Fri Apr 14 14:48:18 UTC 2023 I: starting to build comet-ms/bookworm/amd64 on jenkins on '2023-04-14 14:48' Fri Apr 14 14:48:18 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_30/13133/console.log Fri Apr 14 14:48:18 UTC 2023 I: Downloading source for bookworm/comet-ms=2019015+cleaned1-3 --2023-04-14 14:48:18-- http://cdn-fastly.deb.debian.org/debian/pool/main/c/comet-ms/comet-ms_2019015%2bcleaned1-3.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2080 (2.0K) [text/prs.lines.tag] Saving to: ‘comet-ms_2019015+cleaned1-3.dsc’ 0K .. 100% 4.71M=0s 2023-04-14 14:48:18 (4.71 MB/s) - ‘comet-ms_2019015+cleaned1-3.dsc’ saved [2080/2080] Fri Apr 14 14:48:18 UTC 2023 I: comet-ms_2019015+cleaned1-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: comet-ms Binary: comet-ms Architecture: any Version: 2019015+cleaned1-3 Maintainer: The Debichem Group Uploaders: Filippo Rusconi Homepage: http://comet-ms.sourceforge.net Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/debichem-team/comet-ms Vcs-Git: https://salsa.debian.org/debichem-team/comet-ms.git Build-Depends: debhelper-compat (= 12), dpkg-dev (>= 1.16.1~), libmstoolkit-dev (>= 82), libmstoolkit-dev (<< 83), docbook-to-man Package-List: comet-ms deb science optional arch=any Checksums-Sha1: e8ce6f80224671a82f5c9123546c621fba5df7d0 1378100 comet-ms_2019015+cleaned1.orig.tar.gz f95389963663df225018034939d6e4249900b1f4 6596 comet-ms_2019015+cleaned1-3.debian.tar.xz Checksums-Sha256: 27a5c4b89b82d4570485cca98b27a45dd55a640ea297d8188c1c008a6b5234a3 1378100 comet-ms_2019015+cleaned1.orig.tar.gz ed6aa53d308ca0be660491d05d96f493c61778ebb5c6585e68d1182b0d9fb1d2 6596 comet-ms_2019015+cleaned1-3.debian.tar.xz Files: fac4a9263c2b124cb0183dc9bf645f4b 1378100 comet-ms_2019015+cleaned1.orig.tar.gz be62061e3694af78e5393053735248c2 6596 comet-ms_2019015+cleaned1-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEsFMwThfW1Bndm0ZRQatITXaUz0IFAl81tjgACgkQQatITXaU z0IY8A/+PswAVKpaF5KgR2adBwgnBdUOTuQOLDteuqq058yxKxuaDJ0sPGOQO0/r Vv+oHUO688tRZv2cDJyUfqXz1qzEVD5K5S3H1PXxS6pwxp1q2xOmJUFdpNTY9aTR l6068uHT5FMEwcSL+8ypbuAtk1OEriz/HIHMrMsvh5YkxgMMYngHzfKdpArXcjzp Pdb1X9REGA4g90PI1cu27A7FlP/z2RyRymzkq7dfu47SOcCYWGihGloWqzj7qD6s hLfqlE9iTAr5J2j7uxXYGzHAjfzw8KJpYMDcKxN6gioOuGSQ+dmnjWtNv4cxkpJ1 KtlDj8pAU6UFDG2vzZWhbcihnIlkKfsV7L5Ot0Xv11gdNIgu+JwlIV6SwAcjYXnj 2nnaBr3Q55QY0YOj23ccHIxDWBj9RGC6/oIbI668LBXbHByFzeU5t2bse1Z4L5z0 xaOKNhI7vX6vZQmgg9Xakm23d+Fj+QLDj8oB6L62xPif++hUHfQpfYHOXv1YT2gv eOqh3n69p2HlZbmRVq91H6vkimCKH/3YyFR3hmZ2b55uCxnWZ+OTgHAoBVq6qgF/ 355s2TQdMxUWzsOuMmyDqfT2eWpJ2aniRFbb0lae+Y54/SZ309sX/fkNPa11SFLA iXT4DTLogmNkT7dPuODjwNjS6YH6BPqpwFYo5lZWLwJTuUTSFmc= =gvnA -----END PGP SIGNATURE----- Fri Apr 14 14:48:18 UTC 2023 I: Checking whether the package is not for us Fri Apr 14 14:48:18 UTC 2023 I: Starting 1st build on remote node ionos5-amd64.debian.net. Fri Apr 14 14:48:18 UTC 2023 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Fri Apr 14 14:52:19 UTC 2023 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu May 16 09:11:20 -12 2024 I: pbuilder-time-stamp: 1715893880 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [comet-ms_2019015+cleaned1-3.dsc] I: copying [./comet-ms_2019015+cleaned1.orig.tar.gz] I: copying [./comet-ms_2019015+cleaned1-3.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Aug 13 09:52:56 2020 -12 gpgv: using RSA key B053304E17D6D419DD9B465141AB484D7694CF42 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./comet-ms_2019015+cleaned1-3.dsc: no acceptable signature found dpkg-source: info: extracting comet-ms in comet-ms-2019015+cleaned1 dpkg-source: info: unpacking comet-ms_2019015+cleaned1.orig.tar.gz dpkg-source: info: unpacking comet-ms_2019015+cleaned1-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying makefile-to-handle-lib-debian-way-of-doing-things.patch dpkg-source: info: applying cometsearch-makefile-to-handle-lib-debian-way-of-doing-things.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3437212/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=16' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='2e96c3c9ab2e4111b82ead158ad5321a' 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='3437212' PS1='# ' PS2='> ' 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.E4wVXJRa/pbuilderrc_cQg0 --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.E4wVXJRa/b1 --logfile b1/build.log comet-ms_2019015+cleaned1-3.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://85.184.249.68:3128' I: uname -a Linux ionos5-amd64 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 2023 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 2023 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 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 85600 Mar 22 2023 findmnt -rwsr-xr-x 1 root root 35128 Mar 22 2023 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 2023 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 2022 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 2023 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 22 2023 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 2023 more -rwsr-xr-x 1 root root 59704 Mar 22 2023 mount -rwxr-xr-x 1 root root 18744 Mar 22 2023 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Feb 12 2023 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 2022 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed lrwxrwxrwx 1 root root 4 Jan 5 2023 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 2023 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar -rwxr-xr-x 1 root root 14520 Nov 2 2022 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 2023 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 22 2023 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 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 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/3437212/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 12), dpkg-dev (>= 1.16.1~), libmstoolkit-dev (>= 82), libmstoolkit-dev (<< 83), docbook-to-man dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19596 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 12); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libmstoolkit-dev (>= 82); however: Package libmstoolkit-dev is not installed. pbuilder-satisfydepends-dummy depends on libmstoolkit-dev (<< 83); however: Package libmstoolkit-dev is not installed. pbuilder-satisfydepends-dummy depends on docbook-to-man; however: Package docbook-to-man is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} docbook{a} docbook-to-man{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libmstoolkit-dev{a} libmstoolkit82{a} libosp5{a} libpipeline1{a} libsqlite3-dev{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} opensp{a} po-debconf{a} sensible-utils{a} sgml-base{a} sgml-data{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 43 newly installed, 0 to remove and 0 not upgraded. Need to get 23.0 MB of archives. After unpacking 88.5 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 sgml-base all 1.31 [15.4 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 22 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 24 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.1+b3 [687 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 xml-core all 0.18+nmu1 [23.8 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 sgml-data all 2.0.11+nmu1 [179 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 docbook all 4.5-10 [131 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 libosp5 amd64 1.5.2-13+b2 [934 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 opensp amd64 1.5.2-13+b2 [421 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 docbook-to-man amd64 1:2.0.0-45 [77.4 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 libexpat1-dev amd64 2.5.0-1 [150 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 libmstoolkit82 amd64 82-7 [138 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 libsqlite3-dev amd64 3.40.1-2 [1025 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 libmstoolkit-dev amd64 82-7 [140 kB] Fetched 23.0 MB in 0s (74.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sgml-base. (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.) Preparing to unpack .../00-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../03-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../06-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.22.4-10_amd64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.38.1-5+b1_amd64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... 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Reading state information... 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/comet-ms-2019015+cleaned1/ && 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 > ../comet-ms_2019015+cleaned1-3_source.changes dpkg-buildpackage: info: source package comet-ms dpkg-buildpackage: info: source version 2019015+cleaned1-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Filippo Rusconi dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/comet-ms-2019015+cleaned1' rm -f debian/comet-ms.1 make[1]: Leaving directory '/build/comet-ms-2019015+cleaned1' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/comet-ms.substvars debian/files rm -fr -- debian/comet-ms/ debian/tmp/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) debian/rules build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/comet-ms-2019015+cleaned1' docbook-to-man debian/comet-ms.sgml > debian/comet-ms.1 dh_auto_build make -j16 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/comet-ms-2019015+cleaned1' cd CometSearch ; make make[3]: Entering directory '/build/comet-ms-2019015+cleaned1/CometSearch' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. g++ -g -O2 -ffile-prefix-map=/build/comet-ms-2019015+cleaned1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit Threading.cpp -c g++ -g -O2 -ffile-prefix-map=/build/comet-ms-2019015+cleaned1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometInterfaces.cpp -c g++ -g -O2 -ffile-prefix-map=/build/comet-ms-2019015+cleaned1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometSearch.cpp -c In file included from CometSearch.cpp:19: ThreadPool.h: In instantiation of 'ThreadManager::ThreadManager(ThreadPool*) [with T = SearchThreadData*]': ThreadPool.h:69:10: required from 'ThreadPool::ThreadPool(ThreadProc, int, int, int) [with T = SearchThreadData*; ThreadProc = void (*)(SearchThreadData*)]' CometSearch.cpp:138:66: required from here ThreadPool.h:257:13: warning: cast between incompatible function types from 'uint32_t (*)(void*)' {aka 'unsigned int (*)(void*)'} to 'ThreadProc' {aka 'void* (*)(void*)'} [-Wcast-function-type] 257 | reinterpret_cast(ThreadManager::ThreadRoutingFunction), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/comet-ms-2019015+cleaned1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometPreprocess.cpp -c In file included from CometPreprocess.h:21, from CometPreprocess.cpp:19: ThreadPool.h: In instantiation of 'ThreadManager::ThreadManager(ThreadPool*) [with T = PreprocessThreadData*]': ThreadPool.h:69:10: required from 'ThreadPool::ThreadPool(ThreadProc, int, int, int) [with T = PreprocessThreadData*; ThreadProc = void (*)(PreprocessThreadData*)]' CometPreprocess.cpp:74:65: required from here ThreadPool.h:257:13: warning: cast between incompatible function types from 'uint32_t (*)(void*)' {aka 'unsigned int (*)(void*)'} to 'ThreadProc' {aka 'void* (*)(void*)'} [-Wcast-function-type] 257 | reinterpret_cast(ThreadManager::ThreadRoutingFunction), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/comet-ms-2019015+cleaned1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometPostAnalysis.cpp -c In file included from CometPostAnalysis.cpp:19: ThreadPool.h: In instantiation of 'ThreadManager::ThreadManager(ThreadPool*) [with T = PostAnalysisThreadData*]': ThreadPool.h:69:10: required from 'ThreadPool::ThreadPool(ThreadProc, int, int, int) [with T = PostAnalysisThreadData*; ThreadProc = void (*)(PostAnalysisThreadData*)]' CometPostAnalysis.cpp:46:38: required from here ThreadPool.h:257:13: warning: cast between incompatible function types from 'uint32_t (*)(void*)' {aka 'unsigned int (*)(void*)'} to 'ThreadProc' {aka 'void* (*)(void*)'} [-Wcast-function-type] 257 | reinterpret_cast(ThreadManager::ThreadRoutingFunction), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/comet-ms-2019015+cleaned1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometMassSpecUtils.cpp -c g++ -g -O2 -ffile-prefix-map=/build/comet-ms-2019015+cleaned1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometWriteOut.cpp -c CometWriteOut.cpp: In static member function 'static bool CometWriteOut::PrintResults(int, bool, FILE*)': CometWriteOut.cpp:124:32: warning: '%.5d' directive writing between 5 and 11 bytes into a region of size between 0 and 1022 [-Wformat-overflow=] 124 | sprintf(szOutput, "%s/%s.%.5d.%.5d.%d.out", | ^~~~ CometWriteOut.cpp:124:14: note: 'sprintf' output between 20 and 1064 bytes into a destination of size 1024 124 | sprintf(szOutput, "%s/%s.%.5d.%.5d.%d.out", | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 125 | g_staticParams.inputFile.szBaseName, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 126 | pStr, | ~~~~~ 127 | pQuery->_spectrumInfoInternal.iScanNumber, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 128 | pQuery->_spectrumInfoInternal.iScanNumber, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 129 | pQuery->_spectrumInfoInternal.iChargeState); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometWriteOut.cpp:115:35: warning: '%s' directive writing up to 511 bytes into a region of size between 506 and 1017 [-Wformat-overflow=] 115 | sprintf(szOutput, "%s_decoy/%s.%.5d.%.5d.%d.out", | ^~ CometWriteOut.cpp:115:14: note: 'sprintf' output between 26 and 1070 bytes into a destination of size 1024 115 | sprintf(szOutput, "%s_decoy/%s.%.5d.%.5d.%d.out", | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 116 | g_staticParams.inputFile.szBaseName, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 117 | pStr, | ~~~~~ 118 | pQuery->_spectrumInfoInternal.iScanNumber, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 119 | pQuery->_spectrumInfoInternal.iScanNumber, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 120 | pQuery->_spectrumInfoInternal.iChargeState); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometWriteOut.cpp:273:28: warning: '%+d' directive writing between 2 and 11 bytes into a region of size 9 [-Wformat-overflow=] 273 | sprintf(szTempStr, " %+d", iLenMaxDuplicates); | ^~~ CometWriteOut.cpp:273:26: note: directive argument in the range [1, 2147483647] 273 | sprintf(szTempStr, " %+d", iLenMaxDuplicates); | ^~~~~~ CometWriteOut.cpp:273:14: note: 'sprintf' output between 4 and 13 bytes into a destination of size 10 273 | sprintf(szTempStr, " %+d", iLenMaxDuplicates); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometWriteOut.cpp:151:59: warning: '%s' directive writing up to 1023 bytes into a region of size 226 [-Wformat-overflow=] 151 | sprintf(szErrorMsg, " Error - cannot write to file %s.\n", szOutput); | ^~ ~~~~~~~~ CometWriteOut.cpp:151:14: note: 'sprintf' output between 33 and 1056 bytes into a destination of size 256 151 | sprintf(szErrorMsg, " Error - cannot write to file %s.\n", szOutput); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/comet-ms-2019015+cleaned1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometWriteSqt.cpp -c g++ -g -O2 -ffile-prefix-map=/build/comet-ms-2019015+cleaned1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometWritePepXML.cpp -c g++ -g -O2 -ffile-prefix-map=/build/comet-ms-2019015+cleaned1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometWritePercolator.cpp -c g++ -g -O2 -ffile-prefix-map=/build/comet-ms-2019015+cleaned1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometWriteTxt.cpp -c g++ -g -O2 -ffile-prefix-map=/build/comet-ms-2019015+cleaned1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometSearchManager.cpp -c CometSearchManager.cpp: In static member function 'static bool CometSearchManager::WriteIndexedDatabase()': CometSearchManager.cpp:2756:28: warning: '.idx' directive writing 4 bytes into a region of size between 1 and 512 [-Wformat-overflow=] 2756 | sprintf(szIndexFile, "%s.idx", g_staticParams.databaseInfo.szDatabase); | ^~~~ CometSearchManager.cpp:2756:11: note: 'sprintf' output between 5 and 516 bytes into a destination of size 512 2756 | sprintf(szIndexFile, "%s.idx", g_staticParams.databaseInfo.szDatabase); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearchManager.cpp: In member function 'virtual bool CometSearchManager::DoSearch()': CometSearchManager.cpp:416:34: warning: '%d' directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 416 | sprintf(szIsotope, "ISOTOPE%d", g_staticParams.tolerances.iIsotopeError); | ^~ In function 'void PrintOutfileHeader()', inlined from 'virtual bool CometSearchManager::DoSearch()' at CometSearchManager.cpp:1559:25: CometSearchManager.cpp:416:26: note: directive argument in the range [1, 2147483647] 416 | sprintf(szIsotope, "ISOTOPE%d", g_staticParams.tolerances.iIsotopeError); | ^~~~~~~~~~~ CometSearchManager.cpp:416:14: note: 'sprintf' output between 9 and 18 bytes into a destination of size 16 416 | sprintf(szIsotope, "ISOTOPE%d", g_staticParams.tolerances.iIsotopeError); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearchManager.cpp: In member function 'virtual bool CometSearchManager::DoSearch()': CometSearchManager.cpp:1597:71: warning: '%s' directive writing up to 511 bytes into a region of size 218 [-Wformat-overflow=] 1597 | sprintf(szErrorMsg, " Error - cannot read DIA window file \"%s\".\n", g_staticParams.szDIAWindowsFile); | ^~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearchManager.cpp:1597:17: note: 'sprintf' output between 42 and 553 bytes into a destination of size 256 1597 | sprintf(szErrorMsg, " Error - cannot read DIA window file \"%s\".\n", g_staticParams.szDIAWindowsFile); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearchManager.cpp:223:73: warning: '%s' directive writing up to 1023 bytes into a region of size 987 [-Wformat-overflow=] 223 | sprintf(szErrorMsg, " Error - could not create directory \"%s\".\n", szDecoyDir); | ^~ ~~~~~~~~~~ In function 'bool UpdateInputFile(InputFileInfo*)', inlined from 'virtual bool CometSearchManager::DoSearch()' at CometSearchManager.cpp:1606:35: CometSearchManager.cpp:223:20: note: 'sprintf' output between 41 and 1064 bytes into a destination of size 1024 223 | sprintf(szErrorMsg, " Error - could not create directory \"%s\".\n", szDecoyDir); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearchManager.cpp: In member function 'virtual bool CometSearchManager::DoSearch()': CometSearchManager.cpp:1700:76: warning: '%s' directive writing up to 1023 bytes into a region of size 219 [-Wformat-overflow=] 1700 | sprintf(szErrorMsg, " Error - cannot write to decoy file \"%s\".\n", szOutputDecoySQT); | ^~ ~~~~~~~~~~~~~~~~ CometSearchManager.cpp:1700:23: note: 'sprintf' output between 41 and 1064 bytes into a destination of size 256 1700 | sprintf(szErrorMsg, " Error - cannot write to decoy file \"%s\".\n", szOutputDecoySQT); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearchManager.cpp:1675:67: warning: '%s' directive writing up to 1023 bytes into a region of size 225 [-Wformat-overflow=] 1675 | sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputSQT); | ^~ ~~~~~~~~~~~ CometSearchManager.cpp:1675:20: note: 'sprintf' output between 35 and 1058 bytes into a destination of size 256 1675 | sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputSQT); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearchManager.cpp:1763:76: warning: '%s' directive writing up to 1023 bytes into a region of size 219 [-Wformat-overflow=] 1763 | sprintf(szErrorMsg, " Error - cannot write to decoy file \"%s\".\n", szOutputDecoyTxt); | ^~ ~~~~~~~~~~~~~~~~ CometSearchManager.cpp:1763:23: note: 'sprintf' output between 41 and 1064 bytes into a destination of size 256 1763 | sprintf(szErrorMsg, " Error - cannot write to decoy file \"%s\".\n", szOutputDecoyTxt); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearchManager.cpp:1737:67: warning: '%s' directive writing up to 1023 bytes into a region of size 225 [-Wformat-overflow=] 1737 | sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputTxt); | ^~ ~~~~~~~~~~~ CometSearchManager.cpp:1737:20: note: 'sprintf' output between 35 and 1058 bytes into a destination of size 256 1737 | sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputTxt); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearchManager.cpp:1826:76: warning: '%s' directive writing up to 1023 bytes into a region of size 219 [-Wformat-overflow=] 1826 | sprintf(szErrorMsg, " Error - cannot write to decoy file \"%s\".\n", szOutputDecoyPepXML); | ^~ ~~~~~~~~~~~~~~~~~~~ CometSearchManager.cpp:1826:23: note: 'sprintf' output between 41 and 1064 bytes into a destination of size 256 1826 | sprintf(szErrorMsg, " Error - cannot write to decoy file \"%s\".\n", szOutputDecoyPepXML); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearchManager.cpp:1800:67: warning: '%s' directive writing up to 1023 bytes into a region of size 225 [-Wformat-overflow=] 1800 | sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputPepXML); | ^~ ~~~~~~~~~~~~~~ CometSearchManager.cpp:1800:20: note: 'sprintf' output between 35 and 1058 bytes into a destination of size 256 1800 | sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputPepXML); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearchManager.cpp:1854:67: warning: '%s' directive writing up to 1023 bytes into a region of size 225 [-Wformat-overflow=] 1854 | sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputPercolator); | ^~ ~~~~~~~~~~~~~~~~~~ CometSearchManager.cpp:1854:20: note: 'sprintf' output between 35 and 1058 bytes into a destination of size 256 1854 | sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputPercolator); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearchManager.cpp:1975:32: warning: '%s' directive writing up to 255 bytes into a region of size 128 [-Wformat-overflow=] 1975 | sprintf(szOut, "%s", szStatusMsg); | ^~ ~~~~~~~~~~~ CometSearchManager.cpp:1975:23: note: 'sprintf' output between 1 and 256 bytes into a destination of size 128 1975 | sprintf(szOut, "%s", szStatusMsg); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearchManager.cpp:364:66: warning: '%s' directive writing up to 511 bytes into a region of size 508 [-Wformat-overflow=] 364 | sprintf(szOutFileTimeString+strlen(szOutFileTimeString), " on %s", g_staticParams.szHostName); | ^~ ~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void CalcRunTime(time_t)', inlined from 'virtual bool CometSearchManager::DoSearch()' at CometSearchManager.cpp:2111:24: CometSearchManager.cpp:364:11: note: 'sprintf' output between 5 and 516 bytes into a destination of size 512 364 | sprintf(szOutFileTimeString+strlen(szOutFileTimeString), " on %s", g_staticParams.szHostName); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/comet-ms-2019015+cleaned1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometCheckForUpdates.cpp -c CometCheckForUpdates.cpp: In static member function 'static void CometCheckForUpdates::SendAnalyticsHit()': CometCheckForUpdates.cpp:161:11: warning: '%s' directive output may be truncated writing up to 1023 bytes into a region of size between 895 and 898 [-Wformat-truncation=] 161 | "%s\r\n", host, (int)strlen(postData), postData); | ^~ ~~~~~~~~ CometCheckForUpdates.cpp:156:12: note: 'snprintf' output between 129 and 1155 bytes into a destination of size 1024 156 | snprintf(message, 1024, | ~~~~~~~~^~~~~~~~~~~~~~~ 157 | "POST /collect HTTP/1.1\r\n" | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 158 | "Host: %s\r\n" | ~~~~~~~~~~~~~~ 159 | "Content-type: application/x-www-form-urlencoded\r\n" | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 160 | "Content-length: %d\r\n\r\n" | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 161 | "%s\r\n", host, (int)strlen(postData), postData); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ar rcs libcometsearch.a Threading.o CometInterfaces.o CometSearch.o CometPreprocess.o CometPostAnalysis.o CometMassSpecUtils.o CometWriteOut.o CometWriteSqt.o CometWritePepXML.o CometWritePercolator.o CometWriteTxt.o CometSearchManager.o CometCheckForUpdates.o make[3]: Leaving directory '/build/comet-ms-2019015+cleaned1/CometSearch' g++ -g -O2 -ffile-prefix-map=/build/comet-ms-2019015+cleaned1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch CometSearch/CometCheckForUpdates.cpp CometSearch/CometMassSpecUtils.cpp CometSearch/CometPreprocess.cpp CometSearch/CometSearchManager.cpp CometSearch/CometWritePepXML.cpp CometSearch/CometWriteSqt.cpp CometSearch/Threading.cpp CometSearch/CometInterfaces.cpp CometSearch/CometPostAnalysis.cpp CometSearch/CometSearch.cpp CometSearch/CometWriteOut.cpp CometSearch/CometWritePercolator.cpp CometSearch/CometWriteTxt.cpp Comet.cpp -c CometSearch/CometCheckForUpdates.cpp: In static member function 'static void CometCheckForUpdates::SendAnalyticsHit()': CometSearch/CometCheckForUpdates.cpp:146:17: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 146 | char *host = "www.google-analytics.com"; | ^~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearch/CometCheckForUpdates.cpp:161:11: warning: '%s' directive output may be truncated writing up to 1023 bytes into a region of size between 895 and 898 [-Wformat-truncation=] 161 | "%s\r\n", host, (int)strlen(postData), postData); | ^~ ~~~~~~~~ CometSearch/CometCheckForUpdates.cpp:156:12: note: 'snprintf' output between 129 and 1155 bytes into a destination of size 1024 156 | snprintf(message, 1024, | ~~~~~~~~^~~~~~~~~~~~~~~ 157 | "POST /collect HTTP/1.1\r\n" | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 158 | "Host: %s\r\n" | ~~~~~~~~~~~~~~ 159 | "Content-type: application/x-www-form-urlencoded\r\n" | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 160 | "Content-length: %d\r\n\r\n" | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 161 | "%s\r\n", host, (int)strlen(postData), postData); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from CometSearch/CometPreprocess.h:21, from CometSearch/CometPreprocess.cpp:19: CometSearch/ThreadPool.h: In instantiation of 'ThreadManager::ThreadManager(ThreadPool*) [with T = PreprocessThreadData*]': CometSearch/ThreadPool.h:69:10: required from 'ThreadPool::ThreadPool(ThreadProc, int, int, int) [with T = PreprocessThreadData*; ThreadProc = void (*)(PreprocessThreadData*)]' CometSearch/CometPreprocess.cpp:74:65: required from here CometSearch/ThreadPool.h:257:13: warning: cast between incompatible function types from 'uint32_t (*)(void*)' {aka 'unsigned int (*)(void*)'} to 'ThreadProc' {aka 'void* (*)(void*)'} [-Wcast-function-type] 257 | reinterpret_cast(ThreadManager::ThreadRoutingFunction), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearch/CometSearchManager.cpp: In static member function 'static bool CometSearchManager::WriteIndexedDatabase()': CometSearch/CometSearchManager.cpp:2756:28: warning: '.idx' directive writing 4 bytes into a region of size between 1 and 512 [-Wformat-overflow=] 2756 | sprintf(szIndexFile, "%s.idx", g_staticParams.databaseInfo.szDatabase); | ^~~~ CometSearch/CometSearchManager.cpp:2756:11: note: 'sprintf' output between 5 and 516 bytes into a destination of size 512 2756 | sprintf(szIndexFile, "%s.idx", g_staticParams.databaseInfo.szDatabase); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearch/CometSearchManager.cpp: In member function 'virtual bool CometSearchManager::DoSearch()': CometSearch/CometSearchManager.cpp:416:34: warning: '%d' directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 416 | sprintf(szIsotope, "ISOTOPE%d", g_staticParams.tolerances.iIsotopeError); | ^~ In function 'void PrintOutfileHeader()', inlined from 'virtual bool CometSearchManager::DoSearch()' at CometSearch/CometSearchManager.cpp:1559:25: CometSearch/CometSearchManager.cpp:416:26: note: directive argument in the range [1, 2147483647] 416 | sprintf(szIsotope, "ISOTOPE%d", g_staticParams.tolerances.iIsotopeError); | ^~~~~~~~~~~ CometSearch/CometSearchManager.cpp:416:14: note: 'sprintf' output between 9 and 18 bytes into a destination of size 16 416 | sprintf(szIsotope, "ISOTOPE%d", g_staticParams.tolerances.iIsotopeError); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearch/CometSearchManager.cpp: In member function 'virtual bool CometSearchManager::DoSearch()': CometSearch/CometSearchManager.cpp:1597:71: warning: '%s' directive writing up to 511 bytes into a region of size 218 [-Wformat-overflow=] 1597 | sprintf(szErrorMsg, " Error - cannot read DIA window file \"%s\".\n", g_staticParams.szDIAWindowsFile); | ^~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearch/CometSearchManager.cpp:1597:17: note: 'sprintf' output between 42 and 553 bytes into a destination of size 256 1597 | sprintf(szErrorMsg, " Error - cannot read DIA window file \"%s\".\n", g_staticParams.szDIAWindowsFile); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearch/CometSearchManager.cpp:223:73: warning: '%s' directive writing up to 1023 bytes into a region of size 987 [-Wformat-overflow=] 223 | sprintf(szErrorMsg, " Error - could not create directory \"%s\".\n", szDecoyDir); | ^~ ~~~~~~~~~~ In function 'bool UpdateInputFile(InputFileInfo*)', inlined from 'virtual bool CometSearchManager::DoSearch()' at CometSearch/CometSearchManager.cpp:1606:35: CometSearch/CometSearchManager.cpp:223:20: note: 'sprintf' output between 41 and 1064 bytes into a destination of size 1024 223 | sprintf(szErrorMsg, " Error - could not create directory \"%s\".\n", szDecoyDir); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearch/CometSearchManager.cpp: In member function 'virtual bool CometSearchManager::DoSearch()': CometSearch/CometSearchManager.cpp:1700:76: warning: '%s' directive writing up to 1023 bytes into a region of size 219 [-Wformat-overflow=] 1700 | sprintf(szErrorMsg, " Error - cannot write to decoy file \"%s\".\n", szOutputDecoySQT); | ^~ ~~~~~~~~~~~~~~~~ CometSearch/CometSearchManager.cpp:1700:23: note: 'sprintf' output between 41 and 1064 bytes into a destination of size 256 1700 | sprintf(szErrorMsg, " Error - cannot write to decoy file \"%s\".\n", szOutputDecoySQT); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearch/CometSearchManager.cpp:1675:67: warning: '%s' directive writing up to 1023 bytes into a region of size 225 [-Wformat-overflow=] 1675 | sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputSQT); | ^~ ~~~~~~~~~~~ CometSearch/CometSearchManager.cpp:1675:20: note: 'sprintf' output between 35 and 1058 bytes into a destination of size 256 1675 | sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputSQT); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearch/CometSearchManager.cpp:1763:76: warning: '%s' directive writing up to 1023 bytes into a region of size 219 [-Wformat-overflow=] 1763 | sprintf(szErrorMsg, " Error - cannot write to decoy file \"%s\".\n", szOutputDecoyTxt); | ^~ ~~~~~~~~~~~~~~~~ CometSearch/CometSearchManager.cpp:1763:23: note: 'sprintf' output between 41 and 1064 bytes into a destination of size 256 1763 | sprintf(szErrorMsg, " Error - cannot write to decoy file \"%s\".\n", szOutputDecoyTxt); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearch/CometSearchManager.cpp:1737:67: warning: '%s' directive writing up to 1023 bytes into a region of size 225 [-Wformat-overflow=] 1737 | sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputTxt); | ^~ ~~~~~~~~~~~ CometSearch/CometSearchManager.cpp:1737:20: note: 'sprintf' output between 35 and 1058 bytes into a destination of size 256 1737 | sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputTxt); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearch/CometSearchManager.cpp:1826:76: warning: '%s' directive writing up to 1023 bytes into a region of size 219 [-Wformat-overflow=] 1826 | sprintf(szErrorMsg, " Error - cannot write to decoy file \"%s\".\n", szOutputDecoyPepXML); | ^~ ~~~~~~~~~~~~~~~~~~~ CometSearch/CometSearchManager.cpp:1826:23: note: 'sprintf' output between 41 and 1064 bytes into a destination of size 256 1826 | sprintf(szErrorMsg, " Error - cannot write to decoy file \"%s\".\n", szOutputDecoyPepXML); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearch/CometSearchManager.cpp:1800:67: warning: '%s' directive writing up to 1023 bytes into a region of size 225 [-Wformat-overflow=] 1800 | sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputPepXML); | ^~ ~~~~~~~~~~~~~~ CometSearch/CometSearchManager.cpp:1800:20: note: 'sprintf' output between 35 and 1058 bytes into a destination of size 256 1800 | sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputPepXML); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearch/CometSearchManager.cpp:1854:67: warning: '%s' directive writing up to 1023 bytes into a region of size 225 [-Wformat-overflow=] 1854 | sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputPercolator); | ^~ ~~~~~~~~~~~~~~~~~~ CometSearch/CometSearchManager.cpp:1854:20: note: 'sprintf' output between 35 and 1058 bytes into a destination of size 256 1854 | sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputPercolator); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearch/CometSearchManager.cpp:1975:32: warning: '%s' directive writing up to 255 bytes into a region of size 128 [-Wformat-overflow=] 1975 | sprintf(szOut, "%s", szStatusMsg); | ^~ ~~~~~~~~~~~ CometSearch/CometSearchManager.cpp:1975:23: note: 'sprintf' output between 1 and 256 bytes into a destination of size 128 1975 | sprintf(szOut, "%s", szStatusMsg); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearch/CometSearchManager.cpp:364:66: warning: '%s' directive writing up to 511 bytes into a region of size 508 [-Wformat-overflow=] 364 | sprintf(szOutFileTimeString+strlen(szOutFileTimeString), " on %s", g_staticParams.szHostName); | ^~ ~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void CalcRunTime(time_t)', inlined from 'virtual bool CometSearchManager::DoSearch()' at CometSearch/CometSearchManager.cpp:2111:24: CometSearch/CometSearchManager.cpp:364:11: note: 'sprintf' output between 5 and 516 bytes into a destination of size 512 364 | sprintf(szOutFileTimeString+strlen(szOutFileTimeString), " on %s", g_staticParams.szHostName); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearch/CometWritePepXML.cpp: In static member function 'static void CometWritePepXML::ReadInstrument(char*, char*)': CometSearch/CometWritePepXML.cpp:910:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 910 | GetVal(szMsInstrumentElement, "\"msModel\" value", szModel); | ^~~~~~~~~~~~~~~~~~~ CometSearch/CometWritePepXML.cpp:911:52: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 911 | GetVal(szMsInstrumentElement, "\"msManufacturer\" value", szManufacturer); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from CometSearch/CometPostAnalysis.cpp:19: CometSearch/ThreadPool.h: In instantiation of 'ThreadManager::ThreadManager(ThreadPool*) [with T = PostAnalysisThreadData*]': CometSearch/ThreadPool.h:69:10: required from 'ThreadPool::ThreadPool(ThreadProc, int, int, int) [with T = PostAnalysisThreadData*; ThreadProc = void (*)(PostAnalysisThreadData*)]' CometSearch/CometPostAnalysis.cpp:46:38: required from here CometSearch/ThreadPool.h:257:13: warning: cast between incompatible function types from 'uint32_t (*)(void*)' {aka 'unsigned int (*)(void*)'} to 'ThreadProc' {aka 'void* (*)(void*)'} [-Wcast-function-type] 257 | reinterpret_cast(ThreadManager::ThreadRoutingFunction), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearch/CometSearch.cpp: In member function 'int CometSearch::twiddle(int*, int*, int*, int*)': CometSearch/CometSearch.cpp:4973:17: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 4973 | register int i, j, k; | ^ CometSearch/CometSearch.cpp:4973:20: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 4973 | register int i, j, k; | ^ CometSearch/CometSearch.cpp:4973:23: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 4973 | register int i, j, k; | ^ In file included from CometSearch/CometSearch.cpp:19: CometSearch/ThreadPool.h: In instantiation of 'ThreadManager::ThreadManager(ThreadPool*) [with T = SearchThreadData*]': CometSearch/ThreadPool.h:69:10: required from 'ThreadPool::ThreadPool(ThreadProc, int, int, int) [with T = SearchThreadData*; ThreadProc = void (*)(SearchThreadData*)]' CometSearch/CometSearch.cpp:138:66: required from here CometSearch/ThreadPool.h:257:13: warning: cast between incompatible function types from 'uint32_t (*)(void*)' {aka 'unsigned int (*)(void*)'} to 'ThreadProc' {aka 'void* (*)(void*)'} [-Wcast-function-type] 257 | reinterpret_cast(ThreadManager::ThreadRoutingFunction), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearch/CometWriteOut.cpp: In static member function 'static bool CometWriteOut::PrintResults(int, bool, FILE*)': CometSearch/CometWriteOut.cpp:124:32: warning: '%.5d' directive writing between 5 and 11 bytes into a region of size between 0 and 1022 [-Wformat-overflow=] 124 | sprintf(szOutput, "%s/%s.%.5d.%.5d.%d.out", | ^~~~ CometSearch/CometWriteOut.cpp:124:14: note: 'sprintf' output between 20 and 1064 bytes into a destination of size 1024 124 | sprintf(szOutput, "%s/%s.%.5d.%.5d.%d.out", | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 125 | g_staticParams.inputFile.szBaseName, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 126 | pStr, | ~~~~~ 127 | pQuery->_spectrumInfoInternal.iScanNumber, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 128 | pQuery->_spectrumInfoInternal.iScanNumber, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 129 | pQuery->_spectrumInfoInternal.iChargeState); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearch/CometWriteOut.cpp:115:35: warning: '%s' directive writing up to 511 bytes into a region of size between 506 and 1017 [-Wformat-overflow=] 115 | sprintf(szOutput, "%s_decoy/%s.%.5d.%.5d.%d.out", | ^~ CometSearch/CometWriteOut.cpp:115:14: note: 'sprintf' output between 26 and 1070 bytes into a destination of size 1024 115 | sprintf(szOutput, "%s_decoy/%s.%.5d.%.5d.%d.out", | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 116 | g_staticParams.inputFile.szBaseName, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 117 | pStr, | ~~~~~ 118 | pQuery->_spectrumInfoInternal.iScanNumber, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 119 | pQuery->_spectrumInfoInternal.iScanNumber, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 120 | pQuery->_spectrumInfoInternal.iChargeState); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearch/CometWriteOut.cpp:273:28: warning: '%+d' directive writing between 2 and 11 bytes into a region of size 9 [-Wformat-overflow=] 273 | sprintf(szTempStr, " %+d", iLenMaxDuplicates); | ^~~ CometSearch/CometWriteOut.cpp:273:26: note: directive argument in the range [1, 2147483647] 273 | sprintf(szTempStr, " %+d", iLenMaxDuplicates); | ^~~~~~ CometSearch/CometWriteOut.cpp:273:14: note: 'sprintf' output between 4 and 13 bytes into a destination of size 10 273 | sprintf(szTempStr, " %+d", iLenMaxDuplicates); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometSearch/CometWriteOut.cpp:151:59: warning: '%s' directive writing up to 1023 bytes into a region of size 226 [-Wformat-overflow=] 151 | sprintf(szErrorMsg, " Error - cannot write to file %s.\n", szOutput); | ^~ ~~~~~~~~ CometSearch/CometWriteOut.cpp:151:14: note: 'sprintf' output between 33 and 1056 bytes into a destination of size 256 151 | sprintf(szErrorMsg, " Error - cannot write to file %s.\n", szOutput); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Comet.cpp: In function 'void ProcessCmdLine(int, char**, char*, std::vector&, CometInterfaces::ICometSearchManager*)': Comet.cpp:1396:75: warning: '%s' directive writing up to 511 bytes into a region of size 235 [-Wformat-overflow=] 1396 | sprintf(szErrorMsg+strlen(szErrorMsg), " Error - input file \"%s\" not found.\n", pInputFileInfo->szFileName); | ^~ Comet.cpp:1396:20: note: 'sprintf' output between 35 and 546 bytes into a destination of size 256 1396 | sprintf(szErrorMsg+strlen(szErrorMsg), " Error - input file \"%s\" not found.\n", pInputFileInfo->szFileName); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd CometSearch ; make make[3]: Entering directory '/build/comet-ms-2019015+cleaned1/CometSearch' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. ar rcs libcometsearch.a Threading.o CometInterfaces.o CometSearch.o CometPreprocess.o CometPostAnalysis.o CometMassSpecUtils.o CometWriteOut.o CometWriteSqt.o CometWritePepXML.o CometWritePercolator.o CometWriteTxt.o CometSearchManager.o CometCheckForUpdates.o make[3]: Leaving directory '/build/comet-ms-2019015+cleaned1/CometSearch' g++ Comet.o CometSearch/CometCheckForUpdates.o CometSearch/CometMassSpecUtils.o CometSearch/CometPreprocess.o CometSearch/CometSearchManager.o CometSearch/CometWritePepXML.o CometSearch/CometWriteSqt.o CometSearch/Threading.o CometSearch/CometInterfaces.o CometSearch/CometPostAnalysis.o CometSearch/CometSearch.o CometSearch/CometWriteOut.o CometSearch/CometWritePercolator.o CometSearch/CometWriteTxt.o -o comet-ms -g -O2 -ffile-prefix-map=/build/comet-ms-2019015+cleaned1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -L/usr/lib -lmstoolkitlite -lm -lpthread make[2]: Leaving directory '/build/comet-ms-2019015+cleaned1' make[1]: Leaving directory '/build/comet-ms-2019015+cleaned1' dh_auto_test create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep rm -f -- debian/comet-ms.substvars rm -fr -- debian/.debhelper/generated/comet-ms/ debian/comet-ms/ debian/tmp/ dh_installdirs install -m0755 -d debian/comet-ms/usr/bin dh_auto_install --destdir=debian/comet-ms/ install -m0755 -d /build/comet-ms-2019015\+cleaned1/debian/comet-ms dh_install install -m0755 -d debian/comet-ms/usr/bin cp --reflink=auto -a ./comet-ms debian/comet-ms/usr/bin/ dh_installdocs install -m0755 -d debian/comet-ms/usr/share/doc/comet-ms install -p -m0644 debian/copyright debian/comet-ms/usr/share/doc/comet-ms/copyright dh_installchangelogs install -m0755 -d debian/comet-ms/usr/share/doc/comet-ms install -p -m0644 debian/.debhelper/generated/comet-ms/dh_installchangelogs.dch.trimmed debian/comet-ms/usr/share/doc/comet-ms/changelog.Debian dh_installman install -m0755 -d debian/comet-ms/usr/share/man/man1/ install -p -m0644 ./debian/comet-ms.1 debian/comet-ms/usr/share/man/man1/comet-ms.1 man-recode --to-code UTF-8 --suffix .dh-new debian/comet-ms/usr/share/man/man1/comet-ms.1 mv debian/comet-ms/usr/share/man/man1/comet-ms.1.dh-new debian/comet-ms/usr/share/man/man1/comet-ms.1 chmod 0644 -- debian/comet-ms/usr/share/man/man1/comet-ms.1 dh_perl dh_link dh_strip_nondeterminism dh_compress cd debian/comet-ms chmod a-x usr/share/doc/comet-ms/changelog.Debian usr/share/man/man1/comet-ms.1 gzip -9nf usr/share/doc/comet-ms/changelog.Debian usr/share/man/man1/comet-ms.1 cd '/build/comet-ms-2019015+cleaned1' dh_fixperms find debian/comet-ms -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/comet-ms ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/comet-ms/usr/share/doc -type f -a -true -a ! -regex 'debian/comet-ms/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/comet-ms/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/comet-ms/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/comet-ms -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/comet-ms/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing dh_dwz dwz -- debian/comet-ms/usr/bin/comet-ms dh_strip install -m0755 -d debian/.debhelper/comet-ms/dbgsym-root/usr/lib/debug/.build-id/8a objcopy --only-keep-debug --compress-debug-sections debian/comet-ms/usr/bin/comet-ms debian/.debhelper/comet-ms/dbgsym-root/usr/lib/debug/.build-id/8a/421b392caa69163de33811d6e7f084585f508d.debug chmod 0644 -- debian/.debhelper/comet-ms/dbgsym-root/usr/lib/debug/.build-id/8a/421b392caa69163de33811d6e7f084585f508d.debug chown 0:0 -- debian/.debhelper/comet-ms/dbgsym-root/usr/lib/debug/.build-id/8a/421b392caa69163de33811d6e7f084585f508d.debug strip --remove-section=.comment --remove-section=.note debian/comet-ms/usr/bin/comet-ms objcopy --add-gnu-debuglink debian/.debhelper/comet-ms/dbgsym-root/usr/lib/debug/.build-id/8a/421b392caa69163de33811d6e7f084585f508d.debug debian/comet-ms/usr/bin/comet-ms install -m0755 -d debian/.debhelper/comet-ms/dbgsym-root/usr/share/doc ln -s comet-ms debian/.debhelper/comet-ms/dbgsym-root/usr/share/doc/comet-ms-dbgsym install -m0755 -d debian/.debhelper/comet-ms dh_makeshlibs rm -f debian/comet-ms/DEBIAN/shlibs dh_shlibdeps install -m0755 -d debian/comet-ms/DEBIAN dpkg-shlibdeps -Tdebian/comet-ms.substvars debian/comet-ms/usr/bin/comet-ms dh_installdeb install -m0755 -d debian/comet-ms/DEBIAN dh_gencontrol install -m0755 -d debian/comet-ms/DEBIAN echo misc:Depends= >> debian/comet-ms.substvars echo misc:Pre-Depends= >> debian/comet-ms.substvars install -m0755 -d debian/.debhelper/comet-ms/dbgsym-root/DEBIAN dpkg-gencontrol -pcomet-ms -ldebian/changelog -Tdebian/comet-ms.substvars -Pdebian/.debhelper/comet-ms/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=comet-ms-dbgsym "-DDepends=comet-ms (= \${binary:Version})" "-DDescription=debug symbols for comet-ms" -DBuild-Ids=8a421b392caa69163de33811d6e7f084585f508d -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/comet-ms/dbgsym-root/DEBIAN/control chown 0:0 -- debian/.debhelper/comet-ms/dbgsym-root/DEBIAN/control dpkg-gencontrol -pcomet-ms -ldebian/changelog -Tdebian/comet-ms.substvars -Pdebian/comet-ms chmod 0644 -- debian/comet-ms/DEBIAN/control chown 0:0 -- debian/comet-ms/DEBIAN/control dh_md5sums install -m0755 -d debian/comet-ms/DEBIAN cd debian/comet-ms >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/comet-ms/DEBIAN/md5sums chown 0:0 -- debian/comet-ms/DEBIAN/md5sums install -m0755 -d debian/.debhelper/comet-ms/dbgsym-root/DEBIAN cd debian/.debhelper/comet-ms/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/comet-ms/dbgsym-root/DEBIAN/md5sums chown 0:0 -- debian/.debhelper/comet-ms/dbgsym-root/DEBIAN/md5sums dh_builddeb dpkg-deb --build debian/comet-ms .. dpkg-deb --root-owner-group --build debian/.debhelper/comet-ms/dbgsym-root .. dpkg-deb: building package 'comet-ms' in '../comet-ms_2019015+cleaned1-3_amd64.deb'. dpkg-deb: building package 'comet-ms-dbgsym' in '../comet-ms-dbgsym_2019015+cleaned1-3_amd64.deb'. dpkg-genbuildinfo --build=binary -O../comet-ms_2019015+cleaned1-3_amd64.buildinfo dpkg-genchanges --build=binary -O../comet-ms_2019015+cleaned1-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration 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/3437212 and its subdirectories I: Current time: Thu May 16 09:15:19 -12 2024 I: pbuilder-time-stamp: 1715894119 Fri Apr 14 14:52:20 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net. Fri Apr 14 14:52:20 UTC 2023 I: Preparing to do remote build '2' on ionos11-amd64.debian.net. Fri Apr 14 14:55:02 UTC 2023 I: Deleting $TMPDIR on ionos11-amd64.debian.net. Fri Apr 14 14:55:02 UTC 2023 I: comet-ms_2019015+cleaned1-3_amd64.changes: Format: 1.8 Date: Thu, 13 Aug 2020 23:49:04 +0200 Source: comet-ms Binary: comet-ms comet-ms-dbgsym Architecture: amd64 Version: 2019015+cleaned1-3 Distribution: unstable Urgency: low Maintainer: The Debichem Group Changed-By: Filippo Rusconi Description: comet-ms - Tandem mass spectrometry (MS/MS) search engine Closes: 929760 Changes: comet-ms (2019015+cleaned1-3) unstable; urgency=low . * d/rules: Fix problem with invoking 'make' for building the software. Replace with dh_auto_build (thanks to Helmut Grohne for the report and the patch; Closes: #929760) Checksums-Sha1: 40b14b45d996f12d2919321c82596db79ac8e623 1887264 comet-ms-dbgsym_2019015+cleaned1-3_amd64.deb d88e93c486ccc537d03291145a749a7cbf5ddbb2 5593 comet-ms_2019015+cleaned1-3_amd64.buildinfo 2e5c32c43f31411bf9b8b4a626ddbb987b015220 828172 comet-ms_2019015+cleaned1-3_amd64.deb Checksums-Sha256: b0950ba6eb0253e7a4b4536d9e98fa7181b80b26520524cc98bb539e547e9228 1887264 comet-ms-dbgsym_2019015+cleaned1-3_amd64.deb 518bc9aaeb99b02f52390f1c012e28d30612bebf527724d11c90f4d40976c5fe 5593 comet-ms_2019015+cleaned1-3_amd64.buildinfo fe964e8c792cae605d56dbddd1b01061be0df0a1e3db2a09285b28f4fc88183a 828172 comet-ms_2019015+cleaned1-3_amd64.deb Files: f5df3f999019eee1bd0469139f213ece 1887264 debug optional comet-ms-dbgsym_2019015+cleaned1-3_amd64.deb d90b1b7158aefa903a15da41faee56c1 5593 science optional comet-ms_2019015+cleaned1-3_amd64.buildinfo 2b9c7f1b05e35247856fb711d7dfdf78 828172 science optional comet-ms_2019015+cleaned1-3_amd64.deb Fri Apr 14 14:55:04 UTC 2023 I: diffoscope 240 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.E4wVXJRa/comet-ms_2019015+cleaned1-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.E4wVXJRa/comet-ms_2019015+cleaned1-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.E4wVXJRa/comet-ms_2019015+cleaned1-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.E4wVXJRa/b1/comet-ms_2019015+cleaned1-3_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.E4wVXJRa/b2/comet-ms_2019015+cleaned1-3_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.368s) 0.368s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.046s) 0.046s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Fri Apr 14 14:55:20 UTC 2023 I: diffoscope 240 found no differences in the changes files, and a .buildinfo file also exists. Fri Apr 14 14:55:20 UTC 2023 I: comet-ms from bookworm built successfully and reproducibly on amd64. Fri Apr 14 14:55:23 UTC 2023 I: Submitting .buildinfo files to external archives: Fri Apr 14 14:55:23 UTC 2023 I: Submitting 8.0K b1/comet-ms_2019015+cleaned1-3_amd64.buildinfo.asc Fri Apr 14 14:55:24 UTC 2023 I: Submitting 8.0K b2/comet-ms_2019015+cleaned1-3_amd64.buildinfo.asc Fri Apr 14 14:55:25 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Apr 14 14:55:25 UTC 2023 I: Done submitting .buildinfo files. Fri Apr 14 14:55:25 UTC 2023 I: Removing signed comet-ms_2019015+cleaned1-3_amd64.buildinfo.asc files: removed './b1/comet-ms_2019015+cleaned1-3_amd64.buildinfo.asc' removed './b2/comet-ms_2019015+cleaned1-3_amd64.buildinfo.asc'