I: pbuilder: network access will be disabled during build
I: Current time: Wed Aug 25 07:32:34 +14 2021
I: pbuilder-time-stamp: 1629826354
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.0_cR1AEO/trustedkeys.kbx': General error
gpgv: Signature made Fri Aug 14 11:52:56 2020 +14
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/8159/tmp/hooks/D01_modify_environment starting
debug: Running on cbxi4a.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
Removing 'diversion of /bin/sh to /bin/sh.distrib by dash'
Adding 'diversion of /bin/sh to /bin/sh.distrib by bash'
Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash'
Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash'
I: Setting pbuilder2's login shell to /bin/bash
I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
I: user script /srv/workspace/pbuilder/8159/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/8159/tmp/hooks/D02_print_environment starting
I: set
BASH=/bin/sh
BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath
BASH_ALIASES=()
BASH_ARGC=()
BASH_ARGV=()
BASH_CMDS=()
BASH_LINENO=([0]="12" [1]="0")
BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf")
BASH_VERSION='5.1.4(1)-release'
BUILDDIR=/build
BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
BUILDUSERNAME=pbuilder2
BUILD_ARCH=armhf
DEBIAN_FRONTEND=noninteractive
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=4'
DIRSTACK=()
DISTRIBUTION=
EUID=0
FUNCNAME=([0]="Echo" [1]="main")
GROUPS=()
HOME=/root
HOSTNAME=i-capture-the-hostname
HOSTTYPE=arm
HOST_ARCH=armhf
IFS='
'
INVOCATION_ID=e00ca581787f4481833fa71fe570e7a7
LANG=C
LANGUAGE=it_CH:it
LC_ALL=C
MACHTYPE=arm-unknown-linux-gnueabihf
MAIL=/var/mail/root
OPTERR=1
OPTIND=1
OSTYPE=linux-gnueabihf
PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
PBCURRENTCOMMANDLINEOPERATION=build
PBUILDER_OPERATION=build
PBUILDER_PKGDATADIR=/usr/share/pbuilder
PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
PBUILDER_SYSCONFDIR=/etc
PIPESTATUS=([0]="0")
POSIXLY_CORRECT=y
PPID=8159
PS4='+ '
PWD=/
SHELL=/bin/bash
SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
SHLVL=3
SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.bXshi7g6cb/pbuilderrc_VtHu --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.bXshi7g6cb/b2 --logfile b2/build.log comet-ms_2019015+cleaned1-3.dsc'
SUDO_GID=113
SUDO_UID=107
SUDO_USER=jenkins
TERM=unknown
TZ=/usr/share/zoneinfo/Etc/GMT-14
UID=0
USER=root
_='I: set'
http_proxy=http://10.0.0.15:8000/
I: uname -a
Linux i-capture-the-hostname 5.10.0-8-armmp #1 SMP Debian 5.10.46-4 (2021-08-03) armv7l GNU/Linux
I: ls -l /bin
total 3580
-rwxr-xr-x 1 root root 816764 Aug 5 10:25 bash
-rwxr-xr-x 3 root root 26052 Jul 21 2020 bunzip2
-rwxr-xr-x 3 root root 26052 Jul 21 2020 bzcat
lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff
lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe
lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep
-rwxr-xr-x 3 root root 26052 Jul 21 2020 bzip2
-rwxr-xr-x 1 root root 9636 Jul 21 2020 bzip2recover
lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore
-rwxr-xr-x 1 root root 26668 Sep 23 2020 cat
-rwxr-xr-x 1 root root 43104 Sep 23 2020 chgrp
-rwxr-xr-x 1 root root 38984 Sep 23 2020 chmod
-rwxr-xr-x 1 root root 43112 Sep 23 2020 chown
-rwxr-xr-x 1 root root 92616 Sep 23 2020 cp
-rwxr-xr-x 1 root root 75524 Dec 11 2020 dash
-rwxr-xr-x 1 root root 75880 Sep 23 2020 date
-rwxr-xr-x 1 root root 55436 Sep 23 2020 dd
-rwxr-xr-x 1 root root 59912 Sep 23 2020 df
-rwxr-xr-x 1 root root 96764 Sep 23 2020 dir
-rwxr-xr-x 1 root root 55012 Jul 29 09:09 dmesg
lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname
-rwxr-xr-x 1 root root 22508 Sep 23 2020 echo
-rwxr-xr-x 1 root root 28 Nov 10 2020 egrep
-rwxr-xr-x 1 root root 22496 Sep 23 2020 false
-rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep
-rwxr-xr-x 1 root root 47492 Jul 29 09:09 findmnt
-rwsr-xr-x 1 root root 26076 Feb 27 06:12 fusermount
-rwxr-xr-x 1 root root 124508 Nov 10 2020 grep
-rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip
-rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe
-rwxr-xr-x 1 root root 64212 Mar 3 13:30 gzip
-rwxr-xr-x 1 root root 13784 Nov 8 2019 hostname
-rwxr-xr-x 1 root root 43180 Sep 23 2020 ln
-rwxr-xr-x 1 root root 35068 Feb 8 2020 login
-rwxr-xr-x 1 root root 96764 Sep 23 2020 ls
-rwxr-xr-x 1 root root 99940 Jul 29 09:09 lsblk
-rwxr-xr-x 1 root root 51408 Sep 23 2020 mkdir
-rwxr-xr-x 1 root root 43184 Sep 23 2020 mknod
-rwxr-xr-x 1 root root 30780 Sep 23 2020 mktemp
-rwxr-xr-x 1 root root 34408 Jul 29 09:09 more
-rwsr-xr-x 1 root root 34400 Jul 29 09:09 mount
-rwxr-xr-x 1 root root 9824 Jul 29 09:09 mountpoint
-rwxr-xr-x 1 root root 88524 Sep 23 2020 mv
lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 26652 Sep 23 2020 pwd
lrwxrwxrwx 1 root root 4 Aug 5 10:25 rbash -> bash
-rwxr-xr-x 1 root root 30740 Sep 23 2020 readlink
-rwxr-xr-x 1 root root 43104 Sep 23 2020 rm
-rwxr-xr-x 1 root root 30732 Sep 23 2020 rmdir
-rwxr-xr-x 1 root root 14144 Sep 28 2020 run-parts
-rwxr-xr-x 1 root root 76012 Dec 23 2018 sed
lrwxrwxrwx 1 root root 4 Aug 25 07:33 sh -> bash
lrwxrwxrwx 1 root root 4 Aug 21 23:28 sh.distrib -> dash
-rwxr-xr-x 1 root root 22532 Sep 23 2020 sleep
-rwxr-xr-x 1 root root 55360 Sep 23 2020 stty
-rwsr-xr-x 1 root root 46704 Jul 29 09:09 su
-rwxr-xr-x 1 root root 22532 Sep 23 2020 sync
-rwxr-xr-x 1 root root 340872 Feb 17 2021 tar
-rwxr-xr-x 1 root root 9808 Sep 28 2020 tempfile
-rwxr-xr-x 1 root root 67696 Sep 23 2020 touch
-rwxr-xr-x 1 root root 22496 Sep 23 2020 true
-rwxr-xr-x 1 root root 9636 Feb 27 06:12 ulockmgr_server
-rwsr-xr-x 1 root root 22108 Jul 29 09:09 umount
-rwxr-xr-x 1 root root 22520 Sep 23 2020 uname
-rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress
-rwxr-xr-x 1 root root 96764 Sep 23 2020 vdir
-rwxr-xr-x 1 root root 38512 Jul 29 09:09 wdctl
lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat
-rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp
-rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff
-rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep
-rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep
-rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce
-rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep
-rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless
-rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore
-rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew
I: user script /srv/workspace/pbuilder/8159/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: armhf
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
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 ... 19398 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 20.9 MB of archives. After unpacking 74.8 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bullseye/main armhf bsdextrautils armhf 2.36.1-8 [138 kB]
Get: 2 http://deb.debian.org/debian bullseye/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get: 3 http://deb.debian.org/debian bullseye/main armhf groff-base armhf 1.22.4-6 [847 kB]
Get: 4 http://deb.debian.org/debian bullseye/main armhf libpipeline1 armhf 1.5.3-1 [30.1 kB]
Get: 5 http://deb.debian.org/debian bullseye/main armhf man-db armhf 2.9.4-2 [1319 kB]
Get: 6 http://deb.debian.org/debian bullseye/main armhf sgml-base all 1.30 [15.1 kB]
Get: 7 http://deb.debian.org/debian bullseye/main armhf sensible-utils all 0.0.14 [14.8 kB]
Get: 8 http://deb.debian.org/debian bullseye/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get: 9 http://deb.debian.org/debian bullseye/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get: 10 http://deb.debian.org/debian bullseye/main armhf file armhf 1:5.39-3 [68.1 kB]
Get: 11 http://deb.debian.org/debian bullseye/main armhf gettext-base armhf 0.21-4 [171 kB]
Get: 12 http://deb.debian.org/debian bullseye/main armhf libsigsegv2 armhf 2.13-1 [34.0 kB]
Get: 13 http://deb.debian.org/debian bullseye/main armhf m4 armhf 1.4.18-5 [192 kB]
Get: 14 http://deb.debian.org/debian bullseye/main armhf autoconf all 2.69-14 [313 kB]
Get: 15 http://deb.debian.org/debian bullseye/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get: 16 http://deb.debian.org/debian bullseye/main armhf automake all 1:1.16.3-2 [814 kB]
Get: 17 http://deb.debian.org/debian bullseye/main armhf autopoint all 0.21-4 [510 kB]
Get: 18 http://deb.debian.org/debian bullseye/main armhf libdebhelper-perl all 13.3.4 [189 kB]
Get: 19 http://deb.debian.org/debian bullseye/main armhf libtool all 2.4.6-15 [513 kB]
Get: 20 http://deb.debian.org/debian bullseye/main armhf dh-autoreconf all 20 [17.1 kB]
Get: 21 http://deb.debian.org/debian bullseye/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get: 22 http://deb.debian.org/debian bullseye/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get: 23 http://deb.debian.org/debian bullseye/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB]
Get: 24 http://deb.debian.org/debian bullseye/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB]
Get: 25 http://deb.debian.org/debian bullseye/main armhf libelf1 armhf 0.183-1 [161 kB]
Get: 26 http://deb.debian.org/debian bullseye/main armhf dwz armhf 0.13+20210201-1 [179 kB]
Get: 27 http://deb.debian.org/debian bullseye/main armhf libicu67 armhf 67.1-7 [8319 kB]
Get: 28 http://deb.debian.org/debian bullseye/main armhf libxml2 armhf 2.9.10+dfsg-6.7 [602 kB]
Get: 29 http://deb.debian.org/debian bullseye/main armhf gettext armhf 0.21-4 [1243 kB]
Get: 30 http://deb.debian.org/debian bullseye/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get: 31 http://deb.debian.org/debian bullseye/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get: 32 http://deb.debian.org/debian bullseye/main armhf debhelper all 13.3.4 [1049 kB]
Get: 33 http://deb.debian.org/debian bullseye/main armhf xml-core all 0.18+nmu1 [23.8 kB]
Get: 34 http://deb.debian.org/debian bullseye/main armhf sgml-data all 2.0.11+nmu1 [179 kB]
Get: 35 http://deb.debian.org/debian bullseye/main armhf docbook all 4.5-6 [129 kB]
Get: 36 http://deb.debian.org/debian bullseye/main armhf libosp5 armhf 1.5.2-13+b2 [847 kB]
Get: 37 http://deb.debian.org/debian bullseye/main armhf opensp armhf 1.5.2-13+b2 [405 kB]
Get: 38 http://deb.debian.org/debian bullseye/main armhf docbook-to-man armhf 1:2.0.0-45 [73.1 kB]
Get: 39 http://deb.debian.org/debian bullseye/main armhf libexpat1 armhf 2.2.10-2 [76.3 kB]
Get: 40 http://deb.debian.org/debian bullseye/main armhf libexpat1-dev armhf 2.2.10-2 [123 kB]
Get: 41 http://deb.debian.org/debian bullseye/main armhf libmstoolkit82 armhf 82-7 [117 kB]
Get: 42 http://deb.debian.org/debian bullseye/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [185 kB]
Get: 43 http://deb.debian.org/debian bullseye/main armhf libsqlite3-dev armhf 3.34.1-3 [890 kB]
Get: 44 http://deb.debian.org/debian bullseye/main armhf libmstoolkit-dev armhf 82-7 [130 kB]
Fetched 20.9 MB in 2s (10.6 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package bsdextrautils.
(Reading database ...
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(Reading database ... 100%
(Reading database ... 19398 files and directories currently installed.)
Preparing to unpack .../00-bsdextrautils_2.36.1-8_armhf.deb ...
Unpacking bsdextrautils (2.36.1-8) ...
Selecting previously unselected package libuchardet0:armhf.
Preparing to unpack .../01-libuchardet0_0.0.7-1_armhf.deb ...
Unpacking libuchardet0:armhf (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../02-groff-base_1.22.4-6_armhf.deb ...
Unpacking groff-base (1.22.4-6) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../03-libpipeline1_1.5.3-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.3-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../04-man-db_2.9.4-2_armhf.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_armhf.deb ...
Unpacking libmagic-mgc (1:5.39-3) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../08-libmagic1_1%3a5.39-3_armhf.deb ...
Unpacking libmagic1:armhf (1:5.39-3) ...
Selecting previously unselected package file.
Preparing to unpack .../09-file_1%3a5.39-3_armhf.deb ...
Unpacking file (1:5.39-3) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../10-gettext-base_0.21-4_armhf.deb ...
Unpacking gettext-base (0.21-4) ...
Selecting previously unselected package libsigsegv2:armhf.
Preparing to unpack .../11-libsigsegv2_2.13-1_armhf.deb ...
Unpacking libsigsegv2:armhf (2.13-1) ...
Selecting previously unselected package m4.
Preparing to unpack .../12-m4_1.4.18-5_armhf.deb ...
Unpacking m4 (1.4.18-5) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../13-autoconf_2.69-14_all.deb ...
Unpacking autoconf (2.69-14) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../14-autotools-dev_20180224.1+nmu1_all.deb ...
Unpacking autotools-dev (20180224.1+nmu1) ...
Selecting previously unselected package automake.
Preparing to unpack .../15-automake_1%3a1.16.3-2_all.deb ...
Unpacking automake (1:1.16.3-2) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../16-autopoint_0.21-4_all.deb ...
Unpacking autopoint (0.21-4) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../17-libdebhelper-perl_13.3.4_all.deb ...
Unpacking libdebhelper-perl (13.3.4) ...
Selecting previously unselected package libtool.
Preparing to unpack .../18-libtool_2.4.6-15_all.deb ...
Unpacking libtool (2.4.6-15) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../19-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../20-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libsub-override-perl.
Preparing to unpack .../21-libsub-override-perl_0.09-2_all.deb ...
Unpacking libsub-override-perl (0.09-2) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../22-libfile-stripnondeterminism-perl_1.12.0-1_all.deb ...
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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
hostname: Name or service not known
I: Running cd /build/comet-ms-2019015+cleaned1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../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 <lopippo@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
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 -j4 "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
CometSearch.cpp: In static member function 'static bool CometSearch::RunSearch(int, int, int, int)':
CometSearch.cpp:369:77: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'comet_fileoffset_t' {aka 'long long int'} [-Wformat=]
369 | sprintf(szErrorMsg, " Error realloc(szMods[%ld])\n", iLenAllocMods);
| ~~^ ~~~~~~~~~~~~~
| | |
| | comet_fileoffset_t {aka long long int}
| long int
| %lld
CometSearch.cpp:515:77: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'comet_fileoffset_t' {aka 'long long int'} [-Wformat=]
515 | sprintf(szErrorMsg, " Error realloc(szMods[%ld])\n", iLenAllocMods);
| ~~^ ~~~~~~~~~~~~~
| | |
| | comet_fileoffset_t {aka long long int}
| long int
| %lld
CometSearch.cpp: In member function 'bool CometSearch::IndexSearch()':
CometSearch.cpp:1174:95: warning: format '%zu' expects argument of type 'size_t', but argument 5 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=]
1174 | sprintf(szErr, " Error reading .idx database: min mass %d, max mass %d, num peptides %zu\n", iMinMass, iMaxMass, tNumPeptides);
| ~~^ ~~~~~~~~~~~~
| | |
| unsigned int uint64_t {aka long long unsigned int}
| %llu
In file included from CometSearch.cpp:19:
ThreadPool.h: In instantiation of 'ThreadManager<T>::ThreadManager(ThreadPool<T>*) [with T = SearchThreadData*]':
ThreadPool.h:69:10: required from 'ThreadPool<T>::ThreadPool(ThreadPool<T>::ThreadProc, int, int, int) [with T = SearchThreadData*; ThreadPool<T>::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<ThreadProc>(ThreadManager<T>::ThreadRoutingFunction),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /usr/include/libmstoolkit/MSReader.h:23,
from Common.h:51,
from CometSearch.cpp:17:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PeffModStruct*, std::vector<PeffModStruct> >; _Distance = int; _Tp = PeffModStruct; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PeffModStruct*, std::vector<PeffModStruct> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/libmstoolkit/MSReader.h:23,
from Common.h:51,
from CometSearch.cpp:17:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PeffModStruct*, std::vector<PeffModStruct> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PeffModStruct*, std::vector<PeffModStruct> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PeffModStruct*, std::vector<PeffModStruct> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PeffModStruct*, std::vector<PeffModStruct> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PeffModStruct*, std::vector<PeffModStruct> >' changed in GCC 7.1
1945 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PeffModStruct*, std::vector<PeffModStruct> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PeffModStruct*, std::vector<PeffModStruct> >' changed in GCC 7.1
1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<OBOStruct*, std::vector<OBOStruct> >; _Compare = __gnu_cxx::__ops::_Val_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<OBOStruct*, std::vector<OBOStruct> >' changed in GCC 7.1
1819 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<OBOStruct*, std::vector<OBOStruct> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<OBOStruct*, std::vector<OBOStruct> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<OBOStruct*, std::vector<OBOStruct> >' changed in GCC 7.1
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /usr/include/libmstoolkit/MSReader.h:23,
from Common.h:51,
from CometSearch.cpp:17:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<OBOStruct*, std::vector<OBOStruct> >; _Distance = int; _Tp = OBOStruct; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<OBOStruct*, std::vector<OBOStruct> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/libmstoolkit/MSReader.h:23,
from Common.h:51,
from CometSearch.cpp:17:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<OBOStruct*, std::vector<OBOStruct> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<OBOStruct*, std::vector<OBOStruct> >' changed in GCC 7.1
1945 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<OBOStruct*, std::vector<OBOStruct> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<OBOStruct*, std::vector<OBOStruct> >' changed in GCC 7.1
1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/libmstoolkit/Spectrum.h:20,
from /usr/include/libmstoolkit/MSReader.h:19,
from Common.h:51,
from CometSearch.cpp:17:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const PeffModStruct&}; _Tp = PeffModStruct; _Alloc = std::allocator<PeffModStruct>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<PeffModStruct>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const OBOStruct&}; _Tp = OBOStruct; _Alloc = std::allocator<OBOStruct>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<OBOStruct>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /usr/include/libmstoolkit/Spectrum.h:20,
from /usr/include/libmstoolkit/MSReader.h:19,
from Common.h:51,
from CometSearch.cpp:17:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void CometSearch::ReadOBO(char*, std::vector<OBOStruct>*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<OBOStruct*, std::vector<OBOStruct> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/libmstoolkit/Spectrum.h:20,
from /usr/include/libmstoolkit/MSReader.h:19,
from Common.h:51,
from CometSearch.cpp:17:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const DBIndex&}; _Tp = DBIndex; _Alloc = std::allocator<DBIndex>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<DBIndex>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ProteinEntryStruct&}; _Tp = ProteinEntryStruct; _Alloc = std::allocator<ProteinEntryStruct>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<ProteinEntryStruct>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /usr/include/libmstoolkit/Spectrum.h:20,
from /usr/include/libmstoolkit/MSReader.h:19,
from Common.h:51,
from CometSearch.cpp:17:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void CometSearch::StorePeptide(int, int, int, int, int, char*, double, double, bool, int*, sDBEntry*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'int CometSearch::CheckDuplicate(int, int, int, int, int, int, double, char*, bool, int*, sDBEntry*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'bool CometSearch::MergeVarMods(char*, int, bool*, bool*, std::vector<PeffPositionStruct>*, sDBEntry*, long int*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<DBIndex*, std::vector<DBIndex> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/libmstoolkit/Spectrum.h:20,
from /usr/include/libmstoolkit/MSReader.h:19,
from Common.h:51,
from CometSearch.cpp:17:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /usr/include/libmstoolkit/Spectrum.h:20,
from /usr/include/libmstoolkit/MSReader.h:19,
from Common.h:51,
from CometSearch.cpp:17:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void CometSearch::VariableModSearch(char*, int*, int, int, bool*, sDBEntry*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/libmstoolkit/MSReader.h:23,
from Common.h:51,
from CometSearch.cpp:17:
/usr/include/c++/10/bits/stl_algo.h: In member function 'bool CometSearch::SearchForPeptides(sDBEntry, char*, bool, bool*)':
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PeffModStruct*, std::vector<PeffModStruct> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PeffModStruct*, std::vector<PeffModStruct> >' changed in GCC 7.1
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PeffModStruct*, std::vector<PeffModStruct> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/libmstoolkit/Spectrum.h:20,
from /usr/include/libmstoolkit/MSReader.h:19,
from Common.h:51,
from CometSearch.cpp:17:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<DBIndex*, std::vector<DBIndex> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'bool CometSearch::IndexSearch()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/libmstoolkit/MSReader.h:23,
from Common.h:51,
from CometSearch.cpp:17:
/usr/include/c++/10/bits/stl_algo.h: In static member function 'static bool CometSearch::RunSearch(int, int, int, int)':
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<OBOStruct*, std::vector<OBOStruct> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<OBOStruct*, std::vector<OBOStruct> >' changed in GCC 7.1
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<OBOStruct*, std::vector<OBOStruct> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/libmstoolkit/Spectrum.h:20,
from /usr/include/libmstoolkit/MSReader.h:19,
from Common.h:51,
from CometSearch.cpp:17:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PeffModStruct*, std::vector<PeffModStruct> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
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<T>::ThreadManager(ThreadPool<T>*) [with T = PreprocessThreadData*]':
ThreadPool.h:69:10: required from 'ThreadPool<T>::ThreadPool(ThreadPool<T>::ThreadProc, int, int, int) [with T = PreprocessThreadData*; ThreadPool<T>::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<ThreadProc>(ThreadManager<T>::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<T>::ThreadManager(ThreadPool<T>*) [with T = PostAnalysisThreadData*]':
ThreadPool.h:69:10: required from 'ThreadPool<T>::ThreadPool(ThreadPool<T>::ThreadProc, int, int, int) [with T = PostAnalysisThreadData*; ThreadPool<T>::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<ThreadProc>(ThreadManager<T>::ThreadRoutingFunction),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/libmstoolkit/MSReader.h:23,
from Common.h:51,
from CometPostAnalysis.cpp:17:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const ProteinEntryStruct&, const ProteinEntryStruct&)>]':
/usr/include/c++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >' changed in GCC 7.1
1819 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const ProteinEntryStruct&, const ProteinEntryStruct&)>]':
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >' changed in GCC 7.1
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /usr/include/libmstoolkit/MSReader.h:23,
from Common.h:51,
from CometPostAnalysis.cpp:17:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >; _Distance = int; _Tp = ProteinEntryStruct; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const ProteinEntryStruct&, const ProteinEntryStruct&)>]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/libmstoolkit/MSReader.h:23,
from Common.h:51,
from CometPostAnalysis.cpp:17:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const ProteinEntryStruct&, const ProteinEntryStruct&)>]':
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >' changed in GCC 7.1
1945 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >' changed in GCC 7.1
1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In static member function 'static void CometPostAnalysis::CalculateSP(Results*, int, int)':
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >' changed in GCC 7.1
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >' changed in GCC 7.1
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
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
In file included from /usr/include/c++/10/vector:72,
from /usr/include/libmstoolkit/Spectrum.h:20,
from /usr/include/libmstoolkit/MSReader.h:19,
from Common.h:51,
from CometMassSpecUtils.cpp:21:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/libmstoolkit/Spectrum.h:20,
from /usr/include/libmstoolkit/MSReader.h:19,
from Common.h:51,
from CometMassSpecUtils.cpp:21:
/usr/include/c++/10/bits/stl_vector.h: In static member function 'static void CometMassSpecUtils::GetProteinName(FILE*, comet_fileoffset_t, char*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
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 void CometWriteOut::PrintOutputLine(int, int, int, int, bool, Results*, FILE*, FILE*)':
CometWriteOut.cpp:489:25: warning: '%d' directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=]
489 | sprintf(szTemp, "+%d", iNumTotProteins);
| ^~
CometWriteOut.cpp:489:23: note: directive argument in the range [-134217728, 268435454]
489 | sprintf(szTemp, "+%d", iNumTotProteins);
| ^~~~~
CometWriteOut.cpp:489:14: note: 'sprintf' output between 3 and 12 bytes into a destination of size 10
489 | sprintf(szTemp, "+%d", iNumTotProteins);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 10 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, 268435454]
273 | sprintf(szTempStr, " %+d", iLenMaxDuplicates);
| ^~~~~~
CometWriteOut.cpp:273:14: note: 'sprintf' output between 4 and 12 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
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /usr/include/libmstoolkit/MSReader.h:23,
from Common.h:51,
from CometSearchManager.cpp:17:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >; _Distance = int; _Tp = long long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/libmstoolkit/MSReader.h:23,
from Common.h:51,
from CometSearchManager.cpp:17:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1945 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/libmstoolkit/Spectrum.h:20,
from /usr/include/libmstoolkit/MSReader.h:19,
from Common.h:51,
from CometSearchManager.cpp:17:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Fragment&}; _Tp = Fragment; _Alloc = std::allocator<Fragment>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Fragment>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/libmstoolkit/MSReader.h:23,
from Common.h:51,
from CometSearchManager.cpp:17:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<DBIndex*, std::vector<DBIndex> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const DBIndex&, const DBIndex&)>]':
/usr/include/c++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<DBIndex*, std::vector<DBIndex> >' changed in GCC 7.1
1819 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<DBIndex*, std::vector<DBIndex> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const DBIndex&, const DBIndex&)>]':
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<DBIndex*, std::vector<DBIndex> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<DBIndex*, std::vector<DBIndex> >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /usr/include/libmstoolkit/Spectrum.h:20,
from /usr/include/libmstoolkit/MSReader.h:19,
from Common.h:51,
from CometSearchManager.cpp:17:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual bool CometSearchManager::DoSingleSpectrumSearch(int, double, double*, double*, int, std::string&, std::string&, std::vector<Fragment>&, Scores&)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Fragment*, std::vector<Fragment> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /usr/include/libmstoolkit/MSReader.h:23,
from Common.h:51,
from CometSearchManager.cpp:17:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<DBIndex*, std::vector<DBIndex> >; _Distance = int; _Tp = DBIndex; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const DBIndex&, const DBIndex&)>]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<DBIndex*, std::vector<DBIndex> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/libmstoolkit/MSReader.h:23,
from Common.h:51,
from CometSearchManager.cpp:17:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<DBIndex*, std::vector<DBIndex> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const DBIndex&, const DBIndex&)>]':
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<DBIndex*, std::vector<DBIndex> >' changed in GCC 7.1
1945 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<DBIndex*, std::vector<DBIndex> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<DBIndex*, std::vector<DBIndex> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<DBIndex*, std::vector<DBIndex> >' changed in GCC 7.1
1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/libmstoolkit/MSReader.h:23,
from Common.h:51,
from CometSearchManager.cpp:17:
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<DBIndex*, std::vector<DBIndex> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<DBIndex*, std::vector<DBIndex> >' changed in GCC 7.1
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<DBIndex*, std::vector<DBIndex> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/libmstoolkit/Spectrum.h:20,
from /usr/include/libmstoolkit/MSReader.h:19,
from Common.h:51,
from CometSearchManager.cpp:17:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/libmstoolkit/MSReader.h:23,
from Common.h:51,
from CometSearchManager.cpp:17:
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/libmstoolkit/Spectrum.h:20,
from /usr/include/libmstoolkit/MSReader.h:19,
from Common.h:51,
from CometSearchManager.cpp:17:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/libmstoolkit/MSReader.h:23,
from Common.h:51,
from CometSearchManager.cpp:17:
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<DBIndex*, std::vector<DBIndex> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<DBIndex*, std::vector<DBIndex> >' changed in GCC 7.1
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<DBIndex*, std::vector<DBIndex> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/libmstoolkit/Spectrum.h:20,
from /usr/include/libmstoolkit/MSReader.h:19,
from Common.h:51,
from CometSearchManager.cpp:17:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
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 /usr/include/c++/10/vector:72,
from /usr/include/libmstoolkit/Spectrum.h:20,
from /usr/include/libmstoolkit/MSReader.h:19,
from CometSearch/Common.h:51,
from CometSearch/CometMassSpecUtils.cpp:21:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/libmstoolkit/Spectrum.h:20,
from /usr/include/libmstoolkit/MSReader.h:19,
from CometSearch/Common.h:51,
from CometSearch/CometMassSpecUtils.cpp:21:
/usr/include/c++/10/bits/stl_vector.h: In static member function 'static void CometMassSpecUtils::GetProteinName(FILE*, comet_fileoffset_t, char*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from CometSearch/CometPreprocess.h:21,
from CometSearch/CometPreprocess.cpp:19:
CometSearch/ThreadPool.h: In instantiation of 'ThreadManager<T>::ThreadManager(ThreadPool<T>*) [with T = PreprocessThreadData*]':
CometSearch/ThreadPool.h:69:10: required from 'ThreadPool<T>::ThreadPool(ThreadPool<T>::ThreadProc, int, int, int) [with T = PreprocessThreadData*; ThreadPool<T>::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<ThreadProc>(ThreadManager<T>::ThreadRoutingFunction),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /usr/include/libmstoolkit/MSReader.h:23,
from CometSearch/Common.h:51,
from CometSearch/CometSearchManager.cpp:17:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >; _Distance = int; _Tp = long long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/libmstoolkit/MSReader.h:23,
from CometSearch/Common.h:51,
from CometSearch/CometSearchManager.cpp:17:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1945 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/libmstoolkit/Spectrum.h:20,
from /usr/include/libmstoolkit/MSReader.h:19,
from CometSearch/Common.h:51,
from CometSearch/CometSearchManager.cpp:17:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Fragment&}; _Tp = Fragment; _Alloc = std::allocator<Fragment>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Fragment>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/libmstoolkit/MSReader.h:23,
from CometSearch/Common.h:51,
from CometSearch/CometSearchManager.cpp:17:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<DBIndex*, std::vector<DBIndex> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const DBIndex&, const DBIndex&)>]':
/usr/include/c++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<DBIndex*, std::vector<DBIndex> >' changed in GCC 7.1
1819 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<DBIndex*, std::vector<DBIndex> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const DBIndex&, const DBIndex&)>]':
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<DBIndex*, std::vector<DBIndex> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<DBIndex*, std::vector<DBIndex> >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /usr/include/libmstoolkit/Spectrum.h:20,
from /usr/include/libmstoolkit/MSReader.h:19,
from CometSearch/Common.h:51,
from CometSearch/CometSearchManager.cpp:17:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual bool CometSearchManager::DoSingleSpectrumSearch(int, double, double*, double*, int, std::string&, std::string&, std::vector<Fragment>&, Scores&)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Fragment*, std::vector<Fragment> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /usr/include/libmstoolkit/MSReader.h:23,
from CometSearch/Common.h:51,
from CometSearch/CometSearchManager.cpp:17:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<DBIndex*, std::vector<DBIndex> >; _Distance = int; _Tp = DBIndex; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const DBIndex&, const DBIndex&)>]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<DBIndex*, std::vector<DBIndex> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/libmstoolkit/MSReader.h:23,
from CometSearch/Common.h:51,
from CometSearch/CometSearchManager.cpp:17:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<DBIndex*, std::vector<DBIndex> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const DBIndex&, const DBIndex&)>]':
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<DBIndex*, std::vector<DBIndex> >' changed in GCC 7.1
1945 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<DBIndex*, std::vector<DBIndex> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<DBIndex*, std::vector<DBIndex> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<DBIndex*, std::vector<DBIndex> >' changed in GCC 7.1
1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/libmstoolkit/MSReader.h:23,
from CometSearch/Common.h:51,
from CometSearch/CometSearchManager.cpp:17:
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<DBIndex*, std::vector<DBIndex> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<DBIndex*, std::vector<DBIndex> >' changed in GCC 7.1
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<DBIndex*, std::vector<DBIndex> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/libmstoolkit/Spectrum.h:20,
from /usr/include/libmstoolkit/MSReader.h:19,
from CometSearch/Common.h:51,
from CometSearch/CometSearchManager.cpp:17:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/libmstoolkit/MSReader.h:23,
from CometSearch/Common.h:51,
from CometSearch/CometSearchManager.cpp:17:
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/libmstoolkit/Spectrum.h:20,
from /usr/include/libmstoolkit/MSReader.h:19,
from CometSearch/Common.h:51,
from CometSearch/CometSearchManager.cpp:17:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/libmstoolkit/MSReader.h:23,
from CometSearch/Common.h:51,
from CometSearch/CometSearchManager.cpp:17:
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<DBIndex*, std::vector<DBIndex> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<DBIndex*, std::vector<DBIndex> >' changed in GCC 7.1
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<DBIndex*, std::vector<DBIndex> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/libmstoolkit/Spectrum.h:20,
from /usr/include/libmstoolkit/MSReader.h:19,
from CometSearch/Common.h:51,
from CometSearch/CometSearchManager.cpp:17:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
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<T>::ThreadManager(ThreadPool<T>*) [with T = PostAnalysisThreadData*]':
CometSearch/ThreadPool.h:69:10: required from 'ThreadPool<T>::ThreadPool(ThreadPool<T>::ThreadProc, int, int, int) [with T = PostAnalysisThreadData*; ThreadPool<T>::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<ThreadProc>(ThreadManager<T>::ThreadRoutingFunction),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/libmstoolkit/MSReader.h:23,
from CometSearch/Common.h:51,
from CometSearch/CometPostAnalysis.cpp:17:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const ProteinEntryStruct&, const ProteinEntryStruct&)>]':
/usr/include/c++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >' changed in GCC 7.1
1819 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const ProteinEntryStruct&, const ProteinEntryStruct&)>]':
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >' changed in GCC 7.1
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /usr/include/libmstoolkit/MSReader.h:23,
from CometSearch/Common.h:51,
from CometSearch/CometPostAnalysis.cpp:17:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >; _Distance = int; _Tp = ProteinEntryStruct; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const ProteinEntryStruct&, const ProteinEntryStruct&)>]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/libmstoolkit/MSReader.h:23,
from CometSearch/Common.h:51,
from CometSearch/CometPostAnalysis.cpp:17:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const ProteinEntryStruct&, const ProteinEntryStruct&)>]':
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >' changed in GCC 7.1
1945 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >' changed in GCC 7.1
1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In static member function 'static void CometPostAnalysis::CalculateSP(Results*, int, int)':
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >' changed in GCC 7.1
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >' changed in GCC 7.1
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp: In static member function 'static bool CometSearch::RunSearch(int, int, int, int)':
CometSearch/CometSearch.cpp:369:77: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'comet_fileoffset_t' {aka 'long long int'} [-Wformat=]
369 | sprintf(szErrorMsg, " Error realloc(szMods[%ld])\n", iLenAllocMods);
| ~~^ ~~~~~~~~~~~~~
| | |
| | comet_fileoffset_t {aka long long int}
| long int
| %lld
CometSearch/CometSearch.cpp:515:77: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'comet_fileoffset_t' {aka 'long long int'} [-Wformat=]
515 | sprintf(szErrorMsg, " Error realloc(szMods[%ld])\n", iLenAllocMods);
| ~~^ ~~~~~~~~~~~~~
| | |
| | comet_fileoffset_t {aka long long int}
| long int
| %lld
CometSearch/CometSearch.cpp: In member function 'bool CometSearch::IndexSearch()':
CometSearch/CometSearch.cpp:1174:95: warning: format '%zu' expects argument of type 'size_t', but argument 5 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=]
1174 | sprintf(szErr, " Error reading .idx database: min mass %d, max mass %d, num peptides %zu\n", iMinMass, iMaxMass, tNumPeptides);
| ~~^ ~~~~~~~~~~~~
| | |
| unsigned int uint64_t {aka long long unsigned int}
| %llu
In file included from CometSearch/CometSearch.cpp:19:
CometSearch/ThreadPool.h: In instantiation of 'ThreadManager<T>::ThreadManager(ThreadPool<T>*) [with T = SearchThreadData*]':
CometSearch/ThreadPool.h:69:10: required from 'ThreadPool<T>::ThreadPool(ThreadPool<T>::ThreadProc, int, int, int) [with T = SearchThreadData*; ThreadPool<T>::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<ThreadProc>(ThreadManager<T>::ThreadRoutingFunction),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /usr/include/libmstoolkit/MSReader.h:23,
from CometSearch/Common.h:51,
from CometSearch/CometSearch.cpp:17:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PeffModStruct*, std::vector<PeffModStruct> >; _Distance = int; _Tp = PeffModStruct; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PeffModStruct*, std::vector<PeffModStruct> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/libmstoolkit/MSReader.h:23,
from CometSearch/Common.h:51,
from CometSearch/CometSearch.cpp:17:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PeffModStruct*, std::vector<PeffModStruct> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PeffModStruct*, std::vector<PeffModStruct> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PeffModStruct*, std::vector<PeffModStruct> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PeffModStruct*, std::vector<PeffModStruct> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PeffModStruct*, std::vector<PeffModStruct> >' changed in GCC 7.1
1945 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PeffModStruct*, std::vector<PeffModStruct> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PeffModStruct*, std::vector<PeffModStruct> >' changed in GCC 7.1
1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<OBOStruct*, std::vector<OBOStruct> >; _Compare = __gnu_cxx::__ops::_Val_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<OBOStruct*, std::vector<OBOStruct> >' changed in GCC 7.1
1819 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<OBOStruct*, std::vector<OBOStruct> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<OBOStruct*, std::vector<OBOStruct> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<OBOStruct*, std::vector<OBOStruct> >' changed in GCC 7.1
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /usr/include/libmstoolkit/MSReader.h:23,
from CometSearch/Common.h:51,
from CometSearch/CometSearch.cpp:17:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<OBOStruct*, std::vector<OBOStruct> >; _Distance = int; _Tp = OBOStruct; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<OBOStruct*, std::vector<OBOStruct> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/libmstoolkit/MSReader.h:23,
from CometSearch/Common.h:51,
from CometSearch/CometSearch.cpp:17:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<OBOStruct*, std::vector<OBOStruct> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<OBOStruct*, std::vector<OBOStruct> >' changed in GCC 7.1
1945 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<OBOStruct*, std::vector<OBOStruct> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<OBOStruct*, std::vector<OBOStruct> >' changed in GCC 7.1
1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/libmstoolkit/Spectrum.h:20,
from /usr/include/libmstoolkit/MSReader.h:19,
from CometSearch/Common.h:51,
from CometSearch/CometSearch.cpp:17:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const PeffModStruct&}; _Tp = PeffModStruct; _Alloc = std::allocator<PeffModStruct>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<PeffModStruct>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const OBOStruct&}; _Tp = OBOStruct; _Alloc = std::allocator<OBOStruct>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<OBOStruct>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /usr/include/libmstoolkit/Spectrum.h:20,
from /usr/include/libmstoolkit/MSReader.h:19,
from CometSearch/Common.h:51,
from CometSearch/CometSearch.cpp:17:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void CometSearch::ReadOBO(char*, std::vector<OBOStruct>*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<OBOStruct*, std::vector<OBOStruct> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/libmstoolkit/Spectrum.h:20,
from /usr/include/libmstoolkit/MSReader.h:19,
from CometSearch/Common.h:51,
from CometSearch/CometSearch.cpp:17:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const DBIndex&}; _Tp = DBIndex; _Alloc = std::allocator<DBIndex>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<DBIndex>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ProteinEntryStruct&}; _Tp = ProteinEntryStruct; _Alloc = std::allocator<ProteinEntryStruct>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<ProteinEntryStruct>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /usr/include/libmstoolkit/Spectrum.h:20,
from /usr/include/libmstoolkit/MSReader.h:19,
from CometSearch/Common.h:51,
from CometSearch/CometSearch.cpp:17:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void CometSearch::StorePeptide(int, int, int, int, int, char*, double, double, bool, int*, sDBEntry*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'int CometSearch::CheckDuplicate(int, int, int, int, int, int, double, char*, bool, int*, sDBEntry*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ProteinEntryStruct*, std::vector<ProteinEntryStruct> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'bool CometSearch::MergeVarMods(char*, int, bool*, bool*, std::vector<PeffPositionStruct>*, sDBEntry*, long int*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<DBIndex*, std::vector<DBIndex> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/libmstoolkit/Spectrum.h:20,
from /usr/include/libmstoolkit/MSReader.h:19,
from CometSearch/Common.h:51,
from CometSearch/CometSearch.cpp:17:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /usr/include/libmstoolkit/Spectrum.h:20,
from /usr/include/libmstoolkit/MSReader.h:19,
from CometSearch/Common.h:51,
from CometSearch/CometSearch.cpp:17:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void CometSearch::VariableModSearch(char*, int*, int, int, bool*, sDBEntry*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/libmstoolkit/MSReader.h:23,
from CometSearch/Common.h:51,
from CometSearch/CometSearch.cpp:17:
/usr/include/c++/10/bits/stl_algo.h: In member function 'bool CometSearch::SearchForPeptides(sDBEntry, char*, bool, bool*)':
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PeffModStruct*, std::vector<PeffModStruct> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PeffModStruct*, std::vector<PeffModStruct> >' changed in GCC 7.1
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PeffModStruct*, std::vector<PeffModStruct> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/libmstoolkit/Spectrum.h:20,
from /usr/include/libmstoolkit/MSReader.h:19,
from CometSearch/Common.h:51,
from CometSearch/CometSearch.cpp:17:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<DBIndex*, std::vector<DBIndex> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'bool CometSearch::IndexSearch()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/libmstoolkit/MSReader.h:23,
from CometSearch/Common.h:51,
from CometSearch/CometSearch.cpp:17:
/usr/include/c++/10/bits/stl_algo.h: In static member function 'static bool CometSearch::RunSearch(int, int, int, int)':
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<OBOStruct*, std::vector<OBOStruct> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<OBOStruct*, std::vector<OBOStruct> >' changed in GCC 7.1
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<OBOStruct*, std::vector<OBOStruct> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/libmstoolkit/Spectrum.h:20,
from /usr/include/libmstoolkit/MSReader.h:19,
from CometSearch/Common.h:51,
from CometSearch/CometSearch.cpp:17:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PeffModStruct*, std::vector<PeffModStruct> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
CometSearch/CometWriteOut.cpp: In static member function 'static void CometWriteOut::PrintOutputLine(int, int, int, int, bool, Results*, FILE*, FILE*)':
CometSearch/CometWriteOut.cpp:489:25: warning: '%d' directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=]
489 | sprintf(szTemp, "+%d", iNumTotProteins);
| ^~
CometSearch/CometWriteOut.cpp:489:23: note: directive argument in the range [-134217728, 268435454]
489 | sprintf(szTemp, "+%d", iNumTotProteins);
| ^~~~~
CometSearch/CometWriteOut.cpp:489:14: note: 'sprintf' output between 3 and 12 bytes into a destination of size 10
489 | sprintf(szTemp, "+%d", iNumTotProteins);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 10 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, 268435454]
273 | sprintf(szTempStr, " %+d", iLenMaxDuplicates);
| ^~~~~~
CometSearch/CometWriteOut.cpp:273:14: note: 'sprintf' output between 4 and 12 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);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /usr/include/libmstoolkit/MSReader.h:23,
from CometSearch/Common.h:51,
from Comet.cpp:18:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/libmstoolkit/MSReader.h:23,
from CometSearch/Common.h:51,
from Comet.cpp:18:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1945 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/libmstoolkit/Spectrum.h:20,
from /usr/include/libmstoolkit/MSReader.h:19,
from CometSearch/Common.h:51,
from Comet.cpp:18:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/libmstoolkit/Spectrum.h:20,
from /usr/include/libmstoolkit/MSReader.h:19,
from CometSearch/Common.h:51,
from Comet.cpp:18:
/usr/include/c++/10/bits/stl_vector.h: In function 'void LoadParameters(char*, CometInterfaces::ICometSearchManager*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/libmstoolkit/MSReader.h:23,
from CometSearch/Common.h:51,
from Comet.cpp:18:
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/libmstoolkit/Spectrum.h:20,
from /usr/include/libmstoolkit/MSReader.h:19,
from CometSearch/Common.h:51,
from Comet.cpp:18:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/libmstoolkit/MSReader.h:23,
from CometSearch/Common.h:51,
from Comet.cpp:18:
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
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/03
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/03/1051b373384affdb767ba58ed3fb714f1c0a26.debug
chmod 0644 -- debian/.debhelper/comet-ms/dbgsym-root/usr/lib/debug/.build-id/03/1051b373384affdb767ba58ed3fb714f1c0a26.debug
chown 0:0 -- debian/.debhelper/comet-ms/dbgsym-root/usr/lib/debug/.build-id/03/1051b373384affdb767ba58ed3fb714f1c0a26.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/03/1051b373384affdb767ba58ed3fb714f1c0a26.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
dpkg-shlibdeps: warning: debian/comet-ms/usr/bin/comet-ms contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
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=031051b373384affdb767ba58ed3fb714f1c0a26 -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_armhf.deb'.
dpkg-deb: building package 'comet-ms-dbgsym' in '../comet-ms-dbgsym_2019015+cleaned1-3_armhf.deb'.
dpkg-genbuildinfo --build=binary
dpkg-genchanges --build=binary >../comet-ms_2019015+cleaned1-3_armhf.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: user script /srv/workspace/pbuilder/8159/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/8159/tmp/hooks/B01_cleanup finished
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/8159 and its subdirectories
I: Current time: Wed Aug 25 07:50:11 +14 2021
I: pbuilder-time-stamp: 1629827411