25: /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 54 | class PWIZ_API_DECL const_iterator : public std::iterator | ^~~~~~~~ @@ -4536,16 +5035,18 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 69%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_MGF.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_MGF.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_MGF.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_MGF.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_MGF.cpp -[ 70%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_MSn.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_MSn.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_MSn.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_MSn.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_MSn.cpp -[ 71%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/Base64.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/Base64.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/Base64.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/Base64.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Base64.cpp -[ 73%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumWorkerThreads.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumWorkerThreads.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumWorkerThreads.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumWorkerThreads.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumWorkerThreads.cpp -[ 74%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/IterationListener.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/IterationListener.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/IterationListener.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/IterationListener.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.cpp +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Reader.cpp: In member function 'virtual void pwiz::msdata::Reader::readIds(const std::string&, const std::string&, std::vector >&, const Config&) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Reader.cpp:80:119: warning: unused parameter 'config' [-Wunused-parameter] + 80 | PWIZ_API_DECL void Reader::readIds(const string& filename, const string& head, vector& results, const Config& config) const + | ~~~~~~~~~~~~~~^~~~~~ +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/iterator.hpp: At global scope: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] 769 | virtual void warn_once(const char* msg) const {} @@ -4554,28 +5055,33 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] 853 | virtual void warn_once(const char* msg) const {} | ~~~~~~~~~~~~^~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MGF.hpp:29: +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MSn.hpp:28: /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/mzmlb/Connection_mzMLb.cpp: In constructor 'pwiz::msdata::mzmlb::Connection_mzMLb::Connection_mzMLb(const std::string&, int, int)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/mzmlb/Connection_mzMLb.cpp:142:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 142 | nbytes = (nbytes > chunk_size) ? nbytes : chunk_size; // Set per dataset cache to twice the chunk size please - | ~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp: At global scope: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 75%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/mzmlb/Connection_mzMLb.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/mzmlb/Connection_mzMLb.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/mzmlb/Connection_mzMLb.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/mzmlb/Connection_mzMLb.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/mzmlb/Connection_mzMLb.cpp +[ 82%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumWorkerThreads.cpp.o +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.cpp: In function 'void pwiz::minimxml::SAXParser::parse(std::istream&, Handler&)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.cpp:543:61: warning: offset '1' outside bounds of constant string [-Warray-bounds=] + 543 | Handler::Status status = wrangler.endElement(buffer.c_str()+1, position); + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumWorkerThreads.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumWorkerThreads.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumWorkerThreads.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumWorkerThreads.cpp +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/BinaryDataEncoder.cpp: In member function 'void pwiz::msdata::BinaryDataEncoder::Impl::encode(const double*, size_t, std::string&, size_t*)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/BinaryDataEncoder.cpp:305:37: warning: 'byteCount' may be used uninitialized [-Wmaybe-uninitialized] + 305 | filterArray(byteBuffer, byteCount,compressed); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/BinaryDataEncoder.cpp:131:12: note: 'byteCount' was declared here + 131 | size_t byteCount; + | ^~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/BinaryDataEncoder.cpp:305:37: warning: 'byteBuffer' may be used uninitialized [-Wmaybe-uninitialized] + 305 | filterArray(byteBuffer, byteCount,compressed); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/BinaryDataEncoder.cpp:132:17: note: 'byteBuffer' was declared here + 132 | const void* byteBuffer; + | ^~~~~~~~~~ In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MSn.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MSn.cpp:25: + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:25: /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 54 | class PWIZ_API_DECL const_iterator : public std::iterator | ^~~~~~~~ @@ -4591,8 +5097,14 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 76%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/SHA1.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/SHA1.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/SHA1.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/SHA1.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/SHA1.cpp +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.cpp:549:17: warning: 'inCDATA' may be used uninitialized [-Wmaybe-uninitialized] + 549 | if (inCDATA) + | ^~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.cpp:501:14: note: 'inCDATA' was declared here + 501 | bool inCDATA; + | ^~~~~~~ +[ 84%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/mzmlb/Connection_mzMLb.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/mzmlb/Connection_mzMLb.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/mzmlb/Connection_mzMLb.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/mzmlb/Connection_mzMLb.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/mzmlb/Connection_mzMLb.cpp In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzML.hpp:29, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzML.cpp:26: @@ -4611,10 +5123,48 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.cpp: In function 'void pwiz::util::force_close_handles_to_filepath(const std::string&, bool)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.cpp:350:52: warning: unused parameter 'filepath' [-Wunused-parameter] + 350 | force_close_handles_to_filepath(const std::string &filepath, + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.cpp:351:38: warning: unused parameter 'closeMemoryMappedSections' [-Wunused-parameter] + 351 | bool closeMemoryMappedSections) noexcept(true) + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.cpp: In function 'void pwiz::util::{anonymous}::copy_recursive(const boost::filesystem::path&, const boost::filesystem::path&)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.cpp:686:22: warning: 'void boost::filesystem::copy_directory(const path&, const path&)' is deprecated: Use create_directory() instead [-Wdeprecated-declarations] + 686 | bfs::copy_directory(from, to); + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.hpp:36: +/usr/include/boost/filesystem/operations.hpp:437:13: note: declared here + 437 | inline void copy_directory(path const& from, path const& to) + | ^~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.cpp: In function 'void pwiz::util::{anonymous}::copy_recursive(const boost::filesystem::path&, const boost::filesystem::path&, boost::system::error_code&)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.cpp:710:22: warning: 'void boost::filesystem::copy_directory(const path&, const path&, boost::system::error_code&)' is deprecated: Use create_directory() instead [-Wdeprecated-declarations] + 710 | bfs::copy_directory(from, to, ec); + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +/usr/include/boost/filesystem/operations.hpp:443:13: note: declared here + 443 | inline void copy_directory(path const& from, path const& to, system::error_code& ec) BOOST_NOEXCEPT + | ^~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.cpp: In function 'void pwiz::util::copy_directory(const boost::filesystem::path&, const boost::filesystem::path&, bool, boost::system::error_code*)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.cpp:764:28: warning: 'void boost::filesystem::copy_directory(const path&, const path&, boost::system::error_code&)' is deprecated: Use create_directory() instead [-Wdeprecated-declarations] + 764 | bfs::copy_directory(from, to, *ec); + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ +/usr/include/boost/filesystem/operations.hpp:443:13: note: declared here + 443 | inline void copy_directory(path const& from, path const& to, system::error_code& ec) BOOST_NOEXCEPT + | ^~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.cpp:766:28: warning: 'void boost::filesystem::copy_directory(const path&, const path&)' is deprecated: Use create_directory() instead [-Wdeprecated-declarations] + 766 | bfs::copy_directory(from, to); + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/usr/include/boost/filesystem/operations.hpp:437:13: note: declared here + 437 | inline void copy_directory(path const& from, path const& to) + | ^~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.cpp: In function 'void pwiz::util::check_path_length(const std::string&)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.cpp:967:33: warning: unused parameter 'path' [-Wunused-parameter] + 967 | check_path_length(const string &path) + | ~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumListBase.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_MSn.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_MSn.cpp:26: + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MGF.hpp:27, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MGF.cpp:25: /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 54 | class PWIZ_API_DECL const_iterator : public std::iterator | ^~~~~~~~ @@ -4631,8 +5181,8 @@ 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:25: + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumListBase.hpp:28, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumListBase.cpp:25: /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 54 | class PWIZ_API_DECL const_iterator : public std::iterator | ^~~~~~~~ @@ -4648,11 +5198,10 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 78%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/SHA1Calculator.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/SHA1Calculator.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/SHA1Calculator.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/SHA1Calculator.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/SHA1Calculator.cpp In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumListBase.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumListBase.cpp:25: + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_MGF.hpp:30, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_MGF.cpp:26: /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 54 | class PWIZ_API_DECL const_iterator : public std::iterator | ^~~~~~~~ @@ -4668,8 +5217,16 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 79%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/minimxml/SAXParser.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/minimxml/SAXParser.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/utility/minimxml/SAXParser.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/utility/minimxml/SAXParser.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.cpp +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/iterator.hpp: At global scope: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 85%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/utility/minimxml/SAXParser.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/utility/minimxml/SAXParser.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/utility/minimxml/SAXParser.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/utility/minimxml/SAXParser.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.cpp /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] 769 | virtual void warn_once(const char* msg) const {} @@ -4678,33 +5235,19 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] 853 | virtual void warn_once(const char* msg) const {} | ~~~~~~~~~~~~^~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MSn.hpp:28: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] + 769 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.hpp:31: /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MGF.cpp: In member function 'void pwiz::msdata::Serializer_MGF::Impl::write(std::ostream&, const pwiz::msdata::MSData&, const pwiz::util::IterationListenerRegistry*, bool, bool) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MGF.cpp:73:61: warning: 'std::string boost::filesystem::basename(const path&)' is deprecated: Use path::stem() instead [-Wdeprecated-declarations] - 73 | string thermoBasename = titleIsThermoDTA ? bfs::basename(thermoFilename) : ""; - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.hpp:37, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MGF.cpp:27: -/usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here - 35 | inline std::string basename(const path& p) - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/BinaryDataEncoder.cpp: In member function 'void pwiz::msdata::BinaryDataEncoder::Impl::encode(const double*, size_t, std::string&, size_t*)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/BinaryDataEncoder.cpp:305:37: warning: 'byteCount' may be used uninitialized [-Wmaybe-uninitialized] - 305 | filterArray(byteBuffer, byteCount,compressed); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/BinaryDataEncoder.cpp:131:12: note: 'byteCount' was declared here - 131 | size_t byteCount; - | ^~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/BinaryDataEncoder.cpp:305:37: warning: 'byteBuffer' may be used uninitialized [-Wmaybe-uninitialized] - 305 | filterArray(byteBuffer, byteCount,compressed); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/BinaryDataEncoder.cpp:132:17: note: 'byteBuffer' was declared here - 132 | const void* byteBuffer; - | ^~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] + 853 | virtual void warn_once(const char* msg) const {} + | ~~~~~~~~~~~~^~~ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] 769 | virtual void warn_once(const char* msg) const {} @@ -4713,34 +5256,6 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] 853 | virtual void warn_once(const char* msg) const {} | ~~~~~~~~~~~~^~~ -[ 80%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/minimxml/XMLWriter.cpp.o -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumListBase.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_MGF.hpp:30, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_MGF.cpp:26: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/algorithm:60, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/minimxml/XMLWriter.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/utility/minimxml/XMLWriter.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/utility/minimxml/XMLWriter.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/XMLWriter.cpp -[ 81%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/random_access_compressed_ifstream.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/random_access_compressed_ifstream.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/random_access_compressed_ifstream.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/random_access_compressed_ifstream.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/random_access_compressed_ifstream.cpp -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzML.hpp:31: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] - 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumListBase.hpp:28, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_MSn.hpp:29, @@ -4760,34 +5275,7 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumListBase.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_MGF.hpp:30, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumList_MGF.cpp:26: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/algorithm:60, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] - 769 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] - 853 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzML.cpp:32: +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:32: /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] 585 | virtual Status processingInstruction(const std::string& name, @@ -4822,6 +5310,11 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] 597 | stream_offset position) {return Status::Ok;} | ~~~~~~~~~~~~~~^~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzML.hpp:31: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] + 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] 769 | virtual void warn_once(const char* msg) const {} @@ -4830,30 +5323,7 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] 853 | virtual void warn_once(const char* msg) const {} | ~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/BinaryDataEncoder.cpp: In member function 'void pwiz::msdata::BinaryDataEncoder::Impl::encode(const double*, size_t, std::string&, size_t*)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/BinaryDataEncoder.cpp:305:37: warning: 'byteCount' may be used uninitialized [-Wmaybe-uninitialized] - 305 | filterArray(byteBuffer, byteCount,compressed); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/BinaryDataEncoder.cpp:131:12: note: 'byteCount' was declared here - 131 | size_t byteCount; - | ^~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/BinaryDataEncoder.cpp:305:37: warning: 'byteBuffer' may be used uninitialized [-Wmaybe-uninitialized] - 305 | filterArray(byteBuffer, byteCount,compressed); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/BinaryDataEncoder.cpp:132:17: note: 'byteBuffer' was declared here - 132 | const void* byteBuffer; - | ^~~~~~~~~~ -[ 82%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/BinaryData.cpp.o -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp: At global scope: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/BinaryData.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/BinaryData.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/BinaryData.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.hpp:31: +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MGF.hpp:29: /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} @@ -4866,70 +5336,9 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] 853 | virtual void warn_once(const char* msg) const {} | ~~~~~~~~~~~~^~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Environment.hpp:24, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Std.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Base64.cpp:26: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp: At global scope: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp: At global scope: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:32: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] - 585 | virtual Status processingInstruction(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:586:61: warning: unused parameter 'data' [-Wunused-parameter] - 586 | const std::string& data, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:587:56: warning: unused parameter 'position' [-Wunused-parameter] - 587 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::startElement(const std::string&, const Attributes&, stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:589:52: warning: unused parameter 'name' [-Wunused-parameter] - 589 | virtual Status startElement(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:590:51: warning: unused parameter 'attributes' [-Wunused-parameter] - 590 | const Attributes& attributes, - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:591:47: warning: unused parameter 'position' [-Wunused-parameter] - 591 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::endElement(const std::string&, stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:593:50: warning: unused parameter 'name' [-Wunused-parameter] - 593 | virtual Status endElement(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:594:45: warning: unused parameter 'position' [-Wunused-parameter] - 594 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::characters(const pwiz::minimxml::SAXParser::saxstring&, stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:596:59: warning: unused parameter 'text' [-Wunused-parameter] - 596 | virtual Status characters(const SAXParser::saxstring& text, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] - 597 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/mzmlb/Connection_mzMLb.cpp: In constructor 'pwiz::msdata::mzmlb::Connection_mzMLb::Connection_mzMLb(const std::string&, int, int)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/mzmlb/Connection_mzMLb.cpp:142:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 142 | nbytes = (nbytes > chunk_size) ? nbytes : chunk_size; // Set per dataset cache to twice the chunk size please - | ~~~~~~~^~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.cpp:28: +[ 86%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/utility/minimxml/XMLWriter.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/utility/minimxml/XMLWriter.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/utility/minimxml/XMLWriter.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/utility/minimxml/XMLWriter.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/XMLWriter.cpp +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzML.cpp:32: /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::minimxml::SAXParser::Handler::processingInstruction(const std::string&, const std::string&, stream_offset)': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] 585 | virtual Status processingInstruction(const std::string& name, @@ -4966,42 +5375,12 @@ | ~~~~~~~~~~~~~~^~~~~~~~ In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Environment.hpp:24, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Std.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.cpp:26: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:31: + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: /usr/include/boost/iterator.hpp: At global scope: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] - 769 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] - 853 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::HandlerIndexedMZML::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzML.cpp:278:51: warning: unused parameter 'attributes' [-Wunused-parameter] - 278 | const Attributes& attributes, - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzML.cpp:279:47: warning: unused parameter 'position' [-Wunused-parameter] - 279 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] - 769 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] - 853 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, @@ -5010,6 +5389,8 @@ /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 87%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/Base64.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/Base64.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/Base64.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/Base64.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Base64.cpp In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, @@ -5018,6 +5399,10 @@ /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/mzmlb/Connection_mzMLb.cpp: In constructor 'pwiz::msdata::mzmlb::Connection_mzMLb::Connection_mzMLb(const std::string&, int, int)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/mzmlb/Connection_mzMLb.cpp:142:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 142 | nbytes = (nbytes > chunk_size) ? nbytes : chunk_size; // Set per dataset cache to twice the chunk size please + | ~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MSn.cpp: In member function 'void pwiz::msdata::Serializer_MSn::write(std::ostream&, const pwiz::msdata::MSData&, const pwiz::util::IterationListenerRegistry*, bool, bool) const': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MSn.cpp:552:10: warning: unused parameter 'useWorkerThreads' [-Wunused-parameter] 552 | bool useWorkerThreads, bool continueOnError) const @@ -5033,10 +5418,6 @@ /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 84%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/IntegerSet.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/IntegerSet.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/IntegerSet.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/IntegerSet.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IntegerSet.cpp -[ 85%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/String.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/String.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/String.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/String.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/String.cpp /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] 769 | virtual void warn_once(const char* msg) const {} @@ -5045,21 +5426,6 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] 853 | virtual void warn_once(const char* msg) const {} | ~~~~~~~~~~~~^~~ -[ 86%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/Filesystem.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/Filesystem.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/Filesystem.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/Filesystem.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.cpp -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.cpp:27: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] - 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/iterator.hpp: At global scope: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp: In function 'std::string pwiz::msdata::{anonymous}::translate_SourceFileTypeToRunID(const pwiz::msdata::SourceFile&, pwiz::cv::CVID)': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:149:61: warning: 'std::string boost::filesystem::extension(const path&)' is deprecated: Use path::extension() instead [-Wdeprecated-declarations] 149 | string nameExtension = bal::to_lower_copy(bfs::extension(sf.name)); @@ -5101,7 +5467,6 @@ /usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here 35 | inline std::string basename(const path& p) | ^~~~~~~~ -[ 87%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/Base64.cpp.o /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:172:65: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] 172 | return bfs::basename(bfs::path(sf.location).leaf()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ @@ -5186,31 +5551,20 @@ /usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here 35 | inline std::string basename(const path& p) | ^~~~~~~~ -cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/Base64.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/Base64.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/Base64.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Base64.cpp /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:228:37: warning: 'std::string boost::filesystem::basename(const path&)' is deprecated: Use path::stem() instead [-Wdeprecated-declarations] 228 | return bfs::basename(sf.name); | ~~~~~~~~~~~~~^~~~~~~~~ /usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here 35 | inline std::string basename(const path& p) | ^~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:24: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/algorithm:60, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 89%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/IterationListener.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/IterationListener.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/IterationListener.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/IterationListener.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.cpp +In file included from /usr/include/boost/lexical_cast.hpp:26, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/common/ParamTypes.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/iterator.hpp: At global scope: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp: In function 'std::vector pwiz::msdata::{anonymous}::getPrecursorInfo(const pwiz::msdata::Spectrum&, pwiz::msdata::SpectrumListPtr, pwiz::cv::CVID)': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:454:62: warning: unused parameter 'spectrumListPtr' [-Wunused-parameter] 454 | const SpectrumListPtr spectrumListPtr, @@ -5226,15 +5580,6 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:1027:47: warning: unused parameter 'position' [-Wunused-parameter] 1027 | stream_offset position) | ~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MGF.cpp: In member function 'void pwiz::msdata::Serializer_MGF::Impl::write(std::ostream&, const pwiz::msdata::MSData&, const pwiz::util::IterationListenerRegistry*, bool, bool) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MGF.cpp:73:61: warning: 'std::string boost::filesystem::basename(const path&)' is deprecated: Use path::stem() instead [-Wdeprecated-declarations] - 73 | string thermoBasename = titleIsThermoDTA ? bfs::basename(thermoFilename) : ""; - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.hpp:37, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MGF.cpp:27: -/usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here - 35 | inline std::string basename(const path& p) - | ^~~~~~~~ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp: In function 'void pwiz::msdata::{anonymous}::fillInMetadata(pwiz::msdata::MSData&)': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:1139:65: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] 1139 | msd.id = msd.run.id = BFS_STRING(bfs::path(lcp).leaf()); @@ -5270,6 +5615,17 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzXML.cpp:1353:47: warning: unused parameter 'position' [-Wunused-parameter] 1353 | stream_offset position) | ~~~~~~~~~~~~~~^~~~~~~~ +[ 89%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/IterationListener.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/IterationListener.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/IterationListener.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/IterationListener.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.cpp +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzML.cpp: In member function 'virtual pwiz::minimxml::SAXParser::Handler::Status pwiz::msdata::HandlerIndexedMZML::startElement(const std::string&, const pwiz::minimxml::SAXParser::Handler::Attributes&, pwiz::minimxml::SAXParser::Handler::stream_offset)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzML.cpp:278:51: warning: unused parameter 'attributes' [-Wunused-parameter] + 278 | const Attributes& attributes, + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_mzML.cpp:279:47: warning: unused parameter 'position' [-Wunused-parameter] + 279 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +[ 90%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/SHA1.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/SHA1.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/SHA1.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/SHA1.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/SHA1.cpp In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Environment.hpp:24, @@ -5278,204 +5634,16 @@ /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/requires_cxx11.hpp:9, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, - from /usr/include/boost/shared_ptr.hpp:17, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/SHA1Calculator.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/SHA1Calculator.cpp:32: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 91%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/SHA1Calculator.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/SHA1Calculator.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/SHA1Calculator.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/SHA1Calculator.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/SHA1Calculator.cpp In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Environment.hpp:24, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Std.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumWorkerThreads.cpp:24: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/XMLWriter.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/XMLWriter.cpp:25: + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Base64.cpp:26: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 90%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/SHA1Calculator.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/SHA1Calculator.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/SHA1Calculator.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/SHA1Calculator.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/SHA1Calculator.cpp -[ 91%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/SHA1.cpp.o -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp: In instantiation of 'const T& pwiz::util::BinaryData::at(size_type) const [with T = double; const_reference = const double&; size_type = long unsigned int]': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:498:30: required from here - 498 | PWIZ_API_DECL template class BinaryData; - | ^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:256:19: warning: comparison of unsigned expression in '< 0' is always false [-Wtype-limits] - 256 | if (index < 0 || index >= size()) - | ~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp: In instantiation of 'T& pwiz::util::BinaryData::at(size_type) [with T = double; reference = double&; size_type = long unsigned int]': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:498:30: required from here - 498 | PWIZ_API_DECL template class BinaryData; - | ^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:263:19: warning: comparison of unsigned expression in '< 0' is always false [-Wtype-limits] - 263 | if (index < 0 || index >= size()) - | ~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp: In instantiation of 'pwiz::util::BinaryData::Impl::Impl(void*) [with T = double]': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:498:30: required from here - 498 | PWIZ_API_DECL template class BinaryData; - | ^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:58:16: warning: unused parameter 'cliNumericArray' [-Wunused-parameter] - 58 | Impl(void* cliNumericArray) - | ~~~~~~^~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp: In instantiation of 'pwiz::util::BinaryData::Impl& pwiz::util::BinaryData::Impl::operator=(void*) [with T = double]': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:498:30: required from here - 498 | PWIZ_API_DECL template class BinaryData; - | ^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:72:27: warning: unused parameter 'cliNumericArray' [-Wunused-parameter] - 72 | Impl& operator=(void* cliNumericArray) - | ~~~~~~^~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp: In instantiation of 'void pwiz::util::BinaryData::Impl::cacheIterators(pwiz::util::BinaryData&) [with T = double]': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:498:30: required from here - 498 | PWIZ_API_DECL template class BinaryData; - | ^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:313:16: warning: implicitly-declared 'constexpr pwiz::util::BinaryData::iterator& pwiz::util::BinaryData::iterator::operator=(const pwiz::util::BinaryData::iterator&)' is deprecated [-Wdeprecated-copy] - 313 | begin_ = iterator(binaryData, true); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:113:9: note: because 'pwiz::util::BinaryData::iterator' has user-provided 'pwiz::util::BinaryData::iterator::iterator(const pwiz::util::BinaryData::iterator&) [with T = double]' - 113 | iterator(const iterator& rhs) : current_(rhs.current_) {} - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:314:14: warning: implicitly-declared 'constexpr pwiz::util::BinaryData::iterator& pwiz::util::BinaryData::iterator::operator=(const pwiz::util::BinaryData::iterator&)' is deprecated [-Wdeprecated-copy] - 314 | end_ = iterator(binaryData, false); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:113:9: note: because 'pwiz::util::BinaryData::iterator' has user-provided 'pwiz::util::BinaryData::iterator::iterator(const pwiz::util::BinaryData::iterator&) [with T = double]' - 113 | iterator(const iterator& rhs) : current_(rhs.current_) {} - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:315:17: warning: implicitly-declared 'constexpr pwiz::util::BinaryData::const_iterator& pwiz::util::BinaryData::const_iterator::operator=(const pwiz::util::BinaryData::const_iterator&)' is deprecated [-Wdeprecated-copy] - 315 | cbegin_ = const_iterator(binaryData, true); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:79:9: note: because 'pwiz::util::BinaryData::const_iterator' has user-provided 'pwiz::util::BinaryData::const_iterator::const_iterator(const pwiz::util::BinaryData::const_iterator&) [with T = double]' - 79 | const_iterator(const const_iterator& rhs) : current_(rhs.current_) {} - | ^~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:316:15: warning: implicitly-declared 'constexpr pwiz::util::BinaryData::const_iterator& pwiz::util::BinaryData::const_iterator::operator=(const pwiz::util::BinaryData::const_iterator&)' is deprecated [-Wdeprecated-copy] - 316 | cend_ = const_iterator(binaryData, false); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:79:9: note: because 'pwiz::util::BinaryData::const_iterator' has user-provided 'pwiz::util::BinaryData::const_iterator::const_iterator(const pwiz::util::BinaryData::const_iterator&) [with T = double]' - 79 | const_iterator(const const_iterator& rhs) : current_(rhs.current_) {} - | ^~~~~~~~~~~~~~ -cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/SHA1.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/SHA1.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/SHA1.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/SHA1.cpp -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp: In instantiation of 'const T& pwiz::util::BinaryData::at(size_type) const [with T = float; const_reference = const float&; size_type = long unsigned int]': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:499:30: required from here - 499 | PWIZ_API_DECL template class BinaryData; - | ^~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:256:19: warning: comparison of unsigned expression in '< 0' is always false [-Wtype-limits] - 256 | if (index < 0 || index >= size()) - | ~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp: In instantiation of 'T& pwiz::util::BinaryData::at(size_type) [with T = float; reference = float&; size_type = long unsigned int]': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:499:30: required from here - 499 | PWIZ_API_DECL template class BinaryData; - | ^~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:263:19: warning: comparison of unsigned expression in '< 0' is always false [-Wtype-limits] - 263 | if (index < 0 || index >= size()) - | ~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp: In instantiation of 'pwiz::util::BinaryData::Impl::Impl(void*) [with T = float]': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:499:30: required from here - 499 | PWIZ_API_DECL template class BinaryData; - | ^~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:58:16: warning: unused parameter 'cliNumericArray' [-Wunused-parameter] - 58 | Impl(void* cliNumericArray) - | ~~~~~~^~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp: In instantiation of 'pwiz::util::BinaryData::Impl& pwiz::util::BinaryData::Impl::operator=(void*) [with T = float]': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:499:30: required from here - 499 | PWIZ_API_DECL template class BinaryData; - | ^~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:72:27: warning: unused parameter 'cliNumericArray' [-Wunused-parameter] - 72 | Impl& operator=(void* cliNumericArray) - | ~~~~~~^~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp: In instantiation of 'void pwiz::util::BinaryData::Impl::cacheIterators(pwiz::util::BinaryData&) [with T = float]': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:499:30: required from here - 499 | PWIZ_API_DECL template class BinaryData; - | ^~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:313:16: warning: implicitly-declared 'constexpr pwiz::util::BinaryData::iterator& pwiz::util::BinaryData::iterator::operator=(const pwiz::util::BinaryData::iterator&)' is deprecated [-Wdeprecated-copy] - 313 | begin_ = iterator(binaryData, true); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:113:9: note: because 'pwiz::util::BinaryData::iterator' has user-provided 'pwiz::util::BinaryData::iterator::iterator(const pwiz::util::BinaryData::iterator&) [with T = float]' - 113 | iterator(const iterator& rhs) : current_(rhs.current_) {} - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:314:14: warning: implicitly-declared 'constexpr pwiz::util::BinaryData::iterator& pwiz::util::BinaryData::iterator::operator=(const pwiz::util::BinaryData::iterator&)' is deprecated [-Wdeprecated-copy] - 314 | end_ = iterator(binaryData, false); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:113:9: note: because 'pwiz::util::BinaryData::iterator' has user-provided 'pwiz::util::BinaryData::iterator::iterator(const pwiz::util::BinaryData::iterator&) [with T = float]' - 113 | iterator(const iterator& rhs) : current_(rhs.current_) {} - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:315:17: warning: implicitly-declared 'constexpr pwiz::util::BinaryData::const_iterator& pwiz::util::BinaryData::const_iterator::operator=(const pwiz::util::BinaryData::const_iterator&)' is deprecated [-Wdeprecated-copy] - 315 | cbegin_ = const_iterator(binaryData, true); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:79:9: note: because 'pwiz::util::BinaryData::const_iterator' has user-provided 'pwiz::util::BinaryData::const_iterator::const_iterator(const pwiz::util::BinaryData::const_iterator&) [with T = float]' - 79 | const_iterator(const const_iterator& rhs) : current_(rhs.current_) {} - | ^~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:316:15: warning: implicitly-declared 'constexpr pwiz::util::BinaryData::const_iterator& pwiz::util::BinaryData::const_iterator::operator=(const pwiz::util::BinaryData::const_iterator&)' is deprecated [-Wdeprecated-copy] - 316 | cend_ = const_iterator(binaryData, false); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:79:9: note: because 'pwiz::util::BinaryData::const_iterator' has user-provided 'pwiz::util::BinaryData::const_iterator::const_iterator(const pwiz::util::BinaryData::const_iterator&) [with T = float]' - 79 | const_iterator(const const_iterator& rhs) : current_(rhs.current_) {} - | ^~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp: In instantiation of 'const T& pwiz::util::BinaryData::at(size_type) const [with T = long int; const_reference = const long int&; size_type = long unsigned int]': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:500:30: required from here - 500 | PWIZ_API_DECL template class BinaryData; - | ^~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:256:19: warning: comparison of unsigned expression in '< 0' is always false [-Wtype-limits] - 256 | if (index < 0 || index >= size()) - | ~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp: In instantiation of 'T& pwiz::util::BinaryData::at(size_type) [with T = long int; reference = long int&; size_type = long unsigned int]': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:500:30: required from here - 500 | PWIZ_API_DECL template class BinaryData; - | ^~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:263:19: warning: comparison of unsigned expression in '< 0' is always false [-Wtype-limits] - 263 | if (index < 0 || index >= size()) - | ~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp: In instantiation of 'pwiz::util::BinaryData::Impl::Impl(void*) [with T = long int]': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:500:30: required from here - 500 | PWIZ_API_DECL template class BinaryData; - | ^~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:58:16: warning: unused parameter 'cliNumericArray' [-Wunused-parameter] - 58 | Impl(void* cliNumericArray) - | ~~~~~~^~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp: In instantiation of 'pwiz::util::BinaryData::Impl& pwiz::util::BinaryData::Impl::operator=(void*) [with T = long int]': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:500:30: required from here - 500 | PWIZ_API_DECL template class BinaryData; - | ^~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:72:27: warning: unused parameter 'cliNumericArray' [-Wunused-parameter] - 72 | Impl& operator=(void* cliNumericArray) - | ~~~~~~^~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp: In instantiation of 'void pwiz::util::BinaryData::Impl::cacheIterators(pwiz::util::BinaryData&) [with T = long int]': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:500:30: required from here - 500 | PWIZ_API_DECL template class BinaryData; - | ^~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:313:16: warning: implicitly-declared 'constexpr pwiz::util::BinaryData::iterator& pwiz::util::BinaryData::iterator::operator=(const pwiz::util::BinaryData::iterator&)' is deprecated [-Wdeprecated-copy] - 313 | begin_ = iterator(binaryData, true); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:113:9: note: because 'pwiz::util::BinaryData::iterator' has user-provided 'pwiz::util::BinaryData::iterator::iterator(const pwiz::util::BinaryData::iterator&) [with T = long int]' - 113 | iterator(const iterator& rhs) : current_(rhs.current_) {} - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:314:14: warning: implicitly-declared 'constexpr pwiz::util::BinaryData::iterator& pwiz::util::BinaryData::iterator::operator=(const pwiz::util::BinaryData::iterator&)' is deprecated [-Wdeprecated-copy] - 314 | end_ = iterator(binaryData, false); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:113:9: note: because 'pwiz::util::BinaryData::iterator' has user-provided 'pwiz::util::BinaryData::iterator::iterator(const pwiz::util::BinaryData::iterator&) [with T = long int]' - 113 | iterator(const iterator& rhs) : current_(rhs.current_) {} - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:315:17: warning: implicitly-declared 'constexpr pwiz::util::BinaryData::const_iterator& pwiz::util::BinaryData::const_iterator::operator=(const pwiz::util::BinaryData::const_iterator&)' is deprecated [-Wdeprecated-copy] - 315 | cbegin_ = const_iterator(binaryData, true); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:79:9: note: because 'pwiz::util::BinaryData::const_iterator' has user-provided 'pwiz::util::BinaryData::const_iterator::const_iterator(const pwiz::util::BinaryData::const_iterator&) [with T = long int]' - 79 | const_iterator(const const_iterator& rhs) : current_(rhs.current_) {} - | ^~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:316:15: warning: implicitly-declared 'constexpr pwiz::util::BinaryData::const_iterator& pwiz::util::BinaryData::const_iterator::operator=(const pwiz::util::BinaryData::const_iterator&)' is deprecated [-Wdeprecated-copy] - 316 | cend_ = const_iterator(binaryData, false); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:79:9: note: because 'pwiz::util::BinaryData::const_iterator' has user-provided 'pwiz::util::BinaryData::const_iterator::const_iterator(const pwiz::util::BinaryData::const_iterator&) [with T = long int]' - 79 | const_iterator(const const_iterator& rhs) : current_(rhs.current_) {} - | ^~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.cpp:54:21: warning: WIN32 is NOT defined - 54 | #pragma GCC warning "WIN32 is NOT defined" - | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumWorkerThreads.hpp:26, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumWorkerThreads.cpp:26: @@ -5531,8 +5699,6 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] 597 | stream_offset position) {return Status::Ok;} | ~~~~~~~~~~~~~~^~~~~~~~ -[ 92%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/random_access_compressed_ifstream.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/random_access_compressed_ifstream.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/random_access_compressed_ifstream.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/random_access_compressed_ifstream.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/random_access_compressed_ifstream.cpp /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] 769 | virtual void warn_once(const char* msg) const {} @@ -5541,7 +5707,6 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] 853 | virtual void warn_once(const char* msg) const {} | ~~~~~~~~~~~~^~~ -[ 93%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/BinaryData.cpp.o In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.hpp:31: @@ -5549,57 +5714,31 @@ /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/BinaryData.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/BinaryData.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/BinaryData.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp -[ 95%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/IntegerSet.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/IntegerSet.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/IntegerSet.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/IntegerSet.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IntegerSet.cpp -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumWorkerThreads.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumWorkerThreads.cpp:26: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | class PWIZ_API_DECL const_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /usr/include/c++/14/stdexcept:39, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Exception.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Std.hpp:28: -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:88:48: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 88 | class PWIZ_API_DECL iterator : public std::iterator - | ^~~~~~~~ -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/requires_cxx11.hpp:9, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/iostreams/device/file_descriptor.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/random_access_compressed_ifstream.cpp:69: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::SpectrumListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:769:40: warning: unused parameter 'msg' [-Wunused-parameter] - 769 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp: In member function 'virtual void pwiz::msdata::ChromatogramListSimple::warn_once(const char*) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/MSData.hpp:853:40: warning: unused parameter 'msg' [-Wunused-parameter] - 853 | virtual void warn_once(const char* msg) const {} - | ~~~~~~~~~~~~^~~ -[ 96%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/String.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/String.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/String.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/String.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/String.cpp -[ 97%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/Filesystem.cpp.o -cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/Filesystem.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/Filesystem.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/Filesystem.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.cpp +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MGF.cpp: In member function 'void pwiz::msdata::Serializer_MGF::Impl::write(std::ostream&, const pwiz::msdata::MSData&, const pwiz::util::IterationListenerRegistry*, bool, bool) const': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MGF.cpp:73:61: warning: 'std::string boost::filesystem::basename(const path&)' is deprecated: Use path::stem() instead [-Wdeprecated-declarations] + 73 | string thermoBasename = titleIsThermoDTA ? bfs::basename(thermoFilename) : ""; + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.hpp:37, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/Serializer_MGF.cpp:27: +/usr/include/boost/filesystem/convenience.hpp:35:20: note: declared here + 35 | inline std::string basename(const path& p) + | ^~~~~~~~ +[ 92%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/random_access_compressed_ifstream.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/random_access_compressed_ifstream.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/random_access_compressed_ifstream.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/random_access_compressed_ifstream.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/random_access_compressed_ifstream.cpp In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Environment.hpp:24, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Std.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IntegerSet.cpp:26: + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.cpp:26: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 93%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/BinaryData.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/BinaryData.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/BinaryData.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/BinaryData.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp +[ 95%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/IntegerSet.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/IntegerSet.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/IntegerSet.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/IntegerSet.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IntegerSet.cpp +[ 96%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/String.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/String.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/String.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/String.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/String.cpp /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumWorkerThreads.cpp: In constructor 'pwiz::msdata::SpectrumWorkerThreads::Impl::Impl(const pwiz::msdata::SpectrumList&, bool, bool)': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumWorkerThreads.cpp:337:22: warning: 'pwiz::msdata::SpectrumWorkerThreads::Impl::taskMRU_' will be initialized after [-Wreorder] 337 | mru_list taskMRU_; @@ -5610,22 +5749,28 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumWorkerThreads.cpp:60:5: warning: when initialized here [-Wreorder] 60 | Impl(const SpectrumList& sl, bool useWorkerThreads, bool continueOnError) | ^~~~ +In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.cpp:27: +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] + 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +[ 97%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/Filesystem.cpp.o +cd /build/reproducible-path/libpwizlite-3.0.8/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_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DHDF_NO_NAMESPACE -DNO_STATIC_CAST -DOLD_HEADER_FILENAME -DWITHOUT_MZ5 -I/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src -I/build/reproducible-path/libpwizlite-3.0.8/src -I/build/reproducible-path/libpwizlite-3.0.8/src/boost -isystem /usr/include/hdf5/serial -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/Filesystem.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/Filesystem.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/Filesystem.cpp.o -c /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.cpp +In file included from /usr/include/boost/smart_ptr/detail/requires_cxx11.hpp:9, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, + from /usr/include/boost/shared_ptr.hpp:17, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/SHA1Calculator.hpp:28, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/SHA1Calculator.cpp:32: +/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' + 10 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Environment.hpp:24, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Std.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Base64.cpp:26: + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/XMLWriter.hpp:29, + from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/XMLWriter.cpp:25: /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IntegerSet.cpp: In member function 'void pwiz::util::IntegerSet::insert(Interval)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IntegerSet.cpp:138:79: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 138 | if (eraseBegin != intervals_.end() && eraseBegin->begin <= interval.begin && eraseBegin->end >= interval.end || - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IntegerSet.cpp: In member function 'bool pwiz::util::IntegerSet::Iterator::operator==(const pwiz::util::IntegerSet::Iterator&) const': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IntegerSet.cpp:325:63: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 325 | return (it_!=end_ && that.it_!=that.end_ && it_==that.it_ && value_==that.value_ || - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:24: /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 54 | class PWIZ_API_DECL const_iterator : public std::iterator @@ -5642,43 +5787,6 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Environment.hpp:24, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Std.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.cpp:26: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumWorkerThreads.cpp: In constructor 'pwiz::msdata::SpectrumWorkerThreads::Impl::Impl(const pwiz::msdata::SpectrumList&, bool, bool)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumWorkerThreads.cpp:337:22: warning: 'pwiz::msdata::SpectrumWorkerThreads::Impl::taskMRU_' will be initialized after [-Wreorder] - 337 | mru_list taskMRU_; - | ^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumWorkerThreads.cpp:334:10: warning: 'bool pwiz::msdata::SpectrumWorkerThreads::Impl::continueOnError_' [-Wreorder] - 334 | bool continueOnError_; - | ^~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/data/msdata/SpectrumWorkerThreads.cpp:60:5: warning: when initialized here [-Wreorder] - 60 | Impl(const SpectrumList& sl, bool useWorkerThreads, bool continueOnError) - | ^~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/random_access_compressed_ifstream.cpp: In member function 'std::streampos pwiz::util::random_access_compressed_streambuf::my_seekg(std::streampos, std::ios_base::seekdir, std::ios_base::openmode)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/random_access_compressed_ifstream.cpp:824:138: warning: unused parameter 'Mode' [-Wunused-parameter] - 824 | std::streampos random_access_compressed_streambuf::my_seekg(std::streampos offset, std::ios_base::seekdir whence,std::ios_base::openmode Mode) { - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/random_access_compressed_ifstream.cpp: In member function 'std::streampos pwiz::util::chunky_streambuf::my_seekg(boost::iostreams::stream_offset, std::ios_base::seekdir, std::ios_base::openmode)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/random_access_compressed_ifstream.cpp:1199:137: warning: unused parameter 'Mode' [-Wunused-parameter] - 1199 | std::streampos chunky_streambuf::my_seekg(boost::iostreams::stream_offset offset, std::ios_base::seekdir whence,std::ios_base::openmode Mode) { - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /usr/include/boost/smart_ptr/detail/requires_cxx11.hpp:9, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, - from /usr/include/boost/shared_ptr.hpp:17, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/SHA1Calculator.hpp:28, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/SHA1Calculator.cpp:32: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.cpp:54:21: warning: WIN32 is NOT defined - 54 | #pragma GCC warning "WIN32 is NOT defined" - | ^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp: In instantiation of 'const T& pwiz::util::BinaryData::at(size_type) const [with T = double; const_reference = const double&; size_type = long unsigned int]': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:498:30: required from here 498 | PWIZ_API_DECL template class BinaryData; @@ -5686,11 +5794,6 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:256:19: warning: comparison of unsigned expression in '< 0' is always false [-Wtype-limits] 256 | if (index < 0 || index >= size()) | ~~~~~~^~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.cpp:27: -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] - 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp: In instantiation of 'T& pwiz::util::BinaryData::at(size_type) [with T = double; reference = double&; size_type = long unsigned int]': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.cpp:498:30: required from here 498 | PWIZ_API_DECL template class BinaryData; @@ -5852,13 +5955,9 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/BinaryData.hpp:79:9: note: because 'pwiz::util::BinaryData::const_iterator' has user-provided 'pwiz::util::BinaryData::const_iterator::const_iterator(const pwiz::util::BinaryData::const_iterator&) [with T = long int]' 79 | const_iterator(const const_iterator& rhs) : current_(rhs.current_) {} | ^~~~~~~~~~~~~~ -In file included from /usr/include/boost/lexical_cast.hpp:26, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/XMLWriter.hpp:29, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/XMLWriter.cpp:25: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.cpp:54:21: warning: WIN32 is NOT defined + 54 | #pragma GCC warning "WIN32 is NOT defined" + | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/lexical_cast.hpp:26, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/optimized_lexical_cast.hpp:29, from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Environment.hpp:24, @@ -5883,20 +5982,6 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/IntegerSet.cpp:325:63: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 325 | return (it_!=end_ && that.it_!=that.end_ && it_==that.it_ && value_==that.value_ || | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/function/detail/requires_cxx11.hpp:9, - from /usr/include/boost/function/detail/prologue.hpp:12, - from /usr/include/boost/function.hpp:30, - from /usr/include/boost/algorithm/string/detail/find_iterator.hpp:18, - from /usr/include/boost/algorithm/string/find_iterator.hpp:24, - from /usr/include/boost/algorithm/string/iter_find.hpp:27, - from /usr/include/boost/algorithm/string/split.hpp:16, - from /usr/include/boost/algorithm/string.hpp:23, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/String.hpp:31, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.hpp:34, - from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.cpp:26: -/usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' - 10 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/random_access_compressed_ifstream.cpp: In member function 'std::streampos pwiz::util::random_access_compressed_streambuf::my_seekg(std::streampos, std::ios_base::seekdir, std::ios_base::openmode)': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/random_access_compressed_ifstream.cpp:824:138: warning: unused parameter 'Mode' [-Wunused-parameter] 824 | std::streampos random_access_compressed_streambuf::my_seekg(std::streampos offset, std::ios_base::seekdir whence,std::ios_base::openmode Mode) { @@ -5905,45 +5990,9 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/random_access_compressed_ifstream.cpp:1199:137: warning: unused parameter 'Mode' [-Wunused-parameter] 1199 | std::streampos chunky_streambuf::my_seekg(boost::iostreams::stream_offset offset, std::ios_base::seekdir whence,std::ios_base::openmode Mode) { | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.cpp: In function 'void pwiz::util::force_close_handles_to_filepath(const std::string&, bool)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.cpp:350:52: warning: unused parameter 'filepath' [-Wunused-parameter] - 350 | force_close_handles_to_filepath(const std::string &filepath, - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.cpp:351:38: warning: unused parameter 'closeMemoryMappedSections' [-Wunused-parameter] - 351 | bool closeMemoryMappedSections) noexcept(true) - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.cpp: In function 'void pwiz::util::{anonymous}::copy_recursive(const boost::filesystem::path&, const boost::filesystem::path&)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.cpp:686:22: warning: 'void boost::filesystem::copy_directory(const path&, const path&)' is deprecated: Use create_directory() instead [-Wdeprecated-declarations] - 686 | bfs::copy_directory(from, to); - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.hpp:36: -/usr/include/boost/filesystem/operations.hpp:437:13: note: declared here - 437 | inline void copy_directory(path const& from, path const& to) - | ^~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.cpp: In function 'void pwiz::util::{anonymous}::copy_recursive(const boost::filesystem::path&, const boost::filesystem::path&, boost::system::error_code&)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.cpp:710:22: warning: 'void boost::filesystem::copy_directory(const path&, const path&, boost::system::error_code&)' is deprecated: Use create_directory() instead [-Wdeprecated-declarations] - 710 | bfs::copy_directory(from, to, ec); - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -/usr/include/boost/filesystem/operations.hpp:443:13: note: declared here - 443 | inline void copy_directory(path const& from, path const& to, system::error_code& ec) BOOST_NOEXCEPT - | ^~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.cpp: In function 'void pwiz::util::copy_directory(const boost::filesystem::path&, const boost::filesystem::path&, bool, boost::system::error_code*)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.cpp:764:28: warning: 'void boost::filesystem::copy_directory(const path&, const path&, boost::system::error_code&)' is deprecated: Use create_directory() instead [-Wdeprecated-declarations] - 764 | bfs::copy_directory(from, to, *ec); - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ -/usr/include/boost/filesystem/operations.hpp:443:13: note: declared here - 443 | inline void copy_directory(path const& from, path const& to, system::error_code& ec) BOOST_NOEXCEPT - | ^~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.cpp:766:28: warning: 'void boost::filesystem::copy_directory(const path&, const path&)' is deprecated: Use create_directory() instead [-Wdeprecated-declarations] - 766 | bfs::copy_directory(from, to); - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/usr/include/boost/filesystem/operations.hpp:437:13: note: declared here - 437 | inline void copy_directory(path const& from, path const& to) - | ^~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.cpp: In function 'void pwiz::util::check_path_length(const std::string&)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.cpp:967:33: warning: unused parameter 'path' [-Wunused-parameter] - 967 | check_path_length(const string &path) - | ~~~~~~~~~~~~~~^~~~ +[ 98%] Linking CXX shared library libpwizlite.so +cd /build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/pwizlite-shared.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -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 -shared -Wl,-soname,libpwizlite.so.3 -o libpwizlite.so.3.0.8 "CMakeFiles/pwizlite-shared.dir/pwiz/data/common/ParamTypes.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/common/CVTranslator.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/common/cv.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/common/diff_std.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/ChromatogramList_mzML.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/LegacyAdapter.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSNumpress.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/References.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumInfo.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_BTDX.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_mzML.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_mzXML.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Version.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/BinaryDataEncoder.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/DefaultReaderList.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/IO.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Index_mzML.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSData.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSDataFile.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Reader.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_MGF.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_MSn.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_mzML.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_mzXML.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumListBase.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_MGF.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_MSn.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumWorkerThreads.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/mzmlb/Connection_mzMLb.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/utility/minimxml/SAXParser.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/utility/minimxml/XMLWriter.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/Base64.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/IterationListener.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/SHA1.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/SHA1Calculator.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/random_access_compressed_ifstream.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/BinaryData.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/IntegerSet.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/String.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/Filesystem.cpp.o" -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial: /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_thread.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 /usr/lib/x86_64-linux-gnu/libz.so -Wl,--no-as-needed /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_cpp.so -Wl,--as-needed /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 In file included from /usr/include/boost/function/detail/requires_cxx11.hpp:9, from /usr/include/boost/function/detail/prologue.hpp:12, from /usr/include/boost/function.hpp:30, @@ -5958,6 +6007,9 @@ /usr/include/boost/iterator.hpp:10:1: note: '#pragma message: This header is deprecated. Use instead.' 10 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +cd /build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_symlink_library libpwizlite.so.3.0.8 libpwizlite.so.3 libpwizlite.so +make[3]: Leaving directory '/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu' +[ 98%] Built target pwizlite-shared /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.cpp: In function 'void pwiz::util::force_close_handles_to_filepath(const std::string&, bool)': /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/misc/Filesystem.cpp:350:52: warning: unused parameter 'filepath' [-Wunused-parameter] 350 | force_close_handles_to_filepath(const std::string &filepath, @@ -6007,27 +6059,11 @@ /build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.cpp:501:14: note: 'inCDATA' was declared here 501 | bool inCDATA; | ^~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.cpp: In function 'void pwiz::minimxml::SAXParser::parse(std::istream&, Handler&)': -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.cpp:543:61: warning: offset '1' outside bounds of constant string [-Warray-bounds=] - 543 | Handler::Status status = wrangler.endElement(buffer.c_str()+1, position); - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.cpp:549:17: warning: 'inCDATA' may be used uninitialized [-Wmaybe-uninitialized] - 549 | if (inCDATA) - | ^~ -/build/reproducible-path/libpwizlite-3.0.8/src/pwiz/utility/minimxml/SAXParser.cpp:501:14: note: 'inCDATA' was declared here - 501 | bool inCDATA; - | ^~~~~~~ -[ 98%] Linking CXX static library libpwizlite.a +[100%] Linking CXX static library libpwizlite.a cd /build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/pwizlite-static.dir/cmake_clean_target.cmake cd /build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/pwizlite-static.dir/link.txt --verbose=1 /usr/bin/ar qc libpwizlite.a "CMakeFiles/pwizlite-static.dir/pwiz/data/common/ParamTypes.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/common/CVTranslator.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/common/cv.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/common/diff_std.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/ChromatogramList_mzML.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/LegacyAdapter.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSNumpress.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/References.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumInfo.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_BTDX.cpp.o" 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"CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumListBase.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_MGF.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_MSn.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumWorkerThreads.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/mzmlb/Connection_mzMLb.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/utility/minimxml/SAXParser.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/utility/minimxml/XMLWriter.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/Base64.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/IterationListener.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/SHA1.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/SHA1Calculator.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/random_access_compressed_ifstream.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/BinaryData.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/IntegerSet.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/String.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/Filesystem.cpp.o" -[100%] Linking CXX shared library libpwizlite.so -cd /build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/pwizlite-shared.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/libpwizlite-3.0.8=. -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 -shared -Wl,-soname,libpwizlite.so.3 -o libpwizlite.so.3.0.8 "CMakeFiles/pwizlite-shared.dir/pwiz/data/common/ParamTypes.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/common/CVTranslator.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/common/cv.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/common/diff_std.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/ChromatogramList_mzML.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/LegacyAdapter.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSNumpress.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/References.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumInfo.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_BTDX.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_mzML.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_mzXML.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Version.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/BinaryDataEncoder.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/DefaultReaderList.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/IO.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Index_mzML.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSData.cpp.o" 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"CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/IterationListener.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/SHA1.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/SHA1Calculator.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/random_access_compressed_ifstream.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/BinaryData.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/IntegerSet.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/String.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/Filesystem.cpp.o" -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial: /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_thread.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 /usr/lib/x86_64-linux-gnu/libz.so -Wl,--no-as-needed /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_cpp.so -Wl,--as-needed /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/bin/ranlib libpwizlite.a -cd /build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_symlink_library libpwizlite.so.3.0.8 libpwizlite.so.3 libpwizlite.so -make[3]: Leaving directory '/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu' -[100%] Built target pwizlite-shared make[3]: Leaving directory '/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu' [100%] Built target pwizlite-static make[2]: Leaving directory '/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu' @@ -6040,7 +6076,7 @@ dh_testroot -O--build-system=cmake dh_prep -O--build-system=cmake dh_auto_install -O--build-system=cmake - cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/libpwizlite-3.0.8/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j20 install DESTDIR=/build/reproducible-path/libpwizlite-3.0.8/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/libpwizlite-3.0.8 -B/build/reproducible-path/libpwizlite-3.0.8/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -6074,24 +6110,24 @@ dh_strip -a -O--build-system=cmake dh_makeshlibs -a -O--build-system=cmake dh_shlibdeps -a -O--build-system=cmake -dpkg-shlibdeps: warning: symbol H5T_NATIVE_FLOAT_g used by debian/libpwizlite3t64/usr/lib/x86_64-linux-gnu/libpwizlite.so.3.0.8 found in none of the libraries -dpkg-shlibdeps: warning: symbol H5Dwrite used by debian/libpwizlite3t64/usr/lib/x86_64-linux-gnu/libpwizlite.so.3.0.8 found in none of the libraries -dpkg-shlibdeps: warning: symbol H5Aopen used by debian/libpwizlite3t64/usr/lib/x86_64-linux-gnu/libpwizlite.so.3.0.8 found in none of the libraries -dpkg-shlibdeps: warning: symbol H5Tget_native_type used by debian/libpwizlite3t64/usr/lib/x86_64-linux-gnu/libpwizlite.so.3.0.8 found in none of the libraries -dpkg-shlibdeps: warning: symbol H5Tget_size used by debian/libpwizlite3t64/usr/lib/x86_64-linux-gnu/libpwizlite.so.3.0.8 found in none of the libraries -dpkg-shlibdeps: warning: symbol H5Pset_deflate used by debian/libpwizlite3t64/usr/lib/x86_64-linux-gnu/libpwizlite.so.3.0.8 found in none of the libraries -dpkg-shlibdeps: warning: symbol H5Dclose used by debian/libpwizlite3t64/usr/lib/x86_64-linux-gnu/libpwizlite.so.3.0.8 found in none of the libraries -dpkg-shlibdeps: warning: symbol H5Tset_size used by debian/libpwizlite3t64/usr/lib/x86_64-linux-gnu/libpwizlite.so.3.0.8 found in none of the libraries -dpkg-shlibdeps: warning: symbol H5Aclose used by debian/libpwizlite3t64/usr/lib/x86_64-linux-gnu/libpwizlite.so.3.0.8 found in none of the libraries +dpkg-shlibdeps: warning: symbol H5Tcreate used by debian/libpwizlite3t64/usr/lib/x86_64-linux-gnu/libpwizlite.so.3.0.8 found in none of the libraries +dpkg-shlibdeps: warning: symbol H5T_NATIVE_SCHAR_g used by debian/libpwizlite3t64/usr/lib/x86_64-linux-gnu/libpwizlite.so.3.0.8 found in none of the libraries dpkg-shlibdeps: warning: symbol H5Sget_simple_extent_dims used by debian/libpwizlite3t64/usr/lib/x86_64-linux-gnu/libpwizlite.so.3.0.8 found in none of the libraries +dpkg-shlibdeps: warning: symbol H5Tset_strpad used by debian/libpwizlite3t64/usr/lib/x86_64-linux-gnu/libpwizlite.so.3.0.8 found in none of the libraries +dpkg-shlibdeps: warning: symbol H5Pset_fletcher32 used by debian/libpwizlite3t64/usr/lib/x86_64-linux-gnu/libpwizlite.so.3.0.8 found in none of the libraries +dpkg-shlibdeps: warning: symbol H5Pset_cache used by debian/libpwizlite3t64/usr/lib/x86_64-linux-gnu/libpwizlite.so.3.0.8 found in none of the libraries +dpkg-shlibdeps: warning: symbol H5Pget_chunk_cache used by debian/libpwizlite3t64/usr/lib/x86_64-linux-gnu/libpwizlite.so.3.0.8 found in none of the libraries +dpkg-shlibdeps: warning: symbol H5Aget_type used by debian/libpwizlite3t64/usr/lib/x86_64-linux-gnu/libpwizlite.so.3.0.8 found in none of the libraries +dpkg-shlibdeps: warning: symbol H5Pset_shuffle used by debian/libpwizlite3t64/usr/lib/x86_64-linux-gnu/libpwizlite.so.3.0.8 found in none of the libraries +dpkg-shlibdeps: warning: symbol H5T_NATIVE_DOUBLE_g used by debian/libpwizlite3t64/usr/lib/x86_64-linux-gnu/libpwizlite.so.3.0.8 found in none of the libraries dpkg-shlibdeps: warning: 43 other similar warnings have been skipped (use -v to see them all) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/libpwizlite3t64/usr/lib/x86_64-linux-gnu/libpwizlite.so.3.0.8 was not linked against libhdf5_serial_cpp.so.103 (it uses none of the library's symbols) dh_installdeb -O--build-system=cmake dh_gencontrol -O--build-system=cmake dh_md5sums -O--build-system=cmake dh_builddeb -O--build-system=cmake -dpkg-deb: building package 'libpwizlite-dev' in '../libpwizlite-dev_3.0.8-1_amd64.deb'. dpkg-deb: building package 'libpwizlite3t64-dbgsym' in '../libpwizlite3t64-dbgsym_3.0.8-1_amd64.deb'. +dpkg-deb: building package 'libpwizlite-dev' in '../libpwizlite-dev_3.0.8-1_amd64.deb'. dpkg-deb: building package 'libpwizlite3t64' in '../libpwizlite3t64_3.0.8-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../libpwizlite_3.0.8-1_amd64.buildinfo dpkg-genchanges --build=binary -O../libpwizlite_3.0.8-1_amd64.changes @@ -6100,12 +6136,14 @@ 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/1194285/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1194285/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/393612 and its subdirectories -I: Current time: Sun Dec 21 06:20:37 -12 2025 -I: pbuilder-time-stamp: 1766341237 +I: removing directory /srv/workspace/pbuilder/1194285 and its subdirectories +I: Current time: Tue Nov 19 02:00:55 +14 2024 +I: pbuilder-time-stamp: 1731931255