Fri Jul 30 00:30:27 UTC 2021 I: starting to build comet-ms/bullseye/arm64 on jenkins on '2021-07-30 00:30' Fri Jul 30 00:30:27 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_6/16541/console.log Fri Jul 30 00:30:27 UTC 2021 I: Downloading source for bullseye/comet-ms=2019015+cleaned1-3 --2021-07-30 00:30:27-- http://cdn-fastly.deb.debian.org/debian/pool/main/c/comet-ms/comet-ms_2019015+cleaned1-3.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2080 (2.0K) Saving to: ‘comet-ms_2019015+cleaned1-3.dsc’ 0K .. 100% 170M=0s 2021-07-30 00:30:27 (170 MB/s) - ‘comet-ms_2019015+cleaned1-3.dsc’ saved [2080/2080] Fri Jul 30 00:30:27 UTC 2021 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 Jul 30 00:30:27 UTC 2021 I: Checking whether the package is not for us Fri Jul 30 00:30:27 UTC 2021 I: Starting 1st build on remote node codethink10-arm64.debian.net. Fri Jul 30 00:30:27 UTC 2021 I: Preparing to do remote build '1' on codethink10-arm64.debian.net. Fri Jul 30 00:35:40 UTC 2021 I: Deleting $TMPDIR on codethink10-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Jul 29 12:30:30 -12 2021 I: pbuilder-time-stamp: 1627605030 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration 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: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.UNQUXg3y/trustedkeys.kbx': General error 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: failed to verify signature on ./comet-ms_2019015+cleaned1-3.dsc 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/19155/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' DISTRIBUTION='' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' 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='19155' 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/tmp.bCbKTfx8pI/pbuilderrc_mxyz --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.bCbKTfx8pI/b1 --logfile b1/build.log comet-ms_2019015+cleaned1-3.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink10-arm64 4.15.0-151-generic #157-Ubuntu SMP Fri Jul 9 21:03:48 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 -rwxr-xr-x 1 root root 1282512 Jun 21 14:26 bash -rwxr-xr-x 3 root root 34808 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 14264 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 39832 Sep 22 2020 cat -rwxr-xr-x 1 root root 64512 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 60368 Sep 22 2020 chmod -rwxr-xr-x 1 root root 64528 Sep 22 2020 chown -rwxr-xr-x 1 root root 138896 Sep 22 2020 cp -rwxr-xr-x 1 root root 129544 Dec 10 2020 dash -rwxr-xr-x 1 root root 101384 Sep 22 2020 date -rwxr-xr-x 1 root root 80984 Sep 22 2020 dd -rwxr-xr-x 1 root root 89824 Sep 22 2020 df -rwxr-xr-x 1 root root 143088 Sep 22 2020 dir -rwxr-xr-x 1 root root 76152 Feb 7 02:38 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 35632 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 31512 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 64856 Feb 7 02:38 findmnt -rwsr-xr-x 1 root root 34824 Feb 26 04:12 fusermount -rwxr-xr-x 1 root root 178400 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe -rwxr-xr-x 1 root root 93744 Mar 2 11:30 gzip -rwxr-xr-x 1 root root 18440 Nov 6 2019 hostname -rwxr-xr-x 1 root root 68720 Sep 22 2020 ln -rwxr-xr-x 1 root root 52720 Feb 7 2020 login -rwxr-xr-x 1 root root 143088 Sep 22 2020 ls -rwxr-xr-x 1 root root 161960 Feb 7 02:38 lsblk -rwxr-xr-x 1 root root 85200 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 68744 Sep 22 2020 mknod -rwxr-xr-x 1 root root 43976 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 51368 Feb 7 02:38 more -rwsr-xr-x 1 root root 51360 Feb 7 02:38 mount -rwxr-xr-x 1 root root 14496 Feb 7 02:38 mountpoint -rwxr-xr-x 1 root root 134808 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35720 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Jun 21 14:26 rbash -> bash -rwxr-xr-x 1 root root 43872 Sep 22 2020 readlink -rwxr-xr-x 1 root root 68592 Sep 22 2020 rm -rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jul 26 21:25 sh -> dash -rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep -rwxr-xr-x 1 root root 72640 Sep 22 2020 stty -rwsr-xr-x 1 root root 67776 Feb 7 02:38 su -rwxr-xr-x 1 root root 35672 Sep 22 2020 sync -rwxr-xr-x 1 root root 535768 Feb 16 21:55 tar -rwxr-xr-x 1 root root 10568 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 89120 Sep 22 2020 touch -rwxr-xr-x 1 root root 31512 Sep 22 2020 true -rwxr-xr-x 1 root root 14264 Feb 26 04:12 ulockmgr_server -rwsr-xr-x 1 root root 30880 Feb 7 02:38 umount -rwxr-xr-x 1 root root 35640 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress -rwxr-xr-x 1 root root 143088 Sep 22 2020 vdir -rwxr-xr-x 1 root root 59584 Feb 7 02:38 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew I: user script /srv/workspace/pbuilder/19155/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: arm64 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 ... 19646 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} libicu67{a} libmagic-mgc{a} libmagic1{a} libmstoolkit-dev{a} libmstoolkit82{a} libosp5{a} libpipeline1{a} libsigsegv2{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, 44 newly installed, 0 to remove and 0 not upgraded. Need to get 21.2 MB of archives. After unpacking 81.6 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main arm64 bsdextrautils arm64 2.36.1-7 [141 kB] Get: 2 http://deb.debian.org/debian bullseye/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main arm64 groff-base arm64 1.22.4-6 [883 kB] Get: 4 http://deb.debian.org/debian bullseye/main arm64 libpipeline1 arm64 1.5.3-1 [33.0 kB] Get: 5 http://deb.debian.org/debian bullseye/main arm64 man-db arm64 2.9.4-2 [1336 kB] Get: 6 http://deb.debian.org/debian bullseye/main arm64 sgml-base all 1.30 [15.1 kB] Get: 7 http://deb.debian.org/debian bullseye/main arm64 sensible-utils all 0.0.14 [14.8 kB] Get: 8 http://deb.debian.org/debian bullseye/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB] Get: 9 http://deb.debian.org/debian bullseye/main arm64 libmagic1 arm64 1:5.39-3 [121 kB] Get: 10 http://deb.debian.org/debian bullseye/main arm64 file arm64 1:5.39-3 [69.1 kB] Get: 11 http://deb.debian.org/debian bullseye/main arm64 gettext-base arm64 0.21-4 [173 kB] Get: 12 http://deb.debian.org/debian bullseye/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main arm64 m4 arm64 1.4.18-5 [199 kB] Get: 14 http://deb.debian.org/debian bullseye/main arm64 autoconf all 2.69-14 [313 kB] Get: 15 http://deb.debian.org/debian bullseye/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 16 http://deb.debian.org/debian bullseye/main arm64 automake all 1:1.16.3-2 [814 kB] Get: 17 http://deb.debian.org/debian bullseye/main arm64 autopoint all 0.21-4 [510 kB] Get: 18 http://deb.debian.org/debian bullseye/main arm64 libdebhelper-perl all 13.3.4 [189 kB] Get: 19 http://deb.debian.org/debian bullseye/main arm64 libtool all 2.4.6-15 [513 kB] Get: 20 http://deb.debian.org/debian bullseye/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 21 http://deb.debian.org/debian bullseye/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 22 http://deb.debian.org/debian bullseye/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 23 http://deb.debian.org/debian bullseye/main arm64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 24 http://deb.debian.org/debian bullseye/main arm64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 25 http://deb.debian.org/debian bullseye/main arm64 libelf1 arm64 0.183-1 [164 kB] Get: 26 http://deb.debian.org/debian bullseye/main arm64 dwz arm64 0.13+20210201-1 [155 kB] Get: 27 http://deb.debian.org/debian bullseye/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get: 28 http://deb.debian.org/debian bullseye/main arm64 libxml2 arm64 2.9.10+dfsg-6.7 [629 kB] Get: 29 http://deb.debian.org/debian bullseye/main arm64 gettext arm64 0.21-4 [1261 kB] Get: 30 http://deb.debian.org/debian bullseye/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 31 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 32 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB] Get: 33 http://deb.debian.org/debian bullseye/main arm64 xml-core all 0.18+nmu1 [23.8 kB] Get: 34 http://deb.debian.org/debian bullseye/main arm64 sgml-data all 2.0.11+nmu1 [179 kB] Get: 35 http://deb.debian.org/debian bullseye/main arm64 docbook all 4.5-6 [129 kB] Get: 36 http://deb.debian.org/debian bullseye/main arm64 libosp5 arm64 1.5.2-13+b2 [884 kB] Get: 37 http://deb.debian.org/debian bullseye/main arm64 opensp arm64 1.5.2-13+b2 [414 kB] Get: 38 http://deb.debian.org/debian bullseye/main arm64 docbook-to-man arm64 1:2.0.0-45 [75.6 kB] Get: 39 http://deb.debian.org/debian bullseye/main arm64 libexpat1 arm64 2.2.10-2 [83.1 kB] Get: 40 http://deb.debian.org/debian bullseye/main arm64 libexpat1-dev arm64 2.2.10-2 [126 kB] Get: 41 http://deb.debian.org/debian bullseye/main arm64 libmstoolkit82 arm64 82-7 [120 kB] Get: 42 http://deb.debian.org/debian bullseye/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2 [189 kB] Get: 43 http://deb.debian.org/debian bullseye/main arm64 libsqlite3-dev arm64 3.34.1-3 [911 kB] Get: 44 http://deb.debian.org/debian bullseye/main arm64 libmstoolkit-dev arm64 82-7 [131 kB] Fetched 21.2 MB in 0s (43.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19646 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-7_arm64.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../01-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_arm64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../03-libpipeline1_1.5.3-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_arm64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package sgml-base. Preparing to unpack .../05-sgml-base_1.30_all.deb ... Unpacking sgml-base (1.30) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../06-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../07-libmagic-mgc_1%3a5.39-3_arm64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../08-libmagic1_1%3a5.39-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.39-3) ... Selecting previously unselected package file. 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Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.25.3-1.1). 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 arm64 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 -j8 "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 -fdebug-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 -fdebug-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 -fdebug-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(ThreadPool::ThreadProc, int, int, int) [with T = SearchThreadData*; ThreadPool::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 -fdebug-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(ThreadPool::ThreadProc, int, int, int) [with T = PreprocessThreadData*; ThreadPool::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 -fdebug-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(ThreadPool::ThreadProc, int, int, int) [with T = PostAnalysisThreadData*; ThreadPool::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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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); | ^~ 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: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); | ^~ ~~~~~~~~~~ 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: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); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-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 -fdebug-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(ThreadPool::ThreadProc, int, int, int) [with T = PreprocessThreadData*; ThreadPool::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); | ^~ 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: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); | ^~ ~~~~~~~~~~ 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: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/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(ThreadPool::ThreadProc, int, int, int) [with T = PostAnalysisThreadData*; ThreadPool::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), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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(ThreadPool::ThreadProc, int, int, int) [with T = SearchThreadData*; ThreadPool::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); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -fdebug-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 -d debian/comet-ms/usr/bin dh_auto_install dh_install cp --reflink=auto -a ./comet-ms debian/comet-ms/usr/bin/ install -d debian/.debhelper/generated/comet-ms dh_installdocs install -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 -p -m0644 debian/changelog debian/comet-ms/usr/share/doc/comet-ms/changelog.Debian dh_installman install -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 -d debian/.debhelper/comet-ms/dbgsym-root/usr/lib/debug/.build-id/d2 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/d2/4ffcccd8c190b9b6a3af5f152524bd861fb7cf.debug chmod 0644 -- debian/.debhelper/comet-ms/dbgsym-root/usr/lib/debug/.build-id/d2/4ffcccd8c190b9b6a3af5f152524bd861fb7cf.debug chown 0:0 -- debian/.debhelper/comet-ms/dbgsym-root/usr/lib/debug/.build-id/d2/4ffcccd8c190b9b6a3af5f152524bd861fb7cf.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/d2/4ffcccd8c190b9b6a3af5f152524bd861fb7cf.debug debian/comet-ms/usr/bin/comet-ms install -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 dh_makeshlibs rm -f debian/comet-ms/DEBIAN/shlibs dh_shlibdeps install -d debian/comet-ms/DEBIAN dpkg-shlibdeps -Tdebian/comet-ms.substvars debian/comet-ms/usr/bin/comet-ms dh_installdeb dh_gencontrol echo misc:Depends= >> debian/comet-ms.substvars echo misc:Pre-Depends= >> debian/comet-ms.substvars install -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=d24ffcccd8c190b9b6a3af5f152524bd861fb7cf -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 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 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 --build debian/.debhelper/comet-ms/dbgsym-root .. dpkg-deb: building package 'comet-ms' in '../comet-ms_2019015+cleaned1-3_arm64.deb'. dpkg-deb: building package 'comet-ms-dbgsym' in '../comet-ms-dbgsym_2019015+cleaned1-3_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../comet-ms_2019015+cleaned1-3_arm64.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/19155 and its subdirectories I: Current time: Thu Jul 29 12:35:38 -12 2021 I: pbuilder-time-stamp: 1627605338 Fri Jul 30 00:35:41 UTC 2021 I: 1st build successful. Starting 2nd build on remote node codethink11-arm64.debian.net. Fri Jul 30 00:35:41 UTC 2021 I: Preparing to do remote build '2' on codethink11-arm64.debian.net. Fri Jul 30 00:40:28 UTC 2021 I: Deleting $TMPDIR on codethink11-arm64.debian.net. Fri Jul 30 00:40:29 UTC 2021 I: comet-ms_2019015+cleaned1-3_arm64.changes: Format: 1.8 Date: Thu, 13 Aug 2020 23:49:04 +0200 Source: comet-ms Binary: comet-ms comet-ms-dbgsym Architecture: arm64 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: 256faceddb784c364513e8ce20a426720ff09b25 1759748 comet-ms-dbgsym_2019015+cleaned1-3_arm64.deb b679fb1e206b4013b4bc968a3220c1093398c0d7 5300 comet-ms_2019015+cleaned1-3_arm64.buildinfo 5dbedba6ef1ebb83582db2d1e3c825e7b1924556 785752 comet-ms_2019015+cleaned1-3_arm64.deb Checksums-Sha256: b796bcba17fd14a930575fe603006d0ac5ccbc66eb7a15ad082f5bf2b8070928 1759748 comet-ms-dbgsym_2019015+cleaned1-3_arm64.deb 95e8c99a431d515f08de45c360e4658e6bf0805adb6dfd32c32e127474924433 5300 comet-ms_2019015+cleaned1-3_arm64.buildinfo f5dda4577babbd9ab368bfd34b95b535ca95cf3b22090f49ddf751c0b3159731 785752 comet-ms_2019015+cleaned1-3_arm64.deb Files: 51c2d00aabe4f60ce33248f58fa14868 1759748 debug optional comet-ms-dbgsym_2019015+cleaned1-3_arm64.deb 7a4d62c454259b8d766bdbc5f32e3dbe 5300 science optional comet-ms_2019015+cleaned1-3_arm64.buildinfo ab9ff0ceb88c2bd695b2c9e38d925482 785752 science optional comet-ms_2019015+cleaned1-3_arm64.deb Fri Jul 30 00:40:30 UTC 2021 I: diffoscope 177 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.bCbKTfx8pI/comet-ms_2019015+cleaned1-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.bCbKTfx8pI/comet-ms_2019015+cleaned1-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.bCbKTfx8pI/comet-ms_2019015+cleaned1-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.bCbKTfx8pI/b1/comet-ms_2019015+cleaned1-3_arm64.changes /srv/reproducible-results/rbuild-debian/tmp.bCbKTfx8pI/b2/comet-ms_2019015+cleaned1-3_arm64.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: 0.339s) 0.339s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.063s) 0.062s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Fri Jul 30 00:40:33 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Fri Jul 30 00:40:33 UTC 2021 I: comet-ms from bullseye built successfully and reproducibly on arm64. Fri Jul 30 00:40:34 UTC 2021 I: Submitting .buildinfo files to external archives: Fri Jul 30 00:40:34 UTC 2021 I: Submitting 8.0K b1/comet-ms_2019015+cleaned1-3_arm64.buildinfo.asc Fri Jul 30 00:40:36 UTC 2021 I: Submitting 8.0K b2/comet-ms_2019015+cleaned1-3_arm64.buildinfo.asc Fri Jul 30 00:40:37 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Jul 30 00:40:37 UTC 2021 I: Done submitting .buildinfo files. Fri Jul 30 00:40:37 UTC 2021 I: Removing signed comet-ms_2019015+cleaned1-3_arm64.buildinfo.asc files: removed './b1/comet-ms_2019015+cleaned1-3_arm64.buildinfo.asc' removed './b2/comet-ms_2019015+cleaned1-3_arm64.buildinfo.asc'