I: pbuilder: network access will be disabled during build I: Current time: Sat Apr 27 17:33:13 +14 2024 I: pbuilder-time-stamp: 1714188793 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [tracetuner_3.0.6~beta+dfsg-3.dsc] I: copying [./tracetuner_3.0.6~beta+dfsg.orig.tar.xz] I: copying [./tracetuner_3.0.6~beta+dfsg-3.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Dec 4 22:53:28 2020 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./tracetuner_3.0.6~beta+dfsg-3.dsc: no acceptable signature found dpkg-source: info: extracting tracetuner in tracetuner-3.0.6~beta+dfsg dpkg-source: info: unpacking tracetuner_3.0.6~beta+dfsg.orig.tar.xz dpkg-source: info: unpacking tracetuner_3.0.6~beta+dfsg-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hardening.patch dpkg-source: info: applying fix_format_security.patch dpkg-source: info: applying cross.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2989067/tmp/hooks/D01_modify_environment starting debug: Running on codethink02-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Apr 27 03:33 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/2989067/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2989067/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=b79c988430e44f1d9281c465a8a2c1b1 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=2989067 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.ssRJtKR3/pbuilderrc_jxqj --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ssRJtKR3/b2 --logfile b2/build.log tracetuner_3.0.6~beta+dfsg-3.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 21 07:15 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2989067/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19937 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 31 newly installed, 0 to remove and 0 not upgraded. Need to get 19.6 MB of archives. After unpacking 77.2 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-2+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic1 arm64 1:5.45-2+b1 [100 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-2+b1 [43.2 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-3+b1 [1126 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.39.3-6 [90.0 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.12.0-3 [1385 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b2 [624 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.15.3 [901 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3.1 [915 kB] Fetched 19.6 MB in 0s (41.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19937 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-2+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-2+b1) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../02-libmagic1_1%3a5.45-2+b1_arm64.deb ... Unpacking libmagic1:arm64 (1:5.45-2+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-2+b1_arm64.deb ... Unpacking file (1:5.45-2+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_arm64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-3+b1_arm64.deb ... Unpacking groff-base (1.23.0-3+b1) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.39.3-6_arm64.deb ... Unpacking bsdextrautils (2.39.3-6) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.7-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.12.0-3_arm64.deb ... Unpacking man-db (2.12.0-3) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../22-libelf1t64_0.191-1+b1_arm64.deb ... Unpacking libelf1t64:arm64 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../24-libicu72_72.1-4+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-4+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.3+b2_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.3+b2) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-14+b1_arm64.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../30-zlib1g-dev_1%3a1.3.dfsg-3.1_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.3.dfsg-3.1) ... Setting up libpipeline1:arm64 (1.5.7-2) ... Setting up libicu72:arm64 (72.1-4+b1) ... Setting up bsdextrautils (2.39.3-6) ... Setting up libmagic-mgc (1:5.45-2+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libmagic1:arm64 (1:5.45-2+b1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-2+b1) ... Setting up libelf1t64:arm64 (0.191-1+b1) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-14) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg-3.1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3+b2) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-3+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.15.3) ... Processing triggers for libc-bin (2.37-18) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/2989067/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/2989067/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/tracetuner-3.0.6~beta+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../tracetuner_3.0.6~beta+dfsg-3_source.changes dpkg-buildpackage: info: source package tracetuner dpkg-buildpackage: info: source version 3.0.6~beta+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --sourcedirectory=src --no-parallel debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/tracetuner-3.0.6~beta+dfsg' dh_auto_clean cd src && make -j1 clean make[2]: Entering directory '/build/reproducible-path/tracetuner-3.0.6~beta+dfsg/src' cd compute_qv; make clean make[3]: Entering directory '/build/reproducible-path/tracetuner-3.0.6~beta+dfsg/src/compute_qv' make[3]: Leaving directory '/build/reproducible-path/tracetuner-3.0.6~beta+dfsg/src/compute_qv' cd mktrain; make clean make[3]: Entering directory '/build/reproducible-path/tracetuner-3.0.6~beta+dfsg/src/mktrain' make[3]: Leaving directory '/build/reproducible-path/tracetuner-3.0.6~beta+dfsg/src/mktrain' cd mklut; make clean make[3]: Entering directory '/build/reproducible-path/tracetuner-3.0.6~beta+dfsg/src/mklut' make[3]: Leaving directory '/build/reproducible-path/tracetuner-3.0.6~beta+dfsg/src/mklut' cd mkchk; make clean make[3]: Entering directory '/build/reproducible-path/tracetuner-3.0.6~beta+dfsg/src/mkchk' make[3]: Leaving directory '/build/reproducible-path/tracetuner-3.0.6~beta+dfsg/src/mkchk' make[2]: Leaving directory '/build/reproducible-path/tracetuner-3.0.6~beta+dfsg/src' rm -rf lib obj rel make[1]: Leaving directory '/build/reproducible-path/tracetuner-3.0.6~beta+dfsg' dh_autoreconf_clean -O--sourcedirectory=src -O--no-parallel dh_clean -O--sourcedirectory=src -O--no-parallel rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/tracetuner.substvars debian/files rm -fr -- debian/tracetuner/ 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 --sourcedirectory=src --no-parallel dh_update_autotools_config -O--sourcedirectory=src -O--no-parallel dh_autoreconf -O--sourcedirectory=src -O--no-parallel dh_auto_configure -O--sourcedirectory=src -O--no-parallel dh_auto_build -O--sourcedirectory=src -O--no-parallel cd src && make -j1 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/tracetuner-3.0.6~beta+dfsg/src' for dir in compute_qv mktrain mklut mkchk ; \ do (cd $dir; make EXTRACFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tracetuner-3.0.6~beta+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic" LDFLAGS="-Wl,-z,relro -Wl,-z,now -Wl,--as-needed" all); \ done make[2]: Entering directory '/build/reproducible-path/tracetuner-3.0.6~beta+dfsg/src/compute_qv' mkdir -p ../../obj/Linux /usr/bin/gcc -g -Wall -I../mktrain -DOS_NAME='"Linux"' -I. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tracetuner-3.0.6~beta+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c main.c -o ../../obj/Linux/main.o main.c: In function 'main': main.c:2000:45: warning: the comparison will always evaluate as 'true' for the address of 'ConsensusName' will never be NULL [-Waddress] 2000 | if (ConsensusSpecified && ConsensusName != NULL) { | ^~ main.c:73:13: note: 'ConsensusName' declared here 73 | static char ConsensusName[BUFLEN]; /* path of consensus file */ | ^~~~~~~~~~~~~ main.c:1692:27: warning: '__builtin_strncpy' specified bound 256 equals destination size [-Wstringop-truncation] 1692 | (void)strncpy(options.tal_dir, argv[++optind], | ^ main.c:1676:27: warning: '__builtin_strncpy' specified bound 256 equals destination size [-Wstringop-truncation] 1676 | (void)strncpy(options.tab_dir, argv[++optind], | ^ main.c:1663:27: warning: '__builtin_strncpy' specified bound 256 equals destination size [-Wstringop-truncation] 1663 | (void)strncpy(options.tip_dir, argv[++optind], | ^ main.c:1644:21: warning: '__builtin_strncpy' specified bound 1000 equals destination size [-Wstringop-truncation] 1644 | strncpy(FastaDirName, argv[++optind], sizeof(FastaDirName)); | ^ main.c:1636:21: warning: '__builtin_strncpy' specified bound 1000 equals destination size [-Wstringop-truncation] 1636 | strncpy(multiseqFileName, argv[++optind], | ^ main.c:1587:21: warning: '__builtin_strncpy' specified bound 1000 equals destination size [-Wstringop-truncation] 1587 | strncpy(QualRptName, argv[++optind], sizeof(QualRptName)); | ^ main.c:1580:21: warning: '__builtin_strncpy' specified bound 1000 equals destination size [-Wstringop-truncation] 1580 | strncpy(QualDirName, argv[++optind], sizeof(QualDirName)); | ^ main.c:1572:21: warning: '__builtin_strncpy' specified bound 1000 equals destination size [-Wstringop-truncation] 1572 | strncpy(multiqualFileName, argv[++optind], | ^ main.c:1546:21: warning: '__builtin_strncpy' specified bound 1000 equals destination size [-Wstringop-truncation] 1546 | strncpy(MultiFastaFilesDirName, argv[++optind], | ^ main.c:1485:27: warning: '__builtin_strncpy' specified bound 256 equals destination size [-Wstringop-truncation] 1485 | (void)strncpy(options.inp_phd_dir, argv[++optind], | ^ main.c:1450:27: warning: '__builtin_strncpy' specified bound 256 equals destination size [-Wstringop-truncation] 1450 | (void)strncpy(options.hpr_dir, argv[++optind], | ^ main.c:1421:27: warning: '__builtin_strncpy' specified bound 1000 equals destination size [-Wstringop-truncation] 1421 | (void)strncpy(InputName, argv[++optind], | ^ main.c:1386:27: warning: '__builtin_strncpy' specified bound 1000 equals destination size [-Wstringop-truncation] 1386 | (void)strncpy(InputName, argv[++optind], | ^ main.c:1391:27: warning: '__builtin_strncpy' specified bound 1000 equals destination size [-Wstringop-truncation] 1391 | (void)strncpy(PhdDirName, argv[++optind], | ^ main.c:1397:27: warning: '__builtin_strncpy' specified bound 1000 equals destination size [-Wstringop-truncation] 1397 | (void)strncpy(SCFDirName, argv[++optind], | ^ main.c:1400:27: warning: '__builtin_strncpy' output may be truncated copying 256 bytes from a string of length 999 [-Wstringop-truncation] 1400 | (void)strncpy(options.scf_dir, SCFDirName, | ^ main.c:1376:27: warning: '__builtin_strncpy' specified bound 256 equals destination size [-Wstringop-truncation] 1376 | (void)strncpy(options.poly_dir, argv[++optind], | ^ main.c:1346:27: warning: '__builtin_strncpy' specified bound 1000 equals destination size [-Wstringop-truncation] 1346 | (void)strncpy(ConsensusName, argv[++optind], | ^ mkdir -p ../../obj/Linux /usr/bin/gcc -g -Wall -I../mktrain -DOS_NAME='"Linux"' -I. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tracetuner-3.0.6~beta+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c ../mktrain/Btk_match_data.c -o ../../obj/Linux/Btk_match_data.o mkdir -p ../../obj/Linux /usr/bin/gcc -g -Wall -I../mktrain -DOS_NAME='"Linux"' -I. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tracetuner-3.0.6~beta+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c ../mktrain/Btk_compute_match.c -o ../../obj/Linux/Btk_compute_match.o ../mktrain/Btk_compute_match.c: In function 'find_best_region': ../mktrain/Btk_compute_match.c:658:13: warning: this 'else' clause does not guard... [-Wmisleading-indentation] 658 | else | ^~~~ ../mktrain/Btk_compute_match.c:660:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else' 660 | max=i; | ^~~ mkdir -p ../../obj/Linux /usr/bin/gcc -g -Wall -I../mktrain -DOS_NAME='"Linux"' -I. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tracetuner-3.0.6~beta+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c ../mktrain/Btk_sw.c -o ../../obj/Linux/Btk_sw.o mkdir -p ../../obj/Linux /usr/bin/gcc -g -Wall -I../mktrain -DOS_NAME='"Linux"' -I. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tracetuner-3.0.6~beta+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c Btk_process_indels.c -o ../../obj/Linux/Btk_process_indels.o Btk_process_indels.c: In function 'get_autocorrelation_indel_size': Btk_process_indels.c:644:42: warning: variable 'max_height' set but not used [-Wunused-but-set-variable] 644 | float *ans[NUM_COLORS], height = 0., max_height = 0.; | ^~~~~~~~~~ Btk_process_indels.c:642:25: warning: variable 'best_color' set but not used [-Wunused-but-set-variable] 642 | int i, j, color, best_color, n=1; | ^~~~~~~~~~ Btk_process_indels.c: In function 'get_autocorrelation': Btk_process_indels.c:409:5: warning: 'correl' accessing 4 bytes in a region of size 0 [-Wstringop-overflow=] 409 | correl(data1-1, data2-1, n, ans-1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Btk_process_indels.c:409:5: note: referencing argument 1 of type 'float[0]' Btk_process_indels.c:409:5: warning: 'correl' accessing 4 bytes in a region of size 0 [-Wstringop-overflow=] Btk_process_indels.c:409:5: note: referencing argument 2 of type 'float[0]' Btk_process_indels.c:409:5: note: referencing argument 4 of type 'float[0]' In file included from Btk_process_indels.c:39: nr.h:54:6: note: in a call to function 'correl' 54 | void correl(float data1[], float data2[], unsigned long n, float ans[]); | ^~~~~~ Btk_process_indels.c: In function 'Btk_process_indels': Btk_process_indels.c:2471:9: warning: '__builtin___strncpy_chk' specified bound depends on the length of the source argument [-Wstringop-truncation] 2471 | strncpy(prefix_name, options.file_name, prefix_len-1); | ^ Btk_process_indels.c:2470:22: note: length computed here 2470 | prefix_len = strlen(options.file_name) - strlen(suffix); | ^~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p ../../obj/Linux /usr/bin/gcc -g -Wall -I../mktrain -DOS_NAME='"Linux"' -I. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tracetuner-3.0.6~beta+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c Btk_atod.c -o ../../obj/Linux/Btk_atod.o mkdir -p ../../obj/Linux /usr/bin/gcc -g -Wall -I../mktrain -DOS_NAME='"Linux"' -I. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tracetuner-3.0.6~beta+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c Btk_compute_qv.c -o ../../obj/Linux/Btk_compute_qv.o mkdir -p ../../obj/Linux /usr/bin/gcc -g -Wall -I../mktrain -DOS_NAME='"Linux"' -I. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tracetuner-3.0.6~beta+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c Btk_call_bases.c -o ../../obj/Linux/Btk_call_bases.o Btk_call_bases.c: In function 'get_best_peak_color_and_index_by_base_and_location': Btk_call_bases.c:2988:28: warning: variable 'new_location' set but not used [-Wunused-but-set-variable] 2988 | int new_peak_index, new_location = location; | ^~~~~~~~~~~~ Btk_call_bases.c: In function 'call_peak_by_location_color_and_index': Btk_call_bases.c:3199:41: warning: variable 'r' set but not used [-Wunused-but-set-variable] 3199 | int i = base_ind, jc = color, j, l, r, k; | ^ Btk_call_bases.c: In function 'mark_called_peaks': Btk_call_bases.c:3547:28: warning: variable 'cd_length' set but not used [-Wunused-but-set-variable] 3547 | int Case, cd_index, cd_length; | ^~~~~~~~~ Btk_call_bases.c:3547:18: warning: variable 'cd_index' set but not used [-Wunused-but-set-variable] 3547 | int Case, cd_index, cd_length; | ^~~~~~~~ Btk_call_bases.c: In function 'Btk_call_bases': Btk_call_bases.c:3697:32: warning: variable 'cweight' set but not used [-Wunused-but-set-variable] 3697 | double height2, nweight, cweight; | ^~~~~~~ Btk_call_bases.c:3697:23: warning: variable 'nweight' set but not used [-Wunused-but-set-variable] 3697 | double height2, nweight, cweight; | ^~~~~~~ Btk_call_bases.c:3691:14: warning: variable 'debug' set but not used [-Wunused-but-set-variable] 3691 | char *debug, base, *context=NULL; | ^~~~~ Btk_call_bases.c: At top level: Btk_call_bases.c:117:25: warning: 'gSpacEst0' defined but not used [-Wunused-const-variable=] 117 | static const double gSpacEst0 = 12.0; | ^~~~~~~~~ mkdir -p ../../obj/Linux /usr/bin/gcc -g -Wall -I../mktrain -DOS_NAME='"Linux"' -I. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tracetuner-3.0.6~beta+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c Btk_process_raw_data.c -o ../../obj/Linux/Btk_process_raw_data.o Btk_process_raw_data.c: In function 'estimate_spacing_variation_of_shifted_peaks': Btk_process_raw_data.c:1142:26: warning: variable 'cd1' set but not used [-Wunused-but-set-variable] 1142 | ColorData *cd0, *cd1; | ^~~ Btk_process_raw_data.c:1142:20: warning: variable 'cd0' set but not used [-Wunused-but-set-variable] 1142 | ColorData *cd0, *cd1; | ^~~ Btk_process_raw_data.c: In function 'make_DP_mobility_shifts': Btk_process_raw_data.c:2299:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 2299 | if (DEBUG_CURTIS && options->Verbose > 2 ) | ^~ Btk_process_raw_data.c:2300:28: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 2300 | putc('o', stderr); fflush(stderr); | ^~~~~~ Btk_process_raw_data.c:2650:17: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 2650 | for ( color=0; color < NUM_COLORS; color++ ) | ^~~ Btk_process_raw_data.c:2652:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 2652 | fprintf(fp, " %8.3g\n", shift_err[i]); | ^~~~~~~ Btk_process_raw_data.c: In function 'normalize_signals': Btk_process_raw_data.c:2956:40: warning: ordered comparison of pointer with integer zero [-Wpedantic] 2956 | norm_factor[i] = (num_peaks>0) ? ave_int[i][m] : -1; | ^ Btk_process_raw_data.c: In function 'make_multicomponent_iteration': Btk_process_raw_data.c:3305:21: warning: variable 'best_pos' set but not used [-Wunused-but-set-variable] 3305 | int best_pos; | ^~~~~~~~ Btk_process_raw_data.c:3247:15: warning: variable 'det4' set but not used [-Wunused-but-set-variable] 3247 | float det4; | ^~~~ Btk_process_raw_data.c: In function 'mobility_shift_curve': Btk_process_raw_data.c:1257:5: warning: 'fpoly' accessing 4 bytes in a region of size 0 [-Wstringop-overflow=] 1257 | fpoly(scan, powers-1, poly_degree); // compute powers of scan; put in array p | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Btk_process_raw_data.c:1257:5: note: referencing argument 2 of type 'float[0]' In file included from Btk_process_raw_data.c:44: util.h:49:6: note: in a call to function 'fpoly' 49 | void fpoly(float x, float p[], int np); | ^~~~~ Btk_process_raw_data.c: In function 'make_DP_mobility_shifts': Btk_process_raw_data.c:2567:17: warning: 'fpoly' accessing 4 bytes in a region of size 0 [-Wstringop-overflow=] 2567 | fpoly(peaks[i]->ipos+shift_flag[color], powers-1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2568 | POLYFIT_DEGREE+1); | ~~~~~~~~~~~~~~~~~ Btk_process_raw_data.c:2567:17: note: referencing argument 2 of type 'float[0]' util.h:49:6: note: in a call to function 'fpoly' 49 | void fpoly(float x, float p[], int np); | ^~~~~ Btk_process_raw_data.c: In function 'make_DP_mobility_shifts.isra': Btk_process_raw_data.c:2567:17: warning: array subscript -1 is outside array bounds of 'float[6]' [-Warray-bounds=] 2567 | fpoly(peaks[i]->ipos+shift_flag[color], powers-1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2568 | POLYFIT_DEGREE+1); | ~~~~~~~~~~~~~~~~~ Btk_process_raw_data.c:1992:19: note: at offset -4 into object 'powers' of size 24 1992 | float powers[POLYFIT_DEGREE+1]; | ^~~~~~ mkdir -p ../../obj/Linux /usr/bin/gcc -g -Wall -I../mktrain -DOS_NAME='"Linux"' -I. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tracetuner-3.0.6~beta+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c util.c -o ../../obj/Linux/util.o util.c: In function 'mobShiftQuality': util.c:980:17: warning: variable 'count' set but not used [-Wunused-but-set-variable] 980 | int count[MAX_CHUNKS]; | ^~~~~ util.c: In function 'polyfit': util.c:192:5: warning: 'lfit' accessing 4 bytes in a region of size 0 [-Wstringop-overflow=] 192 | lfit(x-1, y-1, sig-1, n_data, a-1, ia-1, na, v, &chisq, fpoly); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util.c:192:5: note: referencing argument 6 of type 'int[0]' In file included from util.c:45: nr.h:63:6: note: in a call to function 'lfit' 63 | void lfit(float x[], float y[], float sig[], int ndat, float a[], int ia[], | ^~~~ mkdir -p ../../obj/Linux /usr/bin/gcc -g -Wall -I../mktrain -DOS_NAME='"Linux"' -I. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tracetuner-3.0.6~beta+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c nr.c -o ../../obj/Linux/nr.o nr.c: In function 'gaussj': nr.c:487:13: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 487 | if (ipiv[j] != 1) | ^~ nr.c:497:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 497 | ++(ipiv[icol]); | ^~ mkdir -p ../../obj/Linux /usr/bin/gcc -g -Wall -I../mktrain -DOS_NAME='"Linux"' -I. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tracetuner-3.0.6~beta+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c Btk_process_peaks.c -o ../../obj/Linux/Btk_process_peaks.o Btk_process_peaks.c: In function 'colordata_detect_peaks': Btk_process_peaks.c:524:45: warning: variable 'relative_width' set but not used [-Wunused-but-set-variable] 524 | sum_peak_width, average10_width, relative_width; | ^~~~~~~~~~~~~~ Btk_process_peaks.c: In function 'add_one_peak': Btk_process_peaks.c:2307:35: warning: variable 'p2' set but not used [-Wunused-but-set-variable] 2307 | Peak peak0, peak1, *p0, *p1, *p2; | ^~ Btk_process_peaks.c:2307:17: warning: variable 'peak1' set but not used [-Wunused-but-set-variable] 2307 | Peak peak0, peak1, *p0, *p1, *p2; | ^~~~~ Btk_process_peaks.c:2307:10: warning: variable 'peak0' set but not used [-Wunused-but-set-variable] 2307 | Peak peak0, peak1, *p0, *p1, *p2; | ^~~~~ Btk_process_peaks.c: In function 'fit_single_peak': Btk_process_peaks.c:2651:45: warning: variable 'x2' set but not used [-Wunused-but-set-variable] 2651 | double sum_exp = 0., sum_exp2 = 0., x2, B; | ^~ mkdir -p ../../obj/Linux /usr/bin/gcc -g -Wall -I../mktrain -DOS_NAME='"Linux"' -I. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tracetuner-3.0.6~beta+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c Btk_qv_io.c -o ../../obj/Linux/Btk_qv_io.o Btk_qv_io.c: In function 'Btk_read_sample_file': Btk_qv_io.c:770:46: warning: ordered comparison of pointer with integer zero [-Wpedantic] 770 | if ((options.inp_phd == 0) && (num_bases > 0)) { | ^ Btk_qv_io.c:649:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 649 | fread(magic, 1, 2, fp); | ^~~~~~~~~~~~~~~~~~~~~~ Btk_qv_io.c: In function 'output_scf_file': Btk_qv_io.c:2636:5: warning: '__builtin_strncpy' output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation] 2636 | strncpy(header.version, (scf_version == 2) ? "2.00" : "3.00", 4); | ^ Btk_qv_io.c: In function 'Btk_read_sample_file': Btk_qv_io.c:945:66: warning: '%s' directive writing up to 999 bytes into a region of size 231 [-Wformat-overflow=] 945 | sprintf(message->text, "Could not read phd file: %s\n", | ^~ 946 | phd_file_name); | ~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:906, from Btk_qv_io.c:27: In function 'sprintf', inlined from 'Btk_read_sample_file' at Btk_qv_io.c:945:17: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 27 and 1026 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 ()); | ~~~~~~~~~~~~~~~~~ Btk_qv_io.c: In function 'Btk_read_sample_file': Btk_qv_io.c:918:62: warning: '%s' directive writing up to 999 bytes into a region of size 231 [-Wformat-overflow=] 918 | sprintf(message->text, "Could not read phd file: %s\n", | ^~ 919 | phd_file_name); | ~~~~~~~~~~~~~ In function 'sprintf', inlined from 'Btk_read_sample_file' at Btk_qv_io.c:918:13: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 27 and 1026 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 ()); | ~~~~~~~~~~~~~~~~~ Btk_qv_io.c: In function 'Btk_output_poly_file': Btk_qv_io.c:2962:59: warning: '%s' directive writing up to 1023 bytes into a region of size 230 [-Wformat-overflow=] 2962 | sprintf(message->text, "Unable to open POLY file '%s'\n", | ^~ 2963 | poly_name); | ~~~~~~~~~ In function 'sprintf', inlined from 'Btk_output_poly_file' at Btk_qv_io.c:2962:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 29 and 1052 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 ()); | ~~~~~~~~~~~~~~~~~ Btk_qv_io.c: In function 'Btk_output_poly_file_old': Btk_qv_io.c:3104:59: warning: '%s' directive writing up to 1023 bytes into a region of size 230 [-Wformat-overflow=] 3104 | sprintf(message->text, "Unable to open POLY file '%s'\n", | ^~ 3105 | poly_name); | ~~~~~~~~~ In function 'sprintf', inlined from 'Btk_output_poly_file_old' at Btk_qv_io.c:3104:9: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 29 and 1052 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 ()); | ~~~~~~~~~~~~~~~~~ mkdir -p ../../obj/Linux /usr/bin/gcc -g -Wall -I../mktrain -DOS_NAME='"Linux"' -I. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tracetuner-3.0.6~beta+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c Btk_compute_tp.c -o ../../obj/Linux/Btk_compute_tp.o Btk_compute_tp.c: In function 'get_peak_height_ratio': Btk_compute_tp.c:340:58: warning: variable 'bad_ipos' set but not used [-Wunused-but-set-variable] 340 | double max_uncalled_ipos = -1, min_called_ipos = -1, bad_ipos; | ^~~~~~~~ Btk_compute_tp.c: In function 'get_peak_spacing_ratio': Btk_compute_tp.c:394:17: warning: variable 'bad_ipos' set but not used [-Wunused-but-set-variable] 394 | double psr, bad_ipos, ipos; | ^~~~~~~~ Btk_compute_tp.c: At top level: Btk_compute_tp.c:634:54: warning: argument 3 of type 'double *[4]' with mismatched bound [-Warray-parameter=] 634 | Btk_compute_tp(Data *data, char *color2base, double *params[NUM_PARAMS], | ~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from Btk_compute_tp.c:48: Btk_compute_tp.h:31:43: note: previously declared as 'double *[]' 31 | extern int Btk_compute_tp(Data *, char *, double *[], ReadInfo *, | ^~~~~~~~~~ mkdir -p ../../obj/Linux /usr/bin/gcc -g -Wall -I../mktrain -DOS_NAME='"Linux"' -I. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tracetuner-3.0.6~beta+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c Btk_compute_tpars.c -o ../../obj/Linux/Btk_compute_tpars.o Btk_compute_tpars.c: In function 'data_create': Btk_compute_tpars.c:215:33: warning: argument to 'sizeof' in 'memset' call is the same expression as the destination; did you mean to dereference it? [-Wsizeof-pointer-memaccess] 215 | (void)memset(data, 0, sizeof(data)); | ^ Btk_compute_tpars.c: In function 'Btk_compute_tpars': Btk_compute_tpars.c:804:38: warning: the comparison will always evaluate as 'false' for the address of 'color_data' will never be NULL [-Waddress] 804 | if ((&data.color_data[i] == NULL) || | ^~ In file included from Btk_compute_tpars.c:42: Btk_qv_data.h:150:16: note: 'color_data' declared here 150 | ColorData color_data[NUM_COLORS]; /* chromatograms */ | ^~~~~~~~~~ mkdir -p ../../obj/Linux /usr/bin/gcc -g -Wall -I../mktrain -DOS_NAME='"Linux"' -I. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tracetuner-3.0.6~beta+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c Btk_get_mixed_bases.c -o ../../obj/Linux/Btk_get_mixed_bases.o Btk_get_mixed_bases.c: In function 'mixed_base': Btk_get_mixed_bases.c:142:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 142 | else if (((b1 == 'G') && (b2 == 'T')) || ((b1 == 'T') && (b2 == 'G'))) | ^~ Btk_get_mixed_bases.c:145:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 145 | return 'N'; | ^~~~~~ Btk_get_mixed_bases.c: In function 'find_alternative_peaks': Btk_get_mixed_bases.c:473:34: warning: ordered comparison of pointer with integer zero [-Wpedantic] 473 | if ((num_peaks_found > 0) && | ^ Btk_get_mixed_bases.c: In function 'call_mixed_bases': Btk_get_mixed_bases.c:744:55: warning: variable 'cweight' set but not used [-Wunused-but-set-variable] 744 | double ratio, ave_wiheight, wiheight, nweight=1., cweight=1.; | ^~~~~~~ Btk_get_mixed_bases.c:744:43: warning: variable 'nweight' set but not used [-Wunused-but-set-variable] 744 | double ratio, ave_wiheight, wiheight, nweight=1., cweight=1.; | ^~~~~~~ Btk_get_mixed_bases.c:740:24: warning: variable 'pos' set but not used [-Wunused-but-set-variable] 740 | int i, j, k, n, pos, jbest, kbest, curr_num2, prev_right_bound=0; | ^~~ Btk_get_mixed_bases.c:739:25: warning: variable 'context' set but not used [-Wunused-but-set-variable] 739 | char base, base2,*context = NULL; | ^~~~~~~ Btk_get_mixed_bases.c:739:18: warning: variable 'base2' set but not used [-Wunused-but-set-variable] 739 | char base, base2,*context = NULL; | ^~~~~ Btk_get_mixed_bases.c:739:12: warning: variable 'base' set but not used [-Wunused-but-set-variable] 739 | char base, base2,*context = NULL; | ^~~~ Btk_get_mixed_bases.c: In function 'Btk_get_mixed_bases': Btk_get_mixed_bases.c:1365:31: warning: variable 'res' set but not used [-Wunused-but-set-variable] 1365 | double ratio, wratio, res, w1, w2; | ^~~ Btk_get_mixed_bases.c:1365:23: warning: variable 'wratio' set but not used [-Wunused-but-set-variable] 1365 | double ratio, wratio, res, w1, w2; | ^~~~~~ In file included from Btk_get_mixed_bases.c:34: Btk_qv.h:119:23: warning: 'altbases' may be used uninitialized [-Wmaybe-uninitialized] 119 | #define FREE(x) if((x)!=NULL) {free((char *)(x));(x)=NULL;} | ^ Btk_get_mixed_bases.c:1439:5: note: in expansion of macro 'FREE' 1439 | FREE(altbases); | ^~~~ Btk_get_mixed_bases.c:1206:14: note: 'altbases' declared here 1206 | AltBase *altbases; | ^~~~~~~~ Btk_qv.h:119:23: warning: 'altbases' may be used uninitialized [-Wmaybe-uninitialized] 119 | #define FREE(x) if((x)!=NULL) {free((char *)(x));(x)=NULL;} | ^ Btk_get_mixed_bases.c:1439:5: note: in expansion of macro 'FREE' 1439 | FREE(altbases); | ^~~~ Btk_get_mixed_bases.c:1206:14: note: 'altbases' declared here 1206 | AltBase *altbases; | ^~~~~~~~ Btk_qv.h:119:23: warning: 'altbases' may be used uninitialized [-Wmaybe-uninitialized] 119 | #define FREE(x) if((x)!=NULL) {free((char *)(x));(x)=NULL;} | ^ Btk_get_mixed_bases.c:1439:5: note: in expansion of macro 'FREE' 1439 | FREE(altbases); | ^~~~ Btk_get_mixed_bases.c:1206:14: note: 'altbases' declared here 1206 | AltBase *altbases; | ^~~~~~~~ Btk_qv.h:119:23: warning: 'altbases' may be used uninitialized [-Wmaybe-uninitialized] 119 | #define FREE(x) if((x)!=NULL) {free((char *)(x));(x)=NULL;} | ^ Btk_get_mixed_bases.c:1439:5: note: in expansion of macro 'FREE' 1439 | FREE(altbases); | ^~~~ Btk_get_mixed_bases.c:1206:14: note: 'altbases' declared here 1206 | AltBase *altbases; | ^~~~~~~~ mkdir -p ../../obj/Linux /usr/bin/gcc -g -Wall -I../mktrain -DOS_NAME='"Linux"' -I. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tracetuner-3.0.6~beta+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c Btk_lookup_table.c -o ../../obj/Linux/Btk_lookup_table.o mkdir -p ../../obj/Linux /usr/bin/gcc -g -Wall -I../mktrain -DOS_NAME='"Linux"' -I. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tracetuner-3.0.6~beta+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c Btk_qv_funs.c -o ../../obj/Linux/Btk_qv_funs.o mkdir -p ../../obj/Linux /usr/bin/gcc -g -Wall -I../mktrain -DOS_NAME='"Linux"' -I. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tracetuner-3.0.6~beta+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c ABI_Toolkit.c -o ../../obj/Linux/ABI_Toolkit.o mkdir -p ../../obj/Linux /usr/bin/gcc -g -Wall -I../mktrain -DOS_NAME='"Linux"' -I. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tracetuner-3.0.6~beta+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c Btk_default_table.c -o ../../obj/Linux/Btk_default_table.o mkdir -p ../../obj/Linux /usr/bin/gcc -g -Wall -I../mktrain -DOS_NAME='"Linux"' -I. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tracetuner-3.0.6~beta+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c FileHandler.c -o ../../obj/Linux/FileHandler.o mkdir -p ../../obj/Linux /usr/bin/gcc -g -Wall -I../mktrain -DOS_NAME='"Linux"' -I. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tracetuner-3.0.6~beta+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c SCF_Toolkit.c -o ../../obj/Linux/SCF_Toolkit.o mkdir -p ../../obj/Linux /usr/bin/gcc -g -Wall -I../mktrain -DOS_NAME='"Linux"' -I. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tracetuner-3.0.6~beta+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c context_table.c -o ../../obj/Linux/context_table.o mkdir -p ../../obj/Linux /usr/bin/gcc -g -Wall -I../mktrain -DOS_NAME='"Linux"' -I. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tracetuner-3.0.6~beta+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c tracepoly.c -o ../../obj/Linux/tracepoly.o tracepoly.c: In function 'gaussj': tracepoly.c:631:13: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 631 | if (ipiv[j] != 1) | ^~ tracepoly.c:641:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 641 | ++(ipiv[icol]); | ^~ tracepoly.c: At top level: tracepoly.c:1111:29: warning: argument 2 of type 'double[4][4000]' with mismatched bound [-Warray-parameter=] 1111 | double xx_a[4][MaxNumBases], double yy_a[4][MaxNumBases], | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from tracepoly.c:37: tracepoly.h:64:37: note: previously declared as 'double[][4000]' 64 | int readGetCoefficients(ReadInfo *, double [][MaxNumBases], | ^~~~~~~~~~~~~~~~~~~~~~ tracepoly.c:1111:58: warning: argument 3 of type 'double[4][4000]' with mismatched bound [-Warray-parameter=] 1111 | double xx_a[4][MaxNumBases], double yy_a[4][MaxNumBases], | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ tracepoly.h:65:25: note: previously declared as 'double[][4000]' 65 | double [][MaxNumBases], int [], int); | ^~~~~~~~~~~~~~~~~~~~~~ tracepoly.c:1112:26: warning: argument 4 of type 'int[4]' with mismatched bound [-Warray-parameter=] 1112 | int num_xy_a[4], int read_num ) | ~~~~^~~~~~~~~~~ tracepoly.h:65:49: note: previously declared as 'int[]' 65 | double [][MaxNumBases], int [], int); | ^~~~~~ tracepoly.c: In function 'func_legendre_1based': tracepoly.c:137:9: warning: 'func_legendre_1based_sub' accessing 8 bytes in a region of size 0 [-Wstringop-overflow=] 137 | func_legendre_1based_sub( fa, x, ptemp0-1, n ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tracepoly.c:137:9: note: referencing argument 3 of type 'double[0]' tracepoly.c:103:1: note: in a call to function 'func_legendre_1based_sub' 103 | func_legendre_1based_sub( FuncArgs* fa, double x, double pl[], int nl ) | ^~~~~~~~~~~~~~~~~~~~~~~~ tracepoly.c: In function 'legendre_fit': tracepoly.c:790:5: warning: 'lfit' accessing 4 bytes in a region of size 0 [-Wstringop-overflow=] 790 | lfit(fa, x-1, y-1, sig-1, n_data, a-1, ia-1, na, v, &chisq, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 791 | func_legendre_1based); | ~~~~~~~~~~~~~~~~~~~~~ tracepoly.c:790:5: note: referencing argument 7 of type 'int[0]' tracepoly.c:699:1: note: in a call to function 'lfit' 699 | lfit(FuncArgs* fa, | ^~~~ tracepoly.c: In function 'func_legendre_1based': tracepoly.c:137:9: warning: array subscript -1 is outside array bounds of 'double[3]' [-Warray-bounds=] 137 | func_legendre_1based_sub( fa, x, ptemp0-1, n ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tracepoly.c:132:27: note: at offset -8 into object 'ptemp0' of size 24 132 | double *pl0 = pl1+1, ptemp0[2*NumCoef-1]; | ^~~~~~ In function 'legendre_fit', inlined from 'traceGetCoef.isra' at tracepoly.c:947:9: tracepoly.c:790:5: warning: array subscript -1 is outside array bounds of 'double[8000]' [-Warray-bounds=] 790 | lfit(fa, x-1, y-1, sig-1, n_data, a-1, ia-1, na, v, &chisq, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 791 | func_legendre_1based); | ~~~~~~~~~~~~~~~~~~~~~ tracepoly.c: In function 'traceGetCoef.isra': tracepoly.c:895:12: note: at offset -8 into object 'xxxx' of size 64000 895 | double xxxx[2*MaxNumBases], yyyy[2*MaxNumBases], sigma[2*MaxNumBases]; | ^~~~ In function 'legendre_fit', inlined from 'traceGetCoef.isra' at tracepoly.c:947:9: tracepoly.c:790:5: warning: array subscript -1 is outside array bounds of 'double[8000]' [-Warray-bounds=] 790 | lfit(fa, x-1, y-1, sig-1, n_data, a-1, ia-1, na, v, &chisq, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 791 | func_legendre_1based); | ~~~~~~~~~~~~~~~~~~~~~ tracepoly.c: In function 'traceGetCoef.isra': tracepoly.c:895:33: note: at offset -8 into object 'yyyy' of size 64000 895 | double xxxx[2*MaxNumBases], yyyy[2*MaxNumBases], sigma[2*MaxNumBases]; | ^~~~ In function 'legendre_fit', inlined from 'traceGetCoef.isra' at tracepoly.c:947:9: tracepoly.c:790:5: warning: array subscript -1 is outside array bounds of 'double[8000]' [-Warray-bounds=] 790 | lfit(fa, x-1, y-1, sig-1, n_data, a-1, ia-1, na, v, &chisq, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 791 | func_legendre_1based); | ~~~~~~~~~~~~~~~~~~~~~ tracepoly.c: In function 'traceGetCoef.isra': tracepoly.c:895:54: note: at offset -8 into object 'sigma' of size 64000 895 | double xxxx[2*MaxNumBases], yyyy[2*MaxNumBases], sigma[2*MaxNumBases]; | ^~~~~ In function 'legendre_fit', inlined from 'traceGetCoef.isra' at tracepoly.c:947:9: tracepoly.c:790:5: warning: array subscript -1 is outside array bounds of 'double[8000]' [-Warray-bounds=] 790 | lfit(fa, x-1, y-1, sig-1, n_data, a-1, ia-1, na, v, &chisq, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 791 | func_legendre_1based); | ~~~~~~~~~~~~~~~~~~~~~ tracepoly.c: In function 'traceGetCoef.isra': tracepoly.c:895:12: note: at offset -8 into object 'xxxx' of size 64000 895 | double xxxx[2*MaxNumBases], yyyy[2*MaxNumBases], sigma[2*MaxNumBases]; | ^~~~ In function 'legendre_fit', inlined from 'traceGetCoef.isra' at tracepoly.c:947:9: tracepoly.c:790:5: warning: array subscript -1 is outside array bounds of 'double[8000]' [-Warray-bounds=] 790 | lfit(fa, x-1, y-1, sig-1, n_data, a-1, ia-1, na, v, &chisq, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 791 | func_legendre_1based); | ~~~~~~~~~~~~~~~~~~~~~ tracepoly.c: In function 'traceGetCoef.isra': tracepoly.c:895:33: note: at offset -8 into object 'yyyy' of size 64000 895 | double xxxx[2*MaxNumBases], yyyy[2*MaxNumBases], sigma[2*MaxNumBases]; | ^~~~ In function 'legendre_fit', inlined from 'traceGetCoef.isra' at tracepoly.c:947:9: tracepoly.c:790:5: warning: array subscript -1 is outside array bounds of 'double[8000]' [-Warray-bounds=] 790 | lfit(fa, x-1, y-1, sig-1, n_data, a-1, ia-1, na, v, &chisq, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 791 | func_legendre_1based); | ~~~~~~~~~~~~~~~~~~~~~ tracepoly.c: In function 'traceGetCoef.isra': tracepoly.c:895:54: note: at offset -8 into object 'sigma' of size 64000 895 | double xxxx[2*MaxNumBases], yyyy[2*MaxNumBases], sigma[2*MaxNumBases]; | ^~~~~ In function 'func_legendre_1based', inlined from 'func_legendre_0based' at tracepoly.c:153:5, inlined from 'traceEvalPoly' at tracepoly.c:839:5, inlined from 'traceCalcCutoff' at tracepoly.c:875:13: tracepoly.c:137:9: warning: array subscript -1 is outside array bounds of 'double[3]' [-Warray-bounds=] 137 | func_legendre_1based_sub( fa, x, ptemp0-1, n ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tracepoly.c: In function 'traceCalcCutoff': tracepoly.c:132:27: note: at offset -8 into object 'ptemp0' of size 24 132 | double *pl0 = pl1+1, ptemp0[2*NumCoef-1]; | ^~~~~~ In function 'func_legendre_1based', inlined from 'func_legendre_0based' at tracepoly.c:153:5, inlined from 'traceEvalPoly' at tracepoly.c:839:5: tracepoly.c:137:9: warning: array subscript -1 is outside array bounds of 'double[3]' [-Warray-bounds=] 137 | func_legendre_1based_sub( fa, x, ptemp0-1, n ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tracepoly.c: In function 'traceEvalPoly': tracepoly.c:132:27: note: at offset -8 into object 'ptemp0' of size 24 132 | double *pl0 = pl1+1, ptemp0[2*NumCoef-1]; | ^~~~~~ /usr/bin/ar rc ../../lib/Linux/libtt.a ../../obj/Linux/Btk_match_data.o ../../obj/Linux/Btk_compute_match.o ../../obj/Linux/Btk_sw.o ../../obj/Linux/Btk_process_indels.o ../../obj/Linux/Btk_atod.o ../../obj/Linux/Btk_compute_qv.o ../../obj/Linux/Btk_call_bases.o ../../obj/Linux/Btk_process_raw_data.o ../../obj/Linux/util.o ../../obj/Linux/nr.o ../../obj/Linux/Btk_process_peaks.o ../../obj/Linux/Btk_qv_io.o ../../obj/Linux/Btk_compute_tp.o ../../obj/Linux/Btk_compute_tpars.o ../../obj/Linux/Btk_get_mixed_bases.o ../../obj/Linux/Btk_lookup_table.o ../../obj/Linux/Btk_qv_funs.o ../../obj/Linux/ABI_Toolkit.o ../../obj/Linux/Btk_default_table.o ../../obj/Linux/FileHandler.o ../../obj/Linux/SCF_Toolkit.o ../../obj/Linux/context_table.o ../../obj/Linux/tracepoly.o /usr/bin/gcc -g -Wall -I../mktrain -DOS_NAME='"Linux"' -I. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tracetuner-3.0.6~beta+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed ../../obj/Linux/main.o ../../lib/Linux/libtt.a -lm -o ../../rel/Linux/ttuner -Wl,-z,relro -Wl,-z,now -Wl,--as-needed make[2]: Leaving directory '/build/reproducible-path/tracetuner-3.0.6~beta+dfsg/src/compute_qv' make[2]: Entering directory '/build/reproducible-path/tracetuner-3.0.6~beta+dfsg/src/mktrain' mkdir -p ../../obj/Linux /usr/bin/gcc -g -Wall -I../compute_qv -I. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tracetuner-3.0.6~beta+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c train.c -o ../../obj/Linux/train.o train.c: In function 'main': train.c:1431:26: warning: '__builtin_strncpy' specified bound 1000 equals destination size [-Wstringop-truncation] 1431 | (void)strncpy(InputName, argv[++optind], sizeof(InputName)); | ^ train.c:1400:23: warning: '__builtin_strncpy' specified bound 1000 equals destination size [-Wstringop-truncation] 1400 | (void)strncpy(OutputName, argv[++optind], sizeof(OutputName)); | ^ train.c:1357:27: warning: '__builtin_strncpy' specified bound 1000 equals destination size [-Wstringop-truncation] 1357 | (void)strncpy(inp_phd_dir, argv[++optind], | ^ train.c:1511:23: warning: '__builtin_strncpy' specified bound 1000 equals destination size [-Wstringop-truncation] 1511 | (void)strncpy(VectorName, argv[++optind], sizeof(VectorName)); | ^ train.c:1501:23: warning: '__builtin_strncpy' specified bound 1000 equals destination size [-Wstringop-truncation] 1501 | (void)strncpy(SiteName, argv[++optind], sizeof(SiteName)); break; | ^ train.c:1437:23: warning: '__builtin_strncpy' specified bound 1000 equals destination size [-Wstringop-truncation] 1437 | (void)strncpy(PrimerName, argv[++optind], sizeof(PrimerName)); | ^ train.c:1297:23: warning: '__builtin_strncpy' specified bound 1000 equals destination size [-Wstringop-truncation] 1297 | (void)strncpy(ConsensusName, argv[++optind], | ^ mkdir -p ../../obj/Linux /usr/bin/gcc -g -Wall -I../compute_qv -I. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tracetuner-3.0.6~beta+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c train_data.c -o ../../obj/Linux/train_data.o train_data.c: In function 'append_to_train_data': train_data.c:217:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 217 | if (Verbose > 0) | ^~ train_data.c:220:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 220 | fprintf(fout, "# Clear range start :%4d end:%4d\n", | ^~~~~~~ /usr/bin/gcc -g -Wall -I../compute_qv -I. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tracetuner-3.0.6~beta+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed ../../obj/Linux/train.o ../../obj/Linux/train_data.o ../../obj/Linux/Btk_compute_match.o ../../obj/Linux/Btk_match_data.o ../../obj/Linux/Btk_sw.o ../../lib/Linux/libtt.a -lm -o ../../rel/Linux/train -Wl,-z,relro -Wl,-z,now -Wl,--as-needed mkdir -p ../../obj/Linux /usr/bin/gcc -g -Wall -I../compute_qv -I. -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tracetuner-3.0.6~beta+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c trainphd.c -o ../../obj/Linux/trainphd.o trainphd.c: In function 'process_projectfile': trainphd.c:653:13: warning: variable 'buffer2' set but not used [-Wunused-but-set-variable] 653 | char buffer2[BUFLEN]; | ^~~~~~~ trainphd.c: In function 'main': trainphd.c:931:35: error: format not a string literal and no format arguments [-Werror=format-security] 931 | fprintf(stderr, message.text); | ~~~~~~~^~~~~ trainphd.c:940:35: error: format not a string literal and no format arguments [-Werror=format-security] 940 | fprintf(stderr, message.text); | ~~~~~~~^~~~~ trainphd.c:959:40: error: format not a string literal and no format arguments [-Werror=format-security] 959 | fprintf(stderr, message.text); | ~~~~~~~^~~~~ trainphd.c:967:44: error: format not a string literal and no format arguments [-Werror=format-security] 967 | fprintf(stderr, message.text); | ~~~~~~~^~~~~ trainphd.c:1011:40: error: format not a string literal and no format arguments [-Werror=format-security] 1011 | fprintf(stderr, message.text); | ~~~~~~~^~~~~ trainphd.c:1018:40: error: format not a string literal and no format arguments [-Werror=format-security] 1018 | fprintf(stderr, message.text); | ~~~~~~~^~~~~ trainphd.c:1084:40: error: format not a string literal and no format arguments [-Werror=format-security] 1084 | fprintf(stderr, message.text); | ~~~~~~~^~~~~ trainphd.c:1091:40: error: format not a string literal and no format arguments [-Werror=format-security] 1091 | fprintf(stderr, message.text); | ~~~~~~~^~~~~ trainphd.c:1123:35: error: format not a string literal and no format arguments [-Werror=format-security] 1123 | fprintf(stderr, message.text); | ~~~~~~~^~~~~ trainphd.c:1128:35: error: format not a string literal and no format arguments [-Werror=format-security] 1128 | fprintf(stderr, message.text); | ~~~~~~~^~~~~ trainphd.c:1134:40: error: format not a string literal and no format arguments [-Werror=format-security] 1134 | fprintf(stderr, message.text); | ~~~~~~~^~~~~ trainphd.c:1139:40: error: format not a string literal and no format arguments [-Werror=format-security] 1139 | fprintf(stderr, message.text); | ~~~~~~~^~~~~ trainphd.c:608:17: warning: '__builtin___strncpy_chk' specified bound depends on the length of the source argument [-Wstringop-truncation] 608 | strncpy(path2, string, strlen(string)-strlen(name)); // remove the phd.1 suffix | ^ In function 'process_dir', inlined from 'main' at trainphd.c:1095:17: trainphd.c:608:40: note: length computed here 608 | strncpy(path2, string, strlen(string)-strlen(name)); // remove the phd.1 suffix | ^~~~~~~~~~~~~~ trainphd.c: In function 'main': trainphd.c:735:17: warning: '__builtin___strncpy_chk' specified bound depends on the length of the source argument [-Wstringop-truncation] 735 | strncpy(tabFileName, string, strlen(string)-strlen(name)); // remove the phd.1 suffix | ^ In function 'process_projectfile', inlined from 'main' at trainphd.c:1105:13: trainphd.c:735:46: note: length computed here 735 | strncpy(tabFileName, string, strlen(string)-strlen(name)); // remove the phd.1 suffix | ^~~~~~~~~~~~~~ trainphd.c: In function 'main': trainphd.c:1041:25: warning: '__builtin___strncpy_chk' specified bound depends on the length of the source argument [-Wstringop-truncation] 1041 | strncpy(tab_file_name, string, strlen(string)-strlen(name)); | ^ trainphd.c:1041:56: note: length computed here 1041 | strncpy(tab_file_name, string, strlen(string)-strlen(name)); | ^~~~~~~~~~~~~~ trainphd.c:896:19: warning: '__builtin_strncpy' specified bound 1000 equals destination size [-Wstringop-truncation] 896 | (void)strncpy(tab_dir_name, optarg, sizeof(tab_dir_name)); | ^ trainphd.c:856:19: warning: '__builtin_strncpy' specified bound 1000 equals destination size [-Wstringop-truncation] 856 | (void)strncpy(OutputName, optarg, sizeof(OutputName)); | ^ trainphd.c:864:19: warning: '__builtin_strncpy' specified bound 1000 equals destination size [-Wstringop-truncation] 864 | (void)strncpy(InputName, optarg, sizeof(InputName)); | ^ trainphd.c:860:19: warning: '__builtin_strncpy' specified bound 1000 equals destination size [-Wstringop-truncation] 860 | (void)strncpy(InputName, optarg, sizeof(InputName)); | ^ trainphd.c:818:19: warning: '__builtin_strncpy' specified bound 1000 equals destination size [-Wstringop-truncation] 818 | (void)strncpy(VectorName, optarg, sizeof(VectorName)); | ^ trainphd.c:822:19: warning: '__builtin_strncpy' specified bound 1000 equals destination size [-Wstringop-truncation] 822 | (void)strncpy(SiteName, optarg, sizeof(SiteName)); | ^ trainphd.c:814:19: warning: '__builtin_strncpy' specified bound 1000 equals destination size [-Wstringop-truncation] 814 | (void)strncpy(PrimerName, optarg, sizeof(PrimerName)); | ^ trainphd.c:849:19: warning: '__builtin_strncpy' specified bound 1000 equals destination size [-Wstringop-truncation] 849 | (void)strncpy(ConsensusName, optarg, sizeof(ConsensusName)); | ^ cc1: some warnings being treated as errors make[2]: *** [../include.mk:180: ../../obj/Linux/trainphd.o] Error 1 make[2]: Leaving directory '/build/reproducible-path/tracetuner-3.0.6~beta+dfsg/src/mktrain' make[2]: Entering directory '/build/reproducible-path/tracetuner-3.0.6~beta+dfsg/src/mklut' mkdir -p ../../obj/Linux /usr/bin/gcc -g -Wall -I../compute_qv -I../mktrain -I. -I/home/gdenisov/build/include/io_lib -I../../../jtc_tt -I. -I../../../io_lib -I../../../io_lib/utils -I../mkchk -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tracetuner-3.0.6~beta+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c lut.c -o ../../obj/Linux/lut.o lut.c: In function 'read_bases_and_populate_bins': lut.c:438:26: warning: variable 'cchar' set but not used [-Wunused-but-set-variable] 438 | char schar, cchar; /* Sample and consensus characters. */ | ^~~~~ lut.c:437:25: warning: variable 'cpos' set but not used [-Wunused-but-set-variable] 437 | int spos, cpos; /* Sample and consensus positions. */ | ^~~~ lut.c:437:19: warning: variable 'spos' set but not used [-Wunused-but-set-variable] 437 | int spos, cpos; /* Sample and consensus positions. */ | ^~~~ lut.c: In function 'create_qv_table_via_dynamic_programming': lut.c:894:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation] 894 | for (i = 1; i < (MAX_QV / 10); i++) | ^~~ lut.c:899:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' 899 | fprintf(fout, "\n"); | ^~~~~~~ lut.c: In function 'compress_params_array': lut.c:1012:13: warning: variable 'max_weight' set but not used [-Wunused-but-set-variable] 1012 | int max_weight=0, *wn; | ^~~~~~~~~~ lut.c: In function 'read_and_sort_trace_parameters': lut.c:1112:21: warning: variable 'cchar' set but not used [-Wunused-but-set-variable] 1112 | char schar, cchar; /* Sample and consensus characters. */ | ^~~~~ lut.c:1111:20: warning: variable 'cpos' set but not used [-Wunused-but-set-variable] 1111 | int spos, cpos; /* Sample and consensus positions. */ | ^~~~ lut.c:1111:14: warning: variable 'spos' set but not used [-Wunused-but-set-variable] 1111 | int spos, cpos; /* Sample and consensus positions. */ | ^~~~ lut.c: In function 'main': lut.c:1404:15: warning: passing argument 1 of 'time' makes pointer from integer without a cast [-Wint-conversion] 1404 | t1 = time((time_t) NULL); | ^ | | | long int In file included from lut.c:45: /usr/include/time.h:76:29: note: expected 'time_t *' {aka 'long int *'} but argument is of type 'long int' 76 | extern time_t time (time_t *__timer) __THROW; | ~~~~~~~~^~~~~~~ lut.c:1449:34: warning: format '%d' expects argument of type 'int *', but argument 3 has type 'unsigned int *' [-Wformat=] 1449 | sscanf(optarg, "%d", &threshold_count); | ~^ ~~~~~~~~~~~~~~~~ | | | | | unsigned int * | int * | %d lut.c:1520:15: warning: passing argument 1 of 'time' makes pointer from integer without a cast [-Wint-conversion] 1520 | t2 = time((time_t) NULL); | ^ | | | long int /usr/include/time.h:76:29: note: expected 'time_t *' {aka 'long int *'} but argument is of type 'long int' 76 | extern time_t time (time_t *__timer) __THROW; | ~~~~~~~~^~~~~~~ lut.c:1573:15: warning: passing argument 1 of 'time' makes pointer from integer without a cast [-Wint-conversion] 1573 | t2 = time((time_t) NULL); | ^ | | | long int /usr/include/time.h:76:29: note: expected 'time_t *' {aka 'long int *'} but argument is of type 'long int' 76 | extern time_t time (time_t *__timer) __THROW; | ~~~~~~~~^~~~~~~ lut.c:1604:15: warning: passing argument 1 of 'time' makes pointer from integer without a cast [-Wint-conversion] 1604 | t2 = time((time_t) NULL); | ^ | | | long int /usr/include/time.h:76:29: note: expected 'time_t *' {aka 'long int *'} but argument is of type 'long int' 76 | extern time_t time (time_t *__timer) __THROW; | ~~~~~~~~^~~~~~~ lut.c:1645:15: warning: passing argument 1 of 'time' makes pointer from integer without a cast [-Wint-conversion] 1645 | t2 = time((time_t) NULL); | ^ | | | long int /usr/include/time.h:76:29: note: expected 'time_t *' {aka 'long int *'} but argument is of type 'long int' 76 | extern time_t time (time_t *__timer) __THROW; | ~~~~~~~~^~~~~~~ lut.c:1459:23: warning: '__builtin_strncpy' specified bound 1000 equals destination size [-Wstringop-truncation] 1459 | (void)strncpy(OutputName, optarg, sizeof(OutputName)); | ^ mkdir -p ../../obj/Linux /usr/bin/gcc -g -Wall -I../compute_qv -I../mktrain -I. -I/home/gdenisov/build/include/io_lib -I../../../jtc_tt -I. -I../../../io_lib -I../../../io_lib/utils -I../mkchk -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tracetuner-3.0.6~beta+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c select.c -o ../../obj/Linux/select.o mkdir -p ../../obj/Linux /usr/bin/gcc -g -Wall -I../compute_qv -I../mktrain -I. -I/home/gdenisov/build/include/io_lib -I../../../jtc_tt -I. -I../../../io_lib -I../../../io_lib/utils -I../mkchk -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tracetuner-3.0.6~beta+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c func_name.c -o ../../obj/Linux/func_name.o mkdir -p ../../obj/Linux /usr/bin/gcc -g -Wall -I../compute_qv -I../mktrain -I. -I/home/gdenisov/build/include/io_lib -I../../../jtc_tt -I. -I../../../io_lib -I../../../io_lib/utils -I../mkchk -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tracetuner-3.0.6~beta+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c get_thresholds.c -o ../../obj/Linux/get_thresholds.o mkdir -p ../../obj/Linux /usr/bin/gcc -g -Wall -I../compute_qv -I../mktrain -I. -I/home/gdenisov/build/include/io_lib -I../../../jtc_tt -I. -I../../../io_lib -I../../../io_lib/utils -I../mkchk -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tracetuner-3.0.6~beta+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c ../mkchk/check_data.c -o ../../obj/Linux/check_data.o ../mkchk/check_data.c: In function 'get_bases': ../mkchk/check_data.c:47:25: warning: variable 'cpos' set but not used [-Wunused-but-set-variable] 47 | int spos, cpos; /* Sample and consensus positions. */ | ^~~~ ../mkchk/check_data.c:47:19: warning: variable 'spos' set but not used [-Wunused-but-set-variable] 47 | int spos, cpos; /* Sample and consensus positions. */ | ^~~~ g++ ../../obj/Linux/lut.o ../../obj/Linux/select.o ../../obj/Linux/func_name.o ../../obj/Linux/get_thresholds.o ../../obj/Linux/check_data.o -o ../../rel/Linux/lut -lm -lz ../../lib/Linux/libtt.a -Wl,-z,relro -Wl,-z,now -Wl,--as-needed make[2]: Leaving directory '/build/reproducible-path/tracetuner-3.0.6~beta+dfsg/src/mklut' make[2]: Entering directory '/build/reproducible-path/tracetuner-3.0.6~beta+dfsg/src/mkchk' mkdir -p ../../obj/Linux /usr/bin/gcc -g -Wall -I../compute_qv -I../mktrain -I../mklut -I. -I -I../../../jtc_tt -I. -I../../../io_lib -I../../../io_lib/utils -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tracetuner-3.0.6~beta+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c checkbc.c -o ../../obj/Linux/checkbc.o g++ ../../obj/Linux/checkbc.o ../../obj/Linux/check_data.o ../../lib/Linux/libtt.a -lm -lz -o ../../rel/Linux/checkbc -lm -lz ../../lib/Linux/libtt.a -Wl,-z,relro -Wl,-z,now -Wl,--as-needed mkdir -p ../../obj/Linux /usr/bin/gcc -g -Wall -I../compute_qv -I../mktrain -I../mklut -I. -I -I../../../jtc_tt -I. -I../../../io_lib -I../../../io_lib/utils -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tracetuner-3.0.6~beta+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c checkqv.c -o ../../obj/Linux/checkqv.o checkqv.c: In function 'crossValidate': checkqv.c:84:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 84 | if (base[i].schar != '-') | ^~ checkqv.c:87:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 87 | qv = get_quality_value(base[i].parameter[0], | ^~ g++ ../../obj/Linux/checkqv.o ../../obj/Linux/check_data.o ../../lib/Linux/libtt.a -lm -lz -o ../../rel/Linux/checkqv -lm -lz ../../lib/Linux/libtt.a -Wl,-z,relro -Wl,-z,now -Wl,--as-needed mkdir -p ../../obj/Linux /usr/bin/gcc -g -Wall -I../compute_qv -I../mktrain -I../mklut -I. -I -I../../../jtc_tt -I. -I../../../io_lib -I../../../io_lib/utils -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tracetuner-3.0.6~beta+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c checkbcphd.c -o ../../obj/Linux/checkbcphd.o checkbcphd.c: In function 'errorStatswithQVs': checkbcphd.c:197:18: warning: unknown escape sequence: '\%' 197 | char c = '\%'; | ^~~~ checkbcphd.c:50:51: warning: variable 'qvo' set but not used [-Wunused-but-set-variable] 50 | Nqvp[MAXNUMBINS+1], qvp[MAXNUMBINS+1], qvo[MAXNUMBINS+1]; | ^~~ checkbcphd.c:50:32: warning: variable 'qvp' set but not used [-Wunused-but-set-variable] 50 | Nqvp[MAXNUMBINS+1], qvp[MAXNUMBINS+1], qvo[MAXNUMBINS+1]; | ^~~ g++ ../../obj/Linux/checkbcphd.o ../../obj/Linux/check_data.o ../../lib/Linux/libtt.a -lm -lz -o ../../rel/Linux/checkbcphd -lm -lz ../../lib/Linux/libtt.a -Wl,-z,relro -Wl,-z,now -Wl,--as-needed mkdir -p ../../obj/Linux /usr/bin/gcc -g -Wall -I../compute_qv -I../mktrain -I../mklut -I. -I -I../../../jtc_tt -I. -I../../../io_lib -I../../../io_lib/utils -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tracetuner-3.0.6~beta+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -c checkqvphd.c -o ../../obj/Linux/checkqvphd.o g++ ../../obj/Linux/checkqvphd.o ../../obj/Linux/check_data.o ../../lib/Linux/libtt.a -lm -lz -o ../../rel/Linux/checkqvphd -lm -lz ../../lib/Linux/libtt.a -Wl,-z,relro -Wl,-z,now -Wl,--as-needed make[2]: Leaving directory '/build/reproducible-path/tracetuner-3.0.6~beta+dfsg/src/mkchk' make[1]: Leaving directory '/build/reproducible-path/tracetuner-3.0.6~beta+dfsg/src' dh_auto_test -O--sourcedirectory=src -O--no-parallel rm -fr -- /tmp/dh-xdg-rundir-1xuKq0U6 create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src -O--no-parallel dh_prep -O--sourcedirectory=src -O--no-parallel rm -f -- debian/tracetuner.substvars rm -fr -- debian/.debhelper/generated/tracetuner/ debian/tracetuner/ debian/tmp/ dh_installdirs -O--sourcedirectory=src -O--no-parallel install -m0755 -d debian/tracetuner/usr/bin debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/tracetuner-3.0.6~beta+dfsg' dh_auto_install install -m0755 -d /build/reproducible-path/tracetuner-3.0.6\~beta\+dfsg/debian/tracetuner find rel -mindepth 2 -type f | xargs -r mv --target-directory=/build/reproducible-path/tracetuner-3.0.6~beta+dfsg/debian/tracetuner/usr/bin/ make[1]: Leaving directory '/build/reproducible-path/tracetuner-3.0.6~beta+dfsg' dh_installdocs -O--sourcedirectory=src -O--no-parallel install -m0755 -d debian/tracetuner/usr/share/doc/tracetuner install -m0755 -d debian/tracetuner/usr/share/doc/tracetuner cp --reflink=auto -a ./src/README debian/tracetuner/usr/share/doc/tracetuner cp --reflink=auto -a ./doc/RELEASE_NOTES debian/tracetuner/usr/share/doc/tracetuner chmod -R u\+rw,go=rX debian/tracetuner/usr/share/doc install -p -m0644 debian/README.Debian debian/tracetuner/usr/share/doc/tracetuner/README.Debian install -p -m0644 debian/copyright debian/tracetuner/usr/share/doc/tracetuner/copyright dh_installchangelogs -O--sourcedirectory=src -O--no-parallel install -m0755 -d debian/tracetuner/usr/share/doc/tracetuner install -p -m0644 debian/.debhelper/generated/tracetuner/dh_installchangelogs.dch.trimmed debian/tracetuner/usr/share/doc/tracetuner/changelog.Debian dh_installman -O--sourcedirectory=src -O--no-parallel install -m0755 -d debian/tracetuner/usr/share/man/man1/ install -p -m0644 ./debian/mans/train.1 debian/tracetuner/usr/share/man/man1/train.1 install -m0755 -d debian/tracetuner/usr/share/man/man1/ install -p -m0644 ./debian/mans/trainphd.1 debian/tracetuner/usr/share/man/man1/trainphd.1 install -m0755 -d debian/tracetuner/usr/share/man/man1/ install -p -m0644 ./debian/mans/ttuner.1 debian/tracetuner/usr/share/man/man1/ttuner.1 man-recode --to-code UTF-8 --suffix .dh-new debian/tracetuner/usr/share/man/man1/train.1 man-recode --to-code UTF-8 --suffix .dh-new debian/tracetuner/usr/share/man/man1/ttuner.1 man-recode --to-code UTF-8 --suffix .dh-new debian/tracetuner/usr/share/man/man1/trainphd.1 mv debian/tracetuner/usr/share/man/man1/train.1.dh-new debian/tracetuner/usr/share/man/man1/train.1 chmod 0644 -- debian/tracetuner/usr/share/man/man1/train.1 mv debian/tracetuner/usr/share/man/man1/trainphd.1.dh-new debian/tracetuner/usr/share/man/man1/trainphd.1 chmod 0644 -- debian/tracetuner/usr/share/man/man1/trainphd.1 mv debian/tracetuner/usr/share/man/man1/ttuner.1.dh-new debian/tracetuner/usr/share/man/man1/ttuner.1 chmod 0644 -- debian/tracetuner/usr/share/man/man1/ttuner.1 dh_installsystemduser -O--sourcedirectory=src -O--no-parallel dh_perl -O--sourcedirectory=src -O--no-parallel dh_link -O--sourcedirectory=src -O--no-parallel dh_strip_nondeterminism -O--sourcedirectory=src -O--no-parallel dh_compress -O--sourcedirectory=src -O--no-parallel cd debian/tracetuner chmod a-x usr/share/doc/tracetuner/README usr/share/doc/tracetuner/RELEASE_NOTES usr/share/doc/tracetuner/changelog.Debian usr/share/man/man1/train.1 usr/share/man/man1/trainphd.1 usr/share/man/man1/ttuner.1 gzip -9nf usr/share/doc/tracetuner/README usr/share/doc/tracetuner/RELEASE_NOTES usr/share/doc/tracetuner/changelog.Debian usr/share/man/man1/train.1 usr/share/man/man1/trainphd.1 usr/share/man/man1/ttuner.1 cd '/build/reproducible-path/tracetuner-3.0.6~beta+dfsg' dh_fixperms -O--sourcedirectory=src -O--no-parallel find debian/tracetuner ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/tracetuner/usr/share/doc -type f -a -true -a ! -regex 'debian/tracetuner/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/tracetuner/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/tracetuner/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/tracetuner -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/tracetuner/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing -O--sourcedirectory=src -O--no-parallel dh_dwz -a -O--sourcedirectory=src -O--no-parallel install -m0755 -d debian/tracetuner/usr/lib/debug/.dwz/aarch64-linux-gnu dwz -mdebian/tracetuner/usr/lib/debug/.dwz/aarch64-linux-gnu/tracetuner.debug -M/usr/lib/debug/.dwz/aarch64-linux-gnu/tracetuner.debug -- debian/tracetuner/usr/bin/checkbc debian/tracetuner/usr/bin/checkbcphd debian/tracetuner/usr/bin/checkqv debian/tracetuner/usr/bin/checkqvphd debian/tracetuner/usr/bin/lut debian/tracetuner/usr/bin/train debian/tracetuner/usr/bin/ttuner objcopy --compress-debug-sections debian/tracetuner/usr/lib/debug/.dwz/aarch64-linux-gnu/tracetuner.debug chmod 0644 -- debian/tracetuner/usr/lib/debug/.dwz/aarch64-linux-gnu/tracetuner.debug dh_strip -a -O--sourcedirectory=src -O--no-parallel install -m0755 -d debian/.debhelper/tracetuner/dbgsym-root/usr/lib/debug/.build-id/3d objcopy --only-keep-debug --compress-debug-sections debian/tracetuner/usr/bin/ttuner debian/.debhelper/tracetuner/dbgsym-root/usr/lib/debug/.build-id/3d/11656e7fa50f4cf95d1677dd738044f77e5ba6.debug chmod 0644 -- debian/.debhelper/tracetuner/dbgsym-root/usr/lib/debug/.build-id/3d/11656e7fa50f4cf95d1677dd738044f77e5ba6.debug strip --remove-section=.comment --remove-section=.note debian/tracetuner/usr/bin/ttuner objcopy --add-gnu-debuglink debian/.debhelper/tracetuner/dbgsym-root/usr/lib/debug/.build-id/3d/11656e7fa50f4cf95d1677dd738044f77e5ba6.debug debian/tracetuner/usr/bin/ttuner install -m0755 -d debian/.debhelper/tracetuner/dbgsym-root/usr/lib/debug/.build-id/92 objcopy --only-keep-debug --compress-debug-sections debian/tracetuner/usr/bin/train debian/.debhelper/tracetuner/dbgsym-root/usr/lib/debug/.build-id/92/10cb56a92336be30ca9c26617185300a5778e8.debug chmod 0644 -- debian/.debhelper/tracetuner/dbgsym-root/usr/lib/debug/.build-id/92/10cb56a92336be30ca9c26617185300a5778e8.debug strip --remove-section=.comment --remove-section=.note debian/tracetuner/usr/bin/train objcopy --add-gnu-debuglink debian/.debhelper/tracetuner/dbgsym-root/usr/lib/debug/.build-id/92/10cb56a92336be30ca9c26617185300a5778e8.debug debian/tracetuner/usr/bin/train install -m0755 -d debian/.debhelper/tracetuner/dbgsym-root/usr/lib/debug/.build-id/e6 objcopy --only-keep-debug --compress-debug-sections debian/tracetuner/usr/bin/checkqv debian/.debhelper/tracetuner/dbgsym-root/usr/lib/debug/.build-id/e6/ad99372591b22d8eda34f2d61634e04575cbfc.debug chmod 0644 -- debian/.debhelper/tracetuner/dbgsym-root/usr/lib/debug/.build-id/e6/ad99372591b22d8eda34f2d61634e04575cbfc.debug strip --remove-section=.comment --remove-section=.note debian/tracetuner/usr/bin/checkqv objcopy --add-gnu-debuglink debian/.debhelper/tracetuner/dbgsym-root/usr/lib/debug/.build-id/e6/ad99372591b22d8eda34f2d61634e04575cbfc.debug debian/tracetuner/usr/bin/checkqv install -m0755 -d debian/.debhelper/tracetuner/dbgsym-root/usr/lib/debug/.build-id/f0 objcopy --only-keep-debug --compress-debug-sections debian/tracetuner/usr/bin/lut debian/.debhelper/tracetuner/dbgsym-root/usr/lib/debug/.build-id/f0/0fb3b02eb2978c2fd148ea13b63f010e0024ff.debug chmod 0644 -- debian/.debhelper/tracetuner/dbgsym-root/usr/lib/debug/.build-id/f0/0fb3b02eb2978c2fd148ea13b63f010e0024ff.debug strip --remove-section=.comment --remove-section=.note debian/tracetuner/usr/bin/lut objcopy --add-gnu-debuglink debian/.debhelper/tracetuner/dbgsym-root/usr/lib/debug/.build-id/f0/0fb3b02eb2978c2fd148ea13b63f010e0024ff.debug debian/tracetuner/usr/bin/lut install -m0755 -d debian/.debhelper/tracetuner/dbgsym-root/usr/lib/debug/.build-id/25 objcopy --only-keep-debug --compress-debug-sections debian/tracetuner/usr/bin/checkbcphd debian/.debhelper/tracetuner/dbgsym-root/usr/lib/debug/.build-id/25/879192cd33ca21fa3b8e476eec6796306d1b35.debug chmod 0644 -- debian/.debhelper/tracetuner/dbgsym-root/usr/lib/debug/.build-id/25/879192cd33ca21fa3b8e476eec6796306d1b35.debug strip --remove-section=.comment --remove-section=.note debian/tracetuner/usr/bin/checkbcphd objcopy --add-gnu-debuglink debian/.debhelper/tracetuner/dbgsym-root/usr/lib/debug/.build-id/25/879192cd33ca21fa3b8e476eec6796306d1b35.debug debian/tracetuner/usr/bin/checkbcphd install -m0755 -d debian/.debhelper/tracetuner/dbgsym-root/usr/lib/debug/.build-id/cd objcopy --only-keep-debug --compress-debug-sections debian/tracetuner/usr/bin/checkbc debian/.debhelper/tracetuner/dbgsym-root/usr/lib/debug/.build-id/cd/491f86cbd1509f298bfa4c790538053a044989.debug chmod 0644 -- debian/.debhelper/tracetuner/dbgsym-root/usr/lib/debug/.build-id/cd/491f86cbd1509f298bfa4c790538053a044989.debug strip --remove-section=.comment --remove-section=.note debian/tracetuner/usr/bin/checkbc objcopy --add-gnu-debuglink debian/.debhelper/tracetuner/dbgsym-root/usr/lib/debug/.build-id/cd/491f86cbd1509f298bfa4c790538053a044989.debug debian/tracetuner/usr/bin/checkbc install -m0755 -d debian/.debhelper/tracetuner/dbgsym-root/usr/lib/debug/.build-id/c2 objcopy --only-keep-debug --compress-debug-sections debian/tracetuner/usr/bin/checkqvphd debian/.debhelper/tracetuner/dbgsym-root/usr/lib/debug/.build-id/c2/1a2f45e9a9e6777fb850062f489ec0464d73e4.debug chmod 0644 -- debian/.debhelper/tracetuner/dbgsym-root/usr/lib/debug/.build-id/c2/1a2f45e9a9e6777fb850062f489ec0464d73e4.debug strip --remove-section=.comment --remove-section=.note debian/tracetuner/usr/bin/checkqvphd objcopy --add-gnu-debuglink debian/.debhelper/tracetuner/dbgsym-root/usr/lib/debug/.build-id/c2/1a2f45e9a9e6777fb850062f489ec0464d73e4.debug debian/tracetuner/usr/bin/checkqvphd install -m0755 -d debian/.debhelper/tracetuner/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/tracetuner/usr/lib/debug/.dwz/aarch64-linux-gnu debian/.debhelper/tracetuner/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/tracetuner/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/tracetuner/usr/lib/debug install -m0755 -d debian/.debhelper/tracetuner/dbgsym-root/usr/share/doc ln -s tracetuner debian/.debhelper/tracetuner/dbgsym-root/usr/share/doc/tracetuner-dbgsym install -m0755 -d debian/.debhelper/tracetuner dh_makeshlibs -a -O--sourcedirectory=src -O--no-parallel rm -f debian/tracetuner/DEBIAN/shlibs dh_shlibdeps -a -O--sourcedirectory=src -O--no-parallel install -m0755 -d debian/tracetuner/DEBIAN dpkg-shlibdeps -Tdebian/tracetuner.substvars debian/tracetuner/usr/bin/ttuner debian/tracetuner/usr/bin/train debian/tracetuner/usr/bin/checkqv debian/tracetuner/usr/bin/lut debian/tracetuner/usr/bin/checkbcphd debian/tracetuner/usr/bin/checkbc debian/tracetuner/usr/bin/checkqvphd dh_installdeb -O--sourcedirectory=src -O--no-parallel install -m0755 -d debian/tracetuner/DEBIAN dh_gencontrol -O--sourcedirectory=src -O--no-parallel install -m0755 -d debian/tracetuner/DEBIAN echo misc:Depends= >> debian/tracetuner.substvars echo misc:Pre-Depends= >> debian/tracetuner.substvars install -m0755 -d debian/.debhelper/tracetuner/dbgsym-root/DEBIAN dpkg-gencontrol -ptracetuner -ldebian/changelog -Tdebian/tracetuner.substvars -cdebian/control -Pdebian/.debhelper/tracetuner/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=tracetuner-dbgsym "-DDepends=tracetuner (= \${binary:Version})" "-DDescription=debug symbols for tracetuner" "-DBuild-Ids=25879192cd33ca21fa3b8e476eec6796306d1b35 3d11656e7fa50f4cf95d1677dd738044f77e5ba6 9210cb56a92336be30ca9c26617185300a5778e8 c21a2f45e9a9e6777fb850062f489ec0464d73e4 cd491f86cbd1509f298bfa4c790538053a044989 e6ad99372591b22d8eda34f2d61634e04575cbfc f00fb3b02eb2978c2fd148ea13b63f010e0024ff" -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/tracetuner/dbgsym-root/DEBIAN/control dpkg-gencontrol -ptracetuner -ldebian/changelog -Tdebian/tracetuner.substvars -cdebian/control -Pdebian/tracetuner chmod 0644 -- debian/tracetuner/DEBIAN/control dh_md5sums -O--sourcedirectory=src -O--no-parallel install -m0755 -d debian/tracetuner/DEBIAN cd debian/tracetuner >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/tracetuner/DEBIAN/md5sums install -m0755 -d debian/.debhelper/tracetuner/dbgsym-root/DEBIAN cd debian/.debhelper/tracetuner/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/tracetuner/dbgsym-root/DEBIAN/md5sums dh_builddeb -O--sourcedirectory=src -O--no-parallel dpkg-deb --root-owner-group --build debian/.debhelper/tracetuner/dbgsym-root .. dpkg-deb --root-owner-group --build debian/tracetuner .. dpkg-deb: building package 'tracetuner-dbgsym' in '../tracetuner-dbgsym_3.0.6~beta+dfsg-3_arm64.deb'. dpkg-deb: building package 'tracetuner' in '../tracetuner_3.0.6~beta+dfsg-3_arm64.deb'. dpkg-genbuildinfo --build=binary -O../tracetuner_3.0.6~beta+dfsg-3_arm64.buildinfo dpkg-genchanges --build=binary -O../tracetuner_3.0.6~beta+dfsg-3_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/2989067/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2989067/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2989067 and its subdirectories I: Current time: Sat Apr 27 17:34:59 +14 2024 I: pbuilder-time-stamp: 1714188899