Diff of the two buildlogs: -- --- b1/build.log 2025-11-18 17:42:14.119009697 +0000 +++ b2/build.log 2025-11-18 17:51:56.227695963 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Nov 18 05:32:00 -12 2025 -I: pbuilder-time-stamp: 1763487120 +I: Current time: Tue Dec 22 14:05:17 +14 2026 +I: pbuilder-time-stamp: 1797897917 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -30,52 +30,84 @@ dpkg-source: info: applying fix-debian-compileinfo.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/4032766/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1894827/tmp/hooks/D01_modify_environment starting +debug: Running on infom02-amd64. +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 Dec 22 00:05 /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/1894827/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1894827/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='amd64' + 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]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 nocheck' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='ed55bc0fab174abbbfe22544db47d66d' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='4032766' - PS1='# ' - PS2='> ' + INVOCATION_ID=22f7dff80de141d6b2e196d13e51fd7d + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-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=1894827 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.f3Z1kYoh/pbuilderrc_cpiW --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.f3Z1kYoh/b1 --logfile b1/build.log mira_4.9.6-11.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + 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.f3Z1kYoh/pbuilderrc_U0Os --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.f3Z1kYoh/b2 --logfile b2/build.log mira_4.9.6-11.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom01-amd64 6.12.57+deb13-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.57-1 (2025-11-05) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.57+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.57-1 (2025-11-05) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/4032766/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1894827/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -326,7 +358,7 @@ Get: 183 http://deb.debian.org/debian forky/main amd64 libgoogle-perftools-dev amd64 2.16-1 [468 kB] Get: 184 http://deb.debian.org/debian forky/main amd64 xxd amd64 2:9.1.1882-1 [100.0 kB] Get: 185 http://deb.debian.org/debian forky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] -Fetched 495 MB in 6s (81.3 MB/s) +Fetched 495 MB in 12s (42.3 MB/s) Preconfiguring packages ... Selecting previously unselected package autoconf-archive. (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 ... 19862 files and directories currently installed.) @@ -941,8 +973,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Nov 18 17:37:28 UTC 2025. -Universal Time is now: Tue Nov 18 17:37:28 UTC 2025. +Local time is now: Tue Dec 22 00:10:09 UTC 2026. +Universal Time is now: Tue Dec 22 00:10:09 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:amd64 (1.83.0-5) ... @@ -1113,7 +1145,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/mira-4.9.6/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../mira_4.9.6-11_source.changes +I: user script /srv/workspace/pbuilder/1894827/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/1894827/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/mira-4.9.6/ && 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 > ../mira_4.9.6-11_source.changes dpkg-buildpackage: info: source package mira dpkg-buildpackage: info: source version 4.9.6-11 dpkg-buildpackage: info: source distribution unstable @@ -1293,8 +1329,8 @@ checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking xargs -n works... yes -checking whether UID '1111' is supported by ustar format... yes -checking whether GID '1111' is supported by ustar format... yes +checking whether UID '2222' is supported by ustar format... yes +checking whether GID '2222' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking for a sed that does not truncate output... /usr/bin/sed checking whether to add --prefix as include path... yes @@ -1656,7 +1692,7 @@ # see bug #812681 find -name '*.ll' | sed -e 's/[.]ll$/.cc/' | xargs rm -f dh_auto_build - make -j12 + make -j16 make[2]: Entering directory '/build/reproducible-path/mira-4.9.6' make all-recursive make[3]: Entering directory '/build/reproducible-path/mira-4.9.6' @@ -1691,7 +1727,7 @@ g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o phd.o phd.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o scf.o scf.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o ncbiinfoxml.o ncbiinfoxml.C -/bin/bash ../../ylwrap exp_flexer.ll lex.yy.c exp_flexer.cc -- flex +/bin/sh ../../ylwrap exp_flexer.ll lex.yy.c exp_flexer.cc -- flex g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o exp_flexer.o exp_flexer.cc rm -f libmirafio.a ar cr libmirafio.a annotationmappings.o exp.o generalio.o fasta.o fastq-mira.o phd.o scf.o ncbiinfoxml.o exp_flexer.o @@ -1740,8 +1776,8 @@ Making all in mira make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/mira' Making .H out of .xxd adaptorsforclip.454.xxd.H -Making .H out of .xxd adaptorsforclip.solexa.xxd.H Making .H out of .xxd adaptorsforclip.iontor.xxd.H +Making .H out of .xxd adaptorsforclip.solexa.xxd.H Making .H out of .xxd adaptorsregex.solexa.xxd.H Making .H out of .xxd adaptorsregex.iontor.xxd.H Making .H out of .xxd seqforfilter_phix174.solexa.xxd.H @@ -1760,19 +1796,10 @@ g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o align.o align.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_info.o assembly_info.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_buildcontigs.o assembly_buildcontigs.C -hashstats.C:1088:9: warning: 'CEBUG' redefined - 1088 | #define CEBUG(bla) {cout << bla; cout.flush();} - | ^~~~~ -hashstats.C:83:9: note: this is the location of the previous definition - 83 | #define CEBUG(bla) - | ^~~~~ -hashstats.C:1197:9: warning: 'CEBUG' redefined - 1197 | #define CEBUG(bla) - | ^~~~~ -hashstats.C:1088:9: note: this is the location of the previous definition - 1088 | #define CEBUG(bla) {cout << bla; cout.flush();} - | ^~~~~ g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_io.o assembly_io.C +g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_misc.o assembly_misc.C +g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_output.o assembly_output.C +g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_pbcorrect.o assembly_pbcorrect.C assembly_buildcontigs.C:80:9: warning: 'CEBUG' redefined 80 | #define CEBUG(bla) {cout << bla; cout.flush(); } | ^~~~~ @@ -1815,6 +1842,37 @@ assembly_buildcontigs.C:2043:9: note: this is the location of the previous definition 2043 | #define VCOUT(bla) {if(verbose) {cout << bla;} } | ^~~~~ +hashstats.C:1088:9: warning: 'CEBUG' redefined + 1088 | #define CEBUG(bla) {cout << bla; cout.flush();} + | ^~~~~ +hashstats.C:83:9: note: this is the location of the previous definition + 83 | #define CEBUG(bla) + | ^~~~~ +hashstats.C:1197:9: warning: 'CEBUG' redefined + 1197 | #define CEBUG(bla) + | ^~~~~ +hashstats.C:1088:9: note: this is the location of the previous definition + 1088 | #define CEBUG(bla) {cout << bla; cout.flush();} + | ^~~~~ +assembly_misc.C:1871:9: warning: 'CEBUG' redefined + 1871 | #define CEBUG(bla) {cout << bla; cout.flush();} + | ^~~~~ +assembly_misc.C:55:9: note: this is the location of the previous definition + 55 | #define CEBUG(bla) + | ^~~~~ +assembly_misc.C:1905:9: warning: 'CEBUG' redefined + 1905 | #define CEBUG(bla) + | ^~~~~ +assembly_misc.C:1871:9: note: this is the location of the previous definition + 1871 | #define CEBUG(bla) {cout << bla; cout.flush();} + | ^~~~~ +g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_reduceskimhits.o assembly_reduceskimhits.C +assembly_pbcorrect.C:59:9: warning: 'CEBUG' redefined + 59 | #define CEBUG(bla) { if(docebug) {cout << bla; cout.flush();}} + | ^~~~~ +assembly_pbcorrect.C:45:9: note: this is the location of the previous definition + 45 | #define CEBUG(bla) + | ^~~~~ In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9, from /usr/include/boost/container_hash/hash.hpp:14, from /usr/include/boost/functional/hash/hash.hpp:6, @@ -1832,20 +1890,6 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9, - from /usr/include/boost/container_hash/hash.hpp:14, - from /usr/include/boost/functional/hash/hash.hpp:6, - from /usr/include/boost/bimap/relation/mutant_relation.hpp:29, - from /usr/include/boost/bimap/detail/bimap_core.hpp:38, - from /usr/include/boost/bimap/bimap.hpp:61, - from /usr/include/boost/bimap.hpp:13, - from ../../src/io/annotationmappings.H:36, - from ../../src/mira/multitag.H:39, - from ../../src/mira/read.H:38, - from read.C:28: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/system/detail/requires_cxx11.hpp:9, from /usr/include/boost/system/detail/config.hpp:11, from /usr/include/boost/system/detail/error_category.hpp:13, @@ -1874,7 +1918,8 @@ from ../../src/mira/pcrcontainer.H:30, from ../../src/mira/contig.H:42, from ../../src/mira/assembly_info.H:33, - from assembly_info.C:28: + from assembly.H:33, + from assembly.C:28: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -1891,7 +1936,9 @@ from ../../src/mira/readpool.H:41, from ../../src/mira/pcrcontainer.H:30, from ../../src/mira/contig.H:42, - from contig_analysis.C:28: + from ../../src/mira/assembly_info.H:33, + from ../../src/mira/assembly_output.H:32, + from assembly_output.C:33: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -1909,22 +1956,7 @@ from ../../src/mira/pcrcontainer.H:30, from ../../src/mira/contig.H:42, from ../../src/mira/assembly_info.H:33, - from assembly.H:33, - from estassembly.C:25: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/system/detail/requires_cxx11.hpp:9, - from /usr/include/boost/system/detail/config.hpp:11, - from /usr/include/boost/system/detail/error_category.hpp:13, - from /usr/include/boost/system/detail/error_code.hpp:14, - from /usr/include/boost/system/errc.hpp:14, - from /usr/include/boost/system/system_error.hpp:9, - from /usr/include/boost/thread/exceptions.hpp:22, - from /usr/include/boost/thread/pthread/mutex.hpp:14, - from /usr/include/boost/thread/mutex.hpp:16, - from ../../src/mira/hashstats.H:27, - from hashstats_sdbg.C:43: + from assembly_info.C:28: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -1938,62 +1970,7 @@ from ../../src/io/annotationmappings.H:36, from ../../src/mira/multitag.H:39, from ../../src/mira/read.H:38, - from ../../src/mira/readpool.H:41, - from ../../src/mira/pcrcontainer.H:30, - from ../../src/mira/contig.H:42, - from ../../src/mira/assembly_info.H:33, - from assembly.H:33, - from assembly.C:28: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -read.C: In member function 'void Read::dumpAsReadname(std::ostream&)': -read.C:1242:25: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=] - 1242 | sprintf(buffer, "%x", this) ; - | ~^ ~~~~ - | | | - | | Read* - | unsigned int -read.C: In member function 'void Read::dumpAsFASTA(std::ostream&, bool, bool, bool)': -read.C:1273:25: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=] - 1273 | sprintf(buffer, "%x", this) ; - | ~^ ~~~~ - | | | - | | Read* - | unsigned int -read.C: In member function 'void Read::dumpAsFASTQ(std::ostream&, bool, bool, bool)': -read.C:1357:25: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=] - 1357 | sprintf(buffer, "%x", this) ; - | ~^ ~~~~ - | | | - | | Read* - | unsigned int -read.C: In member function 'void Read::dumpAsFASTAQual(std::ostream&, bool, bool, bool)': -read.C:1458:25: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=] - 1458 | sprintf(buffer, "%x", this) ; - | ~^ ~~~~ - | | | - | | Read* - | unsigned int -read.C: In member function 'void Read::dumpAsCAF(std::ostream&)': -read.C:1530:25: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=] - 1530 | sprintf(buffer, "%x", this) ; - | ~^ ~~~~ - | | | - | | Read* - | unsigned int -read.C: In member function 'void Read::dumpAsMAF(std::ostream&)': -read.C:1945:25: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=] - 1945 | sprintf(buffer, "%x", this) ; - | ~^ ~~~~ - | | | - | | Read* - | unsigned int -In file included from /usr/include/boost/function/detail/requires_cxx11.hpp:9, - from /usr/include/boost/function/detail/prologue.hpp:12, - from /usr/include/boost/function.hpp:30, - from ../../src/mira/skim.H:25, - from skim.C:23: + from read.C:28: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -2010,44 +1987,16 @@ from ../../src/mira/readpool.H:41, from ../../src/mira/pcrcontainer.H:30, from ../../src/mira/contig.H:42, - from ../../src/mira/assembly_info.H:33, - from ../../src/mira/assembly.H:33, - from assembly_buildcontigs.C:28: + from contig_analysis.C:28: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_misc.o assembly_misc.C -assembly_misc.C:1871:9: warning: 'CEBUG' redefined - 1871 | #define CEBUG(bla) {cout << bla; cout.flush();} - | ^~~~~ -assembly_misc.C:55:9: note: this is the location of the previous definition - 55 | #define CEBUG(bla) - | ^~~~~ -assembly_misc.C:1905:9: warning: 'CEBUG' redefined - 1905 | #define CEBUG(bla) - | ^~~~~ -assembly_misc.C:1871:9: note: this is the location of the previous definition - 1871 | #define CEBUG(bla) {cout << bla; cout.flush();} - | ^~~~~ In file included from /usr/include/boost/lexical_cast.hpp:26, from ../../src/util/fileanddisk.H:43, from assembly_io.C:28: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_output.o assembly_output.C -In file included from /usr/include/boost/system/detail/requires_cxx11.hpp:9, - from /usr/include/boost/system/detail/config.hpp:11, - from /usr/include/boost/system/detail/error_category.hpp:13, - from /usr/include/boost/system/error_category.hpp:10, - from /usr/include/boost/filesystem/detail/path_traits.hpp:25, - from /usr/include/boost/filesystem/path.hpp:21, - from /usr/include/boost/filesystem.hpp:16, - from assembly_misc.C:32: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_pbcorrect.o assembly_pbcorrect.C In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9, from /usr/include/boost/container_hash/hash.hpp:14, from /usr/include/boost/functional/hash/hash.hpp:6, @@ -2062,17 +2011,11 @@ from ../../src/mira/pcrcontainer.H:30, from ../../src/mira/contig.H:42, from ../../src/mira/assembly_info.H:33, - from ../../src/mira/assembly_output.H:32, - from assembly_output.C:33: + from ../../src/mira/assembly.H:33, + from assembly_buildcontigs.C:28: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -assembly_pbcorrect.C:59:9: warning: 'CEBUG' redefined - 59 | #define CEBUG(bla) { if(docebug) {cout << bla; cout.flush();}} - | ^~~~~ -assembly_pbcorrect.C:45:9: note: this is the location of the previous definition - 45 | #define CEBUG(bla) - | ^~~~~ In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9, from /usr/include/boost/container_hash/hash.hpp:14, from /usr/include/boost/functional/hash/hash.hpp:6, @@ -2087,12 +2030,68 @@ from ../../src/mira/pcrcontainer.H:30, from ../../src/mira/contig.H:42, from ../../src/mira/assembly_info.H:33, - from ../../src/mira/assembly.H:33, - from assembly_pbcorrect.C:26: + from assembly.H:33, + from estassembly.C:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_reduceskimhits.o assembly_reduceskimhits.C +In file included from /usr/include/boost/system/detail/requires_cxx11.hpp:9, + from /usr/include/boost/system/detail/config.hpp:11, + from /usr/include/boost/system/detail/error_category.hpp:13, + from /usr/include/boost/system/detail/error_code.hpp:14, + from /usr/include/boost/system/errc.hpp:14, + from /usr/include/boost/system/system_error.hpp:9, + from /usr/include/boost/thread/exceptions.hpp:22, + from /usr/include/boost/thread/pthread/mutex.hpp:14, + from /usr/include/boost/thread/mutex.hpp:16, + from ../../src/mira/hashstats.H:27, + from hashstats_sdbg.C:43: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +read.C: In member function 'void Read::dumpAsReadname(std::ostream&)': +read.C:1242:25: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=] + 1242 | sprintf(buffer, "%x", this) ; + | ~^ ~~~~ + | | | + | | Read* + | unsigned int +read.C: In member function 'void Read::dumpAsFASTA(std::ostream&, bool, bool, bool)': +read.C:1273:25: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=] + 1273 | sprintf(buffer, "%x", this) ; + | ~^ ~~~~ + | | | + | | Read* + | unsigned int +read.C: In member function 'void Read::dumpAsFASTQ(std::ostream&, bool, bool, bool)': +read.C:1357:25: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=] + 1357 | sprintf(buffer, "%x", this) ; + | ~^ ~~~~ + | | | + | | Read* + | unsigned int +read.C: In member function 'void Read::dumpAsFASTAQual(std::ostream&, bool, bool, bool)': +read.C:1458:25: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=] + 1458 | sprintf(buffer, "%x", this) ; + | ~^ ~~~~ + | | | + | | Read* + | unsigned int +read.C: In member function 'void Read::dumpAsCAF(std::ostream&)': +read.C:1530:25: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=] + 1530 | sprintf(buffer, "%x", this) ; + | ~^ ~~~~ + | | | + | | Read* + | unsigned int +read.C: In member function 'void Read::dumpAsMAF(std::ostream&)': +read.C:1945:25: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=] + 1945 | sprintf(buffer, "%x", this) ; + | ~^ ~~~~ + | | | + | | Read* + | unsigned int +g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_swalign.o assembly_swalign.C assembly_reduceskimhits.C:1111:9: warning: 'CEBUG' redefined 1111 | #define CEBUG(bla) {cout << bla; cout.flush();} | ^~~~~ @@ -2141,6 +2140,45 @@ assembly_reduceskimhits.C:2808:9: note: this is the location of the previous definition 2808 | #define CEBUG(bla) {cout << bla; cout.flush();} | ^~~~~ +In file included from /usr/include/boost/system/detail/requires_cxx11.hpp:9, + from /usr/include/boost/system/detail/config.hpp:11, + from /usr/include/boost/system/detail/error_category.hpp:13, + from /usr/include/boost/system/error_category.hpp:10, + from /usr/include/boost/filesystem/detail/path_traits.hpp:25, + from /usr/include/boost/filesystem/path.hpp:21, + from /usr/include/boost/filesystem.hpp:16, + from assembly_misc.C:32: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9, + from /usr/include/boost/container_hash/hash.hpp:14, + from /usr/include/boost/functional/hash/hash.hpp:6, + from /usr/include/boost/bimap/relation/mutant_relation.hpp:29, + from /usr/include/boost/bimap/detail/bimap_core.hpp:38, + from /usr/include/boost/bimap/bimap.hpp:61, + from /usr/include/boost/bimap.hpp:13, + from ../../src/io/annotationmappings.H:36, + from ../../src/mira/multitag.H:39, + from ../../src/mira/read.H:38, + from ../../src/mira/readpool.H:41, + from ../../src/mira/pcrcontainer.H:30, + from ../../src/mira/contig.H:42, + from ../../src/mira/assembly_info.H:33, + from ../../src/mira/assembly.H:33, + from assembly_pbcorrect.C:26: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/function/detail/requires_cxx11.hpp:9, + from /usr/include/boost/function/detail/prologue.hpp:12, + from /usr/include/boost/function.hpp:30, + from ../../src/mira/skim.H:25, + from skim.C:23: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o contig_consensus.o contig_consensus.C In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9, from /usr/include/boost/container_hash/hash.hpp:14, from /usr/include/boost/functional/hash/hash.hpp:6, @@ -2160,7 +2198,6 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o assembly_swalign.o assembly_swalign.C In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9, from /usr/include/boost/container_hash/hash.hpp:14, from /usr/include/boost/functional/hash/hash.hpp:6, @@ -2180,9 +2217,7 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o contig_consensus.o contig_consensus.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o contig_covanalysis.o contig_covanalysis.C -g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o contig_edit.o contig_edit.C In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9, from /usr/include/boost/container_hash/hash.hpp:14, from /usr/include/boost/functional/hash/hash.hpp:6, @@ -2217,6 +2252,37 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o contig_edit.o contig_edit.C +g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o contig_featureinfo.o contig_featureinfo.C +g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o contig_output.o contig_output.C +g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o contig_pairconsistency.o contig_pairconsistency.C +g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o dataprocessing.o dataprocessing.C +contig_featureinfo.C:512:9: warning: 'CEBUGF2' redefined + 512 | #define CEBUGF2 + | ^~~~~~~ +contig_featureinfo.C:473:9: note: this is the location of the previous definition + 473 | #define CEBUGF2(bla) + | ^~~~~~~ +contig_pairconsistency.C:313:9: warning: 'CEBUG' redefined + 313 | #define CEBUG(bla) + | ^~~~~ +contig_pairconsistency.C:34:9: note: this is the location of the previous definition + 34 | #define CEBUG(bla) {cout << bla; cout.flush();} + | ^~~~~ +contig_pairconsistency.C:315:9: warning: 'CEBUG' redefined + 315 | #define CEBUG(bla) {cout << bla; cout.flush();} + | ^~~~~ +contig_pairconsistency.C:313:9: note: this is the location of the previous definition + 313 | #define CEBUG(bla) + | ^~~~~ +contig_pairconsistency.C:399:9: warning: 'CEBUG' redefined + 399 | #define CEBUG(bla) + | ^~~~~ +contig_pairconsistency.C:315:9: note: this is the location of the previous definition + 315 | #define CEBUG(bla) {cout << bla; cout.flush();} + | ^~~~~ +g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o dynamic.o dynamic.C +g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o gbf_parse.o gbf_parse.C In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9, from /usr/include/boost/container_hash/hash.hpp:14, from /usr/include/boost/functional/hash/hash.hpp:6, @@ -2234,14 +2300,6 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o contig_featureinfo.o contig_featureinfo.C -g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o contig_output.o contig_output.C -contig_featureinfo.C:512:9: warning: 'CEBUGF2' redefined - 512 | #define CEBUGF2 - | ^~~~~~~ -contig_featureinfo.C:473:9: note: this is the location of the previous definition - 473 | #define CEBUGF2(bla) - | ^~~~~~~ In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9, from /usr/include/boost/container_hash/hash.hpp:14, from /usr/include/boost/functional/hash/hash.hpp:6, @@ -2276,27 +2334,7 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o contig_pairconsistency.o contig_pairconsistency.C -g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o dataprocessing.o dataprocessing.C -contig_pairconsistency.C:313:9: warning: 'CEBUG' redefined - 313 | #define CEBUG(bla) - | ^~~~~ -contig_pairconsistency.C:34:9: note: this is the location of the previous definition - 34 | #define CEBUG(bla) {cout << bla; cout.flush();} - | ^~~~~ -contig_pairconsistency.C:315:9: warning: 'CEBUG' redefined - 315 | #define CEBUG(bla) {cout << bla; cout.flush();} - | ^~~~~ -contig_pairconsistency.C:313:9: note: this is the location of the previous definition - 313 | #define CEBUG(bla) - | ^~~~~ -contig_pairconsistency.C:399:9: warning: 'CEBUG' redefined - 399 | #define CEBUG(bla) - | ^~~~~ -contig_pairconsistency.C:315:9: note: this is the location of the previous definition - 315 | #define CEBUG(bla) {cout << bla; cout.flush();} - | ^~~~~ -g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o dynamic.o dynamic.C +g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o gff_parse.o gff_parse.C In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9, from /usr/include/boost/container_hash/hash.hpp:14, from /usr/include/boost/functional/hash/hash.hpp:6, @@ -2314,8 +2352,6 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o gbf_parse.o gbf_parse.C -g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o gff_parse.o gff_parse.C In file included from /usr/include/boost/system/detail/requires_cxx11.hpp:9, from /usr/include/boost/system/detail/config.hpp:11, from /usr/include/boost/system/detail/error_category.hpp:13, @@ -2344,6 +2380,7 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o maf_parse.o maf_parse.C In file included from /usr/include/boost/function/detail/requires_cxx11.hpp:9, from /usr/include/boost/function/detail/prologue.hpp:12, from /usr/include/boost/function.hpp:30, @@ -2373,24 +2410,8 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o maf_parse.o maf_parse.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o manifest.o manifest.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o multitag.o multitag.C -/bin/bash ../../ylwrap parameters_flexer.ll lex.yy.c parameters_flexer.cc -- flex -g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o parameters.o parameters.C -g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o pcrcontainer.o pcrcontainer.C -In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9, - from /usr/include/boost/container_hash/hash.hpp:14, - from /usr/include/boost/functional/hash/hash.hpp:6, - from /usr/include/boost/bimap/relation/mutant_relation.hpp:29, - from /usr/include/boost/bimap/detail/bimap_core.hpp:38, - from /usr/include/boost/bimap/bimap.hpp:61, - from /usr/include/boost/bimap.hpp:13, - from ../../src/io/annotationmappings.H:36, - from multitag.C:28: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9, from /usr/include/boost/container_hash/hash.hpp:14, from /usr/include/boost/functional/hash/hash.hpp:6, @@ -2409,7 +2430,12 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +/bin/sh ../../ylwrap parameters_flexer.ll lex.yy.c parameters_flexer.cc -- flex +g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o parameters.o parameters.C +g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o pcrcontainer.o pcrcontainer.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o ppathfinder.o ppathfinder.C +g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o preventinitfiasco.o preventinitfiasco.C +g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o readgrouplib.o readgrouplib.C In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9, from /usr/include/boost/container_hash/hash.hpp:14, from /usr/include/boost/functional/hash/hash.hpp:6, @@ -2418,11 +2444,7 @@ from /usr/include/boost/bimap/bimap.hpp:61, from /usr/include/boost/bimap.hpp:13, from ../../src/io/annotationmappings.H:36, - from ../../src/mira/multitag.H:39, - from ../../src/mira/read.H:38, - from ../../src/mira/readpool.H:41, - from ../../src/mira/pcrcontainer.H:30, - from pcrcontainer.C:27: + from multitag.C:28: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -2446,6 +2468,18 @@ from /usr/include/boost/bimap/bimap.hpp:61, from /usr/include/boost/bimap.hpp:13, from ../../src/io/annotationmappings.H:36, + from preventinitfiasco.C:30: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9, + from /usr/include/boost/container_hash/hash.hpp:14, + from /usr/include/boost/functional/hash/hash.hpp:6, + from /usr/include/boost/bimap/relation/mutant_relation.hpp:29, + from /usr/include/boost/bimap/detail/bimap_core.hpp:38, + from /usr/include/boost/bimap/bimap.hpp:61, + from /usr/include/boost/bimap.hpp:13, + from ../../src/io/annotationmappings.H:36, from ../../src/mira/multitag.H:39, from ../../src/mira/read.H:38, from ../../src/mira/readpool.H:41, @@ -2456,8 +2490,6 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o preventinitfiasco.o preventinitfiasco.C -g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o readgrouplib.o readgrouplib.C In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9, from /usr/include/boost/container_hash/hash.hpp:14, from /usr/include/boost/functional/hash/hash.hpp:6, @@ -2466,13 +2498,19 @@ from /usr/include/boost/bimap/bimap.hpp:61, from /usr/include/boost/bimap.hpp:13, from ../../src/io/annotationmappings.H:36, - from preventinitfiasco.C:30: + from ../../src/mira/multitag.H:39, + from ../../src/mira/read.H:38, + from ../../src/mira/readpool.H:41, + from ../../src/mira/pcrcontainer.H:30, + from pcrcontainer.C:27: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o readlotstat.o readlotstat.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o readpool.o readpool.C g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o readpool_io.o readpool_io.C +g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o sam_collect.o sam_collect.C +g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o scaffolder.o scaffolder.C In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9, from /usr/include/boost/container_hash/hash.hpp:14, from /usr/include/boost/functional/hash/hash.hpp:6, @@ -2488,8 +2526,15 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o sam_collect.o sam_collect.C -g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o scaffolder.o scaffolder.C +scaffolder.C:203:9: warning: 'CEBUG' redefined + 203 | #define CEBUG(bla) + | ^~~~~ +scaffolder.C:84:9: note: this is the location of the previous definition + 84 | #define CEBUG(bla) {cout << bla; cout.flush(); } + | ^~~~~ +g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o seqtohash.o seqtohash.C +g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o simplebloomfilter.o simplebloomfilter.C +g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o skim_lowbph.o skim_lowbph.C In file included from /usr/include/boost/function/detail/requires_cxx11.hpp:9, from /usr/include/boost/function/detail/prologue.hpp:12, from /usr/include/boost/function.hpp:30, @@ -2502,14 +2547,6 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -scaffolder.C:203:9: warning: 'CEBUG' redefined - 203 | #define CEBUG(bla) - | ^~~~~ -scaffolder.C:84:9: note: this is the location of the previous definition - 84 | #define CEBUG(bla) {cout << bla; cout.flush(); } - | ^~~~~ -g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o seqtohash.o seqtohash.C -g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o simplebloomfilter.o simplebloomfilter.C In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9, from /usr/include/boost/container_hash/hash.hpp:14, from /usr/include/boost/functional/hash/hash.hpp:6, @@ -2523,11 +2560,11 @@ from ../../src/mira/readpool.H:41, from ../../src/mira/pcrcontainer.H:30, from ../../src/mira/contig.H:42, - from ../../src/mira/maf_parse.H:38, - from sam_collect.C:31: + from scaffolder.C:28: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o warnings.o warnings.C In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9, from /usr/include/boost/container_hash/hash.hpp:14, from /usr/include/boost/functional/hash/hash.hpp:6, @@ -2541,16 +2578,15 @@ from ../../src/mira/readpool.H:41, from ../../src/mira/pcrcontainer.H:30, from ../../src/mira/contig.H:42, - from scaffolder.C:28: + from ../../src/mira/maf_parse.H:38, + from sam_collect.C:31: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o skim_lowbph.o skim_lowbph.C -g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o warnings.o warnings.C rm -f libmiraestass.a ar cr libmiraestass.a estassembly.o -ranlib libmiraestass.a g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o parameters_flexer.o parameters_flexer.cc +ranlib libmiraestass.a In file included from /usr/include/boost/function/detail/requires_cxx11.hpp:9, from /usr/include/boost/function/detail/prologue.hpp:12, from /usr/include/boost/function.hpp:30, @@ -2567,7 +2603,7 @@ Making all in caf make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/caf' g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o caf.o caf.C -/bin/bash ../../ylwrap caf_flexer.ll lex.yy.c caf_flexer.cc -- flex +/bin/sh ../../ylwrap caf_flexer.ll lex.yy.c caf_flexer.cc -- flex g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o caf_flexer.o caf_flexer.cc In file included from /usr/include/boost/lexical_cast.hpp:26, from ../../src/util/fileanddisk.H:43, @@ -2724,7 +2760,7 @@ rm -f libmemorc.a ar cr libmemorc.a memorc.o ranlib libmemorc.a -/bin/bash ../../libtool --tag=CXX --mode=link g++ -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf/ -L/usr/lib/x86_64-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib -o main main.o -lmiraerrorhandling -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 +/bin/sh ../../libtool --tag=CXX --mode=link g++ -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf/ -L/usr/lib/x86_64-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib -o main main.o -lmiraerrorhandling -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 libtool: link: g++ -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -Wl,-z -Wl,relro -Wl,-z -Wl,now -o main main.o -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf/ -L/usr/lib/x86_64-linux-gnu -L/usr/lib -lmiraerrorhandling -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 -fopenmp -pthread make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/memorc' Making all in modules @@ -2779,7 +2815,8 @@ from ../../src/mira/contig.H:42, from ../../src/mira/assembly_info.H:33, from ../../src/mira/assembly.H:33, - from mod_dbgreplay.C:4: + from ../../src/modules/mod_diff.H:34, + from mod_diff.C:29: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -2798,24 +2835,7 @@ from ../../src/mira/contig.H:42, from ../../src/mira/assembly_info.H:33, from ../../src/mira/assembly.H:33, - from ../../src/modules/mod_diff.H:34, - from mod_diff.C:29: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9, - from /usr/include/boost/container_hash/hash.hpp:14, - from /usr/include/boost/functional/hash/hash.hpp:6, - from /usr/include/boost/bimap/relation/mutant_relation.hpp:29, - from /usr/include/boost/bimap/detail/bimap_core.hpp:38, - from /usr/include/boost/bimap/bimap.hpp:61, - from /usr/include/boost/bimap.hpp:13, - from ../../src/io/annotationmappings.H:36, - from ../../src/mira/multitag.H:39, - from ../../src/mira/read.H:38, - from ../../src/mira/readpool.H:41, - from ../../src/modules/mod_convert.H:34, - from mod_convert.C:29: + from mod_memestim.C:36: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -2834,7 +2854,7 @@ from ../../src/mira/contig.H:42, from ../../src/mira/assembly_info.H:33, from ../../src/mira/assembly.H:33, - from mod_memestim.C:36: + from mod_dbgreplay.C:4: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -2849,9 +2869,8 @@ from ../../src/mira/multitag.H:39, from ../../src/mira/read.H:38, from ../../src/mira/readpool.H:41, - from ../../src/mira/readpool_io.H:45, - from ../../src/modules/mod_mer.H:35, - from mod_mer.C:27: + from ../../src/modules/mod_convert.H:34, + from mod_convert.C:29: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -2883,6 +2902,23 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/container_hash/detail/requires_cxx11.hpp:9, + from /usr/include/boost/container_hash/hash.hpp:14, + from /usr/include/boost/functional/hash/hash.hpp:6, + from /usr/include/boost/bimap/relation/mutant_relation.hpp:29, + from /usr/include/boost/bimap/detail/bimap_core.hpp:38, + from /usr/include/boost/bimap/bimap.hpp:61, + from /usr/include/boost/bimap.hpp:13, + from ../../src/io/annotationmappings.H:36, + from ../../src/mira/multitag.H:39, + from ../../src/mira/read.H:38, + from ../../src/mira/readpool.H:41, + from ../../src/mira/readpool_io.H:45, + from ../../src/modules/mod_mer.H:35, + from mod_mer.C:27: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/system/detail/requires_cxx11.hpp:9, from /usr/include/boost/system/detail/config.hpp:11, from /usr/include/boost/system/detail/error_category.hpp:13, @@ -2958,10 +2994,10 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -/bin/bash ../../libtool --tag=CXX --mode=link g++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/x86_64-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib -o mira mira.o quirks.o compileinfo.itxt.xxd.o -lmiraversion -lmiramodules -lmiradebuggersupport -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 -/bin/bash ../../libtool --tag=CXX --mode=link g++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/x86_64-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib -o miratest miratest.o compileinfo.itxt.xxd.o -lmiraversion -lmiramodules -lmiradebuggersupport -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 -libtool: link: g++ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -Wl,-z -Wl,relro -Wl,-z -Wl,now -o mira mira.o quirks.o compileinfo.itxt.xxd.o -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/x86_64-linux-gnu -L/usr/lib -lmiraversion -lmiramodules -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 -fopenmp -pthread +/bin/sh ../../libtool --tag=CXX --mode=link g++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/x86_64-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib -o miratest miratest.o compileinfo.itxt.xxd.o -lmiraversion -lmiramodules -lmiradebuggersupport -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 +/bin/sh ../../libtool --tag=CXX --mode=link g++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/x86_64-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib -o mira mira.o quirks.o compileinfo.itxt.xxd.o -lmiraversion -lmiramodules -lmiradebuggersupport -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 libtool: link: g++ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -Wl,-z -Wl,relro -Wl,-z -Wl,now -o miratest miratest.o compileinfo.itxt.xxd.o -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/x86_64-linux-gnu -L/usr/lib -lmiraversion -lmiramodules -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 -fopenmp -pthread +libtool: link: g++ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -Wl,-z -Wl,relro -Wl,-z -Wl,now -o mira mira.o quirks.o compileinfo.itxt.xxd.o -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/x86_64-linux-gnu -L/usr/lib -lmiraversion -lmiramodules -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 -fopenmp -pthread make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/progs' make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/progs' Making all in other @@ -3000,7 +3036,7 @@ debian/rules override_dh_auto_build-indep make[1]: Entering directory '/build/reproducible-path/mira-4.9.6' dh_auto_build --sourcedir=doc - cd doc && make -j12 INSTALL="install --strip-program=true" + cd doc && make -j16 INSTALL="install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/mira-4.9.6/doc' Making all in docbook make[3]: Entering directory '/build/reproducible-path/mira-4.9.6/doc/docbook' @@ -3017,6 +3053,15 @@ Making .html out of _part.xml chap_logfiles_part.html Making .html out of _part.xml chap_maf_part.html Making .html out of _part.xml chap_reference_part.html +Making .html out of _part.xml chap_installation_part.html +Making .html out of _part.xml chap_intro_part.html +Making .html out of _part.xml chap_sra_part.html +Making .html out of _part.xml chap_results_part.html +Build the book set list... +Build the book set list... +Making .html out of _part.xml chap_seqadvice_part.html +Making .html out of _part.xml chap_bonus_part.html +Making .html out of _part.xml chap_preface_part.html ERROR: xref linking to chap_dataprep has no generated link text. Error: no ID for constraint linkend: "chap_dataprep". ERROR: xref linking to chap_denovo has no generated link text. @@ -3041,24 +3086,15 @@ Error: no ID for constraint linkend: "sect_ref_manifest_readgroups". ERROR: xref linking to sect_ref_manifest_parameters has no generated link text. Error: no ID for constraint linkend: "sect_ref_manifest_parameters". -Making .html out of _part.xml chap_installation_part.html -Making .html out of _part.xml chap_intro_part.html -Making .html out of _part.xml chap_results_part.html -Making .html out of _part.xml chap_sra_part.html -Making .html out of _part.xml chap_seqadvice_part.html -Making .html out of _part.xml chap_bonus_part.html -Making .html out of _part.xml chap_preface_part.html Element emph in namespace '' encountered in note, but no template matches. -Build the book set list... -Build the book set list... -Element emph in namespace '' encountered in note, but no template matches. -Build the listings... Build the listings... +Element emph in namespace '' encountered in note, but no template matches. XSLT stylesheets DocBook - LaTeX 2e (0.3.12) =================================================== No template matches copyright in chapterinfo. No template matches year in copyright. No template matches holder in copyright. +Build the listings... Build book_3rdparty.pdf XSLT stylesheets DocBook - LaTeX 2e (0.3.12) =================================================== @@ -3241,129 +3277,11 @@ make[3]: Leaving directory '/build/reproducible-path/mira-4.9.6/doc' make[2]: Leaving directory '/build/reproducible-path/mira-4.9.6/doc' make[1]: Leaving directory '/build/reproducible-path/mira-4.9.6' - rm -f debian/mira-doc.debhelper.log debian/mira-rfam-12s-rrna.debhelper.log - debian/rules override_dh_auto_test-arch -make[1]: Entering directory '/build/reproducible-path/mira-4.9.6' -make check -make[2]: Entering directory '/build/reproducible-path/mira-4.9.6' -make check-recursive -make[3]: Entering directory '/build/reproducible-path/mira-4.9.6' -Making check in man -make[4]: Entering directory '/build/reproducible-path/mira-4.9.6/man' -make[4]: Nothing to be done for 'check'. -make[4]: Leaving directory '/build/reproducible-path/mira-4.9.6/man' -Making check in src -make[4]: Entering directory '/build/reproducible-path/mira-4.9.6/src' -Making check in debuggersupport -make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/debuggersupport' -make[5]: Nothing to be done for 'check'. -make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/debuggersupport' -Making check in io -make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/io' -make check-am -make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/io' -make[6]: Nothing to be done for 'check-am'. -make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/io' -make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/io' -Making check in stdinc -make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/stdinc' -make[5]: Nothing to be done for 'check'. -make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/stdinc' -Making check in errorhandling -make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/errorhandling' -make[5]: Nothing to be done for 'check'. -make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/errorhandling' -Making check in util -make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/util' -make[5]: Nothing to be done for 'check'. -make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/util' -Making check in mira -make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/mira' -make check-am -make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/mira' -make[6]: Nothing to be done for 'check-am'. -make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/mira' -make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/mira' -Making check in caf -make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/caf' -make[5]: Nothing to be done for 'check'. -make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/caf' -Making check in memorc -make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/memorc' -make[5]: Nothing to be done for 'check'. -make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/memorc' -Making check in modules -make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/modules' -make[5]: Nothing to be done for 'check'. -make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/modules' -Making check in support -make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/support' -make[5]: Nothing to be done for 'check'. -make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/support' -Making check in scripts -make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/scripts' -make[5]: Nothing to be done for 'check'. -make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/scripts' -Making check in version -make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/version' -make check-am -make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/version' -make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/version' -make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/version' -Making check in progs -make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/progs' -Making .C out of .xxd compileinfo.itxt -make check-am -make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/progs' -Making .C out of .xxd compileinfo.itxt -g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o compileinfo.itxt.xxd.o compileinfo.itxt.xxd.C -/bin/bash ../../libtool --tag=CXX --mode=link g++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/x86_64-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib -o mira mira.o quirks.o compileinfo.itxt.xxd.o -lmiraversion -lmiramodules -lmiradebuggersupport -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 -libtool: link: g++ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -Wl,-z -Wl,relro -Wl,-z -Wl,now -o mira mira.o quirks.o compileinfo.itxt.xxd.o -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/x86_64-linux-gnu -L/usr/lib -lmiraversion -lmiramodules -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 -fopenmp -pthread -/bin/bash ../../libtool --tag=CXX --mode=link g++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/x86_64-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib -o miratest miratest.o compileinfo.itxt.xxd.o -lmiraversion -lmiramodules -lmiradebuggersupport -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 -libtool: link: g++ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -Wl,-z -Wl,relro -Wl,-z -Wl,now -o miratest miratest.o compileinfo.itxt.xxd.o -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/x86_64-linux-gnu -L/usr/lib -lmiraversion -lmiramodules -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 -fopenmp -pthread -make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/progs' -make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/progs' -Making check in other -make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other' -Making check in sls -make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other/sls' -Making check in mira-createsls -make[7]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls' -Making check in bin -make[8]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls/bin' -make[8]: Nothing to be done for 'check'. -make[8]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls/bin' -make[8]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls' -make[8]: Nothing to be done for 'check-am'. -make[8]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls' -make[7]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other/sls/mira-createsls' -make[7]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other/sls' -make[7]: Nothing to be done for 'check-am'. -make[7]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other/sls' -make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other/sls' -make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/other' -make[6]: Nothing to be done for 'check-am'. -make[6]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other' -make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src/other' -make[5]: Entering directory '/build/reproducible-path/mira-4.9.6/src' -make[5]: Nothing to be done for 'check-am'. -make[5]: Leaving directory '/build/reproducible-path/mira-4.9.6/src' -make[4]: Leaving directory '/build/reproducible-path/mira-4.9.6/src' -make[4]: Entering directory '/build/reproducible-path/mira-4.9.6' -make[4]: Nothing to be done for 'check-am'. -make[4]: Leaving directory '/build/reproducible-path/mira-4.9.6' -make[3]: Leaving directory '/build/reproducible-path/mira-4.9.6' -make[2]: Leaving directory '/build/reproducible-path/mira-4.9.6' -make[1]: Leaving directory '/build/reproducible-path/mira-4.9.6' - debian/rules override_dh_auto_test-indep -make[1]: Entering directory '/build/reproducible-path/mira-4.9.6' -echo no tests for -indep -no tests for -indep -make[1]: Leaving directory '/build/reproducible-path/mira-4.9.6' create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/mira-assembler.substvars debian/mira-rfam-12s-rrna.substvars debian/mira-doc.substvars rm -fr -- debian/.debhelper/generated/mira-assembler/ debian/mira-assembler/ debian/tmp/ debian/.debhelper/generated/mira-rfam-12s-rrna/ debian/mira-rfam-12s-rrna/ debian/.debhelper/generated/mira-doc/ debian/mira-doc/ + rm -f debian/mira-doc.debhelper.log debian/mira-rfam-12s-rrna.debhelper.log debian/rules override_dh_auto_install-arch make[1]: Entering directory '/build/reproducible-path/mira-4.9.6' make install DESTDIR=/build/reproducible-path/mira-4.9.6/debian/mira-assembler @@ -3481,14 +3399,14 @@ make[6]: Entering directory '/build/reproducible-path/mira-4.9.6/src/progs' Making .C out of .xxd compileinfo.itxt g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.9.6\" -DPACKAGE_STRING=\"mira\ 4.9.6\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.9.6\" -DHAVE_OPENMP=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict__ -DHAVE_MALLOC=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DHAVE_GZOFFSET=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -c -o compileinfo.itxt.xxd.o compileinfo.itxt.xxd.C -/bin/bash ../../libtool --tag=CXX --mode=link g++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/x86_64-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib -o mira mira.o quirks.o compileinfo.itxt.xxd.o -lmiraversion -lmiramodules -lmiradebuggersupport -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 +/bin/sh ../../libtool --tag=CXX --mode=link g++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/x86_64-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib -o mira mira.o quirks.o compileinfo.itxt.xxd.o -lmiraversion -lmiramodules -lmiradebuggersupport -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 libtool: link: g++ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -Wl,-z -Wl,relro -Wl,-z -Wl,now -o mira mira.o quirks.o compileinfo.itxt.xxd.o -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/x86_64-linux-gnu -L/usr/lib -lmiraversion -lmiramodules -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 -fopenmp -pthread -/bin/bash ../../libtool --tag=CXX --mode=link g++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/x86_64-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib -o miratest miratest.o compileinfo.itxt.xxd.o -lmiraversion -lmiramodules -lmiradebuggersupport -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 +/bin/sh ../../libtool --tag=CXX --mode=link g++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/x86_64-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib -o miratest miratest.o compileinfo.itxt.xxd.o -lmiraversion -lmiramodules -lmiradebuggersupport -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 libtool: link: g++ -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/reproducible-path/mira-4.9.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include -O3 -funroll-loops -I/usr/include -I/usr/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -Werror=unused-value -std=c++14 -fopenmp -Wl,-z -Wl,relro -Wl,-z -Wl,now -o miratest miratest.o compileinfo.itxt.xxd.o -L../version -L../modules -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf -L/usr/lib/x86_64-linux-gnu -L/usr/lib -lmiraversion -lmiramodules -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lmirafmttext -lboost_thread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2 -fopenmp -pthread make[7]: Entering directory '/build/reproducible-path/mira-4.9.6/src/progs' Making .C out of .xxd compileinfo.itxt /usr/bin/mkdir -p '/build/reproducible-path/mira-4.9.6/debian/mira-assembler/usr/bin' - /bin/bash ../../libtool --mode=install /usr/bin/install -c mira '/build/reproducible-path/mira-4.9.6/debian/mira-assembler/usr/bin' + /bin/sh ../../libtool --mode=install /usr/bin/install -c mira '/build/reproducible-path/mira-4.9.6/debian/mira-assembler/usr/bin' libtool: install: /usr/bin/install -c mira /build/reproducible-path/mira-4.9.6/debian/mira-assembler/usr/bin/mira make install-exec-hook make[8]: Entering directory '/build/reproducible-path/mira-4.9.6/src/progs' @@ -3596,12 +3514,12 @@ install -m0755 -d debian/mira-assembler/usr/share/doc/mira-assembler install -p -m0644 debian/.debhelper/generated/mira-assembler/dh_installchangelogs.dch.trimmed debian/mira-assembler/usr/share/doc/mira-assembler/changelog.Debian install -p -m0644 src/mira/CHANGES.txt debian/mira-assembler/usr/share/doc/mira-assembler/changelog - install -m0755 -d debian/mira-doc/usr/share/doc/mira-doc - install -p -m0644 debian/.debhelper/generated/mira-doc/dh_installchangelogs.dch.trimmed debian/mira-doc/usr/share/doc/mira-doc/changelog.Debian - install -p -m0644 src/mira/CHANGES.txt debian/mira-doc/usr/share/doc/mira-doc/changelog install -m0755 -d debian/mira-rfam-12s-rrna/usr/share/doc/mira-rfam-12s-rrna install -p -m0644 debian/.debhelper/generated/mira-rfam-12s-rrna/dh_installchangelogs.dch.trimmed debian/mira-rfam-12s-rrna/usr/share/doc/mira-rfam-12s-rrna/changelog.Debian install -p -m0644 src/mira/CHANGES.txt debian/mira-rfam-12s-rrna/usr/share/doc/mira-rfam-12s-rrna/changelog + install -m0755 -d debian/mira-doc/usr/share/doc/mira-doc + install -p -m0644 debian/.debhelper/generated/mira-doc/dh_installchangelogs.dch.trimmed debian/mira-doc/usr/share/doc/mira-doc/changelog.Debian + install -p -m0644 src/mira/CHANGES.txt debian/mira-doc/usr/share/doc/mira-doc/changelog make[1]: Leaving directory '/build/reproducible-path/mira-4.9.6' dh_installman man-recode --to-code UTF-8 --suffix .dh-new debian/mira-assembler/usr/share/man/man1/mira.1 @@ -3610,94 +3528,94 @@ man-recode --to-code UTF-8 --suffix .dh-new debian/mira-assembler/usr/share/man/man1/miradiff.1 man-recode --to-code UTF-8 --suffix .dh-new debian/mira-assembler/usr/share/man/man1/miramem.1 man-recode --to-code UTF-8 --suffix .dh-new debian/mira-assembler/usr/share/man/man1/miramer.1 - mv debian/mira-assembler/usr/share/man/man1/miraconvert.1.dh-new debian/mira-assembler/usr/share/man/man1/miraconvert.1 - chmod 0644 -- debian/mira-assembler/usr/share/man/man1/miraconvert.1 - mv debian/mira-assembler/usr/share/man/man1/miramem.1.dh-new debian/mira-assembler/usr/share/man/man1/miramem.1 - chmod 0644 -- debian/mira-assembler/usr/share/man/man1/miramem.1 - mv debian/mira-assembler/usr/share/man/man1/miradiff.1.dh-new debian/mira-assembler/usr/share/man/man1/miradiff.1 - chmod 0644 -- debian/mira-assembler/usr/share/man/man1/miradiff.1 - mv debian/mira-assembler/usr/share/man/man1/mirabait.1.dh-new debian/mira-assembler/usr/share/man/man1/mirabait.1 - chmod 0644 -- debian/mira-assembler/usr/share/man/man1/mirabait.1 mv debian/mira-assembler/usr/share/man/man1/mira.1.dh-new debian/mira-assembler/usr/share/man/man1/mira.1 chmod 0644 -- debian/mira-assembler/usr/share/man/man1/mira.1 + mv debian/mira-assembler/usr/share/man/man1/mirabait.1.dh-new debian/mira-assembler/usr/share/man/man1/mirabait.1 + chmod 0644 -- debian/mira-assembler/usr/share/man/man1/mirabait.1 mv debian/mira-assembler/usr/share/man/man1/miramer.1.dh-new debian/mira-assembler/usr/share/man/man1/miramer.1 chmod 0644 -- debian/mira-assembler/usr/share/man/man1/miramer.1 + mv debian/mira-assembler/usr/share/man/man1/miradiff.1.dh-new debian/mira-assembler/usr/share/man/man1/miradiff.1 + chmod 0644 -- debian/mira-assembler/usr/share/man/man1/miradiff.1 + mv debian/mira-assembler/usr/share/man/man1/miramem.1.dh-new debian/mira-assembler/usr/share/man/man1/miramem.1 + chmod 0644 -- debian/mira-assembler/usr/share/man/man1/miramem.1 + mv debian/mira-assembler/usr/share/man/man1/miraconvert.1.dh-new debian/mira-assembler/usr/share/man/man1/miraconvert.1 + chmod 0644 -- debian/mira-assembler/usr/share/man/man1/miraconvert.1 dh_lintian install -m0755 -d debian/mira-assembler/usr/share/lintian/overrides install -p -m0644 debian/mira-assembler.lintian-overrides debian/mira-assembler/usr/share/lintian/overrides/mira-assembler dh_perl dh_link - rm -f debian/mira-assembler/usr/bin/miramer - ln -s mira debian/mira-assembler/usr/bin/miramer - rm -f debian/mira-assembler/usr/bin/miramem - ln -s mira debian/mira-assembler/usr/bin/miramem - rm -f debian/mira-assembler/usr/bin/mirabait - ln -s mira debian/mira-assembler/usr/bin/mirabait rm -f debian/mira-assembler/usr/bin/miraconvert ln -s mira debian/mira-assembler/usr/bin/miraconvert + rm -f debian/mira-assembler/usr/bin/mirabait + ln -s mira debian/mira-assembler/usr/bin/mirabait + rm -f debian/mira-assembler/usr/bin/miramem + ln -s mira debian/mira-assembler/usr/bin/miramem + rm -f debian/mira-assembler/usr/bin/miramer + ln -s mira debian/mira-assembler/usr/bin/miramer dh_strip_nondeterminism Using 1707216070 as canonical time Normalizing debian/mira-rfam-12s-rrna/usr/share/mira/rfam_rrna-21-12.sls.gz using File::StripNondeterminism::handlers::gzip Using 1707216070 as canonical time - Normalizing debian/mira-doc/usr/share/doc/mira-assembler/images/warning.png using File::StripNondeterminism::handlers::png - Normalizing debian/mira-doc/usr/share/doc/mira-assembler/images/note.png using File::StripNondeterminism::handlers::png - Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_sroc_lenski1.png using File::StripNondeterminism::handlers::png + Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/san_autoedit2.png using File::StripNondeterminism::handlers::png Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/454sxa_hybdenovo.png using File::StripNondeterminism::handlers::png - Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/haf_danger_join_ok.png using File::StripNondeterminism::handlers::png + Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/haf5_haf2_contigcoverage.png using File::StripNondeterminism::handlers::png + Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/ion_dh10bgoodB13.png using File::StripNondeterminism::handlers::png + Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/454_autoedit1.png using File::StripNondeterminism::handlers::png Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_unsc_ggcxg1_lenski.png using File::StripNondeterminism::handlers::png - Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/results_miraconvert.png using File::StripNondeterminism::handlers::png - Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_xmastree_lenski1.png using File::StripNondeterminism::handlers::png - Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/haf5_haf2_contigcoverage_ovals.png using File::StripNondeterminism::handlers::png - Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/454_stacks_join.png using File::StripNondeterminism::handlers::png + Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/haf_danger_join_ok.png using File::StripNondeterminism::handlers::png + Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/gcb99_edit.png using File::StripNondeterminism::handlers::png + Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/san_autoedit1.png using File::StripNondeterminism::handlers::png + Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_gcbias_bias2009.png using File::StripNondeterminism::handlers::png + Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/pb_elasticdarkinserts04.png using File::StripNondeterminism::handlers::png + Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_unsc_ggc3_lenski.png using File::StripNondeterminism::handlers::png + Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_mcvc_lenski.png using File::StripNondeterminism::handlers::png Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/haf2_end_nomoredata.png using File::StripNondeterminism::handlers::png - Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_wrmcsrmc_hiding_lenski1.png using File::StripNondeterminism::handlers::png - Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/haf_danger_join_notok.png using File::StripNondeterminism::handlers::png - Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/iontor_indelhpexample.png using File::StripNondeterminism::handlers::png - Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/ion_dh10bdirdepindel.png using File::StripNondeterminism::handlers::png Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/results_mira2other.png using File::StripNondeterminism::handlers::png - Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/gcb99_replocator.png using File::StripNondeterminism::handlers::png - Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_cer_reads1.png using File::StripNondeterminism::handlers::png + Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/pb_elasticdarkinserts02.png using File::StripNondeterminism::handlers::png + Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/pb_elasticdarkinserts03.png using File::StripNondeterminism::handlers::png + Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_wrmcsrmc_hiding_lenski1.png using File::StripNondeterminism::handlers::png + Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/pb_elasticdarkinserts01.png using File::StripNondeterminism::handlers::png Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/srmc_in_454sxahyb_lastpass2.png using File::StripNondeterminism::handlers::png - Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/srmc_in_454sxahyb_lastpass1.png using File::StripNondeterminism::handlers::png - Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/san_autoedit1.png using File::StripNondeterminism::handlers::png Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/srmc_in_454sxahyb_1stpass.png using File::StripNondeterminism::handlers::png - Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/454san_stmu_hybdenovo.png using File::StripNondeterminism::handlers::png - Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_xmastree_lenski2.png using File::StripNondeterminism::handlers::png + Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/srmc_in_454sxahyb_lastpass1.png using File::StripNondeterminism::handlers::png + Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_cer_reads2.png using File::StripNondeterminism::handlers::png Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/haf2_haf5_clearshortrepeat.png using File::StripNondeterminism::handlers::png - Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/pb_elasticdarkinserts04.png using File::StripNondeterminism::handlers::png - Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_unsc_ggcxg2_lenski.png using File::StripNondeterminism::handlers::png - Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_unsc_ggc1_lenski.png using File::StripNondeterminism::handlers::png - Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/haf5_repend_rrna.png using File::StripNondeterminism::handlers::png - Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/pb_elasticdarkinserts01.png using File::StripNondeterminism::handlers::png - Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/pb_elasticdarkinserts02.png using File::StripNondeterminism::handlers::png - Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_gcbias_nobias2008.png using File::StripNondeterminism::handlers::png - Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/haf5_haf2_contigcoverage.png using File::StripNondeterminism::handlers::png + Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_cer_reads1.png using File::StripNondeterminism::handlers::png + Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/ion_dh10bdirdepindel.png using File::StripNondeterminism::handlers::png Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/pb_c227-11-clcr_res.png using File::StripNondeterminism::handlers::png - Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_sroc_lenski2.png using File::StripNondeterminism::handlers::png - Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_unsc_ggc3_lenski.png using File::StripNondeterminism::handlers::png - Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/454_autoedit2.png using File::StripNondeterminism::handlers::png - Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/454_autoedit1.png using File::StripNondeterminism::handlers::png - Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_unsc_ggc2_lenski.png using File::StripNondeterminism::handlers::png - Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/ion_dh10bgoodB13.png using File::StripNondeterminism::handlers::png - Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_mcvc_lenski.png using File::StripNondeterminism::handlers::png - Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_gcbias_bias2009.png using File::StripNondeterminism::handlers::png - Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/san_autoedit2.png using File::StripNondeterminism::handlers::png - Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_cer_reads2.png using File::StripNondeterminism::handlers::png - Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/gcb99_edit.png using File::StripNondeterminism::handlers::png - Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/454sxa_stms_hybdenovo.png using File::StripNondeterminism::handlers::png + Normalizing debian/mira-doc/usr/share/doc/mira-assembler/images/warning.png using File::StripNondeterminism::handlers::png + Normalizing debian/mira-doc/usr/share/doc/mira-assembler/images/note.png using File::StripNondeterminism::handlers::png + Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/454_stacks_join.png using File::StripNondeterminism::handlers::png + Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_xmastree_lenski1.png using File::StripNondeterminism::handlers::png + Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/454san_stmu_hybdenovo.png using File::StripNondeterminism::handlers::png + Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/haf_danger_join_notok.png using File::StripNondeterminism::handlers::png Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_gcbias_comp20082009.png using File::StripNondeterminism::handlers::png - Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/pb_elasticdarkinserts03.png using File::StripNondeterminism::handlers::png + Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/haf5_haf2_contigcoverage_ovals.png using File::StripNondeterminism::handlers::png + Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/results_miraconvert.png using File::StripNondeterminism::handlers::png + Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/454sxa_stms_hybdenovo.png using File::StripNondeterminism::handlers::png + Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/454_autoedit2.png using File::StripNondeterminism::handlers::png Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_unsc_ggc4_lenski.png using File::StripNondeterminism::handlers::png + Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_xmastree_lenski2.png using File::StripNondeterminism::handlers::png + Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_sroc_lenski1.png using File::StripNondeterminism::handlers::png + Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_unsc_ggc2_lenski.png using File::StripNondeterminism::handlers::png + Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_sroc_lenski2.png using File::StripNondeterminism::handlers::png + Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/haf5_repend_rrna.png using File::StripNondeterminism::handlers::png + Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_gcbias_nobias2008.png using File::StripNondeterminism::handlers::png + Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_unsc_ggc1_lenski.png using File::StripNondeterminism::handlers::png + Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/gcb99_replocator.png using File::StripNondeterminism::handlers::png + Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/iontor_indelhpexample.png using File::StripNondeterminism::handlers::png + Normalizing debian/mira-doc/usr/share/doc/mira-assembler/bookfigures/sxa_unsc_ggcxg2_lenski.png using File::StripNondeterminism::handlers::png dh_compress cd debian/mira-assembler - cd debian/mira-doc cd debian/mira-rfam-12s-rrna + cd debian/mira-doc chmod a-x usr/share/doc/mira-rfam-12s-rrna/changelog usr/share/doc/mira-rfam-12s-rrna/changelog.Debian - chmod a-x usr/share/doc/mira-assembler/NEWS usr/share/doc/mira-assembler/changelog usr/share/doc/mira-assembler/changelog.Debian usr/share/doc/mira-assembler/test_data/fasta_estset1/tvc_mini.fasta usr/share/doc/mira-assembler/test_data/fasta_estset1/tvc_mini.fasta.qual usr/share/doc/mira-assembler/test_data/solexa_eco_art/ecoli_backbone_in.gbf usr/share/doc/mira-assembler/test_data/solexa_eco_art/ecoli_in.solexa.fasta usr/share/doc/mira-assembler/test_data/solexa_eco_art/ecoli_in.solexa.fasta.qual usr/share/doc/mira-assembler/test_data/solexa_eco_art/ecoli_straindata_in.txt usr/share/man/man1/mira.1 usr/share/man/man1/mirabait.1 usr/share/man/man1/miraconvert.1 usr/share/man/man1/miradiff.1 usr/share/man/man1/miramem.1 usr/share/man/man1/miramer.1 chmod a-x usr/share/doc/mira-doc/changelog usr/share/doc/mira-doc/changelog.Debian + chmod a-x usr/share/doc/mira-assembler/NEWS usr/share/doc/mira-assembler/changelog usr/share/doc/mira-assembler/changelog.Debian usr/share/doc/mira-assembler/test_data/fasta_estset1/tvc_mini.fasta usr/share/doc/mira-assembler/test_data/fasta_estset1/tvc_mini.fasta.qual usr/share/doc/mira-assembler/test_data/solexa_eco_art/ecoli_backbone_in.gbf usr/share/doc/mira-assembler/test_data/solexa_eco_art/ecoli_in.solexa.fasta usr/share/doc/mira-assembler/test_data/solexa_eco_art/ecoli_in.solexa.fasta.qual usr/share/doc/mira-assembler/test_data/solexa_eco_art/ecoli_straindata_in.txt usr/share/man/man1/mira.1 usr/share/man/man1/mirabait.1 usr/share/man/man1/miraconvert.1 usr/share/man/man1/miradiff.1 usr/share/man/man1/miramem.1 usr/share/man/man1/miramer.1 gzip -9nf usr/share/doc/mira-rfam-12s-rrna/changelog usr/share/doc/mira-rfam-12s-rrna/changelog.Debian - gzip -9nf usr/share/doc/mira-assembler/NEWS usr/share/doc/mira-assembler/changelog usr/share/doc/mira-assembler/changelog.Debian usr/share/doc/mira-assembler/test_data/fasta_estset1/tvc_mini.fasta usr/share/doc/mira-assembler/test_data/fasta_estset1/tvc_mini.fasta.qual usr/share/doc/mira-assembler/test_data/solexa_eco_art/ecoli_backbone_in.gbf usr/share/doc/mira-assembler/test_data/solexa_eco_art/ecoli_in.solexa.fasta usr/share/doc/mira-assembler/test_data/solexa_eco_art/ecoli_in.solexa.fasta.qual usr/share/doc/mira-assembler/test_data/solexa_eco_art/ecoli_straindata_in.txt usr/share/man/man1/mira.1 usr/share/man/man1/mirabait.1 usr/share/man/man1/miraconvert.1 usr/share/man/man1/miradiff.1 usr/share/man/man1/miramem.1 usr/share/man/man1/miramer.1 gzip -9nf usr/share/doc/mira-doc/changelog usr/share/doc/mira-doc/changelog.Debian + gzip -9nf usr/share/doc/mira-assembler/NEWS usr/share/doc/mira-assembler/changelog usr/share/doc/mira-assembler/changelog.Debian usr/share/doc/mira-assembler/test_data/fasta_estset1/tvc_mini.fasta usr/share/doc/mira-assembler/test_data/fasta_estset1/tvc_mini.fasta.qual usr/share/doc/mira-assembler/test_data/solexa_eco_art/ecoli_backbone_in.gbf usr/share/doc/mira-assembler/test_data/solexa_eco_art/ecoli_in.solexa.fasta usr/share/doc/mira-assembler/test_data/solexa_eco_art/ecoli_in.solexa.fasta.qual usr/share/doc/mira-assembler/test_data/solexa_eco_art/ecoli_straindata_in.txt usr/share/man/man1/mira.1 usr/share/man/man1/mirabait.1 usr/share/man/man1/miraconvert.1 usr/share/man/man1/miradiff.1 usr/share/man/man1/miramem.1 usr/share/man/man1/miramer.1 cd '/build/reproducible-path/mira-4.9.6' cd '/build/reproducible-path/mira-4.9.6' cd '/build/reproducible-path/mira-4.9.6' @@ -3706,8 +3624,8 @@ find debian/mira-rfam-12s-rrna ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/mira-doc ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/mira-rfam-12s-rrna/usr/share/doc -type f -a -true -a ! -regex 'debian/mira-rfam-12s-rrna/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 - find debian/mira-doc/usr/share/doc -type f -a -true -a ! -regex 'debian/mira-doc/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/mira-assembler/usr/share/doc -type f -a -true -a ! -regex 'debian/mira-assembler/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 + find debian/mira-doc/usr/share/doc -type f -a -true -a ! -regex 'debian/mira-doc/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/mira-rfam-12s-rrna/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/mira-assembler/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/mira-doc/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 @@ -3744,6 +3662,10 @@ chmod 0755 -- debian/mira-rfam-12s-rrna/DEBIAN/postrm install -m0755 -d debian/mira-doc/DEBIAN dh_gencontrol + install -m0755 -d debian/mira-rfam-12s-rrna/DEBIAN + echo misc:Depends= >> debian/mira-rfam-12s-rrna.substvars + echo misc:Pre-Depends= >> debian/mira-rfam-12s-rrna.substvars + dpkg-gencontrol -pmira-rfam-12s-rrna -ldebian/changelog -Tdebian/mira-rfam-12s-rrna.substvars -cdebian/control -Pdebian/mira-rfam-12s-rrna install -m0755 -d debian/mira-assembler/DEBIAN echo misc:Depends= >> debian/mira-assembler.substvars echo misc:Pre-Depends= >> debian/mira-assembler.substvars @@ -3753,22 +3675,18 @@ echo misc:Depends= >> debian/mira-doc.substvars echo misc:Pre-Depends= >> debian/mira-doc.substvars dpkg-gencontrol -pmira-doc -ldebian/changelog -Tdebian/mira-doc.substvars -cdebian/control -Pdebian/mira-doc - install -m0755 -d debian/mira-rfam-12s-rrna/DEBIAN - echo misc:Depends= >> debian/mira-rfam-12s-rrna.substvars - echo misc:Pre-Depends= >> debian/mira-rfam-12s-rrna.substvars - dpkg-gencontrol -pmira-rfam-12s-rrna -ldebian/changelog -Tdebian/mira-rfam-12s-rrna.substvars -cdebian/control -Pdebian/mira-rfam-12s-rrna chmod 0644 -- debian/mira-rfam-12s-rrna/DEBIAN/control + chmod 0644 -- debian/mira-doc/DEBIAN/control chmod 0644 -- debian/.debhelper/mira-assembler/dbgsym-root/DEBIAN/control dpkg-gencontrol -pmira-assembler -ldebian/changelog -Tdebian/mira-assembler.substvars -cdebian/control -Pdebian/mira-assembler - chmod 0644 -- debian/mira-doc/DEBIAN/control chmod 0644 -- debian/mira-assembler/DEBIAN/control dh_md5sums - install -m0755 -d debian/mira-assembler/DEBIAN install -m0755 -d debian/mira-doc/DEBIAN + install -m0755 -d debian/mira-assembler/DEBIAN install -m0755 -d debian/mira-rfam-12s-rrna/DEBIAN - cd debian/mira-assembler >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums - cd debian/mira-rfam-12s-rrna >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/mira-doc >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums + cd debian/mira-rfam-12s-rrna >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums + cd debian/mira-assembler >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/mira-doc/DEBIAN/md5sums chmod 0644 -- debian/mira-assembler/DEBIAN/md5sums install -m0755 -d debian/.debhelper/mira-assembler/dbgsym-root/DEBIAN @@ -3776,14 +3694,14 @@ chmod 0644 -- debian/mira-rfam-12s-rrna/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/mira-assembler/dbgsym-root/DEBIAN/md5sums dh_builddeb - dpkg-deb --root-owner-group --build debian/.debhelper/mira-assembler/dbgsym-root .. dpkg-deb --root-owner-group --build debian/mira-assembler .. + dpkg-deb --root-owner-group --build debian/.debhelper/mira-assembler/dbgsym-root .. dpkg-deb --root-owner-group --build debian/mira-rfam-12s-rrna .. dpkg-deb --root-owner-group --build debian/mira-doc .. dpkg-deb: building package 'mira-assembler-dbgsym' in '../mira-assembler-dbgsym_4.9.6-11_amd64.deb'. -dpkg-deb: building package 'mira-rfam-12s-rrna' in '../mira-rfam-12s-rrna_4.9.6-11_all.deb'. dpkg-deb: building package 'mira-assembler' in '../mira-assembler_4.9.6-11_amd64.deb'. dpkg-deb: building package 'mira-doc' in '../mira-doc_4.9.6-11_all.deb'. +dpkg-deb: building package 'mira-rfam-12s-rrna' in '../mira-rfam-12s-rrna_4.9.6-11_all.deb'. dpkg-genbuildinfo --build=binary -O../mira_4.9.6-11_amd64.buildinfo dpkg-genchanges --build=binary -O../mira_4.9.6-11_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -3791,12 +3709,14 @@ 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/1894827/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1894827/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/4032766 and its subdirectories -I: Current time: Tue Nov 18 05:42:13 -12 2025 -I: pbuilder-time-stamp: 1763487733 +I: removing directory /srv/workspace/pbuilder/1894827 and its subdirectories +I: Current time: Tue Dec 22 14:14:55 +14 2026 +I: pbuilder-time-stamp: 1797898495