I: pbuilder: network access will be disabled during build I: Current time: Mon Mar 25 21:44:26 +14 2024 I: pbuilder-time-stamp: 1711352666 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 [maq_0.7.1-9.dsc] I: copying [./maq_0.7.1.orig.tar.gz] I: copying [./maq_0.7.1-9.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Nov 16 10:45:18 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 ./maq_0.7.1-9.dsc: no acceptable signature found dpkg-source: info: extracting maq in maq-0.7.1 dpkg-source: info: unpacking maq_0.7.1.orig.tar.gz dpkg-source: info: unpacking maq_0.7.1-9.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 10_prevent_-64_option.patch dpkg-source: info: applying gcc-4.7.patch dpkg-source: info: applying mayhem.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/32453/tmp/hooks/D01_modify_environment starting debug: Running on virt32z. 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 Mar 25 07:44 /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/32453/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/32453/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]="arm-unknown-linux-gnueabihf") 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=armhf DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=arm HOST_ARCH=armhf IFS=' ' INVOCATION_ID=adb487d5199b44f2ad3b6ea94dd69e3d LANG=C LANGUAGE=it_CH:it LC_ALL=C MACHTYPE=arm-unknown-linux-gnueabihf MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnueabihf PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=32453 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.4l1GFUXO/pbuilderrc_1TPd --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.4l1GFUXO/b2 --logfile b2/build.log maq_0.7.1-9.dsc' SUDO_GID=110 SUDO_UID=103 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://10.0.0.15:3142/ I: uname -a Linux i-capture-the-hostname 6.1.0-18-armmp-lpae #1 SMP Debian 6.1.76-1 (2024-02-01) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 22 11:24 /bin -> usr/bin I: user script /srv/workspace/pbuilder/32453/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team 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 ... 19577 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} libelf1{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 19.2 MB of archives. After unpacking 69.8 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-2+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf libmagic1 armhf 1:5.45-2+b1 [97.9 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-2+b1 [42.2 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.21-14+b1 [157 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b1 [65.7 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-3 [1088 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.39.3-6 [81.2 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.7-1+b2 [33.4 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.12.0-3 [1367 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 12 http://deb.debian.org/debian trixie/main armhf autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main armhf autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.14.1 [85.6 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf libsub-override-perl all 0.10-1 [10.6 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian trixie/main armhf libelf1 armhf 0.190-1+b1 [171 kB] Get: 24 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1 [101 kB] Get: 25 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-4+b1 [9070 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.9.14+dfsg-1.3+b2 [599 kB] Get: 27 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.21-14+b1 [1230 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf debhelper all 13.14.1 [890 kB] Get: 31 http://deb.debian.org/debian trixie/main armhf zlib1g-dev armhf 1:1.3.dfsg-3+b1 [904 kB] Fetched 19.2 MB in 0s (85.3 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 ... 19577 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_armhf.deb ... Unpacking libmagic-mgc (1:5.45-2+b1) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../02-libmagic1_1%3a5.45-2+b1_armhf.deb ... Unpacking libmagic1:armhf (1:5.45-2+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-2+b1_armhf.deb ... Unpacking file (1:5.45-2+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_armhf.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-3_armhf.deb ... Unpacking groff-base (1.23.0-3) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.39.3-6_armhf.deb ... Unpacking bsdextrautils (2.39.3-6) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../08-libpipeline1_1.5.7-1+b2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.7-1+b2) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.12.0-3_armhf.deb ... Unpacking man-db (2.12.0-3) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_armhf.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_13.14.1_all.deb ... Unpacking libdebhelper-perl (13.14.1) ... 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 libelf1:armhf. Preparing to unpack .../22-libelf1_0.190-1+b1_armhf.deb ... Unpacking libelf1:armhf (0.190-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1_armhf.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../24-libicu72_72.1-4+b1_armhf.deb ... Unpacking libicu72:armhf (72.1-4+b1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.3+b2_armhf.deb ... Unpacking libxml2:armhf (2.9.14+dfsg-1.3+b2) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-14+b1_armhf.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_13.14.1_all.deb ... Unpacking debhelper (13.14.1) ... Selecting previously unselected package zlib1g-dev:armhf. Preparing to unpack .../30-zlib1g-dev_1%3a1.3.dfsg-3+b1_armhf.deb ... Unpacking zlib1g-dev:armhf (1:1.3.dfsg-3+b1) ... Setting up libpipeline1:armhf (1.5.7-1+b2) ... Setting up libicu72:armhf (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 (13.14.1) ... Setting up libmagic1:armhf (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 autotools-dev (20220109.1) ... Setting up autopoint (0.21-14) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:armhf (1:1.3.dfsg-3+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:armhf (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libelf1:armhf (0.190-1+b1) ... Setting up libxml2:armhf (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 dwz (0.15-1) ... Setting up groff-base (1.23.0-3) ... 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 (13.14.1) ... Processing triggers for libc-bin (2.37-15) ... 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/32453/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/32453/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/maq-0.7.1/ && 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 > ../maq_0.7.1-9_source.changes dpkg-buildpackage: info: source package maq dpkg-buildpackage: info: source version 0.7.1-9 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead dh_autoreconf configure.ac:2: warning: 'AM_CONFIG_HEADER': this macro is obsolete. configure.ac:2: You should use the 'AC_CONFIG_HEADERS' macro instead. ./lib/autoconf/general.m4:2434: AC_DIAGNOSE is expanded from... aclocal.m4:445: AM_CONFIG_HEADER is expanded from... configure.ac:2: the top level configure.ac:39: warning: The macro `AC_STDC_HEADERS' is obsolete. configure.ac:39: You should run autoupdate. ./lib/autoconf/oldnames.m4:75: AC_STDC_HEADERS is expanded from... configure.ac:39: the top level configure.ac:39: warning: The macro `AC_HEADER_STDC' is obsolete. configure.ac:39: You should run autoupdate. ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... ./lib/autoconf/oldnames.m4:75: AC_STDC_HEADERS is expanded from... configure.ac:39: the top level configure.ac:42: warning: AC_OUTPUT should be used without arguments. configure.ac:42: You should run autoupdate. configure.ac:6: installing './compile' dh_auto_configure ./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking build system type... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for zlib.h... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating config.h dh_auto_build make -j4 make[1]: Entering directory '/build/reproducible-path/maq-0.7.1' make all-am make[2]: Entering directory '/build/reproducible-path/maq-0.7.1' gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o main.o main.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o const.o const.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o seq.o seq.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o bfa.o bfa.c g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o read.o read.cc bfa.c: In function 'nst_load_bfa1': bfa.c:31:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 31 | fread(bfa1->name, sizeof(char), len, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bfa.c:32:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 32 | fread(&bfa1->ori_len, sizeof(int), 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bfa.c:33:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 33 | fread(&bfa1->len, sizeof(int), 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bfa.c:35:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 35 | fread(bfa1->seq, sizeof(bit64_t), bfa1->len, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bfa.c:37:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 37 | fread(bfa1->mask, sizeof(bit64_t), bfa1->len, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bfa.c: In function 'nst_bfa_len': bfa.c:46:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 46 | fread(&len, sizeof(int), 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bfa.c:48:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 48 | fread(&len, sizeof(int), 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o fasta2bfa.o fasta2bfa.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o fastq2bfq.o fastq2bfq.c g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o merge.o merge.cc fastq2bfq.c: In function 'fastq2bfq': fastq2bfq.c:30:12: warning: assignment to 'struct gzFile_s **' from incompatible pointer type 'gzFile' {aka 'struct gzFile_s *'} [-Wincompatible-pointer-types] 30 | fp = gzopen(str, "w"); | ^ fastq2bfq.c:36:28: warning: assignment to 'struct gzFile_s **' from incompatible pointer type 'gzFile' {aka 'struct gzFile_s *'} [-Wincompatible-pointer-types] 36 | fp = gzopen(str, "w"); | ^ fastq2bfq.c:47:25: warning: passing argument 1 of 'gzwrite' from incompatible pointer type [-Wincompatible-pointer-types] 47 | gzwrite(fp, &i, sizeof(int)); | ^~ | | | struct gzFile_s ** In file included from fastq2bfq.c:1: /usr/include/zlib.h:1451:36: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' 1451 | ZEXTERN int ZEXPORT gzwrite(gzFile file, voidpc buf, unsigned len); | ~~~~~~~^~~~ fastq2bfq.c:48:25: warning: passing argument 1 of 'gzwrite' from incompatible pointer type [-Wincompatible-pointer-types] 48 | gzwrite(fp, name, sizeof(char) * i); | ^~ | | | struct gzFile_s ** /usr/include/zlib.h:1451:36: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' 1451 | ZEXTERN int ZEXPORT gzwrite(gzFile file, voidpc buf, unsigned len); | ~~~~~~~^~~~ fastq2bfq.c:49:25: warning: passing argument 1 of 'gzwrite' from incompatible pointer type [-Wincompatible-pointer-types] 49 | gzwrite(fp, &l, sizeof(int)); | ^~ | | | struct gzFile_s ** /usr/include/zlib.h:1451:36: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' 1451 | ZEXTERN int ZEXPORT gzwrite(gzFile file, voidpc buf, unsigned len); | ~~~~~~~^~~~ fastq2bfq.c:50:25: warning: passing argument 1 of 'gzwrite' from incompatible pointer type [-Wincompatible-pointer-types] 50 | gzwrite(fp, seq.s, sizeof(char) * l); | ^~ | | | struct gzFile_s ** /usr/include/zlib.h:1451:36: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' 1451 | ZEXTERN int ZEXPORT gzwrite(gzFile file, voidpc buf, unsigned len); | ~~~~~~~^~~~ fastq2bfq.c:53:33: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] 53 | gzclose(fp); | ^~ | | | struct gzFile_s ** /usr/include/zlib.h:1634:39: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' 1634 | ZEXTERN int ZEXPORT gzclose(gzFile file); | ~~~~~~~^~~~ fastq2bfq.c:62:25: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] 62 | gzclose(fp); | ^~ | | | struct gzFile_s ** /usr/include/zlib.h:1634:39: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' 1634 | ZEXTERN int ZEXPORT gzclose(gzFile file); | ~~~~~~~^~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o match_aux.o match_aux.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o match.o match.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o sort_mapping.o sort_mapping.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o assemble.o assemble.cc match.cc: In function 'int alt_cal_mm(bit64_t)': match.cc:58:15: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses] 58 | x = x + (x >> 4) & 0x0F0F0F0F0F0F0F0FLLU; | ~~^~~~~~~~~~ sort_mapping.cc: In function 'int ma_make_pair(const match_aux_t*, const match_info_t*, const match_info_t*, pair_info_t*)': sort_mapping.cc:59:75: warning: suggest parentheses around arithmetic in operand of '^' [-Wparentheses] 59 | p->i1 = (((m1->i1>>24)+(m2->i1>>24))<<24) | (m1->i1^m2->i1&0xffffff); | ~~~~~~^~~~~~~~~ match.cc:61:15: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses] 61 | x = x + (x >> 32) & 0x0000007F; | ~~^~~~~~~~~~~ match.cc: In function 'int alt_cal_err(bit64_t, bit64_t)': match.cc:67:15: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses] 67 | x = x + (x >> 4) & 0x0F0F0F0F0F0F0F0FLLU; | ~~^~~~~~~~~~ match.cc:70:15: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses] 70 | x = x + (x >> 32) & 0x0000007F; | ~~^~~~~~~~~~~ match.cc: In function 'void process_candidate(const required_option_t*, int, bit64_t, match_data_t*, ref_canlist_t*)': match.cc:284:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct ref_canlist_t'; use assignment or value-initialization instead [-Wclass-memaccess] 284 | memset(list, 0, sizeof(ref_canlist_t)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ match.cc:49:16: note: 'struct ref_canlist_t' declared here 49 | typedef struct { | ^ match.cc: In function 'void match_search(const match_aux_t*, match_data_t*, const nst_bfa1_t*, int, ref_canlist_t*)': match.cc:292:17: warning: variable 'n_reads' set but not used [-Wunused-but-set-variable] 292 | bit32_t n_reads; | ^~~~~~~ match.cc: In function 'int ma_match(int, char**)': match.cc:525:31: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fscanf(tmpfp, "%s", adaptor); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ assemble.cc: In function 'base_call_aux_t* assemble_cns_collect(assemble_pos_t*, const assemble_aux_t*)': assemble.cc:106:77: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 106 | if (info>>24 < 4 && (info>>8&0x3f) != 0) info = 4<<24 | info&0xffffff; | ~~~~^~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o pileup.o pileup.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o mapcheck.o mapcheck.cc gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o get_pos.o get_pos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o assopt.o assopt.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o aux_utils.o aux_utils.c g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o rbcc.o rbcc.cc mapcheck.cc: In function 'int ma_mapcheck(int, char**)': mapcheck.cc:60:24: warning: variable 'fpout' set but not used [-Wunused-but-set-variable] 60 | FILE *fp_bfa, *fpout; | ^~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o subsnp.o subsnp.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o pair_stat.o pair_stat.cc rbcc.cc: In function 'hash_map_char* cns_load_dbSNP(FILE*)': rbcc.cc:21:35: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 21 | sprintf(str1, "%s.%d", name, pos); | ^~ In file included from /usr/include/stdio.h:906, from rbcc.cc:7: In function 'int sprintf(char*, const char*, ...)', inlined from 'hash_map_char* cns_load_dbSNP(FILE*)' at rbcc.cc:21:10: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 3 and 268 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 ()); | ~~~~~~~~~~~~~~~~~ subsnp.cc: In function 'hash_map_char* ma_load_snp(FILE*)': subsnp.cc:20:34: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 20 | sprintf(key, "%s.%d", name, pos); | ^~ In file included from /usr/include/stdio.h:906, from subsnp.cc:2: In function 'int sprintf(char*, const char*, ...)', inlined from 'hash_map_char* ma_load_snp(FILE*)' at subsnp.cc:20:10: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 3 and 268 bytes into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o indel_soa.o indel_soa.cc subsnp.cc: In function 'hash_set_char* ma_load_snp_set(FILE*)': subsnp.cc:35:34: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 35 | sprintf(key, "%s.%d", name, pos); | ^~ In function 'int sprintf(char*, const char*, ...)', inlined from 'hash_set_char* ma_load_snp_set(FILE*)' at subsnp.cc:35:10: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 3 and 268 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 ()); | ~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o maqmap.o maqmap.c indel_soa.cc: In function 'void fill_counter(bit32_t*, int, nst_bfa1_t*, gzFile)': indel_soa.cc:42:61: warning: suggest parentheses around '-' inside '<<' [-Wparentheses] 42 | if (int(m1->seq[k]>>6) == int(s>>(31-j<<1)&3)) ++score; | ~~^~ indel_soa.cc:56:61: warning: suggest parentheses around '-' inside '<<' [-Wparentheses] 56 | if (int(m1->seq[k]>>6) == int(s>>(31-j<<1)&3)) ++score; | ~~^~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o maqmap_conv.o maqmap_conv.c g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o altchr.o altchr.cc gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o submap.o submap.c subsnp.cc: In function 'void maq_simucns_core(FILE*, gzFile, FILE*)': subsnp.cc:190:42: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 190 | sprintf(key, "%s.%d", name, pos); | ^~ In function 'int sprintf(char*, const char*, ...)', inlined from 'hash_map_char* load_simu_snp(FILE*)' at subsnp.cc:190:11, inlined from 'void maq_simucns_core(FILE*, gzFile, FILE*)' at subsnp.cc:202:45: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 3 and 268 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 ()); | ~~~~~~~~~~~~~~~~~ subsnp.cc: In function 'void maq_simucns_core(FILE*, gzFile, FILE*)': subsnp.cc:186:50: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 186 | sprintf(key, "%s.%d", name, i); | ^~ In function 'int sprintf(char*, const char*, ...)', inlined from 'hash_map_char* load_simu_snp(FILE*)' at subsnp.cc:186:12, inlined from 'void maq_simucns_core(FILE*, gzFile, FILE*)' at subsnp.cc:202:45: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 3 and 268 bytes into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o rmdup.o rmdup.cc gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o simulate.o simulate.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o genran.o genran.c g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o indel_pe.o indel_pe.cc simulate.c: In function 'maq_simutrain': simulate.c:83:15: warning: assignment to 'struct gzFile_s **' from incompatible pointer type 'gzFile' {aka 'struct gzFile_s *'} [-Wincompatible-pointer-types] 83 | fpout = gzopen(argv[1], "w"); | ^ simulate.c:86:17: warning: passing argument 1 of 'gzwrite' from incompatible pointer type [-Wincompatible-pointer-types] 86 | gzwrite(fpout, fqc, sizeof(fqc_t)); | ^~~~~ | | | struct gzFile_s ** In file included from simulate.c:6: /usr/include/zlib.h:1451:36: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' 1451 | ZEXTERN int ZEXPORT gzwrite(gzFile file, voidpc buf, unsigned len); | ~~~~~~~^~~~ simulate.c:87:17: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] 87 | gzclose(fpout); | ^~~~~ | | | struct gzFile_s ** /usr/include/zlib.h:1634:39: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' 1634 | ZEXTERN int ZEXPORT gzclose(gzFile file); | ~~~~~~~^~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o stdaln.o stdaln.c In file included from /usr/include/string.h:535, from maqmap.h:23, from simulate.c:11: In function 'memset', inlined from 'simustat_core' at simulate.c:386:2: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:59:10: warning: '__builtin___memset_chk' offset [16, 31] is out of the bounds [0, 16] of object 'tc' with type 'int[2][2]' [-Warray-bounds=] 59 | return __builtin___memset_chk (__dest, __ch, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 60 | __glibc_objsize0 (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ simulate.c: In function 'simustat_core': simulate.c:381:19: note: 'tc' declared here 381 | int i, k, tc[2][2]; | ^~ stdaln.c: In function 'aln_local_core': stdaln.c:534:32: warning: variable 'b' set but not used [-Wunused-but-set-variable] 534 | int gap_open, gap_ext, b; | ^ rmdup.cc: In function 'void maq_rmdup_core(gzFile, gzFile)': rmdup.cc:46:32: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-truncation] 46 | strncpy(buf, name, tl-1); | ^ In function 'char* trim_name(char*, char*)', inlined from 'char* trim_name(char*, char*)' at rmdup.cc:39:21, inlined from 'void maq_rmdup_core(gzFile, gzFile)' at rmdup.cc:102:23: rmdup.cc:42:40: note: length computed here 42 | int c1, c2, tl = strlen(name); | ~~~~~~^~~~~~ rmdup.cc: In function 'void maq_rmdup_core(gzFile, gzFile)': rmdup.cc:46:32: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-truncation] 46 | strncpy(buf, name, tl-1); | ^ In function 'char* trim_name(char*, char*)', inlined from 'char* trim_name(char*, char*)' at rmdup.cc:39:21, inlined from 'void maq_rmdup_core(gzFile, gzFile)' at rmdup.cc:94:37: rmdup.cc:42:40: note: length computed here 42 | int c1, c2, tl = strlen(name); | ~~~~~~^~~~~~ rmdup.cc: In function 'void maq_rmdup_core(gzFile, gzFile)': rmdup.cc:46:32: warning: 'char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-truncation] 46 | strncpy(buf, name, tl-1); | ^ In function 'char* trim_name(char*, char*)', inlined from 'char* trim_name(char*, char*)' at rmdup.cc:39:21, inlined from 'void maq_rmdup_core(gzFile, gzFile)' at rmdup.cc:92:31: rmdup.cc:42:40: note: length computed here 42 | int c1, c2, tl = strlen(name); | ~~~~~~^~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o indel_call.o indel_call.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o eland2maq.o eland2maq.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o csmap2ntmap.o csmap2ntmap.cc In file included from stdaln.c:29: stdaln.h:61:23: warning: 'free' called on pointer '*(int **)((char *))' with nonzero offset 4 [-Wfree-nonheap-object] 61 | # define MYFREE free stdaln.c:726:17: note: in expansion of macro 'MYFREE' 726 | MYFREE(s_array[i]); | ^~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o break_pair.o break_pair.c eland2maq.cc: In function 'void eland2maq_core(FILE*, FILE*, gzFile)': eland2maq.cc:88:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 88 | fscanf(fp_eland, "%s", str); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ eland2maq.cc:96:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 96 | fscanf(fp_eland, "%s", str); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ eland2maq.cc:99:31: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 99 | fscanf(fp_eland, "%u%u%u%s%u%s", tmp, tmp+1, tmp+2, str, tmp+3, str2); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ eland2maq.cc: In function 'hash_map_char* read_list(FILE*)': eland2maq.cc:33:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 33 | fscanf(fp, "%s", str); | ~~~~~~^~~~~~~~~~~~~~~ eland2maq.cc: In function 'void novo2maq_core(FILE*, FILE*, gzFile)': eland2maq.cc:323:18: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 323 | fgets( str2, 4096, fp_novo ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o glfgen.o glfgen.cc In file included from break_pair.c:2: break_pair.c: In function 'breakpair': break_pair.c:16:16: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 16 | assert(fp = gzopen(str, "r")); | ^~ glfgen.cc: In function 'glf1_t* glfgen1_core(assemble_pos_t*, const assemble_aux_t*, bit8_t)': glfgen.cc:43:77: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 43 | if (info>>24 < 4 && (info>>8&0x3f) != 0) info = 4<<24 | info&0xffffff; | ~~~~^~~~~~~~~ eland2maq.cc: In function 'void export2maq_core(FILE*, FILE*, gzFile)': eland2maq.cc:563:35: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 563 | sprintf(str2, "%s_%d:%d:%d:%d:%d", str, ti[0], ti[1], ti[2], ti[3], ti[4]); | ^~ In file included from /usr/include/stdio.h:906, from eland2maq.cc:9: In function 'int sprintf(char*, const char*, ...)', inlined from 'void export2maq_core(FILE*, FILE*, gzFile)' at eland2maq.cc:563:10: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 11 and 1084 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o maq main.o const.o seq.o bfa.o read.o fasta2bfa.o fastq2bfq.o merge.o match_aux.o match.o sort_mapping.o assemble.o pileup.o mapcheck.o get_pos.o assopt.o aux_utils.o rbcc.o subsnp.o pair_stat.o indel_soa.o maqmap.o maqmap_conv.o altchr.o submap.o rmdup.o simulate.o genran.o indel_pe.o stdaln.o indel_call.o eland2maq.o csmap2ntmap.o break_pair.o glfgen.o -lm -lz make[2]: Leaving directory '/build/reproducible-path/maq-0.7.1' make[1]: Leaving directory '/build/reproducible-path/maq-0.7.1' dh_auto_test make -j4 check "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/maq-0.7.1' make[1]: Leaving directory '/build/reproducible-path/maq-0.7.1' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/maq/ make -j4 install DESTDIR=/build/reproducible-path/maq-0.7.1/debian/maq AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/maq-0.7.1' make[2]: Entering directory '/build/reproducible-path/maq-0.7.1' /usr/bin/mkdir -p '/build/reproducible-path/maq-0.7.1/debian/maq/usr/bin' make[2]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/maq-0.7.1/debian/maq/usr/bin' /usr/bin/install -c maq '/build/reproducible-path/maq-0.7.1/debian/maq/usr/bin' /usr/bin/install -c scripts/maq.pl scripts/farm-run.pl scripts/maq_plot.pl scripts/maq_eval.pl '/build/reproducible-path/maq-0.7.1/debian/maq/usr/bin' make[2]: Leaving directory '/build/reproducible-path/maq-0.7.1' make[1]: Leaving directory '/build/reproducible-path/maq-0.7.1' dh_install dh_installdocs dh_installchangelogs dh_installexamples debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/maq-0.7.1' dh_installman # when installing via debian/manpages the .pl is stripped and the # files will end up in /usr/share/man/pl/man1 cp -a debian/mans/*.1 debian/maq/usr/share/man/man1 make[1]: Leaving directory '/build/reproducible-path/maq-0.7.1' dh_lintian dh_perl dh_link dh_strip_nondeterminism debian/rules override_dh_compress make[1]: Entering directory '/build/reproducible-path/maq-0.7.1' dh_compress --exclude=.pdf make[1]: Leaving directory '/build/reproducible-path/maq-0.7.1' dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package maq: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package maq: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'maq' in '../maq_0.7.1-9_armhf.deb'. dpkg-deb: building package 'maq-dbgsym' in '../maq-dbgsym_0.7.1-9_armhf.deb'. dpkg-genbuildinfo --build=binary -O../maq_0.7.1-9_armhf.buildinfo dpkg-genchanges --build=binary -O../maq_0.7.1-9_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/32453/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/32453/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/32453 and its subdirectories I: Current time: Mon Mar 25 21:45:31 +14 2024 I: pbuilder-time-stamp: 1711352731