Diff of the two buildlogs: -- --- b1/build.log 2023-04-16 16:01:10.829268404 +0000 +++ b2/build.log 2023-04-16 16:07:45.831748371 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Apr 16 03:53:34 -12 2023 -I: pbuilder-time-stamp: 1681660414 +I: Current time: Sun May 19 12:24:14 +14 2024 +I: pbuilder-time-stamp: 1716071054 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./libpwizlite_3.0.4.orig.tar.gz] I: copying [./libpwizlite_3.0.4-1.debian.tar.xz] I: Extracting source -gpgv: Signature made Tue Mar 15 02:18:45 2022 -12 +gpgv: Signature made Wed Mar 16 04:18:45 2022 +14 gpgv: using RSA key B053304E17D6D419DD9B465141AB484D7694CF42 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./libpwizlite_3.0.4-1.dsc: no acceptable signature found @@ -25,135 +25,167 @@ dpkg-source: info: unpacking libpwizlite_3.0.4-1.debian.tar.xz I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2430257/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3456798/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-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 May 19 12:24 /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/3456798/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3456798/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - 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=15' - DISTRIBUTION='bookworm' - 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]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + 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=16' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='e3bc2cbbbeb942c69c5f51518f62b924' - 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='2430257' - PS1='# ' - PS2='> ' + INVOCATION_ID=789cf06a78b24c0c8cb3bd3d4e9838c4 + 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=3456798 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.ZUjFDmuk/pbuilderrc_nnzd --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ZUjFDmuk/b1 --logfile b1/build.log libpwizlite_3.0.4-1.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + 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.ZUjFDmuk/pbuilderrc_hnlm --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ZUjFDmuk/b2 --logfile b2/build.log --extrapackages usrmerge libpwizlite_3.0.4-1.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://85.184.249.68:3128 I: uname -a - Linux ionos1-amd64 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-0.deb11.5-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.12-1~bpo11+1 (2023-03-05) x86_64 GNU/Linux I: ls -l /bin total 5632 - -rwxr-xr-x 1 root root 1265648 Feb 12 08:05 bash - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat - -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown - -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp - -rwxr-xr-x 1 root root 125640 Jan 5 01:20 dash - -rwxr-xr-x 1 root root 121904 Sep 20 2022 date - -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd - -rwxr-xr-x 1 root root 102200 Sep 20 2022 df - -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir - -rwxr-xr-x 1 root root 88656 Mar 22 22:02 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname - -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 35664 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 85600 Mar 22 22:02 findmnt - -rwsr-xr-x 1 root root 35128 Mar 22 20:35 fusermount - -rwxr-xr-x 1 root root 203152 Jan 24 02:43 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 22680 Dec 19 01:33 hostname - -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln - -rwxr-xr-x 1 root root 53024 Mar 23 00:40 login - -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls - -rwxr-xr-x 1 root root 207168 Mar 22 22:02 lsblk - -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 59712 Mar 22 22:02 more - -rwsr-xr-x 1 root root 59704 Mar 22 22:02 mount - -rwxr-xr-x 1 root root 18744 Mar 22 22:02 mountpoint - -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Feb 12 08:05 rbash -> bash - -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm - -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 27560 Nov 2 04:31 run-parts - -rwxr-xr-x 1 root root 126424 Jan 5 07:55 sed - lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash - -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty - -rwsr-xr-x 1 root root 72000 Mar 22 22:02 su - -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync - -rwxr-xr-x 1 root root 531984 Apr 6 02:25 tar - -rwxr-xr-x 1 root root 14520 Nov 2 04:31 tempfile - -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch - -rwxr-xr-x 1 root root 35664 Sep 20 2022 true - -rwxr-xr-x 1 root root 14568 Mar 22 20:35 ulockmgr_server - -rwsr-xr-x 1 root root 35128 Mar 22 22:02 umount - -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 72024 Mar 22 22:02 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/2430257/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1265648 Feb 13 2023 bash + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 44016 Sep 21 2022 cat + -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown + -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp + -rwxr-xr-x 1 root root 125640 Jan 6 2023 dash + -rwxr-xr-x 1 root root 121904 Sep 21 2022 date + -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd + -rwxr-xr-x 1 root root 102200 Sep 21 2022 df + -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir + -rwxr-xr-x 1 root root 88656 Mar 24 2023 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 2022 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 2022 domainname -> hostname + -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 2023 egrep + -rwxr-xr-x 1 root root 35664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 2023 fgrep + -rwxr-xr-x 1 root root 85600 Mar 24 2023 findmnt + -rwsr-xr-x 1 root root 35128 Mar 23 2023 fusermount + -rwxr-xr-x 1 root root 203152 Jan 25 2023 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22680 Dec 20 2022 hostname + -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln + -rwxr-xr-x 1 root root 53024 Mar 24 2023 login + -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls + -rwxr-xr-x 1 root root 207168 Mar 24 2023 lsblk + -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 59712 Mar 24 2023 more + -rwsr-xr-x 1 root root 59704 Mar 24 2023 mount + -rwxr-xr-x 1 root root 18744 Mar 24 2023 mountpoint + -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 2022 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Feb 13 2023 rbash -> bash + -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm + -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 27560 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 126424 Jan 6 2023 sed + lrwxrwxrwx 1 root root 9 May 19 12:24 sh -> /bin/bash + -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty + -rwsr-xr-x 1 root root 72000 Mar 24 2023 su + -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync + -rwxr-xr-x 1 root root 531984 Apr 7 2023 tar + -rwxr-xr-x 1 root root 14520 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch + -rwxr-xr-x 1 root root 35664 Sep 21 2022 true + -rwxr-xr-x 1 root root 14568 Mar 23 2023 ulockmgr_server + -rwsr-xr-x 1 root root 35128 Mar 24 2023 umount + -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 72024 Mar 24 2023 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 2022 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/3456798/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -297,7 +329,7 @@ Get: 88 http://deb.debian.org/debian bookworm/main amd64 python3-roman all 3.3-3 [9880 B] Get: 89 http://deb.debian.org/debian bookworm/main amd64 python3-docutils all 0.19+dfsg-6 [382 kB] Get: 90 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] -Fetched 64.3 MB in 2s (41.6 MB/s) +Fetched 64.3 MB in 3s (19.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-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 ... 19596 files and directories currently installed.) @@ -678,10 +710,17 @@ Reading package lists... Building dependency tree... Reading state information... +usrmerge is already the newest version (35). fakeroot is already the newest version (1.31-1.2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/libpwizlite-3.0.4/ && 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_3.0.4-1_source.changes +I: user script /srv/workspace/pbuilder/3456798/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +removed '/etc/unsupported-skip-usrmerge-conversion' +The system has been successfully converted. +I: user script /srv/workspace/pbuilder/3456798/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/libpwizlite-3.0.4/ && 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_3.0.4-1_source.changes dpkg-buildpackage: info: source package libpwizlite dpkg-buildpackage: info: source version 3.0.4-1 dpkg-buildpackage: info: source distribution unstable @@ -1238,54 +1277,56 @@ 'boost/enum.hpp' -> '/build/libpwizlite-3.0.4/debian/includes/pwizlite/boost/enum.hpp' make[1]: Leaving directory '/build/libpwizlite-3.0.4' dh_auto_build -O--build-system=cmake - cd obj-x86_64-linux-gnu && make -j15 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/libpwizlite-3.0.4 -B/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/CMakeFiles /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu' 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/libpwizlite-3.0.4/obj-x86_64-linux-gnu' cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libpwizlite-3.0.4 /build/libpwizlite-3.0.4/src /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src/CMakeFiles/pwizlite-static.dir/DependInfo.cmake --color= +make -f src/CMakeFiles/pwizlite-shared.dir/build.make src/CMakeFiles/pwizlite-shared.dir/depend make[3]: Entering directory '/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu' cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libpwizlite-3.0.4 /build/libpwizlite-3.0.4/src /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src/CMakeFiles/pwizlite-shared.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu' +make -f src/CMakeFiles/pwizlite-shared.dir/build.make src/CMakeFiles/pwizlite-shared.dir/build +make[3]: Leaving directory '/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu' -make -f src/CMakeFiles/pwizlite-shared.dir/build.make src/CMakeFiles/pwizlite-shared.dir/build make[3]: Entering directory '/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu' -[ 1%] Building CXX object 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-Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/utility/misc/Base64.cpp +[ 13%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/random_access_compressed_ifstream.cpp.o cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/utility/misc/random_access_compressed_ifstream.cpp -[ 16%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/IntegerSet.cpp.o -[ 17%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/Filesystem.cpp.o +[ 15%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/Filesystem.cpp.o +[ 16%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/Filesystem.cpp.o cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/utility/misc/Filesystem.cpp -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/utility/misc/IntegerSet.cpp -[ 18%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/SHA1.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/utility/misc/SHA1.cpp +[ 17%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/random_access_compressed_ifstream.cpp.o +[ 18%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/IntegerSet.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/utility/misc/Filesystem.cpp +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/utility/misc/random_access_compressed_ifstream.cpp +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/utility/misc/IntegerSet.cpp +[ 20%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/SHA1.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/utility/misc/SHA1.cpp In file included from /build/libpwizlite-3.0.4/src/pwiz/utility/misc/BinaryData.cpp:24: /build/libpwizlite-3.0.4/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 @@ -1456,6 +1497,78 @@ /build/libpwizlite-3.0.4/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 /build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.cpp:28: +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] + 585 | virtual Status processingInstruction(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:586:61: warning: unused parameter 'data' [-Wunused-parameter] + 586 | const std::string& data, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:587:56: warning: unused parameter 'position' [-Wunused-parameter] + 587 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:589:52: warning: unused parameter 'name' [-Wunused-parameter] + 589 | virtual Status startElement(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:590:51: warning: unused parameter 'attributes' [-Wunused-parameter] + 590 | const Attributes& attributes, + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:591:47: warning: unused parameter 'position' [-Wunused-parameter] + 591 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:593:50: warning: unused parameter 'name' [-Wunused-parameter] + 593 | virtual Status endElement(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:594:45: warning: unused parameter 'position' [-Wunused-parameter] + 594 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:596:59: warning: unused parameter 'text' [-Wunused-parameter] + 596 | virtual Status characters(const SAXParser::saxstring& text, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] + 597 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +[ 21%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/SHA1Calculator.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/utility/misc/SHA1Calculator.cpp +In file included from /build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.cpp:28: +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] + 585 | virtual Status processingInstruction(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:586:61: warning: unused parameter 'data' [-Wunused-parameter] + 586 | const std::string& data, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:587:56: warning: unused parameter 'position' [-Wunused-parameter] + 587 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:589:52: warning: unused parameter 'name' [-Wunused-parameter] + 589 | virtual Status startElement(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:590:51: warning: unused parameter 'attributes' [-Wunused-parameter] + 590 | const Attributes& attributes, + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:591:47: warning: unused parameter 'position' [-Wunused-parameter] + 591 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:593:50: warning: unused parameter 'name' [-Wunused-parameter] + 593 | virtual Status endElement(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:594:45: warning: unused parameter 'position' [-Wunused-parameter] + 594 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:596:59: warning: unused parameter 'text' [-Wunused-parameter] + 596 | virtual Status characters(const SAXParser::saxstring& text, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] + 597 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ /build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/misc/BinaryData.cpp:470:30: required from here /build/libpwizlite-3.0.4/src/pwiz/utility/misc/BinaryData.hpp:256:19: warning: comparison of unsigned expression in '< 0' is always false [-Wtype-limits] @@ -1594,102 +1707,24 @@ /build/libpwizlite-3.0.4/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 /build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.cpp:28: -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] - 585 | virtual Status processingInstruction(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:586:61: warning: unused parameter 'data' [-Wunused-parameter] - 586 | const std::string& data, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:587:56: warning: unused parameter 'position' [-Wunused-parameter] - 587 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:589:52: warning: unused parameter 'name' [-Wunused-parameter] - 589 | virtual Status startElement(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:590:51: warning: unused parameter 'attributes' [-Wunused-parameter] - 590 | const Attributes& attributes, - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:591:47: warning: unused parameter 'position' [-Wunused-parameter] - 591 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:593:50: warning: unused parameter 'name' [-Wunused-parameter] - 593 | virtual Status endElement(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:594:45: warning: unused parameter 'position' [-Wunused-parameter] - 594 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:596:59: warning: unused parameter 'text' [-Wunused-parameter] - 596 | virtual Status characters(const SAXParser::saxstring& text, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] - 597 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/misc/IntegerSet.cpp: In member function 'bool pwiz::util::IntegerSet::Iterator::operator==(const pwiz::util::IntegerSet::Iterator&) const': -/build/libpwizlite-3.0.4/src/pwiz/utility/misc/IntegerSet.cpp:307:63: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 307 | return (it_!=end_ && that.it_!=that.end_ && it_==that.it_ && value_==that.value_ || - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -[ 20%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/SHA1Calculator.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/utility/misc/SHA1Calculator.cpp In file included from /build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.cpp:27: /build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': /build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/misc/IntegerSet.cpp: In member function 'bool pwiz::util::IntegerSet::Iterator::operator==(const pwiz::util::IntegerSet::Iterator&) const': +/build/libpwizlite-3.0.4/src/pwiz/utility/misc/IntegerSet.cpp:307:63: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 307 | return (it_!=end_ && that.it_!=that.end_ && it_==that.it_ && value_==that.value_ || + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +[ 22%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/IntegerSet.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/utility/misc/IntegerSet.cpp In file included from /build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.cpp:27: /build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': /build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -[ 21%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/String.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/utility/misc/String.cpp -In file included from /build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.cpp:28: -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] - 585 | virtual Status processingInstruction(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:586:61: warning: unused parameter 'data' [-Wunused-parameter] - 586 | const std::string& data, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:587:56: warning: unused parameter 'position' [-Wunused-parameter] - 587 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:589:52: warning: unused parameter 'name' [-Wunused-parameter] - 589 | virtual Status startElement(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:590:51: warning: unused parameter 'attributes' [-Wunused-parameter] - 590 | const Attributes& attributes, - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:591:47: warning: unused parameter 'position' [-Wunused-parameter] - 591 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:593:50: warning: unused parameter 'name' [-Wunused-parameter] - 593 | virtual Status endElement(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:594:45: warning: unused parameter 'position' [-Wunused-parameter] - 594 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:596:59: warning: unused parameter 'text' [-Wunused-parameter] - 596 | virtual Status characters(const SAXParser::saxstring& text, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] - 597 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -[ 22%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_MGF.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_MGF.cpp -[ 23%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSNumpress.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSNumpress.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSNumpress.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSNumpress.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSNumpress.cpp -[ 25%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_MSn.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_MSn.cpp -[ 26%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/Filesystem.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/utility/misc/Filesystem.cpp +[ 23%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/String.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/utility/misc/String.cpp /build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/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) { @@ -1698,10 +1733,10 @@ /build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/MSNumpress.cpp: In function 'void pwiz::msdata::MSNumpress::encodeInt(int, unsigned char*, size_t*)': -/build/libpwizlite-3.0.4/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) { - | ~~~~~^~~~~~~ +[ 25%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/SHA1.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/utility/misc/SHA1.cpp +[ 26%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_MGF.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_MGF.cpp /build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/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) { @@ -1710,6 +1745,22 @@ /build/libpwizlite-3.0.4/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) { | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 27%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSNumpress.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSNumpress.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSNumpress.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSNumpress.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSNumpress.cpp +[ 28%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_MSn.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_MSn.cpp +[ 30%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumInfo.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumInfo.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumInfo.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumInfo.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumInfo.cpp +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSNumpress.cpp: In function 'void pwiz::msdata::MSNumpress::encodeInt(int, unsigned char*, size_t*)': +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/misc/IntegerSet.cpp: In member function 'bool pwiz::util::IntegerSet::Iterator::operator==(const pwiz::util::IntegerSet::Iterator&) const': +/build/libpwizlite-3.0.4/src/pwiz/utility/misc/IntegerSet.cpp:307:63: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 307 | return (it_!=end_ && that.it_!=that.end_ && it_==that.it_ && value_==that.value_ || + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +[ 31%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/SHA1Calculator.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/utility/misc/SHA1Calculator.cpp In file included from /usr/include/c++/12/iostream:39, from /build/libpwizlite-3.0.4/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]', @@ -1730,11 +1781,13 @@ /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSNumpress.cpp:346:15: note: 'extrapol' was declared here 346 | long long extrapol; | ^~~~~~~~ -[ 27%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumInfo.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumInfo.cpp +[ 32%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/String.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/utility/misc/String.cpp +[ 33%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/IO.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/IO.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/IO.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/IO.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/msdata/IO.cpp In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_MSn.hpp:26, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_MSn.cpp:25: + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumInfo.hpp:29, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumInfo.cpp:27: /build/libpwizlite-3.0.4/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 | ^~~~~~~~ @@ -1750,15 +1803,9 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 28%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/IntegerSet.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/utility/misc/IntegerSet.cpp -[ 30%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/IO.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/IO.cpp -[ 31%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_BTDX.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_BTDX.cpp In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumInfo.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumInfo.cpp:27: + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_MSn.hpp:26, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_MSn.cpp:25: /build/libpwizlite-3.0.4/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 | ^~~~~~~~ @@ -1774,11 +1821,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_MSn.hpp:28: -/build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] - 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +[ 35%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_MGF.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_MGF.cpp In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_MGF.hpp:27, from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_MGF.cpp:25: @@ -1797,10 +1841,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/libpwizlite-3.0.4/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) const': -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_MSn.cpp:524:10: warning: unused parameter 'useWorkerThreads' [-Wunused-parameter] - 524 | bool useWorkerThreads) const - | ~~~~~^~~~~~~~~~~~~~~~ /build/libpwizlite-3.0.4/src/pwiz/utility/misc/Filesystem.cpp: In function 'void pwiz::util::force_close_handles_to_filepath(const std::string&, bool)': /build/libpwizlite-3.0.4/src/pwiz/utility/misc/Filesystem.cpp:256:71: warning: unused parameter 'filepath' [-Wunused-parameter] 256 | PWIZ_API_DECL void force_close_handles_to_filepath(const std::string& filepath, bool closeMemoryMappedSections) noexcept(true) @@ -1812,7 +1852,27 @@ /build/libpwizlite-3.0.4/src/pwiz/utility/misc/Filesystem.cpp:719:52: warning: unused parameter 'path' [-Wunused-parameter] 719 | PWIZ_API_DECL void check_path_length(const string& path) | ~~~~~~~~~~~~~~^~~~ -[ 32%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/SHA1.cpp.o +/build/libpwizlite-3.0.4/src/pwiz/utility/misc/Filesystem.cpp: In function 'void pwiz::util::force_close_handles_to_filepath(const std::string&, bool)': +/build/libpwizlite-3.0.4/src/pwiz/utility/misc/Filesystem.cpp:256:71: warning: unused parameter 'filepath' [-Wunused-parameter] + 256 | PWIZ_API_DECL void force_close_handles_to_filepath(const std::string& filepath, bool closeMemoryMappedSections) noexcept(true) + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/misc/Filesystem.cpp:256:86: warning: unused parameter 'closeMemoryMappedSections' [-Wunused-parameter] + 256 | PWIZ_API_DECL void force_close_handles_to_filepath(const std::string& filepath, bool closeMemoryMappedSections) noexcept(true) + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/misc/Filesystem.cpp: In function 'void pwiz::util::check_path_length(const std::string&)': +/build/libpwizlite-3.0.4/src/pwiz/utility/misc/Filesystem.cpp:719:52: warning: unused parameter 'path' [-Wunused-parameter] + 719 | PWIZ_API_DECL void check_path_length(const string& path) + | ~~~~~~~~~~~~~~^~~~ +In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_MGF.hpp:29: +/build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_MSn.hpp:28: +/build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/IO.hpp:29, from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/IO.cpp:26: @@ -1831,41 +1891,20 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/utility/misc/SHA1.cpp -In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumListBase.hpp:28, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_BTDX.hpp:30, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:26: -/build/libpwizlite-3.0.4/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++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/algorithm:60, - from /build/libpwizlite-3.0.4/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/libpwizlite-3.0.4/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++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_MGF.hpp:29: -/build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/misc/IntegerSet.cpp: In member function 'bool pwiz::util::IntegerSet::Iterator::operator==(const pwiz::util::IntegerSet::Iterator&) const': -/build/libpwizlite-3.0.4/src/pwiz/utility/misc/IntegerSet.cpp:307:63: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 307 | return (it_!=end_ && that.it_!=that.end_ && it_==that.it_ && value_==that.value_ || - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -[ 33%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/ChromatogramList_mzML.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/ChromatogramList_mzML.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/ChromatogramList_mzML.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/ChromatogramList_mzML.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/msdata/ChromatogramList_mzML.cpp -[ 35%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/SHA1Calculator.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/utility/misc/SHA1Calculator.cpp -[ 36%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/String.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/utility/misc/String.cpp +[ 36%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSNumpress.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSNumpress.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSNumpress.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSNumpress.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSNumpress.cpp +[ 37%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_BTDX.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_BTDX.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_BTDX.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_BTDX.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_BTDX.cpp +/build/libpwizlite-3.0.4/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) const': +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_MSn.cpp:524:10: warning: unused parameter 'useWorkerThreads' [-Wunused-parameter] + 524 | bool useWorkerThreads) const + | ~~~~~^~~~~~~~~~~~~~~~ +[ 38%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_MSn.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_MSn.cpp +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSNumpress.cpp: In function 'void pwiz::msdata::MSNumpress::encodeInt(int, unsigned char*, size_t*)': +/build/libpwizlite-3.0.4/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 /build/libpwizlite-3.0.4/src/pwiz/data/msdata/IO.hpp:32: /build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': /build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] @@ -1906,64 +1945,30 @@ /build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:28: -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] - 585 | virtual Status processingInstruction(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:586:61: warning: unused parameter 'data' [-Wunused-parameter] - 586 | const std::string& data, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:587:56: warning: unused parameter 'position' [-Wunused-parameter] - 587 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:589:52: warning: unused parameter 'name' [-Wunused-parameter] - 589 | virtual Status startElement(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:590:51: warning: unused parameter 'attributes' [-Wunused-parameter] - 590 | const Attributes& attributes, - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:591:47: warning: unused parameter 'position' [-Wunused-parameter] - 591 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:593:50: warning: unused parameter 'name' [-Wunused-parameter] - 593 | virtual Status endElement(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:594:45: warning: unused parameter 'position' [-Wunused-parameter] - 594 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:596:59: warning: unused parameter 'text' [-Wunused-parameter] - 596 | virtual Status characters(const SAXParser::saxstring& text, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/ChromatogramListBase.hpp:28, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/ChromatogramList_mzML.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/ChromatogramList_mzML.cpp:26: -/build/libpwizlite-3.0.4/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++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/algorithm:60, - from /build/libpwizlite-3.0.4/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/libpwizlite-3.0.4/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++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 37%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_mzML.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzML.cpp -[ 38%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_MGF.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_MGF.cpp +In file included from /usr/include/c++/12/iostream:39, + from /build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/MSNumpress.cpp:404:26: +/usr/include/c++/12/ostream:202:25: warning: 'y' may be used uninitialized [-Wmaybe-uninitialized] + 202 | { return _M_insert(__n); } + | ~~~~~~~~~^~~~~ +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSNumpress.cpp: In function 'size_t pwiz::msdata::MSNumpress::decodeLinear(const unsigned char*, size_t, double*)': +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSNumpress.cpp:347:15: note: 'y' was declared here + 347 | long long y; + | ^ +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/libpwizlite-3.0.4/src/pwiz/data/msdata/MSNumpress.cpp:403:33: +/usr/include/c++/12/ostream:202:25: warning: 'extrapol' may be used uninitialized [-Wmaybe-uninitialized] + 202 | { return _M_insert(__n); } + | ~~~~~~~~~^~~~~ +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSNumpress.cpp: In function 'size_t pwiz::msdata::MSNumpress::decodeLinear(const unsigned char*, size_t, double*)': +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSNumpress.cpp:346:15: note: 'extrapol' was declared here + 346 | long long extrapol; + | ^~~~~~~~ +[ 40%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/ChromatogramList_mzML.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/ChromatogramList_mzML.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/ChromatogramList_mzML.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/ChromatogramList_mzML.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/msdata/ChromatogramList_mzML.cpp +[ 41%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumInfo.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumInfo.cpp /build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/IO.cpp:81:47: warning: unused parameter 'position' [-Wunused-parameter] 81 | stream_offset position) @@ -2016,8 +2021,6 @@ /build/libpwizlite-3.0.4/src/pwiz/data/msdata/IO.cpp:1660:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 1660 | bool zlib = false; // Handle numpress+zlib | ^~~~ -[ 40%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Version.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/Version.cpp /build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/IO.cpp:2169:35: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 2169 | else if (version == 1 && name == "acquisitionList" /* mzML 1.0 */ || name == "scanList") @@ -2037,80 +2040,9 @@ /build/libpwizlite-3.0.4/src/pwiz/data/msdata/IO.cpp:2787:47: warning: unused parameter 'position' [-Wunused-parameter] 2787 | stream_offset position) | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:121:47: warning: unused parameter 'position' [-Wunused-parameter] - 121 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:162:45: warning: unused parameter 'position' [-Wunused-parameter] - 162 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:356:45: warning: unused parameter 'position' [-Wunused-parameter] - 356 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/IO.hpp:32, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/ChromatogramList_mzML.cpp:27: -/build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/ChromatogramList_mzML.cpp:29: -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] - 585 | virtual Status processingInstruction(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:586:61: warning: unused parameter 'data' [-Wunused-parameter] - 586 | const std::string& data, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:587:56: warning: unused parameter 'position' [-Wunused-parameter] - 587 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:589:52: warning: unused parameter 'name' [-Wunused-parameter] - 589 | virtual Status startElement(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:590:51: warning: unused parameter 'attributes' [-Wunused-parameter] - 590 | const Attributes& attributes, - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:591:47: warning: unused parameter 'position' [-Wunused-parameter] - 591 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:593:50: warning: unused parameter 'name' [-Wunused-parameter] - 593 | virtual Status endElement(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:594:45: warning: unused parameter 'position' [-Wunused-parameter] - 594 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:596:59: warning: unused parameter 'text' [-Wunused-parameter] - 596 | virtual Status characters(const SAXParser::saxstring& text, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] - 597 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -[ 41%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSNumpress.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSNumpress.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSNumpress.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSNumpress.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSNumpress.cpp -/build/libpwizlite-3.0.4/src/pwiz/utility/misc/Filesystem.cpp: In function 'void pwiz::util::force_close_handles_to_filepath(const std::string&, bool)': -/build/libpwizlite-3.0.4/src/pwiz/utility/misc/Filesystem.cpp:256:71: warning: unused parameter 'filepath' [-Wunused-parameter] - 256 | PWIZ_API_DECL void force_close_handles_to_filepath(const std::string& filepath, bool closeMemoryMappedSections) noexcept(true) - | ~~~~~~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/misc/Filesystem.cpp:256:86: warning: unused parameter 'closeMemoryMappedSections' [-Wunused-parameter] - 256 | PWIZ_API_DECL void force_close_handles_to_filepath(const std::string& filepath, bool closeMemoryMappedSections) noexcept(true) - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/misc/Filesystem.cpp: In function 'void pwiz::util::check_path_length(const std::string&)': -/build/libpwizlite-3.0.4/src/pwiz/utility/misc/Filesystem.cpp:719:52: warning: unused parameter 'path' [-Wunused-parameter] - 719 | PWIZ_API_DECL void check_path_length(const string& path) - | ~~~~~~~~~~~~~~^~~~ -[ 42%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSDataFile.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/MSDataFile.cpp -[ 43%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumListBase.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumListBase.cpp In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumListBase.hpp:28, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzML.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzML.cpp:26: + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_MGF.hpp:27, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_MGF.cpp:25: /build/libpwizlite-3.0.4/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 | ^~~~~~~~ @@ -2126,92 +2058,13 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSNumpress.cpp: In function 'void pwiz::msdata::MSNumpress::encodeInt(int, unsigned char*, size_t*)': -/build/libpwizlite-3.0.4/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) { - | ~~~~~^~~~~~~ -[ 45%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_MSn.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_MSn.cpp -In file included from /usr/include/c++/12/iostream:39, - from /build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/MSNumpress.cpp:404:26: -/usr/include/c++/12/ostream:202:25: warning: 'y' may be used uninitialized [-Wmaybe-uninitialized] - 202 | { return _M_insert(__n); } - | ~~~~~~~~~^~~~~ -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSNumpress.cpp: In function 'size_t pwiz::msdata::MSNumpress::decodeLinear(const unsigned char*, size_t, double*)': -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSNumpress.cpp:347:15: note: 'y' was declared here - 347 | long long y; - | ^ -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/libpwizlite-3.0.4/src/pwiz/data/msdata/MSNumpress.cpp:403:33: -/usr/include/c++/12/ostream:202:25: warning: 'extrapol' may be used uninitialized [-Wmaybe-uninitialized] - 202 | { return _M_insert(__n); } - | ~~~~~~~~~^~~~~ -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSNumpress.cpp: In function 'size_t pwiz::msdata::MSNumpress::decodeLinear(const unsigned char*, size_t, double*)': -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSNumpress.cpp:346:15: note: 'extrapol' was declared here - 346 | long long extrapol; - | ^~~~~~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.cpp: In function 'void pwiz::minimxml::SAXParser::parse(std::istream&, Handler&)': -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.cpp:549:17: warning: 'inCDATA' may be used uninitialized [-Wmaybe-uninitialized] - 549 | if (inCDATA) - | ^~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.cpp:501:14: note: 'inCDATA' was declared here - 501 | bool inCDATA; - | ^~~~~~~ -[ 46%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumInfo.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumInfo.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumInfo.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumInfo.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumInfo.cpp -[ 47%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/BinaryDataEncoder.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/BinaryDataEncoder.cpp -In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/IO.hpp:32, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzML.cpp:27: -/build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzML.cpp:29: -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] - 585 | virtual Status processingInstruction(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:586:61: warning: unused parameter 'data' [-Wunused-parameter] - 586 | const std::string& data, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:587:56: warning: unused parameter 'position' [-Wunused-parameter] - 587 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:589:52: warning: unused parameter 'name' [-Wunused-parameter] - 589 | virtual Status startElement(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:590:51: warning: unused parameter 'attributes' [-Wunused-parameter] - 590 | const Attributes& attributes, - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:591:47: warning: unused parameter 'position' [-Wunused-parameter] - 591 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:593:50: warning: unused parameter 'name' [-Wunused-parameter] - 593 | virtual Status endElement(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -[ 48%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_mzXML.cpp.o -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:594:45: warning: unused parameter 'position' [-Wunused-parameter] - 594 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:596:59: warning: unused parameter 'text' [-Wunused-parameter] - 596 | virtual Status characters(const SAXParser::saxstring& text, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] - 597 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.cpp +[ 42%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/IO.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/IO.cpp +[ 43%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_mzML.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_mzML.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_mzML.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_mzML.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzML.cpp In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_MGF.hpp:27, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_MGF.cpp:25: + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_MSn.hpp:26, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_MSn.cpp:25: /build/libpwizlite-3.0.4/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 | ^~~~~~~~ @@ -2228,8 +2081,9 @@ 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSDataFile.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSDataFile.cpp:26: + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumListBase.hpp:28, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_BTDX.hpp:30, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:26: /build/libpwizlite-3.0.4/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 | ^~~~~~~~ @@ -2245,9 +2099,14 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_MGF.hpp:29: +/build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumListBase.hpp:28, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumListBase.cpp:25: + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumInfo.hpp:29, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumInfo.cpp:27: /build/libpwizlite-3.0.4/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 | ^~~~~~~~ @@ -2263,36 +2122,12 @@ /usr/include/c++/12/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/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /build/libpwizlite-3.0.4/src/pwiz/data/common/ParamTypes.hpp:33, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/bind.hpp: At global scope: -/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.cpp: In function 'void pwiz::minimxml::SAXParser::parse(std::istream&, Handler&)': -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.cpp:549:17: warning: 'inCDATA' may be used uninitialized [-Wmaybe-uninitialized] - 549 | if (inCDATA) - | ^~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.cpp:501:14: note: 'inCDATA' was declared here - 501 | bool inCDATA; - | ^~~~~~~ -In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_MGF.hpp:29: -/build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/BinaryDataEncoder.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/BinaryDataEncoder.cpp:26: +[ 45%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Version.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Version.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Version.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Version.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Version.cpp +In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/ChromatogramListBase.hpp:28, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/ChromatogramList_mzML.hpp:29, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/ChromatogramList_mzML.cpp:26: /build/libpwizlite-3.0.4/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 | ^~~~~~~~ @@ -2308,20 +2143,30 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Reader.hpp:28, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSDataFile.hpp:30: +[ 46%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSDataFile.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/MSDataFile.cpp +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.cpp: In function 'void pwiz::minimxml::SAXParser::parse(std::istream&, Handler&)': +/build/libpwizlite-3.0.4/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); + | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_MSn.hpp:28: /build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': /build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/Reader.hpp:29: -/build/libpwizlite-3.0.4/src/pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const': -/build/libpwizlite-3.0.4/src/pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.cpp:549:17: warning: 'inCDATA' may be used uninitialized [-Wmaybe-uninitialized] + 549 | if (inCDATA) + | ^~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.cpp:501:14: note: 'inCDATA' was declared here + 501 | bool inCDATA; + | ^~~~~~~ +[ 47%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_BTDX.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_BTDX.cpp +[ 48%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumListBase.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumListBase.cpp In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_MSn.hpp:26, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_MSn.cpp:25: + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/IO.hpp:29, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/IO.cpp:26: /build/libpwizlite-3.0.4/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 | ^~~~~~~~ @@ -2337,9 +2182,51 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 50%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/BinaryDataEncoder.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/BinaryDataEncoder.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/BinaryDataEncoder.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/BinaryDataEncoder.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/msdata/BinaryDataEncoder.cpp +/build/libpwizlite-3.0.4/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) const': +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_MSn.cpp:524:10: warning: unused parameter 'useWorkerThreads' [-Wunused-parameter] + 524 | bool useWorkerThreads) const + | ~~~~~^~~~~~~~~~~~~~~~ +In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:28: +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] + 585 | virtual Status processingInstruction(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:586:61: warning: unused parameter 'data' [-Wunused-parameter] + 586 | const std::string& data, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:587:56: warning: unused parameter 'position' [-Wunused-parameter] + 587 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:589:52: warning: unused parameter 'name' [-Wunused-parameter] + 589 | virtual Status startElement(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:590:51: warning: unused parameter 'attributes' [-Wunused-parameter] + 590 | const Attributes& attributes, + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:591:47: warning: unused parameter 'position' [-Wunused-parameter] + 591 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:593:50: warning: unused parameter 'name' [-Wunused-parameter] + 593 | virtual Status endElement(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:594:45: warning: unused parameter 'position' [-Wunused-parameter] + 594 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:596:59: warning: unused parameter 'text' [-Wunused-parameter] + 596 | virtual Status characters(const SAXParser::saxstring& text, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumInfo.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumInfo.cpp:27: + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumListBase.hpp:28, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzML.hpp:29, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzML.cpp:26: /build/libpwizlite-3.0.4/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 | ^~~~~~~~ @@ -2355,22 +2242,60 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSDataFile.cpp:35: -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/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/libpwizlite-3.0.4/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 ""; } - | ~~~~~~~~~~~~~~~~~~~^~~~ -[ 50%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSData.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp -[ 51%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/IO.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/IO.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/IO.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/IO.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/msdata/IO.cpp +In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/IO.hpp:32, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/ChromatogramList_mzML.cpp:27: +/build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/ChromatogramList_mzML.cpp:29: +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] + 585 | virtual Status processingInstruction(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:586:61: warning: unused parameter 'data' [-Wunused-parameter] + 586 | const std::string& data, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:587:56: warning: unused parameter 'position' [-Wunused-parameter] + 587 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:589:52: warning: unused parameter 'name' [-Wunused-parameter] + 589 | virtual Status startElement(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:590:51: warning: unused parameter 'attributes' [-Wunused-parameter] + 590 | const Attributes& attributes, + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:591:47: warning: unused parameter 'position' [-Wunused-parameter] + 591 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:593:50: warning: unused parameter 'name' [-Wunused-parameter] + 593 | virtual Status endElement(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:594:45: warning: unused parameter 'position' [-Wunused-parameter] + 594 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:596:59: warning: unused parameter 'text' [-Wunused-parameter] + 596 | virtual Status characters(const SAXParser::saxstring& text, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] + 597 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.cpp: In function 'void pwiz::minimxml::SAXParser::parse(std::istream&, Handler&)': +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.cpp:549:17: warning: 'inCDATA' may be used uninitialized [-Wmaybe-uninitialized] + 549 | if (inCDATA) + | ^~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.cpp:501:14: note: 'inCDATA' was declared here + 501 | bool inCDATA; + | ^~~~~~~ In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumListBase.hpp:28, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:25: + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSDataFile.hpp:29, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSDataFile.cpp:26: /build/libpwizlite-3.0.4/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 | ^~~~~~~~ @@ -2386,13 +2311,10 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_MSn.hpp:28: -/build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp:25: + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumListBase.hpp:28, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_BTDX.hpp:30, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:26: /build/libpwizlite-3.0.4/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 | ^~~~~~~~ @@ -2408,13 +2330,24 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/IO.hpp:32, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:26: +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:121:47: warning: unused parameter 'position' [-Wunused-parameter] + 121 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:162:45: warning: unused parameter 'position' [-Wunused-parameter] + 162 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:356:45: warning: unused parameter 'position' [-Wunused-parameter] + 356 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/IO.hpp:32: /build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': /build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:28: +In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/IO.cpp:28: /build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] 585 | virtual Status processingInstruction(const std::string& name, @@ -2449,15 +2382,9 @@ /build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] 597 | stream_offset position) {return Status::Ok;} | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/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) const': -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_MSn.cpp:524:10: warning: unused parameter 'useWorkerThreads' [-Wunused-parameter] - 524 | bool useWorkerThreads) const - | ~~~~~^~~~~~~~~~~~~~~~ -[ 52%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/LegacyAdapter.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/LegacyAdapter.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/LegacyAdapter.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/LegacyAdapter.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/msdata/LegacyAdapter.cpp In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/IO.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/IO.cpp:26: + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumListBase.hpp:28, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumListBase.cpp:25: /build/libpwizlite-3.0.4/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 | ^~~~~~~~ @@ -2473,79 +2400,13 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/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/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:128:47: warning: unused parameter 'position' [-Wunused-parameter] - 128 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:212:45: warning: unused parameter 'position' [-Wunused-parameter] - 212 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:239:47: warning: unused parameter 'position' [-Wunused-parameter] - 239 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:282:45: warning: unused parameter 'position' [-Wunused-parameter] - 282 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/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/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:701:51: warning: unused parameter 'attributes' [-Wunused-parameter] - 701 | const Attributes& attributes, - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:702:47: warning: unused parameter 'position' [-Wunused-parameter] - 702 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:710:45: warning: unused parameter 'position' [-Wunused-parameter] - 710 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:736:47: warning: unused parameter 'position' [-Wunused-parameter] - 736 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:754:45: warning: unused parameter 'position' [-Wunused-parameter] - 754 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:778:51: warning: unused parameter 'attributes' [-Wunused-parameter] - 778 | const Attributes& attributes, - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:779:47: warning: unused parameter 'position' [-Wunused-parameter] - 779 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:796:59: warning: unused parameter 'text' [-Wunused-parameter] - 796 | virtual Status characters(const SAXParser::saxstring& text, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:797:45: warning: unused parameter 'position' [-Wunused-parameter] - 797 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:885:45: warning: unused parameter 'position' [-Wunused-parameter] - 885 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -[ 53%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_BTDX.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_BTDX.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_BTDX.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_BTDX.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_BTDX.cpp -[ 55%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Reader.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/Reader.cpp -In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/IO.hpp:32: +In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/IO.hpp:32, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzML.cpp:27: /build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': /build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -[ 56%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_MSn.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_MSn.cpp -In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/IO.cpp:28: +In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzML.cpp:29: /build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] 585 | virtual Status processingInstruction(const std::string& name, @@ -2580,9 +2441,25 @@ /build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/LegacyAdapter.hpp:30, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/LegacyAdapter.cpp:27: +In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Reader.hpp:28, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSDataFile.hpp:30: +/build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/Reader.hpp:29: +/build/libpwizlite-3.0.4/src/pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const': +/build/libpwizlite-3.0.4/src/pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 51%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSData.cpp.o +[ 52%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_mzXML.cpp.o +[ 53%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/LegacyAdapter.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_mzXML.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_mzXML.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_mzXML.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.cpp +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/LegacyAdapter.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/LegacyAdapter.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/LegacyAdapter.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/msdata/LegacyAdapter.cpp +In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/BinaryDataEncoder.hpp:29, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/BinaryDataEncoder.cpp:26: /build/libpwizlite-3.0.4/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 | ^~~~~~~~ @@ -2598,22 +2475,27 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual size_t pwiz::msdata::SpectrumList::findAbbreviated(const std::string&, char) const': -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp:1112:21: warning: comparison of unsigned expression in '>= 0' is always true [-Wtype-limits] - 1112 | if ((result >= 0 && result < size()) || s == 0) - | ~~~~~~~^~~~ -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual void pwiz::msdata::SpectrumList::warn_once(const char*) const': -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp:1160:56: warning: unused parameter 'msg' [-Wunused-parameter] - 1160 | PWIZ_API_DECL void SpectrumList::warn_once(const char *msg) const - | ~~~~~~~~~~~~^~~ -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual pwiz::msdata::SpectrumPtr pwiz::msdata::SpectrumListSimple::spectrum(size_t, bool) const': -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp:1204:75: warning: unused parameter 'getBinaryData' [-Wunused-parameter] - 1204 | PWIZ_API_DECL SpectrumPtr SpectrumListSimple::spectrum(size_t index, bool getBinaryData) const - | ~~~~~^~~~~~~~~~~~~ -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual pwiz::msdata::ChromatogramPtr pwiz::msdata::ChromatogramListSimple::chromatogram(size_t, bool) const': -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp:1271:87: warning: unused parameter 'getBinaryData' [-Wunused-parameter] - 1271 | PWIZ_API_DECL ChromatogramPtr ChromatogramListSimple::chromatogram(size_t index, bool getBinaryData) const - | ~~~~~^~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /build/libpwizlite-3.0.4/src/pwiz/data/common/ParamTypes.hpp:33, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/bind.hpp: At global scope: +/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( + | ^~~~~~~~~~~~~~~~~~~~ +In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSDataFile.cpp:35: +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/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/libpwizlite-3.0.4/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/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/IO.cpp:81:47: warning: unused parameter 'position' [-Wunused-parameter] 81 | stream_offset position) @@ -2644,44 +2526,10 @@ /build/libpwizlite-3.0.4/src/pwiz/data/msdata/IO.cpp:694:47: warning: unused parameter 'position' [-Wunused-parameter] 694 | stream_offset position) | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/BinaryDataEncoder.cpp: In member function 'void pwiz::msdata::BinaryDataEncoder::Impl::encode(const double*, size_t, std::string&, size_t*)': -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/BinaryDataEncoder.cpp:302:37: warning: 'byteCount' may be used uninitialized [-Wmaybe-uninitialized] - 302 | filterArray(byteBuffer, byteCount,compressed); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/BinaryDataEncoder.cpp:131:12: note: 'byteCount' was declared here - 131 | size_t byteCount; - | ^~~~~~~~~ -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/BinaryDataEncoder.cpp:302:37: warning: 'byteBuffer' may be used uninitialized [-Wmaybe-uninitialized] - 302 | filterArray(byteBuffer, byteCount,compressed); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/BinaryDataEncoder.cpp:132:17: note: 'byteBuffer' was declared here - 132 | const void* byteBuffer; - | ^~~~~~~~~~ -[ 57%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/ChromatogramList_mzML.cpp.o -In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumListBase.hpp:28, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_BTDX.hpp:30, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:26: -/build/libpwizlite-3.0.4/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 - | ^~~~~~~~ -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/ChromatogramList_mzML.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/ChromatogramList_mzML.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/ChromatogramList_mzML.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/msdata/ChromatogramList_mzML.cpp /build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/IO.cpp:966:47: warning: unused parameter 'position' [-Wunused-parameter] 966 | stream_offset position) | ~~~~~~~~~~~~~~^~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/algorithm:60, - from /build/libpwizlite-3.0.4/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/libpwizlite-3.0.4/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++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ /build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/IO.cpp:1079:47: warning: unused parameter 'position' [-Wunused-parameter] 1079 | stream_offset position) @@ -2704,12 +2552,6 @@ /build/libpwizlite-3.0.4/src/pwiz/data/msdata/IO.cpp:2169:35: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 2169 | else if (version == 1 && name == "acquisitionList" /* mzML 1.0 */ || name == "scanList") | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Reader.hpp:28, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Reader.cpp:26: -/build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/IO.cpp:2438:47: warning: unused parameter 'position' [-Wunused-parameter] 2438 | stream_offset position) @@ -2722,29 +2564,54 @@ /build/libpwizlite-3.0.4/src/pwiz/data/msdata/IO.cpp:2869:31: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 2869 | else if (version == 1 && name == "acquisitionSettings" /* mzML 1.0 */ || | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 55%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/ChromatogramList_mzML.cpp.o /build/libpwizlite-3.0.4/src/pwiz/data/msdata/IO.cpp:2787:47: warning: unused parameter 'position' [-Wunused-parameter] 2787 | stream_offset position) | ~~~~~~~~~~~~~~^~~~~~~~ -In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Reader.hpp:29: -/build/libpwizlite-3.0.4/src/pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const': -/build/libpwizlite-3.0.4/src/pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 58%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_mzML.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_mzML.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_mzML.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_mzML.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzML.cpp +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/ChromatogramList_mzML.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/ChromatogramList_mzML.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/ChromatogramList_mzML.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/msdata/ChromatogramList_mzML.cpp +In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:28: +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] + 585 | virtual Status processingInstruction(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:586:61: warning: unused parameter 'data' [-Wunused-parameter] + 586 | const std::string& data, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:587:56: warning: unused parameter 'position' [-Wunused-parameter] + 587 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:589:52: warning: unused parameter 'name' [-Wunused-parameter] + 589 | virtual Status startElement(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:590:51: warning: unused parameter 'attributes' [-Wunused-parameter] + 590 | const Attributes& attributes, + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:591:47: warning: unused parameter 'position' [-Wunused-parameter] + 591 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:593:50: warning: unused parameter 'name' [-Wunused-parameter] + 593 | virtual Status endElement(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:594:45: warning: unused parameter 'position' [-Wunused-parameter] + 594 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:596:59: warning: unused parameter 'text' [-Wunused-parameter] + 596 | virtual Status characters(const SAXParser::saxstring& text, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Reader.hpp:30: -/build/libpwizlite-3.0.4/src/pwiz/utility/misc/BinaryData.hpp: At global scope: + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp:25: /build/libpwizlite-3.0.4/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++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/memory:63, - 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:17, - from /usr/include/boost/shared_ptr.hpp:17, - from /build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp:29: + from /usr/include/c++/12/algorithm:60, + from /build/libpwizlite-3.0.4/src/pwiz/utility/misc/BinaryData.hpp:29: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -2754,25 +2621,40 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp: In function 'std::string pwiz::msdata::id::translateNativeIDToScanNumber(pwiz::cv::CVID, const std::string&)': -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp:578:13: warning: this statement may fall through [-Wimplicit-fallthrough=] - 578 | if (id.find("controllerType=0 controllerNumber=1") != 0) - | ^~ -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp:583:9: note: here - 583 | case MS_Bruker_Agilent_YEP_nativeID_format: - | ^~~~ -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual size_t pwiz::msdata::SpectrumList::findAbbreviated(const std::string&, char) const': -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp:1115:1: warning: control reaches end of non-void function [-Wreturn-type] - 1115 | } - | ^ -[ 60%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Version.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Version.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Version.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Version.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Version.cpp -[ 61%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSDataFile.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/MSDataFile.cpp In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumListBase.hpp:28, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_MSn.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_MSn.cpp:26: + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.hpp:29, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:25: +/build/libpwizlite-3.0.4/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++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/algorithm:60, + from /build/libpwizlite-3.0.4/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/libpwizlite-3.0.4/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++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:121:47: warning: unused parameter 'position' [-Wunused-parameter] + 121 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:162:45: warning: unused parameter 'position' [-Wunused-parameter] + 162 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:356:45: warning: unused parameter 'position' [-Wunused-parameter] + 356 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/LegacyAdapter.hpp:30, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/LegacyAdapter.cpp:27: /build/libpwizlite-3.0.4/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 | ^~~~~~~~ @@ -2788,10 +2670,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 62%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_mzML.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzML.cpp -[ 63%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Index_mzML.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/Index_mzML.cpp In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/ChromatogramListBase.hpp:28, from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/ChromatogramList_mzML.hpp:29, @@ -2811,9 +2689,15 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 65%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumListBase.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumListBase.cpp -In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:28: +[ 56%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_mzML.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzML.cpp +In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/IO.hpp:32, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:26: +/build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:28: /build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] 585 | virtual Status processingInstruction(const std::string& name, @@ -2848,10 +2732,6 @@ /build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] 597 | stream_offset position) {return Status::Ok;} | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/Reader.cpp:76:119: warning: unused parameter 'config' [-Wunused-parameter] - 76 | PWIZ_API_DECL void Reader::readIds(const string& filename, const string& head, vector& results, const Config& config) const - | ~~~~~~~~~~~~~~^~~~~~ In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/IO.hpp:32, from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/ChromatogramList_mzML.cpp:27: /build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': @@ -2893,9 +2773,102 @@ /build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] 597 | stream_offset position) {return Status::Ok;} | ~~~~~~~~~~~~~~^~~~~~~~ +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual size_t pwiz::msdata::SpectrumList::findAbbreviated(const std::string&, char) const': +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp:1112:21: warning: comparison of unsigned expression in '>= 0' is always true [-Wtype-limits] + 1112 | if ((result >= 0 && result < size()) || s == 0) + | ~~~~~~~^~~~ +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual void pwiz::msdata::SpectrumList::warn_once(const char*) const': +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp:1160:56: warning: unused parameter 'msg' [-Wunused-parameter] + 1160 | PWIZ_API_DECL void SpectrumList::warn_once(const char *msg) const + | ~~~~~~~~~~~~^~~ +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual pwiz::msdata::SpectrumPtr pwiz::msdata::SpectrumListSimple::spectrum(size_t, bool) const': +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp:1204:75: warning: unused parameter 'getBinaryData' [-Wunused-parameter] + 1204 | PWIZ_API_DECL SpectrumPtr SpectrumListSimple::spectrum(size_t index, bool getBinaryData) const + | ~~~~~^~~~~~~~~~~~~ +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual pwiz::msdata::ChromatogramPtr pwiz::msdata::ChromatogramListSimple::chromatogram(size_t, bool) const': +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp:1271:87: warning: unused parameter 'getBinaryData' [-Wunused-parameter] + 1271 | PWIZ_API_DECL ChromatogramPtr ChromatogramListSimple::chromatogram(size_t index, bool getBinaryData) const + | ~~~~~^~~~~~~~~~~~~ +[ 57%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Reader.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/Reader.cpp +[ 58%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Version.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/Version.cpp +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/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/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:128:47: warning: unused parameter 'position' [-Wunused-parameter] + 128 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:212:45: warning: unused parameter 'position' [-Wunused-parameter] + 212 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:239:47: warning: unused parameter 'position' [-Wunused-parameter] + 239 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:282:45: warning: unused parameter 'position' [-Wunused-parameter] + 282 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/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/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:701:51: warning: unused parameter 'attributes' [-Wunused-parameter] + 701 | const Attributes& attributes, + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:702:47: warning: unused parameter 'position' [-Wunused-parameter] + 702 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:710:45: warning: unused parameter 'position' [-Wunused-parameter] + 710 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:736:47: warning: unused parameter 'position' [-Wunused-parameter] + 736 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:754:45: warning: unused parameter 'position' [-Wunused-parameter] + 754 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:778:51: warning: unused parameter 'attributes' [-Wunused-parameter] + 778 | const Attributes& attributes, + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:779:47: warning: unused parameter 'position' [-Wunused-parameter] + 779 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:796:59: warning: unused parameter 'text' [-Wunused-parameter] + 796 | virtual Status characters(const SAXParser::saxstring& text, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:797:45: warning: unused parameter 'position' [-Wunused-parameter] + 797 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:885:45: warning: unused parameter 'position' [-Wunused-parameter] + 885 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp: In function 'std::string pwiz::msdata::id::translateNativeIDToScanNumber(pwiz::cv::CVID, const std::string&)': +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp:578:13: warning: this statement may fall through [-Wimplicit-fallthrough=] + 578 | if (id.find("controllerType=0 controllerNumber=1") != 0) + | ^~ +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp:583:9: note: here + 583 | case MS_Bruker_Agilent_YEP_nativeID_format: + | ^~~~ +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual size_t pwiz::msdata::SpectrumList::findAbbreviated(const std::string&, char) const': +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp:1115:1: warning: control reaches end of non-void function [-Wreturn-type] + 1115 | } + | ^ In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzML.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzML.cpp:26: + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumListBase.hpp:28, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzML.hpp:29, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzML.cpp:26: /build/libpwizlite-3.0.4/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 | ^~~~~~~~ @@ -2911,10 +2884,117 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +[ 60%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSDataFile.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/MSDataFile.cpp +[ 61%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumListBase.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumListBase.cpp +[ 62%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_MSn.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_MSn.cpp +[ 63%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/BinaryDataEncoder.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/BinaryDataEncoder.cpp +In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Reader.hpp:28, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Reader.cpp:26: +/build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/Reader.hpp:29: +/build/libpwizlite-3.0.4/src/pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const': +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Reader.hpp:30: +/build/libpwizlite-3.0.4/src/pwiz/utility/misc/BinaryData.hpp: At global scope: +/build/libpwizlite-3.0.4/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++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/memory:63, + 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:17, + from /usr/include/boost/shared_ptr.hpp:17, + from /build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp:29: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/libpwizlite-3.0.4/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++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/IO.hpp:32, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzML.cpp:27: +/build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzML.cpp:29: +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] + 585 | virtual Status processingInstruction(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:586:61: warning: unused parameter 'data' [-Wunused-parameter] + 586 | const std::string& data, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:587:56: warning: unused parameter 'position' [-Wunused-parameter] + 587 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:589:52: warning: unused parameter 'name' [-Wunused-parameter] + 589 | virtual Status startElement(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:590:51: warning: unused parameter 'attributes' [-Wunused-parameter] + 590 | const Attributes& attributes, + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:591:47: warning: unused parameter 'position' [-Wunused-parameter] + 591 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:593:50: warning: unused parameter 'name' [-Wunused-parameter] + 593 | virtual Status endElement(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:594:45: warning: unused parameter 'position' [-Wunused-parameter] + 594 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:596:59: warning: unused parameter 'text' [-Wunused-parameter] + 596 | virtual Status characters(const SAXParser::saxstring& text, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] + 597 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/BinaryDataEncoder.cpp: In member function 'void pwiz::msdata::BinaryDataEncoder::Impl::encode(const double*, size_t, std::string&, size_t*)': +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/BinaryDataEncoder.cpp:302:37: warning: 'byteCount' may be used uninitialized [-Wmaybe-uninitialized] + 302 | filterArray(byteBuffer, byteCount,compressed); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/BinaryDataEncoder.cpp:131:12: note: 'byteCount' was declared here + 131 | size_t byteCount; + | ^~~~~~~~~ +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/BinaryDataEncoder.cpp:302:37: warning: 'byteBuffer' may be used uninitialized [-Wmaybe-uninitialized] + 302 | filterArray(byteBuffer, byteCount,compressed); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/BinaryDataEncoder.cpp:132:17: note: 'byteBuffer' was declared here + 132 | const void* byteBuffer; + | ^~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /build/libpwizlite-3.0.4/src/pwiz/data/common/ParamTypes.hpp:33, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:30: +/usr/include/boost/bind.hpp: At global scope: +/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( + | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumListBase.hpp:28, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzML.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzML.cpp:26: + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumListBase.cpp:25: /build/libpwizlite-3.0.4/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 | ^~~~~~~~ @@ -2948,21 +3028,16 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:121:47: warning: unused parameter 'position' [-Wunused-parameter] - 121 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:162:45: warning: unused parameter 'position' [-Wunused-parameter] - 162 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_BTDX.cpp:356:45: warning: unused parameter 'position' [-Wunused-parameter] - 356 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ +[ 65%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_mzML.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_mzML.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_mzML.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_mzML.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzML.cpp +[ 66%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Index_mzML.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Index_mzML.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Index_mzML.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Index_mzML.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Index_mzML.cpp +[ 67%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumWorkerThreads.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumWorkerThreads.cpp In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Index_mzML.hpp:28, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Index_mzML.cpp:24: + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumListBase.hpp:28, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_MSn.hpp:29, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_MSn.cpp:26: /build/libpwizlite-3.0.4/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 | ^~~~~~~~ @@ -2978,9 +3053,8 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumListBase.hpp:28, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumListBase.cpp:25: +In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/BinaryDataEncoder.hpp:29, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/BinaryDataEncoder.cpp:26: /build/libpwizlite-3.0.4/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 | ^~~~~~~~ @@ -2996,111 +3070,41 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzML.hpp:31: -/build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzML.cpp:32: -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] - 585 | virtual Status processingInstruction(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:586:61: warning: unused parameter 'data' [-Wunused-parameter] - 586 | const std::string& data, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:587:56: warning: unused parameter 'position' [-Wunused-parameter] - 587 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:589:52: warning: unused parameter 'name' [-Wunused-parameter] - 589 | virtual Status startElement(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:590:51: warning: unused parameter 'attributes' [-Wunused-parameter] - 590 | const Attributes& attributes, - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:591:47: warning: unused parameter 'position' [-Wunused-parameter] - 591 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:593:50: warning: unused parameter 'name' [-Wunused-parameter] - 593 | virtual Status endElement(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:594:45: warning: unused parameter 'position' [-Wunused-parameter] - 594 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:596:59: warning: unused parameter 'text' [-Wunused-parameter] - 596 | virtual Status characters(const SAXParser::saxstring& text, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] - 597 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzML.cpp:205:51: warning: unused parameter 'attributes' [-Wunused-parameter] - 205 | const Attributes& attributes, - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzML.cpp:206:47: warning: unused parameter 'position' [-Wunused-parameter] - 206 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/Reader.cpp:76:119: warning: unused parameter 'config' [-Wunused-parameter] + 76 | PWIZ_API_DECL void Reader::readIds(const string& filename, const string& head, vector& results, const Config& config) const + | ~~~~~~~~~~~~~~^~~~~~ +[ 68%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/References.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/References.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/References.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/References.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/msdata/References.cpp In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Reader.hpp:28, from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSDataFile.hpp:30: /build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': /build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -[ 66%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumWorkerThreads.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumWorkerThreads.cpp In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Reader.hpp:29: /build/libpwizlite-3.0.4/src/pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const': /build/libpwizlite-3.0.4/src/pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 67%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/BinaryDataEncoder.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/BinaryDataEncoder.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/BinaryDataEncoder.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/BinaryDataEncoder.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/msdata/BinaryDataEncoder.cpp -In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/IO.hpp:32, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzML.cpp:27: -/build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzML.cpp:29: -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] - 585 | virtual Status processingInstruction(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:586:61: warning: unused parameter 'data' [-Wunused-parameter] - 586 | const std::string& data, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:587:56: warning: unused parameter 'position' [-Wunused-parameter] - 587 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:589:52: warning: unused parameter 'name' [-Wunused-parameter] - 589 | virtual Status startElement(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:590:51: warning: unused parameter 'attributes' [-Wunused-parameter] - 590 | const Attributes& attributes, - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:591:47: warning: unused parameter 'position' [-Wunused-parameter] - 591 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:593:50: warning: unused parameter 'name' [-Wunused-parameter] - 593 | virtual Status endElement(const std::string& name, - | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:594:45: warning: unused parameter 'position' [-Wunused-parameter] - 594 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:596:59: warning: unused parameter 'text' [-Wunused-parameter] - 596 | virtual Status characters(const SAXParser::saxstring& text, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] - 597 | stream_offset position) {return Status::Ok;} - | ~~~~~~~~~~~~~~^~~~~~~~ -[ 68%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/References.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/References.cpp +In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Index_mzML.hpp:28, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Index_mzML.cpp:24: +/build/libpwizlite-3.0.4/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++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/algorithm:60, + from /build/libpwizlite-3.0.4/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/libpwizlite-3.0.4/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++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSDataFile.cpp:35: /build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/DefaultReaderList.hpp:98:53: warning: unused parameter 'filename' [-Wunused-parameter] @@ -3109,19 +3113,42 @@ /build/libpwizlite-3.0.4/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 /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /build/libpwizlite-3.0.4/src/pwiz/data/common/ParamTypes.hpp:33, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:30: -/usr/include/boost/bind.hpp: At global scope: -/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( - | ^~~~~~~~~~~~~~~~~~~~ +In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzML.hpp:29, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzML.cpp:26: +/build/libpwizlite-3.0.4/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++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/algorithm:60, + from /build/libpwizlite-3.0.4/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/libpwizlite-3.0.4/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++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/References.hpp:29, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/References.cpp:25: +/build/libpwizlite-3.0.4/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++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/algorithm:60, + from /build/libpwizlite-3.0.4/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/libpwizlite-3.0.4/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++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Index_mzML.cpp:26: /build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] @@ -3186,43 +3213,48 @@ /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Index_mzML.cpp:197:47: warning: unused parameter 'position' [-Wunused-parameter] 197 | stream_offset position) | ~~~~~~~~~~~~~~^~~~~~~~ -In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/References.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/References.cpp:25: -/build/libpwizlite-3.0.4/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++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/algorithm:60, - from /build/libpwizlite-3.0.4/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/libpwizlite-3.0.4/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++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/BinaryDataEncoder.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/BinaryDataEncoder.cpp:26: -/build/libpwizlite-3.0.4/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++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/algorithm:60, - from /build/libpwizlite-3.0.4/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/libpwizlite-3.0.4/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++/12/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/SpectrumList_MGF.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_MGF.cpp +In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzML.hpp:31: +/build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzML.cpp:32: +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] + 585 | virtual Status processingInstruction(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:586:61: warning: unused parameter 'data' [-Wunused-parameter] + 586 | const std::string& data, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:587:56: warning: unused parameter 'position' [-Wunused-parameter] + 587 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:589:52: warning: unused parameter 'name' [-Wunused-parameter] + 589 | virtual Status startElement(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:590:51: warning: unused parameter 'attributes' [-Wunused-parameter] + 590 | const Attributes& attributes, + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:591:47: warning: unused parameter 'position' [-Wunused-parameter] + 591 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:593:50: warning: unused parameter 'name' [-Wunused-parameter] + 593 | virtual Status endElement(const std::string& name, + | ~~~~~~~~~~~~~~~~~~~^~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:594:45: warning: unused parameter 'position' [-Wunused-parameter] + 594 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:596:59: warning: unused parameter 'text' [-Wunused-parameter] + 596 | virtual Status characters(const SAXParser::saxstring& text, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +/build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] + 597 | stream_offset position) {return Status::Ok;} + | ~~~~~~~~~~~~~~^~~~~~~~ +[ 70%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_MGF.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_MGF.cpp In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumWorkerThreads.hpp:26, from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumWorkerThreads.cpp:26: @@ -3243,10 +3275,21 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 71%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_mzXML.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_mzXML.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_mzXML.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_mzXML.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.cpp -[ 72%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/DefaultReaderList.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/DefaultReaderList.cpp +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzML.cpp:205:51: warning: unused parameter 'attributes' [-Wunused-parameter] + 205 | const Attributes& attributes, + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzML.cpp:206:47: warning: unused parameter 'position' [-Wunused-parameter] + 206 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +[ 71%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/DefaultReaderList.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/DefaultReaderList.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/DefaultReaderList.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/DefaultReaderList.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/msdata/DefaultReaderList.cpp +[ 72%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_mzXML.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.cpp +[ 73%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSData.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp +[ 75%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_mzXML.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzXML.cpp In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumListBase.hpp:28, from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_MGF.hpp:30, @@ -3266,8 +3309,8 @@ /usr/include/c++/12/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/Serializer_mzXML.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzXML.cpp +[ 76%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/common/ParamTypes.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/common/ParamTypes.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/common/ParamTypes.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/common/ParamTypes.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/common/ParamTypes.cpp In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumListBase.hpp:28, from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.hpp:29, @@ -3287,15 +3330,23 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 75%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSData.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp -[ 76%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/common/ParamTypes.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/common/ParamTypes.cpp -[ 77%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/common/cv.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/common/cv.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/common/cv.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/common/cv.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/common/cv.cpp +[ 77%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/common/cv.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/common/cv.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/common/cv.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/common/cv.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/common/cv.cpp +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/BinaryDataEncoder.cpp: In member function 'void pwiz::msdata::BinaryDataEncoder::Impl::encode(const double*, size_t, std::string&, size_t*)': +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/BinaryDataEncoder.cpp:302:37: warning: 'byteCount' may be used uninitialized [-Wmaybe-uninitialized] + 302 | filterArray(byteBuffer, byteCount,compressed); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/BinaryDataEncoder.cpp:131:12: note: 'byteCount' was declared here + 131 | size_t byteCount; + | ^~~~~~~~~ +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/BinaryDataEncoder.cpp:302:37: warning: 'byteBuffer' may be used uninitialized [-Wmaybe-uninitialized] + 302 | filterArray(byteBuffer, byteCount,compressed); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/BinaryDataEncoder.cpp:132:17: note: 'byteBuffer' was declared here + 132 | const void* byteBuffer; + | ^~~~~~~~~~ In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzXML.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzXML.cpp:25: + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp:25: /build/libpwizlite-3.0.4/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 | ^~~~~~~~ @@ -3311,8 +3362,8 @@ /usr/include/c++/12/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/data/common/CVTranslator.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/common/CVTranslator.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/common/CVTranslator.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/common/CVTranslator.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/common/CVTranslator.cpp +[ 78%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/common/CVTranslator.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/common/CVTranslator.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/common/CVTranslator.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/common/CVTranslator.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/common/CVTranslator.cpp In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/IO.hpp:32, from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:26: /build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': @@ -3354,6 +3405,30 @@ /build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzXML.hpp:29, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzXML.cpp:25: +/build/libpwizlite-3.0.4/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++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/algorithm:60, + from /build/libpwizlite-3.0.4/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/libpwizlite-3.0.4/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++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +[ 80%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/LegacyAdapter.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/LegacyAdapter.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/LegacyAdapter.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/LegacyAdapter.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/msdata/LegacyAdapter.cpp +[ 81%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Reader.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/Reader.cpp +[ 82%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/common/diff_std.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/common/diff_std.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/common/diff_std.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/common/diff_std.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/common/diff_std.cpp In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/DefaultReaderList.cpp:28: /build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] @@ -3519,32 +3594,31 @@ /build/libpwizlite-3.0.4/src/pwiz/data/msdata/DefaultReaderList.cpp:484:51: warning: unused parameter 'config' [-Wunused-parameter] 484 | const Config& config) const | ~~~~~~~~~~~~~~^~~~~~ -In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp:25: -/build/libpwizlite-3.0.4/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++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/algorithm:60, - from /build/libpwizlite-3.0.4/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/libpwizlite-3.0.4/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++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/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){ - | ^ In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzXML.hpp:31: /build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': /build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual size_t pwiz::msdata::SpectrumList::findAbbreviated(const std::string&, char) const': +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp:1112:21: warning: comparison of unsigned expression in '>= 0' is always true [-Wtype-limits] + 1112 | if ((result >= 0 && result < size()) || s == 0) + | ~~~~~~~^~~~ +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual void pwiz::msdata::SpectrumList::warn_once(const char*) const': +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp:1160:56: warning: unused parameter 'msg' [-Wunused-parameter] + 1160 | PWIZ_API_DECL void SpectrumList::warn_once(const char *msg) const + | ~~~~~~~~~~~~^~~ +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual pwiz::msdata::SpectrumPtr pwiz::msdata::SpectrumListSimple::spectrum(size_t, bool) const': +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp:1204:75: warning: unused parameter 'getBinaryData' [-Wunused-parameter] + 1204 | PWIZ_API_DECL SpectrumPtr SpectrumListSimple::spectrum(size_t index, bool getBinaryData) const + | ~~~~~^~~~~~~~~~~~~ +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual pwiz::msdata::ChromatogramPtr pwiz::msdata::ChromatogramListSimple::chromatogram(size_t, bool) const': +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp:1271:87: warning: unused parameter 'getBinaryData' [-Wunused-parameter] + 1271 | PWIZ_API_DECL ChromatogramPtr ChromatogramListSimple::chromatogram(size_t index, bool getBinaryData) const + | ~~~~~^~~~~~~~~~~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/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/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:128:47: warning: unused parameter 'position' [-Wunused-parameter] 128 | stream_offset position) @@ -3602,10 +3676,37 @@ /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_mzXML.cpp:885:45: warning: unused parameter 'position' [-Wunused-parameter] 885 | stream_offset position) | ~~~~~~~~~~~~~~^~~~~~~~ -[ 80%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/common/diff_std.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/common/diff_std.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/common/diff_std.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/common/diff_std.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/common/diff_std.cpp -[ 81%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/LegacyAdapter.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/LegacyAdapter.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/LegacyAdapter.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/LegacyAdapter.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/msdata/LegacyAdapter.cpp +In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Reader.hpp:28, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Reader.cpp:26: +/build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] + 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +[ 83%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_MSn.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_MSn.cpp +In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/LegacyAdapter.hpp:30, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/LegacyAdapter.cpp:27: +/build/libpwizlite-3.0.4/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++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/algorithm:60, + from /build/libpwizlite-3.0.4/src/pwiz/utility/misc/BinaryData.hpp:29: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/libpwizlite-3.0.4/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++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Reader.hpp:29: +/build/libpwizlite-3.0.4/src/pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const': +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzXML.cpp:32: /build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] @@ -3641,21 +3742,51 @@ /build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] 597 | stream_offset position) {return Status::Ok;} | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/BinaryDataEncoder.cpp: In member function 'void pwiz::msdata::BinaryDataEncoder::Impl::encode(const double*, size_t, std::string&, size_t*)': -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/BinaryDataEncoder.cpp:302:37: warning: 'byteCount' may be used uninitialized [-Wmaybe-uninitialized] - 302 | filterArray(byteBuffer, byteCount,compressed); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/BinaryDataEncoder.cpp:131:12: note: 'byteCount' was declared here - 131 | size_t byteCount; - | ^~~~~~~~~ -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/BinaryDataEncoder.cpp:302:37: warning: 'byteBuffer' may be used uninitialized [-Wmaybe-uninitialized] - 302 | filterArray(byteBuffer, byteCount,compressed); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/BinaryDataEncoder.cpp:132:17: note: 'byteBuffer' was declared here - 132 | const void* byteBuffer; - | ^~~~~~~~~~ -[ 82%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Reader.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/Reader.cpp +In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Reader.hpp:30: +/build/libpwizlite-3.0.4/src/pwiz/utility/misc/BinaryData.hpp: At global scope: +/build/libpwizlite-3.0.4/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++/12/bits/stl_algobase.h:65, + from /usr/include/c++/12/memory:63, + 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:17, + from /usr/include/boost/shared_ptr.hpp:17, + from /build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp:29: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/libpwizlite-3.0.4/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++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp: In function 'std::string pwiz::msdata::id::translateNativeIDToScanNumber(pwiz::cv::CVID, const std::string&)': +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp:578:13: warning: this statement may fall through [-Wimplicit-fallthrough=] + 578 | if (id.find("controllerType=0 controllerNumber=1") != 0) + | ^~ +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp:583:9: note: here + 583 | case MS_Bruker_Agilent_YEP_nativeID_format: + | ^~~~ +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual size_t pwiz::msdata::SpectrumList::findAbbreviated(const std::string&, char) const': +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp:1115:1: warning: control reaches end of non-void function [-Wreturn-type] + 1115 | } + | ^ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/common/diff_std.cpp:40:33: warning: unused parameter 'config' [-Wunused-parameter] + 40 | const BaseDiffConfig& config) + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/common/diff_std.cpp:88:33: warning: unused parameter 'config' [-Wunused-parameter] + 88 | const BaseDiffConfig& config) + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~ +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/common/diff_std.cpp:124:33: warning: unused parameter 'config' [-Wunused-parameter] + 124 | const BaseDiffConfig& config) + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzXML.cpp:421:62: warning: unused parameter 'spectrumListPtr' [-Wunused-parameter] 421 | const SpectrumListPtr spectrumListPtr, @@ -3680,24 +3811,6 @@ /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzXML.cpp:1302:47: warning: unused parameter 'position' [-Wunused-parameter] 1302 | stream_offset position) | ~~~~~~~~~~~~~~^~~~~~~~ -[ 83%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_MSn.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_MSn.cpp -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual size_t pwiz::msdata::SpectrumList::findAbbreviated(const std::string&, char) const': -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp:1112:21: warning: comparison of unsigned expression in '>= 0' is always true [-Wtype-limits] - 1112 | if ((result >= 0 && result < size()) || s == 0) - | ~~~~~~~^~~~ -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual void pwiz::msdata::SpectrumList::warn_once(const char*) const': -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp:1160:56: warning: unused parameter 'msg' [-Wunused-parameter] - 1160 | PWIZ_API_DECL void SpectrumList::warn_once(const char *msg) const - | ~~~~~~~~~~~~^~~ -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual pwiz::msdata::SpectrumPtr pwiz::msdata::SpectrumListSimple::spectrum(size_t, bool) const': -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp:1204:75: warning: unused parameter 'getBinaryData' [-Wunused-parameter] - 1204 | PWIZ_API_DECL SpectrumPtr SpectrumListSimple::spectrum(size_t index, bool getBinaryData) const - | ~~~~~^~~~~~~~~~~~~ -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual pwiz::msdata::ChromatogramPtr pwiz::msdata::ChromatogramListSimple::chromatogram(size_t, bool) const': -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp:1271:87: warning: unused parameter 'getBinaryData' [-Wunused-parameter] - 1271 | PWIZ_API_DECL ChromatogramPtr ChromatogramListSimple::chromatogram(size_t index, bool getBinaryData) const - | ~~~~~^~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64, from /usr/include/c++/12/functional:62, from /usr/include/boost/numeric/conversion/converter_policies.hpp:19, @@ -3718,30 +3831,6 @@ /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumWorkerThreads.cpp:240:41: note: 'lruToReset.boost::optional::.boost::optional_detail::tc_optional_base::m_storage' was declared here 240 | boost::optional lruToReset; | ^~~~~~~~~~ -In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/LegacyAdapter.hpp:30, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/LegacyAdapter.cpp:27: -/build/libpwizlite-3.0.4/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++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/algorithm:60, - from /build/libpwizlite-3.0.4/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/libpwizlite-3.0.4/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++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Reader.hpp:28, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Reader.cpp:26: -/build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/common/CVTranslator.cpp: In function 'bool pwiz::data::shouldIgnore(const std::string&, pwiz::cv::CVID, pwiz::cv::CVID)': /build/libpwizlite-3.0.4/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 || @@ -3762,31 +3851,20 @@ /build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/Reader.hpp:29: -/build/libpwizlite-3.0.4/src/pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const': -/build/libpwizlite-3.0.4/src/pwiz/utility/chemistry/MzMobilityWindow.hpp:40:59: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 40 | mobilityBounds.get().first < mobilityValue && mobilityValue < mobilityBounds.get().second; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp: In function 'std::string pwiz::msdata::id::translateNativeIDToScanNumber(pwiz::cv::CVID, const std::string&)': -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp:578:13: warning: this statement may fall through [-Wimplicit-fallthrough=] - 578 | if (id.find("controllerType=0 controllerNumber=1") != 0) - | ^~ -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp:583:9: note: here - 583 | case MS_Bruker_Agilent_YEP_nativeID_format: - | ^~~~ +[ 85%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_mzML.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzML.cpp +[ 86%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Index_mzML.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/Index_mzML.cpp In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Reader.hpp:30: -/build/libpwizlite-3.0.4/src/pwiz/utility/misc/BinaryData.hpp: At global scope: + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumListBase.hpp:28, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_MSn.hpp:29, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_MSn.cpp:26: /build/libpwizlite-3.0.4/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++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/memory:63, - 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:17, - from /usr/include/boost/shared_ptr.hpp:17, - from /build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp:29: + from /usr/include/c++/12/algorithm:60, + from /build/libpwizlite-3.0.4/src/pwiz/utility/misc/BinaryData.hpp:29: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -3796,16 +3874,20 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp: In member function 'virtual size_t pwiz::msdata::SpectrumList::findAbbreviated(const std::string&, char) const': -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.cpp:1115:1: warning: control reaches end of non-void function [-Wreturn-type] - 1115 | } - | ^ -[ 85%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_mzML.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_mzML.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_mzML.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_mzML.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzML.cpp +[ 87%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumWorkerThreads.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumWorkerThreads.cpp +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/Reader.cpp:76:119: warning: unused parameter 'config' [-Wunused-parameter] + 76 | PWIZ_API_DECL void Reader::readIds(const string& filename, const string& head, vector& results, const Config& config) const + | ~~~~~~~~~~~~~~^~~~~~ +In file included from /build/libpwizlite-3.0.4/src/pwiz/data/common/cv.cpp:25067: +/build/libpwizlite-3.0.4/src/pwiz/data/common/cv.inl: In function 'const pwiz::cv::CVTermInfo& pwiz::cv::cvTermInfo(const char*)': +/build/libpwizlite-3.0.4/src/pwiz/data/common/cv.inl:102:23: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] + 102 | for (int o=0;o struct std::iterator' is deprecated [-Wdeprecated-declarations] 54 | class PWIZ_API_DECL const_iterator : public std::iterator | ^~~~~~~~ @@ -3821,26 +3903,13 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/libpwizlite-3.0.4/src/pwiz/data/common/cv.cpp:25067: -/build/libpwizlite-3.0.4/src/pwiz/data/common/cv.inl: In function 'const pwiz::cv::CVTermInfo& pwiz::cv::cvTermInfo(const char*)': -/build/libpwizlite-3.0.4/src/pwiz/data/common/cv.inl:102:23: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] - 102 | for (int o=0;o struct std::iterator' is deprecated [-Wdeprecated-declarations] 54 | class PWIZ_API_DECL const_iterator : public std::iterator | ^~~~~~~~ @@ -3856,21 +3925,15 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 86%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Index_mzML.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Index_mzML.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Index_mzML.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Index_mzML.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Index_mzML.cpp -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/Reader.cpp:76:119: warning: unused parameter 'config' [-Wunused-parameter] - 76 | PWIZ_API_DECL void Reader::readIds(const string& filename, const string& head, vector& results, const Config& config) const - | ~~~~~~~~~~~~~~^~~~~~ -[ 87%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumWorkerThreads.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumWorkerThreads.cpp In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzML.hpp:31: /build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': /build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp:60:48: warning: unused parameter 'updateMessage' [-Wunused-parameter] 60 | virtual Status update(const UpdateMessage& updateMessage) {return Status_Ok;} | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -[ 88%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/References.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/References.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/References.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/References.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/msdata/References.cpp +[ 91%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/DefaultReaderList.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/DefaultReaderList.cpp +[ 92%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_mzXML.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzXML.cpp In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzML.cpp:32: /build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] @@ -3906,16 +3969,9 @@ /build/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:597:45: warning: unused parameter 'position' [-Wunused-parameter] 597 | stream_offset position) {return Status::Ok;} | ~~~~~~~~~~~~~~^~~~~~~~ -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzML.cpp:205:51: warning: unused parameter 'attributes' [-Wunused-parameter] - 205 | const Attributes& attributes, - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzML.cpp:206:47: warning: unused parameter 'position' [-Wunused-parameter] - 206 | stream_offset position) - | ~~~~~~~~~~~~~~^~~~~~~~ In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Index_mzML.hpp:28, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Index_mzML.cpp:24: + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/References.hpp:29, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/References.cpp:25: /build/libpwizlite-3.0.4/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 | ^~~~~~~~ @@ -3931,17 +3987,23 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 90%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_MGF.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_MGF.cpp -[ 91%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/DefaultReaderList.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/DefaultReaderList.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/DefaultReaderList.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/DefaultReaderList.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/msdata/DefaultReaderList.cpp -[ 92%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_mzXML.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzXML.cpp -[ 93%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/common/ParamTypes.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/common/ParamTypes.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/common/ParamTypes.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/common/ParamTypes.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/common/ParamTypes.cpp +[ 93%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/common/ParamTypes.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -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/libpwizlite-3.0.4/src/pwiz/data/common/ParamTypes.cpp +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzML.cpp:205:51: warning: unused parameter 'attributes' [-Wunused-parameter] + 205 | const Attributes& attributes, + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzML.cpp:206:47: warning: unused parameter 'position' [-Wunused-parameter] + 206 | stream_offset position) + | ~~~~~~~~~~~~~~^~~~~~~~ +[ 95%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/common/cv.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/common/cv.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/common/cv.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/common/cv.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/common/cv.cpp +[ 96%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/common/CVTranslator.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/common/CVTranslator.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/common/CVTranslator.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/common/CVTranslator.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/common/CVTranslator.cpp In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/References.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/References.cpp:25: + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumListBase.hpp:28, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_MGF.hpp:30, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_MGF.cpp:26: /build/libpwizlite-3.0.4/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 | ^~~~~~~~ @@ -3958,9 +4020,8 @@ 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumListBase.hpp:28, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_MGF.hpp:30, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumList_MGF.cpp:26: + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzXML.hpp:29, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzXML.cpp:25: /build/libpwizlite-3.0.4/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 | ^~~~~~~~ @@ -3976,8 +4037,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 95%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/common/cv.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/common/cv.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/common/cv.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/common/cv.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/common/cv.cpp In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Index_mzML.cpp:26: /build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] @@ -4043,26 +4102,6 @@ 197 | stream_offset position) | ~~~~~~~~~~~~~~^~~~~~~~ In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzXML.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzXML.cpp:25: -/build/libpwizlite-3.0.4/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++/12/bits/stl_algobase.h:65, - from /usr/include/c++/12/algorithm:60, - from /build/libpwizlite-3.0.4/src/pwiz/utility/misc/BinaryData.hpp:29: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/libpwizlite-3.0.4/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++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -[ 96%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/common/CVTranslator.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/common/CVTranslator.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/common/CVTranslator.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/common/CVTranslator.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/common/CVTranslator.cpp -In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumWorkerThreads.hpp:26, from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/SpectrumWorkerThreads.cpp:26: /build/libpwizlite-3.0.4/src/pwiz/utility/misc/BinaryData.hpp:54:54: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] @@ -4082,14 +4121,12 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 97%] Building CXX object src/CMakeFiles/pwizlite-shared.dir/pwiz/data/common/diff_std.cpp.o -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -Dpwizlite_shared_EXPORTS -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-shared.dir/pwiz/data/common/diff_std.cpp.o -MF CMakeFiles/pwizlite-shared.dir/pwiz/data/common/diff_std.cpp.o.d -o CMakeFiles/pwizlite-shared.dir/pwiz/data/common/diff_std.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/common/diff_std.cpp In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzXML.hpp:31: /build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': /build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/DefaultReaderList.cpp:28: +In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzXML.cpp:32: /build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] 585 | virtual Status processingInstruction(const std::string& name, @@ -4124,39 +4161,7 @@ /build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/Reader.hpp:28, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/DefaultReaderList.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/DefaultReaderList.cpp:29: -/build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/Reader.hpp:29: -/build/libpwizlite-3.0.4/src/pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const': -/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Reader.hpp:30: -/build/libpwizlite-3.0.4/src/pwiz/utility/misc/BinaryData.hpp: At global scope: -/build/libpwizlite-3.0.4/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++/12/string:45, - from /usr/include/c++/12/stdexcept:39, - from /build/libpwizlite-3.0.4/src/pwiz/utility/misc/Exception.hpp:28, - from /build/libpwizlite-3.0.4/src/pwiz/utility/misc/Std.hpp:28, - from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/DefaultReaderList.cpp:26: -/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/libpwizlite-3.0.4/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++/12/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzXML.cpp:32: +In file included from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/DefaultReaderList.cpp:28: /build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/utility/minimxml/SAXParser.hpp:585:61: warning: unused parameter 'name' [-Wunused-parameter] 585 | virtual Status processingInstruction(const std::string& name, @@ -4191,6 +4196,38 @@ /build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/Reader.hpp:28, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/DefaultReaderList.hpp:29, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/DefaultReaderList.cpp:29: +/build/libpwizlite-3.0.4/src/pwiz/utility/misc/IterationListener.hpp: In member function 'virtual pwiz::util::IterationListener::Status pwiz::util::IterationListener::update(const UpdateMessage&)': +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/Reader.hpp:29: +/build/libpwizlite-3.0.4/src/pwiz/utility/chemistry/MzMobilityWindow.hpp: In member function 'bool pwiz::chemistry::MzMobilityWindow::mobilityValueInBounds(double) const': +/build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/MSData.hpp:29, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/Reader.hpp:30: +/build/libpwizlite-3.0.4/src/pwiz/utility/misc/BinaryData.hpp: At global scope: +/build/libpwizlite-3.0.4/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++/12/string:45, + from /usr/include/c++/12/stdexcept:39, + from /build/libpwizlite-3.0.4/src/pwiz/utility/misc/Exception.hpp:28, + from /build/libpwizlite-3.0.4/src/pwiz/utility/misc/Std.hpp:28, + from /build/libpwizlite-3.0.4/src/pwiz/data/msdata/DefaultReaderList.cpp:26: +/usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/libpwizlite-3.0.4/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++/12/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ /build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/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 ""; } @@ -4289,6 +4326,8 @@ /build/libpwizlite-3.0.4/src/pwiz/data/msdata/DefaultReaderList.cpp:484:51: warning: unused parameter 'config' [-Wunused-parameter] 484 | const Config& config) const | ~~~~~~~~~~~~~~^~~~~~ +[ 97%] Building CXX object src/CMakeFiles/pwizlite-static.dir/pwiz/data/common/diff_std.cpp.o +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_THREAD_DYN_LINK -DWITHOUT_MZ5 -I/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src -I/build/libpwizlite-3.0.4/src -I/build/libpwizlite-3.0.4/src/boost -g -O2 -ffile-prefix-map=/build/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wno-unknown-pragmas -Wall -Wextra -fPIC -Wall -std=gnu++17 -MD -MT src/CMakeFiles/pwizlite-static.dir/pwiz/data/common/diff_std.cpp.o -MF CMakeFiles/pwizlite-static.dir/pwiz/data/common/diff_std.cpp.o.d -o CMakeFiles/pwizlite-static.dir/pwiz/data/common/diff_std.cpp.o -c /build/libpwizlite-3.0.4/src/pwiz/data/common/diff_std.cpp /build/libpwizlite-3.0.4/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/libpwizlite-3.0.4/src/pwiz/data/msdata/Serializer_mzXML.cpp:421:62: warning: unused parameter 'spectrumListPtr' [-Wunused-parameter] 421 | const SpectrumListPtr spectrumListPtr, @@ -4333,10 +4372,11 @@ /build/libpwizlite-3.0.4/src/pwiz/data/common/CVTranslator.cpp:153:56: warning: unused parameter 'cvid' [-Wunused-parameter] 153 | bool shouldReplace(const string& key, CVID value, CVID cvid) | ~~~~~^~~~ -[ 98%] Linking CXX static library libpwizlite.a -cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/pwizlite-static.dir/cmake_clean_target.cmake -cd /build/libpwizlite-3.0.4/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/utility/minimxml/XMLWriter.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/utility/minimxml/SAXParser.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/IterationListener.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/BinaryData.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/Base64.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/random_access_compressed_ifstream.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/Filesystem.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/IntegerSet.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/String.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_MGF.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSNumpress.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_MSn.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumInfo.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/IO.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_BTDX.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/ChromatogramList_mzML.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_mzML.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Version.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSDataFile.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumListBase.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/BinaryDataEncoder.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_mzXML.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSData.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/LegacyAdapter.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Reader.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_MSn.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_mzML.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Index_mzML.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumWorkerThreads.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/References.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_MGF.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/DefaultReaderList.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_mzXML.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/common/ParamTypes.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/common/cv.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/common/CVTranslator.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/common/diff_std.cpp.o" +In file included from /build/libpwizlite-3.0.4/src/pwiz/data/common/cv.cpp:25067: +/build/libpwizlite-3.0.4/src/pwiz/data/common/cv.inl: In function 'const pwiz::cv::CVTermInfo& pwiz::cv::cvTermInfo(const char*)': +/build/libpwizlite-3.0.4/src/pwiz/data/common/cv.inl:102:23: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] + 102 | for (int o=0;o::.boost::optional_detail::tc_optional_base::m_storage' was declared here 240 | boost::optional lruToReset; | ^~~~~~~~~~ -make[3]: Leaving directory '/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu' -[ 98%] Built target pwizlite-static -[100%] Linking CXX shared library libpwizlite.so +[ 98%] Linking CXX shared library libpwizlite.so cd /build/libpwizlite-3.0.4/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/libpwizlite-3.0.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libpwizlite.so.3 -o libpwizlite.so.3.0.4 "CMakeFiles/pwizlite-shared.dir/pwiz/utility/minimxml/XMLWriter.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/utility/minimxml/SAXParser.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/IterationListener.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/BinaryData.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/Base64.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/random_access_compressed_ifstream.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/Filesystem.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/utility/misc/IntegerSet.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/String.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_MGF.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSNumpress.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_MSn.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumInfo.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/IO.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_BTDX.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/ChromatogramList_mzML.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_mzML.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Version.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSDataFile.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumListBase.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/BinaryDataEncoder.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_mzXML.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/MSData.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/LegacyAdapter.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Reader.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_MSn.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_mzML.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Index_mzML.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumWorkerThreads.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/References.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/SpectrumList_MGF.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/DefaultReaderList.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/msdata/Serializer_mzXML.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/common/ParamTypes.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/common/cv.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/common/CVTranslator.cpp.o" "CMakeFiles/pwizlite-shared.dir/pwiz/data/common/diff_std.cpp.o" /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_thread.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.74.0 cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_symlink_library libpwizlite.so.3.0.4 libpwizlite.so.3 libpwizlite.so make[3]: Leaving directory '/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu' -[100%] Built target pwizlite-shared +[ 98%] Built target pwizlite-shared +[100%] Linking CXX static library libpwizlite.a +cd /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/pwizlite-static.dir/cmake_clean_target.cmake +cd /build/libpwizlite-3.0.4/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/utility/minimxml/XMLWriter.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/utility/minimxml/SAXParser.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/IterationListener.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/BinaryData.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/Base64.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/random_access_compressed_ifstream.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/Filesystem.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/utility/misc/IntegerSet.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/String.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_MGF.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSNumpress.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_MSn.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumInfo.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/IO.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_BTDX.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/ChromatogramList_mzML.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_mzML.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Version.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSDataFile.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumListBase.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/BinaryDataEncoder.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_mzXML.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/MSData.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/LegacyAdapter.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Reader.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_MSn.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_mzML.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Index_mzML.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumWorkerThreads.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/References.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/SpectrumList_MGF.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/DefaultReaderList.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/msdata/Serializer_mzXML.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/common/ParamTypes.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/common/cv.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/common/CVTranslator.cpp.o" "CMakeFiles/pwizlite-static.dir/pwiz/data/common/diff_std.cpp.o" +/usr/bin/ranlib libpwizlite.a +make[3]: Leaving directory '/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu' +[100%] Built target pwizlite-static make[2]: Leaving directory '/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/libpwizlite-3.0.4/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu' @@ -4393,7 +4432,7 @@ 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 -j15 install DESTDIR=/build/libpwizlite-3.0.4/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j16 install DESTDIR=/build/libpwizlite-3.0.4/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/libpwizlite-3.0.4 -B/build/libpwizlite-3.0.4/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -4429,9 +4468,9 @@ dh_gencontrol -O--build-system=cmake dh_md5sums -O--build-system=cmake dh_builddeb -O--build-system=cmake -dpkg-deb: building package 'libpwizlite3-dbgsym' in '../libpwizlite3-dbgsym_3.0.4-1_amd64.deb'. dpkg-deb: building package 'libpwizlite-dev' in '../libpwizlite-dev_3.0.4-1_amd64.deb'. dpkg-deb: building package 'libpwizlite3' in '../libpwizlite3_3.0.4-1_amd64.deb'. +dpkg-deb: building package 'libpwizlite3-dbgsym' in '../libpwizlite3-dbgsym_3.0.4-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../libpwizlite_3.0.4-1_amd64.buildinfo dpkg-genchanges --build=binary -O../libpwizlite_3.0.4-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -4439,12 +4478,14 @@ 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/3456798/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3456798/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/2430257 and its subdirectories -I: Current time: Sun Apr 16 04:01:10 -12 2023 -I: pbuilder-time-stamp: 1681660870 +I: removing directory /srv/workspace/pbuilder/3456798 and its subdirectories +I: Current time: Sun May 19 12:30:47 +14 2024 +I: pbuilder-time-stamp: 1716071447