sbuild (Debian sbuild) 0.86.3~bpo12+1 (03 November 2024) on debusine-worker-amd64-hades-04.freexian.com
+==============================================================================+
| comet-ms 2019015+cleaned1-4.1 (amd64) Fri, 15 Nov 2024 13:11:24 +0000 |
+==============================================================================+
Package: comet-ms
Version: 2019015+cleaned1-4.1
Source Version: 2019015+cleaned1-4.1
Distribution: sid
Machine Architecture: amd64
Host Architecture: amd64
Build Architecture: amd64
Build Type: binary
I: No tarballs found in /var/lib/debusine/worker/.cache/sbuild
Unpacking /var/lib/debusine/worker/system-images/957754/system.tar.xz to /tmp/tmp.sbuild.vaoxO9z9op...
I: NOTICE: Log filtering will replace 'sbuild-unshare-dummy-location' with '<<CHROOT>>'
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| Chroot Setup Commands |
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rm -f /etc/resolv.conf
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I: Finished running 'rm -f /etc/resolv.conf'.
Finished processing commands.
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Copying /tmp/debusine-fetch-exec-upload-eyzx3wsg/dpkg-dbgsym_1.22.12~1.gbp82cafd_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-eyzx3wsg/dpkg_1.22.12~1.gbp82cafd_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-eyzx3wsg/dselect-dbgsym_1.22.12~1.gbp82cafd_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-eyzx3wsg/dselect_1.22.12~1.gbp82cafd_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-eyzx3wsg/libdpkg-dev_1.22.12~1.gbp82cafd_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-eyzx3wsg/dpkg-dev_1.22.12~1.gbp82cafd_all.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-eyzx3wsg/libdpkg-perl_1.22.12~1.gbp82cafd_all.deb to /<<CHROOT>>...
I: NOTICE: Log filtering will replace 'build/comet-ms-vWc6oi/resolver-jjs93a' with '<<RESOLVERDIR>>'
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Get:1 file:/build/comet-ms-vWc6oi/resolver-q5mYdb/apt_archive ./ InRelease
Ign:1 file:/build/comet-ms-vWc6oi/resolver-q5mYdb/apt_archive ./ InRelease
Get:2 file:/build/comet-ms-vWc6oi/resolver-q5mYdb/apt_archive ./ Release [606 B]
Get:3 http://deb.debian.org/debian sid InRelease [202 kB]
Get:2 file:/build/comet-ms-vWc6oi/resolver-q5mYdb/apt_archive ./ Release [606 B]
Get:4 file:/build/comet-ms-vWc6oi/resolver-q5mYdb/apt_archive ./ Release.gpg
Ign:4 file:/build/comet-ms-vWc6oi/resolver-q5mYdb/apt_archive ./ Release.gpg
Get:5 file:/build/comet-ms-vWc6oi/resolver-q5mYdb/apt_archive ./ Packages [9246 B]
Get:6 http://deb.debian.org/debian sid/main amd64 Packages [10.0 MB]
Get:7 http://deb.debian.org/debian sid/main amd64 Components [4979 kB]
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Reading package lists...
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Building dependency tree...
Reading state information...
Calculating upgrade...
The following packages will be upgraded:
apt bsdextrautils bsdutils dpkg-dev libapt-pkg6.0t64 libaudit-common
libaudit1 libblkid1 libbrotli1 libcap-ng0 libdpkg-perl libglib2.0-0t64
libmount1 libpcre2-8-0 libseccomp2 libselinux1 libsemanage2 libsmartcols1
libuuid1 libxml2 login mount util-linux
23 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Need to get 7670 kB/9654 kB of archives.
After this operation, 366 kB disk space will be freed.
Get:1 file:/build/comet-ms-vWc6oi/resolver-q5mYdb/apt_archive ./ dpkg-dev 1.22.12~1.gbp82cafd [1337 kB]
Get:2 file:/build/comet-ms-vWc6oi/resolver-q5mYdb/apt_archive ./ libdpkg-perl 1.22.12~1.gbp82cafd [647 kB]
Get:3 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.40.2-11 [105 kB]
Get:4 http://deb.debian.org/debian sid/main amd64 bsdextrautils amd64 2.40.2-11 [91.5 kB]
Get:5 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.40.2-11 [168 kB]
Get:6 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.40.2-11 [199 kB]
Get:7 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.40.2-11 [139 kB]
Get:8 http://deb.debian.org/debian sid/main amd64 mount amd64 2.40.2-11 [155 kB]
Get:9 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.40.2-11 [35.9 kB]
Get:10 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.40.2-11 [1213 kB]
Get:11 http://deb.debian.org/debian sid/main amd64 libpcre2-8-0 amd64 10.44-2 [275 kB]
Get:12 http://deb.debian.org/debian sid/main amd64 libselinux1 amd64 3.7-3+b1 [77.0 kB]
Get:13 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0t64 amd64 2.9.11 [1043 kB]
Get:14 http://deb.debian.org/debian sid/main amd64 libseccomp2 amd64 2.5.5-1+b3 [47.4 kB]
Get:15 http://deb.debian.org/debian sid/main amd64 apt amd64 2.9.11 [1362 kB]
Get:16 http://deb.debian.org/debian sid/main amd64 libaudit-common all 1:4.0.2-2 [12.7 kB]
Get:17 http://deb.debian.org/debian sid/main amd64 libcap-ng0 amd64 0.8.5-3+b1 [17.5 kB]
Get:18 http://deb.debian.org/debian sid/main amd64 libaudit1 amd64 1:4.0.2-2 [54.9 kB]
Get:19 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.16.0-2+really2.40.2-11 [81.5 kB]
Get:20 http://deb.debian.org/debian sid/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB]
Get:21 http://deb.debian.org/debian sid/main amd64 libglib2.0-0t64 amd64 2.82.2-3 [1501 kB]
Get:22 http://deb.debian.org/debian sid/main amd64 libsemanage2 amd64 3.7-2+b1 [91.2 kB]
Get:23 http://deb.debian.org/debian sid/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Processing triggers for man-db (2.13.0-1) ...
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| Fetch source files |
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Local sources
-------------
/tmp/debusine-fetch-exec-upload-eyzx3wsg/comet-ms_2019015+cleaned1-4.1.dsc exists in /tmp/debusine-fetch-exec-upload-eyzx3wsg; copying to chroot
I: NOTICE: Log filtering will replace 'build/comet-ms-vWc6oi/comet-ms-2019015+cleaned1' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/comet-ms-vWc6oi' with '<<BUILDDIR>>'
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| Install package build dependencies |
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Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), dpkg-dev (>= 1.16.1.1), libmstoolkit-dev (>= 82), libmstoolkit-dev (<< 83), docbook-to-man, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), dpkg-dev (>= 1.16.1.1), libmstoolkit-dev (>= 82), libmstoolkit-dev (<< 83), docbook-to-man, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
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Reading package lists...
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Reading package lists...
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Install main build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
autoconf automake autopoint autotools-dev build-essential cpp cpp-14
cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu debhelper dh-autoreconf
dh-strip-nondeterminism docbook docbook-to-man dwz fakeroot g++ g++-14
g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-14
gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu libasan8 libc-dev-bin libc6-dev
libcc1-0 libcrypt-dev libdebhelper-perl libelf1t64 libexpat1 libexpat1-dev
libfakeroot libfile-stripnondeterminism-perl libgcc-14-dev libhwasan0
libisl23 libitm1 liblsan0 libmpc3 libmpfr6 libmstoolkit-dev
libmstoolkit82t64 libosp5 libquadmath0 libsqlite3-dev libstdc++-14-dev
libtool libtsan2 libubsan1 linux-libc-dev m4 opensp po-debconf rpcsvc-proto
sgml-base sgml-data xml-core zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc cpp-doc gcc-14-locales
cpp-14-doc dh-make docbook-defguide docbook-dsssl docbook-xml psgml
g++-multilib g++-14-multilib gcc-14-doc gcc-multilib manpages-dev flex bison
gdb gcc-doc gcc-14-multilib gdb-x86-64-linux-gnu libc-devtools glibc-doc
sqlite3-doc libstdc++-14-doc libtool-doc gfortran | fortran95-compiler
gcj-jdk m4-doc doc-base libmail-box-perl sgml-base-doc perlsgml w3-recs
libxml2-utils
Recommended packages:
manpages manpages-dev libarchive-cpio-perl libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev build-essential cpp cpp-14
cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu debhelper dh-autoreconf
dh-strip-nondeterminism docbook docbook-to-man dwz fakeroot g++ g++-14
g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-14
gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu libasan8 libc-dev-bin libc6-dev
libcc1-0 libcrypt-dev libdebhelper-perl libelf1t64 libexpat1 libexpat1-dev
libfakeroot libfile-stripnondeterminism-perl libgcc-14-dev libhwasan0
libisl23 libitm1 liblsan0 libmpc3 libmpfr6 libmstoolkit-dev
libmstoolkit82t64 libosp5 libquadmath0 libsqlite3-dev libstdc++-14-dev
libtool libtsan2 libubsan1 linux-libc-dev m4 opensp po-debconf rpcsvc-proto
sbuild-build-depends-main-dummy sgml-base sgml-data xml-core zlib1g-dev
0 upgraded, 61 newly installed, 0 to remove and 0 not upgraded.
Need to get 74.4 MB of archives.
After this operation, 273 MB of additional disk space will be used.
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Get:2 http://deb.debian.org/debian sid/main amd64 sgml-base all 1.31 [15.4 kB]
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Get:5 http://deb.debian.org/debian sid/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get:6 http://deb.debian.org/debian sid/main amd64 automake all 1:1.16.5-1.3 [823 kB]
Get:7 http://deb.debian.org/debian sid/main amd64 autopoint all 0.22.5-2 [723 kB]
Get:8 http://deb.debian.org/debian sid/main amd64 libc-dev-bin amd64 2.40-3 [51.8 kB]
Get:9 http://deb.debian.org/debian sid/main amd64 linux-libc-dev all 6.11.7-1 [2454 kB]
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Get:38 http://deb.debian.org/debian sid/main amd64 build-essential amd64 12.12 [4624 B]
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Get:48 http://deb.debian.org/debian sid/main amd64 xml-core all 0.19 [20.1 kB]
Get:49 http://deb.debian.org/debian sid/main amd64 sgml-data all 2.0.11+nmu1 [179 kB]
Get:50 http://deb.debian.org/debian sid/main amd64 docbook all 4.5-11 [126 kB]
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Get:56 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.6.4-1 [106 kB]
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Get:58 http://deb.debian.org/debian sid/main amd64 libmstoolkit82t64 amd64 82-7.2 [140 kB]
Get:59 http://deb.debian.org/debian sid/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB]
Get:60 http://deb.debian.org/debian sid/main amd64 libsqlite3-dev amd64 3.46.1-1 [1107 kB]
Get:61 http://deb.debian.org/debian sid/main amd64 libmstoolkit-dev amd64 82-7.2 [140 kB]
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Setting up gcc-14 (14.2.0-8) ...
Setting up g++-14-x86-64-linux-gnu (14.2.0-8) ...
Setting up g++-x86-64-linux-gnu (4:14.2.0-1) ...
Setting up g++-14 (14.2.0-8) ...
Setting up libtool (2.4.7-8) ...
Setting up gcc (4:14.2.0-1) ...
Setting up dh-autoreconf (20) ...
Setting up g++ (4:14.2.0-1) ...
update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
Setting up build-essential (12.12) ...
Setting up debhelper (13.20) ...
Processing triggers for libc-bin (2.40-3) ...
Processing triggers for man-db (2.13.0-1) ...
Processing triggers for sgml-base (1.31) ...
Setting up sgml-data (2.0.11+nmu1) ...
Processing triggers for sgml-base (1.31) ...
Setting up docbook (4.5-11) ...
Processing triggers for sgml-base (1.31) ...
Setting up docbook-to-man (1:2.0.0-47) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
W: Extra package /tmp/debusine-fetch-exec-upload-eyzx3wsg/dpkg-dbgsym_1.22.12~1.gbp82cafd_arm64.deb of architecture arm64 cannot be installed in the chroot
W: Extra package /tmp/debusine-fetch-exec-upload-eyzx3wsg/dpkg_1.22.12~1.gbp82cafd_arm64.deb of architecture arm64 cannot be installed in the chroot
W: Extra package /tmp/debusine-fetch-exec-upload-eyzx3wsg/dselect-dbgsym_1.22.12~1.gbp82cafd_arm64.deb of architecture arm64 cannot be installed in the chroot
W: Extra package /tmp/debusine-fetch-exec-upload-eyzx3wsg/dselect_1.22.12~1.gbp82cafd_arm64.deb of architecture arm64 cannot be installed in the chroot
W: Extra package /tmp/debusine-fetch-exec-upload-eyzx3wsg/libdpkg-dev_1.22.12~1.gbp82cafd_arm64.deb of architecture arm64 cannot be installed in the chroot
Arch check ok (amd64 included in any)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 6.1.0-27-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) amd64 (x86_64)
Toolchain package versions: binutils_2.43.1-5 dpkg-dev_1.22.12~1.gbp82cafd g++-14_14.2.0-8 gcc-14_14.2.0-8 libc6-dev_2.40-3 libstdc++-14-dev_14.2.0-8 libstdc++6_14.2.0-8 linux-libc-dev_6.11.7-1
Package versions: appstream_1.0.3-1+b1 apt_2.9.11 autoconf_2.72-3 automake_1:1.16.5-1.3 autopoint_0.22.5-2 autotools-dev_20220109.1 base-files_13.5 base-passwd_3.6.5 bash_5.2.32-1+b2 binutils_2.43.1-5 binutils-common_2.43.1-5 binutils-x86-64-linux-gnu_2.43.1-5 bsdextrautils_2.40.2-11 bsdutils_1:2.40.2-11 build-essential_12.12 bzip2_1.0.8-6 ca-certificates_20240203 coreutils_9.5-1+b1 cpp_4:14.2.0-1 cpp-14_14.2.0-8 cpp-14-x86-64-linux-gnu_14.2.0-8 cpp-x86-64-linux-gnu_4:14.2.0-1 dash_0.5.12-9 debconf_1.5.87 debhelper_13.20 debian-archive-keyring_2023.4 debianutils_5.20 dh-autoreconf_20 dh-strip-nondeterminism_1.14.0-1 diffstat_1.66-1 diffutils_1:3.10-1 docbook_4.5-11 docbook-to-man_1:2.0.0-47 dpkg_1.22.11 dpkg-dev_1.22.12~1.gbp82cafd dwz_0.15-1+b1 e2fsprogs_1.47.1-1+b1 fakeroot_1.36-1 file_1:5.45-3+b1 findutils_4.10.0-3 g++_4:14.2.0-1 g++-14_14.2.0-8 g++-14-x86-64-linux-gnu_14.2.0-8 g++-x86-64-linux-gnu_4:14.2.0-1 gcc_4:14.2.0-1 gcc-14_14.2.0-8 gcc-14-base_14.2.0-8 gcc-14-x86-64-linux-gnu_14.2.0-8 gcc-x86-64-linux-gnu_4:14.2.0-1 gettext_0.22.5-2 gettext-base_0.22.5-2 gpg_2.2.45-2 gpgconf_2.2.45-2 gpgv_2.2.45-2 grep_3.11-4 groff-base_1.23.0-5 gzip_1.12-1.1 hostname_3.25 init-system-helpers_1.67 intltool-debian_0.35.0+20060710.6 iso-codes_4.17.0-1 libacl1_2.3.2-2+b1 libaliased-perl_0.34-3 libappstream5_1.0.3-1+b1 libapt-pkg-perl_0.1.40+b6 libapt-pkg6.0t64_2.9.11 libarchive-zip-perl_1.68-1 libasan8_14.2.0-8 libassuan9_3.0.1-2 libatomic1_14.2.0-8 libattr1_1:2.5.2-2 libaudit-common_1:4.0.2-2 libaudit1_1:4.0.2-2 libb-hooks-endofscope-perl_0.28-1 libb-hooks-op-check-perl_0.22-3+b2 libberkeleydb-perl_0.66-1 libbinutils_2.43.1-5 libblkid1_2.40.2-11 libbrotli1_1.1.0-2+b6 libbsd0_0.12.2-2 libbz2-1.0_1.0.8-6 libc-bin_2.40-3 libc-dev-bin_2.40-3 libc6_2.40-3 libc6-dev_2.40-3 libcap-ng0_0.8.5-3+b1 libcap2_1:2.66-5+b1 libcapture-tiny-perl_0.48-2 libcc1-0_14.2.0-8 libcgi-pm-perl_4.66-1 libclass-data-inheritable-perl_0.10-1 libclass-inspector-perl_1.36-3 libclass-method-modifiers-perl_2.15-1 libclass-xsaccessor-perl_1.19-4+b4 libclone-perl_0.47-1+b1 libcom-err2_1.47.1-1+b1 libconfig-tiny-perl_2.30-1 libconst-fast-perl_0.014-2 libcpanel-json-xs-perl_4.38-1+b1 libcrypt-dev_1:4.4.36-5 libcrypt1_1:4.4.36-5 libctf-nobfd0_2.43.1-5 libctf0_2.43.1-5 libcurl3t64-gnutls_8.11.0-1 libdata-dpath-perl_0.60-1 libdata-messagepack-perl_1.02-1+b4 libdata-optlist-perl_0.114-1 libdata-validate-domain-perl_0.15-1 libdata-validate-ip-perl_0.31-1 libdata-validate-uri-perl_0.07-3 libdb5.3t64_5.3.28+dfsg2-9 libdebconfclient0_0.273 libdebhelper-perl_13.20 libdevel-callchecker-perl_0.009-1+b1 libdevel-size-perl_0.84-1+b1 libdevel-stacktrace-perl_2.0500-1 libdpkg-perl_1.22.12~1.gbp82cafd libdynaloader-functions-perl_0.004-1 libelf1t64_0.192-4 libemail-address-xs-perl_1.05-1+b4 libencode-locale-perl_1.05-3 libexception-class-perl_1.45-1 libexpat1_2.6.4-1 libexpat1-dev_2.6.4-1 libext2fs2t64_1.47.1-1+b1 libfakeroot_1.36-1 libffi8_3.4.6-1 libfile-basedir-perl_0.09-2 libfile-find-rule-perl_0.34-3 libfile-listing-perl_6.16-1 libfile-sharedir-perl_1.118-3 libfile-stripnondeterminism-perl_1.14.0-1 libfont-ttf-perl_1.06-2 libgcc-14-dev_14.2.0-8 libgcc-s1_14.2.0-8 libgcrypt20_1.11.0-6 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 libglib2.0-0t64_2.82.2-3 libgmp10_2:6.3.0+dfsg-2+b2 libgnutls30t64_3.8.8-2 libgomp1_14.2.0-8 libgpg-error0_1.50-4 libgprofng0_2.43.1-5 libgssapi-krb5-2_1.21.3-3 libhogweed6t64_3.10-1+b1 libhtml-form-perl_6.12-1 libhtml-html5-entities-perl_0.004-3 libhtml-parser-perl_3.83-1+b1 libhtml-tagset-perl_3.24-1 libhtml-tokeparser-simple-perl_3.16-4 libhtml-tree-perl_5.07-3 libhttp-cookies-perl_6.11-1 libhttp-date-perl_6.06-1 libhttp-message-perl_7.00-2 libhttp-negotiate-perl_6.01-2 libhwasan0_14.2.0-8 libicu72_72.1-5+b1 libidn2-0_2.3.7-2+b1 libimport-into-perl_1.002005-2 libio-html-perl_1.004-3 libio-interactive-perl_1.025-1 libio-socket-ssl-perl_2.089-1 libio-string-perl_1.08-4 libipc-run3-perl_0.049-1 libipc-system-simple-perl_1.30-2 libisl23_0.27-1 libiterator-perl_0.03+ds1-2 libiterator-util-perl_0.02+ds1-2 libitm1_14.2.0-8 libjansson4_2.14-2+b3 libjson-maybexs-perl_1.004008-1 libk5crypto3_1.21.3-3 libkeyutils1_1.6.3-4 libkrb5-3_1.21.3-3 libkrb5support0_1.21.3-3 libldap-2.5-0_2.5.18+dfsg-3+b1 liblist-compare-perl_0.55-2 liblist-someutils-perl_0.59-1 liblist-utilsby-perl_0.12-2 liblsan0_14.2.0-8 liblwp-mediatypes-perl_6.04-2 liblwp-protocol-https-perl_6.14-1 liblz1_1.15~pre2-1 liblz4-1_1.9.4-3+b1 liblzma5_5.6.3-1+b1 liblzo2-2_2.10-3+b1 libmagic-mgc_1:5.45-3+b1 libmagic1t64_1:5.45-3+b1 libmarkdown2_2.2.7-2+b1 libmd0_1.1.0-2+b1 libmldbm-perl_2.05-4 libmodule-implementation-perl_0.09-2 libmodule-runtime-perl_0.016-2 libmoo-perl_2.005005-1 libmoox-aliases-perl_0.001006-2 libmount1_2.40.2-11 libmouse-perl_2.5.11-1+b1 libmpc3_1.3.1-1+b3 libmpfr6_4.2.1-1+b2 libmstoolkit-dev_82-7.2 libmstoolkit82t64_82-7.2 libnamespace-clean-perl_0.27-2 libnet-domain-tld-perl_1.75-4 libnet-http-perl_6.23-1 libnet-ipv6addr-perl_1.02-1 libnet-netmask-perl_2.0002-2 libnet-ssleay-perl_1.94-2 libnetaddr-ip-perl_4.079+dfsg-2+b4 libnettle8t64_3.10-1+b1 libnghttp2-14_1.64.0-1 libnghttp3-9_1.4.0-1+b1 libngtcp2-16_1.6.0-1 libngtcp2-crypto-gnutls8_1.6.0-1 libnumber-compare-perl_0.03-3 libosp5_1.5.2-15 libp11-kit0_0.25.5-2+b1 libpackage-stash-perl_0.40-1 libpam-modules_1.5.3-7+b1 libpam-modules-bin_1.5.3-7+b1 libpam-runtime_1.5.3-7 libpam0g_1.5.3-7+b1 libparams-classify-perl_0.015-2+b4 libparams-util-perl_1.102-3+b1 libpath-tiny-perl_0.146-1 libpcre2-8-0_10.44-2 libperl5.40_5.40.0-7 libperlio-gzip-perl_0.20-1+b4 libperlio-utf8-strict-perl_0.010-1+b3 libpipeline1_1.5.8-1 libproc-processtable-perl_0.636-1+b3 libpsl5t64_0.21.2-1.1+b1 libquadmath0_14.2.0-8 libreadline8t64_8.2-5 libregexp-wildcards-perl_1.05-3 librole-tiny-perl_2.002004-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b5 libsasl2-2_2.1.28+dfsg1-8 libsasl2-modules-db_2.1.28+dfsg1-8 libseccomp2_2.5.5-1+b3 libselinux1_3.7-3+b1 libsemanage-common_3.7-2 libsemanage2_3.7-2+b1 libsepol2_3.7-1 libsereal-decoder-perl_5.004+ds-1+b3 libsereal-encoder-perl_5.004+ds-1+b3 libsframe1_2.43.1-5 libsmartcols1_2.40.2-11 libsort-versions-perl_1.62-3 libsqlite3-0_3.46.1-1 libsqlite3-dev_3.46.1-1 libss2_1.47.1-1+b1 libssh2-1t64_1.11.1-1 libssl3t64_3.3.2-2 libstdc++-14-dev_14.2.0-8 libstdc++6_14.2.0-8 libstemmer0d_2.2.0-4+b2 libstrictures-perl_2.000006-1 libsub-exporter-perl_0.990-1 libsub-exporter-progressive-perl_0.001013-3 libsub-identify-perl_0.14-3+b3 libsub-install-perl_0.929-1 libsub-name-perl_0.27-1+b3 libsub-quote-perl_2.006008-1 libsyntax-keyword-try-perl_0.30-1+b1 libsystemd0_257~rc1-4 libtasn1-6_4.19.0-3+b3 libterm-readkey-perl_2.38-2+b4 libtext-glob-perl_0.11-3 libtext-levenshteinxs-perl_0.03-5+b4 libtext-markdown-discount-perl_0.16-1+b3 libtext-xslate-perl_3.5.9-2+b1 libtime-duration-perl_1.21-2 libtime-moment-perl_0.44-2+b4 libtimedate-perl_2.3300-2 libtinfo6_6.5-2+b1 libtool_2.4.7-8 libtry-tiny-perl_0.32-1 libtsan2_14.2.0-8 libubsan1_14.2.0-8 libuchardet0_0.0.8-1+b2 libudev1_257~rc1-4 libunicode-utf8-perl_0.62-2+b3 libunistring5_1.2-1+b1 liburi-perl_5.30-1 libuuid1_2.40.2-11 libvariable-magic-perl_0.64-1+b1 libwww-mechanize-perl_2.19-1 libwww-perl_6.77-1 libwww-robotrules-perl_6.02-1 libxml-libxml-perl_2.0207+dfsg+really+2.0134-5+b1 libxml-namespacesupport-perl_1.12-2 libxml-sax-base-perl_1.09-3 libxml-sax-perl_1.02+dfsg-3 libxml2_2.12.7+dfsg+really2.9.14-0.2+b1 libxmlb2_0.3.21-1 libxs-parse-keyword-perl_0.46-1+b1 libxxhash0_0.8.2-2+b2 libyaml-0-2_0.2.5-1+b2 libyaml-libyaml-perl_0.902.0+ds-2+b1 libzstd1_1.5.6+dfsg-1+b1 lintian_2.120.0 linux-libc-dev_6.11.7-1 login_1:4.16.0-2+really2.40.2-11 login.defs_1:4.16.0-4 logsave_1.47.1-1+b1 lzop_1.04-2 m4_1.4.19-4 make_4.3-4.1 man-db_2.13.0-1 mawk_1.3.4.20240905-1 mount_2.40.2-11 ncurses-base_6.5-2 ncurses-bin_6.5-2+b1 netbase_6.4 opensp_1.5.2-15 openssl_3.3.2-2 openssl-provider-legacy_3.3.2-2 passwd_1:4.16.0-4 patch_2.7.6-7 patchutils_0.4.2-1 perl_5.40.0-7 perl-base_5.40.0-7 perl-modules-5.40_5.40.0-7 perl-openssl-defaults_7+b2 plzip_1.11-2 po-debconf_1.0.21+nmu1 readline-common_8.2-5 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.24 sgml-base_1.31 sgml-data_2.0.11+nmu1 shared-mime-info_2.4-5+b1 sysvinit-utils_3.11-1 t1utils_1.41-4 tar_1.35+dfsg-3 tzdata_2024b-3 ucf_3.0043+nmu1 unzip_6.0-28 util-linux_2.40.2-11 xml-core_0.19 xz-utils_5.6.3-1+b1 zlib1g_1:1.3.dfsg+really1.3.1-1+b1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1+b1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: comet-ms
Binary: comet-ms
Architecture: any
Version: 2019015+cleaned1-4.1
Maintainer: The Debichem Group <debichem-devel@lists.alioth.debian.org>
Uploaders: Filippo Rusconi <lopippo@debian.org>
Homepage: http://comet-ms.sourceforge.net
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/debichem-team/comet-ms
Vcs-Git: https://salsa.debian.org/debichem-team/comet-ms.git
Build-Depends: debhelper-compat (= 13), dpkg-dev (>= 1.16.1.1), libmstoolkit-dev (>= 82), libmstoolkit-dev (<< 83), docbook-to-man
Package-List:
comet-ms deb science optional arch=any
Checksums-Sha1:
e8ce6f80224671a82f5c9123546c621fba5df7d0 1378100 comet-ms_2019015+cleaned1.orig.tar.gz
a104367afb14167d5c6727a659ebabd93e414987 6788 comet-ms_2019015+cleaned1-4.1.debian.tar.xz
Checksums-Sha256:
27a5c4b89b82d4570485cca98b27a45dd55a640ea297d8188c1c008a6b5234a3 1378100 comet-ms_2019015+cleaned1.orig.tar.gz
05004bda0b5db500dff1d6be91d477dc0b4d97b6bf1715b433b9cb15a787a8f9 6788 comet-ms_2019015+cleaned1-4.1.debian.tar.xz
Files:
fac4a9263c2b124cb0183dc9bf645f4b 1378100 comet-ms_2019015+cleaned1.orig.tar.gz
60aaa0e3839d39e2e84ce79171d188bf 6788 comet-ms_2019015+cleaned1-4.1.debian.tar.xz
-----BEGIN PGP SIGNATURE-----
iHUEARYKAB0WIQRCYn6EHZln2oPh+pAhk2s2YA/NiQUCZhrrJgAKCRAhk2s2YA/N
iRrkAQC9i579L3K2MmEuwFS591qWR4TQQq+RmB24pIS1vWdjIQEA1lHf0PSA5PjE
Me0u1TUZP65SzjDJOdrzmplIM882DQI=
=F6go
-----END PGP SIGNATURE-----
gpgv: Signature made Sat Apr 13 20:29:26 2024 UTC
gpgv: using EDDSA key 42627E841D9967DA83E1FA9021936B36600FCD89
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./comet-ms_2019015+cleaned1-4.1.dsc: no acceptable signature found
dpkg-source: info: extracting comet-ms in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking comet-ms_2019015+cleaned1.orig.tar.gz
dpkg-source: info: unpacking comet-ms_2019015+cleaned1-4.1.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
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
HOME=/sbuild-nonexistent
LANG=en_US.UTF-8
LC_ALL=C.UTF-8
LOGNAME=debusine-worker
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SHELL=/bin/sh
USER=debusine-worker
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage --sanitize-env -us -uc -b -rfakeroot
dpkg-buildpackage: info: source package comet-ms
dpkg-buildpackage: info: source version 2019015+cleaned1-4.1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Sebastian Ramacher <sramacher@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -f debian/comet-ms.1
make clean
make[2]: Entering directory '/<<PKGBUILDDIR>>'
rm -f *.o comet-ms
cd CometSearch ; make clean
make[3]: Entering directory '/<<PKGBUILDDIR>>/CometSearch'
rm -f *.o libcometsearch.a
make[3]: Leaving directory '/<<PKGBUILDDIR>>/CometSearch'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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 \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \)
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
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 \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \)
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
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 '/<<PKGBUILDDIR>>'
cd CometSearch ; make
make[3]: Entering directory '/<<PKGBUILDDIR>>/CometSearch'
make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit Threading.cpp -c
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometInterfaces.cpp -c
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometSearch.cpp -c
In file included from CometSearch.cpp:19:
ThreadPool.h: In instantiation of ‘ThreadManager<T>::ThreadManager(ThreadPool<T>*) [with T = SearchThreadData*]’:
ThreadPool.h:69:10: required from ‘ThreadPool<T>::ThreadPool(ThreadProc, int, int, int) [with T = SearchThreadData*; ThreadProc = void (*)(SearchThreadData*)]’
69 | new ThreadManager<T>(this);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch.cpp:138:66: required from here
138 | minNumThreads, maxNumThreads, 1 /*maxNumParamsToQueue*/);
| ^
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),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch.cpp: In static member function ‘static bool CometSearch::RunSearch(int, int, int, int)’:
CometSearch.cpp:312:27: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
312 | fgets(szPeffLine, iLenSzLine, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch.cpp:329:30: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
329 | fgets(szPeffLine+(int)strlen(szPeffLine), iLenSzLine - (int)strlen(szPeffLine), fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch.cpp:673:18: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
673 | fgets(szBuf, sizeof(szBuf), fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch.cpp: In member function ‘void CometSearch::ReadOBO(char*, std::vector<OBOStruct>*)’:
CometSearch.cpp:725:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
725 | fgets(szLineOBO, SIZE_BUF, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch.cpp:777:18: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
777 | fgets(szLineOBO, SIZE_BUF, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch.cpp: In member function ‘bool CometSearch::IndexSearch()’:
CometSearch.cpp:1159:9: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1159 | fread(&lEndOfStruct, sizeof(comet_fileoffset_t), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch.cpp:1166:9: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1166 | fread(&iMinMass, sizeof(int), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch.cpp:1167:9: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1167 | fread(&iMaxMass, sizeof(int), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch.cpp:1168:9: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1168 | fread(&tNumPeptides, sizeof(uint64_t), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch.cpp:1185:9: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1185 | fread(lReadIndex, sizeof(comet_fileoffset_t), iMaxPeptideMass10, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch.cpp:1224:9: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1224 | fread(&sDBI, sizeof(struct DBIndex), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch.cpp:1229:9: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1229 | fread(&lSize, sizeof(long), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch.cpp:1233:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1233 | fread(&tmpoffset, sizeof(comet_fileoffset_t), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch.cpp:1266:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1266 | fread(&sDBI, sizeof(struct DBIndex), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch.cpp:1269:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1269 | fread(&lSize, sizeof(long), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch.cpp:1273:15: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1273 | fread(&tmpoffset, sizeof(comet_fileoffset_t), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch.cpp:1311:18: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1311 | fread(&lSize, sizeof(long), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch.cpp:1316:21: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1316 | fread(&tmpoffset, sizeof(comet_fileoffset_t), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch.cpp:1323:21: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1323 | fread(szTmp, sizeof(char)*WIDTH_REFERENCE, 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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(ThreadProc, int, int, int) [with T = PreprocessThreadData*; ThreadProc = void (*)(PreprocessThreadData*)]’
69 | new ThreadManager<T>(this);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
CometPreprocess.cpp:74:65: required from here
74 | minNumThreads, maxNumThreads, 1 /*maxNumParamsToQueue*/);
| ^
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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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(ThreadProc, int, int, int) [with T = PostAnalysisThreadData*; ThreadProc = void (*)(PostAnalysisThreadData*)]’
69 | new ThreadManager<T>(this);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
CometPostAnalysis.cpp:46:38: required from here
46 | minNumThreads, maxNumThreads);
| ^
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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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
CometMassSpecUtils.cpp: In static member function ‘static void CometMassSpecUtils::GetProteinName(FILE*, comet_fileoffset_t, char*)’:
CometMassSpecUtils.cpp:136:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
136 | fread(&lSize, sizeof(long), 1, fpdb);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometMassSpecUtils.cpp:141:15: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
141 | fread(&tmpoffset, sizeof(comet_fileoffset_t), 1, fpdb);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometMassSpecUtils.cpp:148:15: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
148 | fread(szTmp, sizeof(char)*WIDTH_REFERENCE, 1, fpdb);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometMassSpecUtils.cpp:155:13: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
155 | fscanf(fpdb, "%99s", szProteinName);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometWriteOut.cpp -c
CometWriteOut.cpp: In static member function ‘static bool CometWriteOut::PrintResults(int, bool, FILE*)’:
CometWriteOut.cpp:124:32: warning: ‘%.5d’ directive writing between 5 and 11 bytes into a region of size between 0 and 1022 [-Wformat-overflow=]
124 | sprintf(szOutput, "%s/%s.%.5d.%.5d.%d.out",
| ^~~~
In file included from /usr/include/stdio.h:970,
from /usr/include/c++/14/cstdio:42,
from /usr/include/c++/14/ext/string_conversions.h:45,
from /usr/include/c++/14/bits/basic_string.h:4154,
from /usr/include/c++/14/string:54,
from Common.h:21,
from CometWriteOut.cpp:17:
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘static bool CometWriteOut::PrintResults(int, bool, FILE*)’ at CometWriteOut.cpp:124:14:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 20 and 1064 bytes into a destination of size 1024
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometWriteOut.cpp: In static member function ‘static bool CometWriteOut::PrintResults(int, bool, FILE*)’:
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",
| ^~
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘static bool CometWriteOut::PrintResults(int, bool, FILE*)’ at CometWriteOut.cpp:115:14:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 26 and 1070 bytes into a destination of size 1024
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometWriteOut.cpp: In static member function ‘static bool CometWriteOut::PrintResults(int, bool, FILE*)’:
CometWriteOut.cpp:273:28: warning: ‘%+d’ directive writing between 2 and 11 bytes into a region of size 9 [-Wformat-overflow=]
273 | sprintf(szTempStr, " %+d", iLenMaxDuplicates);
| ^~~
CometWriteOut.cpp:273:26: note: directive argument in the range [1, 2147483647]
273 | sprintf(szTempStr, " %+d", iLenMaxDuplicates);
| ^~~~~~
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘static bool CometWriteOut::PrintResults(int, bool, FILE*)’ at CometWriteOut.cpp:273:14:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 4 and 13 bytes into a destination of size 10
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometWriteOut.cpp: In static member function ‘static bool CometWriteOut::PrintResults(int, bool, FILE*)’:
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);
| ^~ ~~~~~~~~
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘static bool CometWriteOut::PrintResults(int, bool, FILE*)’ at CometWriteOut.cpp:151:14:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 33 and 1056 bytes into a destination of size 256
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometWriteSqt.cpp -c
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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
CometWritePepXML.cpp: In static member function ‘static bool CometWritePepXML::WritePepXMLHeader(FILE*, CometSearchManager&)’:
CometWritePepXML.cpp:100:12: warning: ignoring return value of ‘char* realpath(const char*, char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
100 | realpath(g_staticParams.inputFile.szBaseName, resolvedPathBaseName);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometWritePepXML.cpp:101:12: warning: ignoring return value of ‘char* realpath(const char*, char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
101 | realpath(szRunSummaryBaseName, szRunSummaryResolvedPath);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometWritePercolator.cpp -c
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometWriteTxt.cpp -c
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometSearchManager.cpp -c
CometSearchManager.cpp: In static member function ‘static bool CometSearchManager::WriteIndexedDatabase()’:
CometSearchManager.cpp:2756:28: warning: ‘.idx’ directive writing 4 bytes into a region of size between 1 and 512 [-Wformat-overflow=]
2756 | sprintf(szIndexFile, "%s.idx", g_staticParams.databaseInfo.szDatabase);
| ^~~~
In file included from /usr/include/stdio.h:970,
from /usr/include/c++/14/cstdio:42,
from /usr/include/c++/14/ext/string_conversions.h:45,
from /usr/include/c++/14/bits/basic_string.h:4154,
from /usr/include/c++/14/string:54,
from Common.h:21,
from CometSearchManager.cpp:17:
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘static bool CometSearchManager::WriteIndexedDatabase()’ at CometSearchManager.cpp:2756:11:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 516 bytes into a destination of size 512
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearchManager.cpp: In member function ‘virtual bool CometSearchManager::DoSearch()’:
CometSearchManager.cpp:416:34: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=]
416 | sprintf(szIsotope, "ISOTOPE%d", g_staticParams.tolerances.iIsotopeError);
| ^~
In function ‘void PrintOutfileHeader()’,
inlined from ‘virtual bool CometSearchManager::DoSearch()’ at CometSearchManager.cpp:1559:25:
CometSearchManager.cpp:416:26: note: directive argument in the range [1, 2147483647]
416 | sprintf(szIsotope, "ISOTOPE%d", g_staticParams.tolerances.iIsotopeError);
| ^~~~~~~~~~~
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘void PrintOutfileHeader()’ at CometSearchManager.cpp:416:14,
inlined from ‘virtual bool CometSearchManager::DoSearch()’ at CometSearchManager.cpp:1559:25:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 9 and 18 bytes into a destination of size 16
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearchManager.cpp: In member function ‘virtual bool CometSearchManager::DoSearch()’:
CometSearchManager.cpp:1597:71: warning: ‘%s’ directive writing up to 511 bytes into a region of size 218 [-Wformat-overflow=]
1597 | sprintf(szErrorMsg, " Error - cannot read DIA window file \"%s\".\n", g_staticParams.szDIAWindowsFile);
| ^~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘virtual bool CometSearchManager::DoSearch()’ at CometSearchManager.cpp:1597:17:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 42 and 553 bytes into a destination of size 256
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearchManager.cpp: In member function ‘virtual bool CometSearchManager::DoSearch()’:
CometSearchManager.cpp:223:73: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 987 [-Wformat-overflow=]
223 | sprintf(szErrorMsg, " Error - could not create directory \"%s\".\n", szDecoyDir);
| ^~ ~~~~~~~~~~
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘bool UpdateInputFile(InputFileInfo*)’ at CometSearchManager.cpp:223:20,
inlined from ‘virtual bool CometSearchManager::DoSearch()’ at CometSearchManager.cpp:1606:35:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 41 and 1064 bytes into a destination of size 1024
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearchManager.cpp: In member function ‘virtual bool CometSearchManager::DoSearch()’:
CometSearchManager.cpp:1700:76: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 219 [-Wformat-overflow=]
1700 | sprintf(szErrorMsg, " Error - cannot write to decoy file \"%s\".\n", szOutputDecoySQT);
| ^~ ~~~~~~~~~~~~~~~~
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘virtual bool CometSearchManager::DoSearch()’ at CometSearchManager.cpp:1700:23:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 41 and 1064 bytes into a destination of size 256
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearchManager.cpp: In member function ‘virtual bool CometSearchManager::DoSearch()’:
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);
| ^~ ~~~~~~~~~~~
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘virtual bool CometSearchManager::DoSearch()’ at CometSearchManager.cpp:1675:20:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 35 and 1058 bytes into a destination of size 256
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearchManager.cpp: In member function ‘virtual bool CometSearchManager::DoSearch()’:
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);
| ^~ ~~~~~~~~~~~~~~~~
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘virtual bool CometSearchManager::DoSearch()’ at CometSearchManager.cpp:1763:23:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 41 and 1064 bytes into a destination of size 256
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearchManager.cpp: In member function ‘virtual bool CometSearchManager::DoSearch()’:
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);
| ^~ ~~~~~~~~~~~
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘virtual bool CometSearchManager::DoSearch()’ at CometSearchManager.cpp:1737:20:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 35 and 1058 bytes into a destination of size 256
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearchManager.cpp: In member function ‘virtual bool CometSearchManager::DoSearch()’:
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);
| ^~ ~~~~~~~~~~~~~~~~~~~
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘virtual bool CometSearchManager::DoSearch()’ at CometSearchManager.cpp:1826:23:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 41 and 1064 bytes into a destination of size 256
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearchManager.cpp: In member function ‘virtual bool CometSearchManager::DoSearch()’:
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);
| ^~ ~~~~~~~~~~~~~~
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘virtual bool CometSearchManager::DoSearch()’ at CometSearchManager.cpp:1800:20:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 35 and 1058 bytes into a destination of size 256
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearchManager.cpp: In member function ‘virtual bool CometSearchManager::DoSearch()’:
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);
| ^~ ~~~~~~~~~~~~~~~~~~
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘virtual bool CometSearchManager::DoSearch()’ at CometSearchManager.cpp:1854:20:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 35 and 1058 bytes into a destination of size 256
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearchManager.cpp: In member function ‘virtual bool CometSearchManager::DoSearch()’:
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);
| ^~ ~~~~~~~~~~~
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘virtual bool CometSearchManager::DoSearch()’ at CometSearchManager.cpp:1975:23:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 1 and 256 bytes into a destination of size 128
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearchManager.cpp: In member function ‘virtual bool CometSearchManager::DoSearch()’:
CometSearchManager.cpp:364:66: warning: ‘%s’ directive writing up to 511 bytes into a region of size 508 [-Wformat-overflow=]
364 | sprintf(szOutFileTimeString+strlen(szOutFileTimeString), " on %s", g_staticParams.szHostName);
| ^~ ~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘void CalcRunTime(time_t)’ at CometSearchManager.cpp:364:11,
inlined from ‘virtual bool CometSearchManager::DoSearch()’ at CometSearchManager.cpp:2111:24:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 516 bytes into a destination of size 512
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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);
| ^~ ~~~~~~~~
In file included from /usr/include/stdio.h:970,
from /usr/include/c++/14/cstdio:42,
from /usr/include/c++/14/ext/string_conversions.h:45,
from /usr/include/c++/14/bits/basic_string.h:4154,
from /usr/include/c++/14/string:54,
from Common.h:21,
from CometCheckForUpdates.h:20,
from CometCheckForUpdates.cpp:17:
In function ‘int snprintf(char*, size_t, const char*, ...)’,
inlined from ‘static void CometCheckForUpdates::SendAnalyticsHit()’ at CometCheckForUpdates.cpp:156:12:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 129 and 1155 bytes into a destination of size 1024
68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
69 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
70 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
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 '/<<PKGBUILDDIR>>/CometSearch'
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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);
| ^~ ~~~~~~~~
In file included from /usr/include/stdio.h:970,
from /usr/include/c++/14/cstdio:42,
from /usr/include/c++/14/ext/string_conversions.h:45,
from /usr/include/c++/14/bits/basic_string.h:4154,
from /usr/include/c++/14/string:54,
from CometSearch/Common.h:21,
from CometSearch/CometCheckForUpdates.h:20,
from CometSearch/CometCheckForUpdates.cpp:17:
In function ‘int snprintf(char*, size_t, const char*, ...)’,
inlined from ‘static void CometCheckForUpdates::SendAnalyticsHit()’ at CometSearch/CometCheckForUpdates.cpp:156:12:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 129 and 1155 bytes into a destination of size 1024
68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
69 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
70 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearch/CometMassSpecUtils.cpp: In static member function ‘static void CometMassSpecUtils::GetProteinName(FILE*, comet_fileoffset_t, char*)’:
CometSearch/CometMassSpecUtils.cpp:136:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
136 | fread(&lSize, sizeof(long), 1, fpdb);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometMassSpecUtils.cpp:141:15: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
141 | fread(&tmpoffset, sizeof(comet_fileoffset_t), 1, fpdb);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometMassSpecUtils.cpp:148:15: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
148 | fread(szTmp, sizeof(char)*WIDTH_REFERENCE, 1, fpdb);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometMassSpecUtils.cpp:155:13: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
155 | fscanf(fpdb, "%99s", szProteinName);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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(ThreadProc, int, int, int) [with T = PreprocessThreadData*; ThreadProc = void (*)(PreprocessThreadData*)]’
69 | new ThreadManager<T>(this);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometPreprocess.cpp:74:65: required from here
74 | minNumThreads, maxNumThreads, 1 /*maxNumParamsToQueue*/);
| ^
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),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
| ^~~~
In file included from /usr/include/stdio.h:970,
from /usr/include/c++/14/cstdio:42,
from /usr/include/c++/14/ext/string_conversions.h:45,
from /usr/include/c++/14/bits/basic_string.h:4154,
from /usr/include/c++/14/string:54,
from CometSearch/Common.h:21,
from CometSearch/CometSearchManager.cpp:17:
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘static bool CometSearchManager::WriteIndexedDatabase()’ at CometSearch/CometSearchManager.cpp:2756:11:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 516 bytes into a destination of size 512
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearch/CometSearchManager.cpp: In member function ‘virtual bool CometSearchManager::DoSearch()’:
CometSearch/CometSearchManager.cpp:416:34: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=]
416 | sprintf(szIsotope, "ISOTOPE%d", g_staticParams.tolerances.iIsotopeError);
| ^~
In function ‘void PrintOutfileHeader()’,
inlined from ‘virtual bool CometSearchManager::DoSearch()’ at CometSearch/CometSearchManager.cpp:1559:25:
CometSearch/CometSearchManager.cpp:416:26: note: directive argument in the range [1, 2147483647]
416 | sprintf(szIsotope, "ISOTOPE%d", g_staticParams.tolerances.iIsotopeError);
| ^~~~~~~~~~~
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘void PrintOutfileHeader()’ at CometSearch/CometSearchManager.cpp:416:14,
inlined from ‘virtual bool CometSearchManager::DoSearch()’ at CometSearch/CometSearchManager.cpp:1559:25:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 9 and 18 bytes into a destination of size 16
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearch/CometSearchManager.cpp: In member function ‘virtual bool CometSearchManager::DoSearch()’:
CometSearch/CometSearchManager.cpp:1597:71: warning: ‘%s’ directive writing up to 511 bytes into a region of size 218 [-Wformat-overflow=]
1597 | sprintf(szErrorMsg, " Error - cannot read DIA window file \"%s\".\n", g_staticParams.szDIAWindowsFile);
| ^~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘virtual bool CometSearchManager::DoSearch()’ at CometSearch/CometSearchManager.cpp:1597:17:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 42 and 553 bytes into a destination of size 256
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearch/CometSearchManager.cpp: In member function ‘virtual bool CometSearchManager::DoSearch()’:
CometSearch/CometSearchManager.cpp:223:73: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 987 [-Wformat-overflow=]
223 | sprintf(szErrorMsg, " Error - could not create directory \"%s\".\n", szDecoyDir);
| ^~ ~~~~~~~~~~
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘bool UpdateInputFile(InputFileInfo*)’ at CometSearch/CometSearchManager.cpp:223:20,
inlined from ‘virtual bool CometSearchManager::DoSearch()’ at CometSearch/CometSearchManager.cpp:1606:35:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 41 and 1064 bytes into a destination of size 1024
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearch/CometSearchManager.cpp: In member function ‘virtual bool CometSearchManager::DoSearch()’:
CometSearch/CometSearchManager.cpp:1700:76: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 219 [-Wformat-overflow=]
1700 | sprintf(szErrorMsg, " Error - cannot write to decoy file \"%s\".\n", szOutputDecoySQT);
| ^~ ~~~~~~~~~~~~~~~~
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘virtual bool CometSearchManager::DoSearch()’ at CometSearch/CometSearchManager.cpp:1700:23:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 41 and 1064 bytes into a destination of size 256
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearch/CometSearchManager.cpp: In member function ‘virtual bool CometSearchManager::DoSearch()’:
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);
| ^~ ~~~~~~~~~~~
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘virtual bool CometSearchManager::DoSearch()’ at CometSearch/CometSearchManager.cpp:1675:20:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 35 and 1058 bytes into a destination of size 256
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearch/CometSearchManager.cpp: In member function ‘virtual bool CometSearchManager::DoSearch()’:
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);
| ^~ ~~~~~~~~~~~~~~~~
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘virtual bool CometSearchManager::DoSearch()’ at CometSearch/CometSearchManager.cpp:1763:23:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 41 and 1064 bytes into a destination of size 256
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearch/CometSearchManager.cpp: In member function ‘virtual bool CometSearchManager::DoSearch()’:
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);
| ^~ ~~~~~~~~~~~
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘virtual bool CometSearchManager::DoSearch()’ at CometSearch/CometSearchManager.cpp:1737:20:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 35 and 1058 bytes into a destination of size 256
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearch/CometSearchManager.cpp: In member function ‘virtual bool CometSearchManager::DoSearch()’:
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);
| ^~ ~~~~~~~~~~~~~~~~~~~
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘virtual bool CometSearchManager::DoSearch()’ at CometSearch/CometSearchManager.cpp:1826:23:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 41 and 1064 bytes into a destination of size 256
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearch/CometSearchManager.cpp: In member function ‘virtual bool CometSearchManager::DoSearch()’:
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);
| ^~ ~~~~~~~~~~~~~~
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘virtual bool CometSearchManager::DoSearch()’ at CometSearch/CometSearchManager.cpp:1800:20:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 35 and 1058 bytes into a destination of size 256
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearch/CometSearchManager.cpp: In member function ‘virtual bool CometSearchManager::DoSearch()’:
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);
| ^~ ~~~~~~~~~~~~~~~~~~
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘virtual bool CometSearchManager::DoSearch()’ at CometSearch/CometSearchManager.cpp:1854:20:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 35 and 1058 bytes into a destination of size 256
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearch/CometSearchManager.cpp: In member function ‘virtual bool CometSearchManager::DoSearch()’:
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);
| ^~ ~~~~~~~~~~~
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘virtual bool CometSearchManager::DoSearch()’ at CometSearch/CometSearchManager.cpp:1975:23:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 1 and 256 bytes into a destination of size 128
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearch/CometSearchManager.cpp: In member function ‘virtual bool CometSearchManager::DoSearch()’:
CometSearch/CometSearchManager.cpp:364:66: warning: ‘%s’ directive writing up to 511 bytes into a region of size 508 [-Wformat-overflow=]
364 | sprintf(szOutFileTimeString+strlen(szOutFileTimeString), " on %s", g_staticParams.szHostName);
| ^~ ~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘void CalcRunTime(time_t)’ at CometSearch/CometSearchManager.cpp:364:11,
inlined from ‘virtual bool CometSearchManager::DoSearch()’ at CometSearch/CometSearchManager.cpp:2111:24:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 5 and 516 bytes into a destination of size 512
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometWritePepXML.cpp: In static member function ‘static bool CometWritePepXML::WritePepXMLHeader(FILE*, CometSearchManager&)’:
CometSearch/CometWritePepXML.cpp:100:12: warning: ignoring return value of ‘char* realpath(const char*, char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
100 | realpath(g_staticParams.inputFile.szBaseName, resolvedPathBaseName);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometWritePepXML.cpp:101:12: warning: ignoring return value of ‘char* realpath(const char*, char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
101 | realpath(szRunSummaryBaseName, szRunSummaryResolvedPath);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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(ThreadProc, int, int, int) [with T = PostAnalysisThreadData*; ThreadProc = void (*)(PostAnalysisThreadData*)]’
69 | new ThreadManager<T>(this);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometPostAnalysis.cpp:46:38: required from here
46 | minNumThreads, maxNumThreads);
| ^
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),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp: In member function ‘int CometSearch::twiddle(int*, int*, int*, int*)’:
CometSearch/CometSearch.cpp:4973:17: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
4973 | register int i, j, k;
| ^
CometSearch/CometSearch.cpp:4973:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
4973 | register int i, j, k;
| ^
CometSearch/CometSearch.cpp:4973:23: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
4973 | register int i, j, k;
| ^
In file included from CometSearch/CometSearch.cpp:19:
CometSearch/ThreadPool.h: In instantiation of ‘ThreadManager<T>::ThreadManager(ThreadPool<T>*) [with T = SearchThreadData*]’:
CometSearch/ThreadPool.h:69:10: required from ‘ThreadPool<T>::ThreadPool(ThreadProc, int, int, int) [with T = SearchThreadData*; ThreadProc = void (*)(SearchThreadData*)]’
69 | new ThreadManager<T>(this);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp:138:66: required from here
138 | minNumThreads, maxNumThreads, 1 /*maxNumParamsToQueue*/);
| ^
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),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp: In static member function ‘static bool CometSearch::RunSearch(int, int, int, int)’:
CometSearch/CometSearch.cpp:312:27: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
312 | fgets(szPeffLine, iLenSzLine, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp:329:30: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
329 | fgets(szPeffLine+(int)strlen(szPeffLine), iLenSzLine - (int)strlen(szPeffLine), fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp:673:18: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
673 | fgets(szBuf, sizeof(szBuf), fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp: In member function ‘void CometSearch::ReadOBO(char*, std::vector<OBOStruct>*)’:
CometSearch/CometSearch.cpp:725:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
725 | fgets(szLineOBO, SIZE_BUF, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp:777:18: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
777 | fgets(szLineOBO, SIZE_BUF, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp: In member function ‘bool CometSearch::IndexSearch()’:
CometSearch/CometSearch.cpp:1159:9: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1159 | fread(&lEndOfStruct, sizeof(comet_fileoffset_t), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp:1166:9: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1166 | fread(&iMinMass, sizeof(int), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp:1167:9: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1167 | fread(&iMaxMass, sizeof(int), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp:1168:9: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1168 | fread(&tNumPeptides, sizeof(uint64_t), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp:1185:9: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1185 | fread(lReadIndex, sizeof(comet_fileoffset_t), iMaxPeptideMass10, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp:1224:9: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1224 | fread(&sDBI, sizeof(struct DBIndex), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp:1229:9: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1229 | fread(&lSize, sizeof(long), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp:1233:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1233 | fread(&tmpoffset, sizeof(comet_fileoffset_t), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp:1266:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1266 | fread(&sDBI, sizeof(struct DBIndex), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp:1269:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1269 | fread(&lSize, sizeof(long), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp:1273:15: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1273 | fread(&tmpoffset, sizeof(comet_fileoffset_t), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp:1311:18: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1311 | fread(&lSize, sizeof(long), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp:1316:21: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1316 | fread(&tmpoffset, sizeof(comet_fileoffset_t), 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CometSearch/CometSearch.cpp:1323:21: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1323 | fread(szTmp, sizeof(char)*WIDTH_REFERENCE, 1, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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",
| ^~~~
In file included from /usr/include/stdio.h:970,
from /usr/include/c++/14/cstdio:42,
from /usr/include/c++/14/ext/string_conversions.h:45,
from /usr/include/c++/14/bits/basic_string.h:4154,
from /usr/include/c++/14/string:54,
from CometSearch/Common.h:21,
from CometSearch/CometWriteOut.cpp:17:
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘static bool CometWriteOut::PrintResults(int, bool, FILE*)’ at CometSearch/CometWriteOut.cpp:124:14:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 20 and 1064 bytes into a destination of size 1024
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearch/CometWriteOut.cpp: In static member function ‘static bool CometWriteOut::PrintResults(int, bool, FILE*)’:
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",
| ^~
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘static bool CometWriteOut::PrintResults(int, bool, FILE*)’ at CometSearch/CometWriteOut.cpp:115:14:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 26 and 1070 bytes into a destination of size 1024
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearch/CometWriteOut.cpp: In static member function ‘static bool CometWriteOut::PrintResults(int, bool, FILE*)’:
CometSearch/CometWriteOut.cpp:273:28: warning: ‘%+d’ directive writing between 2 and 11 bytes into a region of size 9 [-Wformat-overflow=]
273 | sprintf(szTempStr, " %+d", iLenMaxDuplicates);
| ^~~
CometSearch/CometWriteOut.cpp:273:26: note: directive argument in the range [1, 2147483647]
273 | sprintf(szTempStr, " %+d", iLenMaxDuplicates);
| ^~~~~~
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘static bool CometWriteOut::PrintResults(int, bool, FILE*)’ at CometSearch/CometWriteOut.cpp:273:14:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 4 and 13 bytes into a destination of size 10
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
CometSearch/CometWriteOut.cpp: In static member function ‘static bool CometWriteOut::PrintResults(int, bool, FILE*)’:
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);
| ^~ ~~~~~~~~
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘static bool CometWriteOut::PrintResults(int, bool, FILE*)’ at CometSearch/CometWriteOut.cpp:151:14:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 33 and 1056 bytes into a destination of size 256
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
Comet.cpp: In function ‘void LoadParameters(char*, CometInterfaces::ICometSearchManager*)’:
Comet.cpp:1143:9: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1143 | fgets(szParamBuf, SIZE_BUF, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
Comet.cpp:1196:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
1196 | fgets(szParamBuf, SIZE_BUF, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
Comet.cpp: In function ‘void ProcessCmdLine(int, char**, char*, std::vector<InputFileInfo*>&, CometInterfaces::ICometSearchManager*)’:
Comet.cpp:1396:75: warning: ‘%s’ directive writing up to 511 bytes into a region of size 235 [-Wformat-overflow=]
1396 | sprintf(szErrorMsg+strlen(szErrorMsg), " Error - input file \"%s\" not found.\n", pInputFileInfo->szFileName);
| ^~
In file included from /usr/include/stdio.h:970,
from /usr/include/c++/14/cstdio:42,
from /usr/include/c++/14/ext/string_conversions.h:45,
from /usr/include/c++/14/bits/basic_string.h:4154,
from /usr/include/c++/14/string:54,
from CometSearch/Common.h:21,
from Comet.cpp:18:
In function ‘int sprintf(char*, const char*, ...)’,
inlined from ‘void ProcessCmdLine(int, char**, char*, std::vector<InputFileInfo*>&, CometInterfaces::ICometSearchManager*)’ at Comet.cpp:1396:20:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: ‘__builtin___sprintf_chk’ output between 35 and 546 bytes into a destination of size 256
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
cd CometSearch ; make
make[3]: Entering directory '/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/CometSearch'
g++ Comet.o CometSearch/CometCheckForUpdates.o CometSearch/CometMassSpecUtils.o CometSearch/CometPreprocess.o CometSearch/CometSearchManager.o CometSearch/CometWritePepXML.o CometSearch/CometWriteSqt.o CometSearch/Threading.o CometSearch/CometInterfaces.o CometSearch/CometPostAnalysis.o CometSearch/CometSearch.o CometSearch/CometWriteOut.o CometSearch/CometWritePercolator.o CometSearch/CometWriteTxt.o -o comet-ms -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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 '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test
rm -fr -- /tmp/dh-xdg-rundir-ZESO8VN8
create-stamp debian/debhelper-build-stamp
dh_prep
rm -f -- debian/comet-ms.substvars
rm -fr -- debian/.debhelper/generated/comet-ms/ debian/comet-ms/ debian/tmp/
dh_installdirs
install -m0755 -d debian/comet-ms/usr/bin
dh_auto_install --destdir=debian/comet-ms/
install -m0755 -d /<<BUILDDIR>>/comet-ms-2019015\+cleaned1/debian/comet-ms
dh_install
install -m0755 -d debian/comet-ms/usr/bin
cp --reflink=auto -a ./comet-ms debian/comet-ms/usr/bin/
dh_installdocs
install -m0755 -d debian/comet-ms/usr/share/doc/comet-ms
install -p -m0644 debian/copyright debian/comet-ms/usr/share/doc/comet-ms/copyright
dh_installchangelogs
install -m0755 -d debian/comet-ms/usr/share/doc/comet-ms
install -p -m0644 debian/.debhelper/generated/comet-ms/dh_installchangelogs.dch.trimmed debian/comet-ms/usr/share/doc/comet-ms/changelog.Debian
dh_installman
install -m0755 -d debian/comet-ms/usr/share/man/man1/
install -p -m0644 ./debian/comet-ms.1 debian/comet-ms/usr/share/man/man1/comet-ms.1
man-recode --to-code UTF-8 --suffix .dh-new debian/comet-ms/usr/share/man/man1/comet-ms.1
mv debian/comet-ms/usr/share/man/man1/comet-ms.1.dh-new debian/comet-ms/usr/share/man/man1/comet-ms.1
chmod 0644 -- debian/comet-ms/usr/share/man/man1/comet-ms.1
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
cd debian/comet-ms
chmod a-x usr/share/doc/comet-ms/changelog.Debian usr/share/man/man1/comet-ms.1
gzip -9nf usr/share/doc/comet-ms/changelog.Debian usr/share/man/man1/comet-ms.1
cd '/<<PKGBUILDDIR>>'
dh_fixperms
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 -a
dwz -- debian/comet-ms/usr/bin/comet-ms
dh_strip -a
install -m0755 -d debian/.debhelper/comet-ms/dbgsym-root/usr/lib/debug/.build-id/1c
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/1c/5b1f21208155f5071c95005e3aeaad4bcca7cc.debug
chmod 0644 -- debian/.debhelper/comet-ms/dbgsym-root/usr/lib/debug/.build-id/1c/5b1f21208155f5071c95005e3aeaad4bcca7cc.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/1c/5b1f21208155f5071c95005e3aeaad4bcca7cc.debug debian/comet-ms/usr/bin/comet-ms
install -m0755 -d debian/.debhelper/comet-ms/dbgsym-root/usr/share/doc
ln -s comet-ms debian/.debhelper/comet-ms/dbgsym-root/usr/share/doc/comet-ms-dbgsym
install -m0755 -d debian/.debhelper/comet-ms
dh_makeshlibs -a
rm -f debian/comet-ms/DEBIAN/shlibs
dh_shlibdeps -a
install -m0755 -d debian/comet-ms/DEBIAN
dpkg-shlibdeps -Tdebian/comet-ms.substvars debian/comet-ms/usr/bin/comet-ms
dh_installdeb
install -m0755 -d debian/comet-ms/DEBIAN
dh_gencontrol
install -m0755 -d debian/comet-ms/DEBIAN
echo misc:Depends= >> debian/comet-ms.substvars
echo misc:Pre-Depends= >> debian/comet-ms.substvars
install -m0755 -d debian/.debhelper/comet-ms/dbgsym-root/DEBIAN
dpkg-gencontrol -pcomet-ms -ldebian/changelog -Tdebian/comet-ms.substvars -cdebian/control -Pdebian/.debhelper/comet-ms/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=comet-ms-dbgsym "-DDepends=comet-ms (= \${binary:Version})" "-DDescription=debug symbols for comet-ms" -DBuild-Ids=1c5b1f21208155f5071c95005e3aeaad4bcca7cc -DSection=debug -UMulti-Arch -UReplaces -UBreaks
chmod 0644 -- debian/.debhelper/comet-ms/dbgsym-root/DEBIAN/control
dpkg-gencontrol -pcomet-ms -ldebian/changelog -Tdebian/comet-ms.substvars -cdebian/control -Pdebian/comet-ms
chmod 0644 -- debian/comet-ms/DEBIAN/control
dh_md5sums
install -m0755 -d debian/comet-ms/DEBIAN
cd debian/comet-ms >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/comet-ms/DEBIAN/md5sums
install -m0755 -d debian/.debhelper/comet-ms/dbgsym-root/DEBIAN
cd debian/.debhelper/comet-ms/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/.debhelper/comet-ms/dbgsym-root/DEBIAN/md5sums
dh_builddeb
dpkg-deb --root-owner-group --build debian/comet-ms ..
dpkg-deb --root-owner-group --build debian/.debhelper/comet-ms/dbgsym-root ..
dpkg-deb: building package 'comet-ms' in '../comet-ms_2019015+cleaned1-4.1_amd64.deb'.
dpkg-deb: building package 'comet-ms-dbgsym' in '../comet-ms-dbgsym_2019015+cleaned1-4.1_amd64.deb'.
dpkg-genbuildinfo --build=binary -O../comet-ms_2019015+cleaned1-4.1_amd64.buildinfo
dpkg-genchanges --build=binary -O../comet-ms_2019015+cleaned1-4.1_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2024-11-15T13:12:48Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
comet-ms_2019015+cleaned1-4.1_amd64.changes:
--------------------------------------------
Format: 1.8
Date: Sat, 13 Apr 2024 22:27:15 +0200
Source: comet-ms
Binary: comet-ms comet-ms-dbgsym
Architecture: amd64
Version: 2019015+cleaned1-4.1
Distribution: sid
Urgency: medium
Maintainer: The Debichem Group <debichem-devel@lists.alioth.debian.org>
Changed-By: Sebastian Ramacher <sramacher@debian.org>
Description:
comet-ms - Tandem mass spectrometry (MS/MS) search engine
Closes: 1068221
Changes:
comet-ms (2019015+cleaned1-4.1) unstable; urgency=medium
.
* Non-maintainer upload.
* debian/control: Remove hard-coded dependency on libmstoolkit82. (Closes:
#1068221)
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Files:
78c6fc0f8ee68445aa3ec866c16d6571 1823828 debug optional comet-ms-dbgsym_2019015+cleaned1-4.1_amd64.deb
7b5d3716bf9991ef5c6a2cfe0f86ce39 5350 science optional comet-ms_2019015+cleaned1-4.1_amd64.buildinfo
fc5c7c133c6b6f1ba083c2913e61e309 830192 science optional comet-ms_2019015+cleaned1-4.1_amd64.deb
+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: comet-ms
Binary: comet-ms comet-ms-dbgsym
Architecture: amd64
Version: 2019015+cleaned1-4.1
Checksums-Md5:
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Checksums-Sha1:
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Checksums-Sha256:
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81f26e9b26f32aca3b40435977d96f2eb2f5e20e639d1d38427e8cb3595ad9b0 830192 comet-ms_2019015+cleaned1-4.1_amd64.deb
Build-Origin: Debian
Build-Architecture: amd64
Build-Date: Fri, 15 Nov 2024 13:12:48 +0000
Build-Path: /<<PKGBUILDDIR>>
Build-Tainted-By:
merged-usr-via-aliased-dirs
Installed-Build-Depends:
autoconf (= 2.72-3),
automake (= 1:1.16.5-1.3),
autopoint (= 0.22.5-2),
autotools-dev (= 20220109.1),
base-files (= 13.5),
base-passwd (= 3.6.5),
bash (= 5.2.32-1+b2),
binutils (= 2.43.1-5),
binutils-common (= 2.43.1-5),
binutils-x86-64-linux-gnu (= 2.43.1-5),
bsdextrautils (= 2.40.2-11),
bsdutils (= 1:2.40.2-11),
build-essential (= 12.12),
bzip2 (= 1.0.8-6),
coreutils (= 9.5-1+b1),
cpp (= 4:14.2.0-1),
cpp-14 (= 14.2.0-8),
cpp-14-x86-64-linux-gnu (= 14.2.0-8),
cpp-x86-64-linux-gnu (= 4:14.2.0-1),
dash (= 0.5.12-9),
debconf (= 1.5.87),
debhelper (= 13.20),
debianutils (= 5.20),
dh-autoreconf (= 20),
dh-strip-nondeterminism (= 1.14.0-1),
diffutils (= 1:3.10-1),
docbook (= 4.5-11),
docbook-to-man (= 1:2.0.0-47),
dpkg (= 1.22.11),
dpkg-dev (= 1.22.12~1.gbp82cafd),
dwz (= 0.15-1+b1),
file (= 1:5.45-3+b1),
findutils (= 4.10.0-3),
g++ (= 4:14.2.0-1),
g++-14 (= 14.2.0-8),
g++-14-x86-64-linux-gnu (= 14.2.0-8),
g++-x86-64-linux-gnu (= 4:14.2.0-1),
gcc (= 4:14.2.0-1),
gcc-14 (= 14.2.0-8),
gcc-14-base (= 14.2.0-8),
gcc-14-x86-64-linux-gnu (= 14.2.0-8),
gcc-x86-64-linux-gnu (= 4:14.2.0-1),
gettext (= 0.22.5-2),
gettext-base (= 0.22.5-2),
grep (= 3.11-4),
groff-base (= 1.23.0-5),
gzip (= 1.12-1.1),
hostname (= 3.25),
init-system-helpers (= 1.67),
intltool-debian (= 0.35.0+20060710.6),
libacl1 (= 2.3.2-2+b1),
libarchive-zip-perl (= 1.68-1),
libasan8 (= 14.2.0-8),
libatomic1 (= 14.2.0-8),
libattr1 (= 1:2.5.2-2),
libaudit-common (= 1:4.0.2-2),
libaudit1 (= 1:4.0.2-2),
libbinutils (= 2.43.1-5),
libblkid1 (= 2.40.2-11),
libbz2-1.0 (= 1.0.8-6),
libc-bin (= 2.40-3),
libc-dev-bin (= 2.40-3),
libc6 (= 2.40-3),
libc6-dev (= 2.40-3),
libcap-ng0 (= 0.8.5-3+b1),
libcap2 (= 1:2.66-5+b1),
libcc1-0 (= 14.2.0-8),
libcrypt-dev (= 1:4.4.36-5),
libcrypt1 (= 1:4.4.36-5),
libctf-nobfd0 (= 2.43.1-5),
libctf0 (= 2.43.1-5),
libdb5.3t64 (= 5.3.28+dfsg2-9),
libdebconfclient0 (= 0.273),
libdebhelper-perl (= 13.20),
libdpkg-perl (= 1.22.12~1.gbp82cafd),
libelf1t64 (= 0.192-4),
libexpat1 (= 2.6.4-1),
libexpat1-dev (= 2.6.4-1),
libfile-stripnondeterminism-perl (= 1.14.0-1),
libgcc-14-dev (= 14.2.0-8),
libgcc-s1 (= 14.2.0-8),
libgdbm-compat4t64 (= 1.24-2),
libgdbm6t64 (= 1.24-2),
libgmp10 (= 2:6.3.0+dfsg-2+b2),
libgomp1 (= 14.2.0-8),
libgprofng0 (= 2.43.1-5),
libhwasan0 (= 14.2.0-8),
libicu72 (= 72.1-5+b1),
libisl23 (= 0.27-1),
libitm1 (= 14.2.0-8),
libjansson4 (= 2.14-2+b3),
liblsan0 (= 14.2.0-8),
liblzma5 (= 5.6.3-1+b1),
libmagic-mgc (= 1:5.45-3+b1),
libmagic1t64 (= 1:5.45-3+b1),
libmd0 (= 1.1.0-2+b1),
libmount1 (= 2.40.2-11),
libmpc3 (= 1.3.1-1+b3),
libmpfr6 (= 4.2.1-1+b2),
libmstoolkit-dev (= 82-7.2),
libmstoolkit82t64 (= 82-7.2),
libosp5 (= 1.5.2-15),
libpam-modules (= 1.5.3-7+b1),
libpam-modules-bin (= 1.5.3-7+b1),
libpam-runtime (= 1.5.3-7),
libpam0g (= 1.5.3-7+b1),
libpcre2-8-0 (= 10.44-2),
libperl5.40 (= 5.40.0-7),
libpipeline1 (= 1.5.8-1),
libquadmath0 (= 14.2.0-8),
libseccomp2 (= 2.5.5-1+b3),
libselinux1 (= 3.7-3+b1),
libsframe1 (= 2.43.1-5),
libsmartcols1 (= 2.40.2-11),
libsqlite3-0 (= 3.46.1-1),
libsqlite3-dev (= 3.46.1-1),
libssl3t64 (= 3.3.2-2),
libstdc++-14-dev (= 14.2.0-8),
libstdc++6 (= 14.2.0-8),
libsystemd0 (= 257~rc1-4),
libtinfo6 (= 6.5-2+b1),
libtool (= 2.4.7-8),
libtsan2 (= 14.2.0-8),
libubsan1 (= 14.2.0-8),
libuchardet0 (= 0.0.8-1+b2),
libudev1 (= 257~rc1-4),
libunistring5 (= 1.2-1+b1),
libuuid1 (= 2.40.2-11),
libxml2 (= 2.12.7+dfsg+really2.9.14-0.2+b1),
libzstd1 (= 1.5.6+dfsg-1+b1),
linux-libc-dev (= 6.11.7-1),
m4 (= 1.4.19-4),
make (= 4.3-4.1),
man-db (= 2.13.0-1),
mawk (= 1.3.4.20240905-1),
ncurses-base (= 6.5-2),
ncurses-bin (= 6.5-2+b1),
opensp (= 1.5.2-15),
openssl-provider-legacy (= 3.3.2-2),
patch (= 2.7.6-7),
perl (= 5.40.0-7),
perl-base (= 5.40.0-7),
perl-modules-5.40 (= 5.40.0-7),
po-debconf (= 1.0.21+nmu1),
rpcsvc-proto (= 1.4.3-1),
sed (= 4.9-2),
sensible-utils (= 0.0.24),
sgml-base (= 1.31),
sgml-data (= 2.0.11+nmu1),
sysvinit-utils (= 3.11-1),
tar (= 1.35+dfsg-3),
util-linux (= 2.40.2-11),
xml-core (= 0.19),
xz-utils (= 5.6.3-1+b1),
zlib1g (= 1:1.3.dfsg+really1.3.1-1+b1),
zlib1g-dev (= 1:1.3.dfsg+really1.3.1-1+b1)
Environment:
DEB_BUILD_OPTIONS="parallel=4"
LANG="C.UTF-8"
LC_COLLATE="C.UTF-8"
LC_CTYPE="C.UTF-8"
SOURCE_DATE_EPOCH="1713040035"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
comet-ms-dbgsym_2019015+cleaned1-4.1_amd64.deb
----------------------------------------------
new Debian package, version 2.0.
size 1823828 bytes: control archive=544 bytes.
388 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: comet-ms-dbgsym
Source: comet-ms
Version: 2019015+cleaned1-4.1
Auto-Built-Package: debug-symbols
Architecture: amd64
Maintainer: The Debichem Group <debichem-devel@lists.alioth.debian.org>
Installed-Size: 1852
Depends: comet-ms (= 2019015+cleaned1-4.1)
Section: debug
Priority: optional
Description: debug symbols for comet-ms
Build-Ids: 1c5b1f21208155f5071c95005e3aeaad4bcca7cc
drwxr-xr-x root/root 0 2024-04-13 20:27 ./
drwxr-xr-x root/root 0 2024-04-13 20:27 ./usr/
drwxr-xr-x root/root 0 2024-04-13 20:27 ./usr/lib/
drwxr-xr-x root/root 0 2024-04-13 20:27 ./usr/lib/debug/
drwxr-xr-x root/root 0 2024-04-13 20:27 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2024-04-13 20:27 ./usr/lib/debug/.build-id/1c/
-rw-r--r-- root/root 1885760 2024-04-13 20:27 ./usr/lib/debug/.build-id/1c/5b1f21208155f5071c95005e3aeaad4bcca7cc.debug
drwxr-xr-x root/root 0 2024-04-13 20:27 ./usr/share/
drwxr-xr-x root/root 0 2024-04-13 20:27 ./usr/share/doc/
lrwxrwxrwx root/root 0 2024-04-13 20:27 ./usr/share/doc/comet-ms-dbgsym -> comet-ms
comet-ms_2019015+cleaned1-4.1_amd64.deb
---------------------------------------
new Debian package, version 2.0.
size 830192 bytes: control archive=860 bytes.
770 bytes, 17 lines control
262 bytes, 4 lines md5sums
Package: comet-ms
Version: 2019015+cleaned1-4.1
Architecture: amd64
Maintainer: The Debichem Group <debichem-devel@lists.alioth.debian.org>
Installed-Size: 2409
Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.0), libmstoolkit82t64 (>= 82), libstdc++6 (>= 13.1)
Section: science
Priority: optional
Homepage: http://comet-ms.sourceforge.net
Description: Tandem mass spectrometry (MS/MS) search engine
Comet is an open source tandem mass spectrometry (MS/MS) sequence
database search engine. It identifies peptides by searching MS/MS
spectra against sequences present in protein sequence databases.
.
This package ships a binary that does MS/MS database
searches. Supported input formats are mzXML, mzML, and ms2
files. Supported output formats are .out, SQT, and pepXML.
drwxr-xr-x root/root 0 2024-04-13 20:27 ./
drwxr-xr-x root/root 0 2024-04-13 20:27 ./usr/
drwxr-xr-x root/root 0 2024-04-13 20:27 ./usr/bin/
-rwxr-xr-x root/root 2452040 2024-04-13 20:27 ./usr/bin/comet-ms
drwxr-xr-x root/root 0 2024-04-13 20:27 ./usr/share/
drwxr-xr-x root/root 0 2024-04-13 20:27 ./usr/share/doc/
drwxr-xr-x root/root 0 2024-04-13 20:27 ./usr/share/doc/comet-ms/
-rw-r--r-- root/root 745 2024-04-13 20:27 ./usr/share/doc/comet-ms/changelog.Debian.gz
-rw-r--r-- root/root 2584 2023-11-24 14:09 ./usr/share/doc/comet-ms/copyright
drwxr-xr-x root/root 0 2024-04-13 20:27 ./usr/share/man/
drwxr-xr-x root/root 0 2024-04-13 20:27 ./usr/share/man/man1/
-rw-r--r-- root/root 668 2024-04-13 20:27 ./usr/share/man/man1/comet-ms.1.gz
lintian
-------
Setup apt archive
-----------------
Merged Build-Depends: lintian
Filtered Build-Depends: lintian
dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-lintian-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [615 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [1291 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [1353 B]
Fetched 3259 B in 0s (0 B/s)
Reading package lists...
Get:1 file:/<<BUILDDIR>>/resolver-q5mYdb/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-q5mYdb/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-q5mYdb/apt_archive ./ Release [606 B]
Get:2 file:/<<BUILDDIR>>/resolver-q5mYdb/apt_archive ./ Release [606 B]
Get:3 file:/<<BUILDDIR>>/resolver-q5mYdb/apt_archive ./ Release.gpg
Ign:3 file:/<<BUILDDIR>>/resolver-q5mYdb/apt_archive ./ Release.gpg
Reading package lists...
Reading package lists...
Install lintian build dependencies (apt-based resolver)
-------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
sbuild-build-depends-lintian-dummy
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 856 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [856 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 856 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-lintian-dummy.
(Reading database ... 23003 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-lintian-dummy_0.invalid.0_amd64.deb ...
Unpacking sbuild-build-depends-lintian-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-lintian-dummy (0.invalid.0) ...
Running lintian...
W: comet-ms changes: distribution-and-changes-mismatch sid unstable
I: Lintian run was successful.
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: amd64
Build Type: binary
Build-Space: 66832
Build-Time: 45
Distribution: sid
Host Architecture: amd64
Install-Time: 15
Job: /tmp/debusine-fetch-exec-upload-eyzx3wsg/comet-ms_2019015+cleaned1-4.1.dsc
Lintian: warn
Machine Architecture: amd64
Package: comet-ms
Package-Time: 84
Source-Version: 2019015+cleaned1-4.1
Space: 66832
Status: successful
Version: 2019015+cleaned1-4.1
--------------------------------------------------------------------------------
Finished at 2024-11-15T13:12:48Z
Build needed 00:01:24, 66832k disk space