Diff of the two buildlogs: -- --- b1/build.log 2020-04-27 21:25:41.790911645 +0000 +++ b2/build.log 2020-04-27 21:52:27.479572001 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun May 30 15:44:46 -12 2021 -I: pbuilder-time-stamp: 1622432686 +I: Current time: Tue Apr 28 11:25:54 +14 2020 +I: pbuilder-time-stamp: 1588022754 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -18,7 +18,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Wed Sep 19 08:41:06 2018 -12 +gpgv: Signature made Thu Sep 20 10:41:06 2018 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -32,6 +32,18 @@ dpkg-source: info: applying man-directory I: using fakeroot in build. I: Installing the build-deps +I: user script /srv/workspace/pbuilder/30754/tmp/hooks/D01_modify_environment starting +debug: Running on profitbricks-build12-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/30754/tmp/hooks/D01_modify_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -301,7 +313,7 @@ Get: 202 http://deb.debian.org/debian buster/main i386 libgoogle-perftools4 i386 2.7-1 [312 kB] Get: 203 http://deb.debian.org/debian buster/main i386 libgoogle-perftools-dev i386 2.7-1 [574 kB] Get: 204 http://deb.debian.org/debian buster/main i386 zlib1g-dev i386 1:1.2.11.dfsg-1 [216 kB] -Fetched 343 MB in 4s (82.5 MB/s) +Fetched 343 MB in 1min 32s (3716 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:i386. (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 ... 19231 files and directories currently installed.) @@ -1163,7 +1175,7 @@ fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/mira-4.9.6/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/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 dpkg-buildpackage: info: source package mira dpkg-buildpackage: info: source version 4.9.6-4 dpkg-buildpackage: info: source distribution unstable @@ -1242,8 +1254,8 @@ checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes -checking whether UID '1111' is supported by ustar format... yes -checking whether GID '1111' is supported by ustar format... yes +checking whether UID '2222' is supported by ustar format... yes +checking whether GID '2222' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking for a sed that does not truncate output... /bin/sed checking whether to add --prefix as include path... yes @@ -1605,7 +1617,7 @@ # see bug #812681 find -name '*.ll' | sed -e 's/[.]ll$/.cc/' | xargs rm dh_auto_build - make -j18 + make -j10 make[2]: Entering directory '/build/mira-4.9.6' make all-recursive make[3]: Entering directory '/build/mira-4.9.6' @@ -1628,8 +1640,8 @@ Making .H out of .xxd mira_ft_set.xxd.H Making .H out of .xxd gap4_ft_so_map.xxd.H Reducing so.obo for smaller so.obo.xxd -Making .H out of .xxd so2xgap4map.xxd.H Making .H out of .xxd oldso2so.xxd.H +Making .H out of .xxd so2xgap4map.xxd.H Making .H out of .xxd so.obo.xxd.H make all-am make[6]: Entering directory '/build/mira-4.9.6/src/io' @@ -1641,7 +1653,7 @@ 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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 cru libmirafio.a annotationmappings.o exp.o generalio.o fasta.o fastq-mira.o phd.o scf.o ncbiinfoxml.o exp_flexer.o @@ -1708,18 +1720,43 @@ 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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 -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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 -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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 -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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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_pbcorrect.C:59: warning: "CEBUG" redefined - #define CEBUG(bla) { if(docebug) {cout << bla; cout.flush();}} +hashstats.C:1088: warning: "CEBUG" redefined + #define CEBUG(bla) {cout << bla; cout.flush();} -assembly_pbcorrect.C:45: note: this is the location of the previous definition +hashstats.C:83: note: this is the location of the previous definition + #define CEBUG(bla) + +hashstats.C:1197: warning: "CEBUG" redefined #define CEBUG(bla) +hashstats.C:1088: note: this is the location of the previous definition + #define CEBUG(bla) {cout << bla; cout.flush();} + +read.C: In member function 'void Read::dumpAsReadname(std::ostream&)': +read.C:1242:23: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=] + sprintf(buffer, "%x", this) ; + ^~~~ +read.C: In member function 'void Read::dumpAsFASTA(std::ostream&, bool, bool, bool)': +read.C:1273:23: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=] + sprintf(buffer, "%x", this) ; + ^~~~ +read.C: In member function 'void Read::dumpAsFASTQ(std::ostream&, bool, bool, bool)': +read.C:1357:23: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=] + sprintf(buffer, "%x", this) ; + ^~~~ +read.C: In member function 'void Read::dumpAsFASTAQual(std::ostream&, bool, bool, bool)': +read.C:1458:23: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=] + sprintf(buffer, "%x", this) ; + ^~~~ +read.C: In member function 'void Read::dumpAsCAF(std::ostream&)': +read.C:1530:23: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=] + sprintf(buffer, "%x", this) ; + ^~~~ +read.C: In member function 'void Read::dumpAsMAF(std::ostream&)': +read.C:1945:23: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=] + sprintf(buffer, "%x", this) ; + ^~~~ +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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 assembly_buildcontigs.C:80: warning: "CEBUG" redefined #define CEBUG(bla) {cout << bla; cout.flush(); } @@ -1762,18 +1799,49 @@ assembly_buildcontigs.C:2043: note: this is the location of the previous definition #define VCOUT(bla) {if(verbose) {cout << bla;} } -hashstats.C:1088: warning: "CEBUG" redefined +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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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: warning: "CEBUG" redefined #define CEBUG(bla) {cout << bla; cout.flush();} -hashstats.C:83: note: this is the location of the previous definition +assembly_misc.C:55: note: this is the location of the previous definition #define CEBUG(bla) -hashstats.C:1197: warning: "CEBUG" redefined +assembly_misc.C:1905: warning: "CEBUG" redefined #define CEBUG(bla) -hashstats.C:1088: note: this is the location of the previous definition +assembly_misc.C:1871: note: this is the location of the previous definition #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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 +assembly_misc.C: In member function 'void Assembly::priv_phahelper(const string&, const string&, uint32, bool, int32, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string)': +assembly_misc.C:376:17: warning: use of an operand of type 'bool' in 'operator++' is deprecated [-Wdeprecated] + countedthisseq++; + ^~ +assembly_misc.C: In instantiation of 'void Assembly::priv_phahelper(const string&, const string&, uint32, bool, int32, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string) [with TVHASH_T = long long unsigned int; std::__cxx11::string = std::__cxx11::basic_string; uint32 = unsigned int; int32 = int]': +assembly_misc.C:471:118: required from here +assembly_misc.C:376:17: warning: use of an operand of type 'bool' in 'operator++' is deprecated [-Wdeprecated] + countedthisseq++; + ~~~~~~~~~~~~~~^~ +assembly_misc.C: In instantiation of 'void Assembly::priv_phahelper(const string&, const string&, uint32, bool, int32, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string) [with TVHASH_T = VLuint<128>; std::__cxx11::string = std::__cxx11::basic_string; uint32 = unsigned int; int32 = int]': +assembly_misc.C:473:119: required from here +assembly_misc.C:376:17: warning: use of an operand of type 'bool' in 'operator++' is deprecated [-Wdeprecated] +assembly_misc.C: In instantiation of 'void Assembly::priv_phahelper(const string&, const string&, uint32, bool, int32, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string) [with TVHASH_T = VLuint<256>; std::__cxx11::string = std::__cxx11::basic_string; uint32 = unsigned int; int32 = int]': +assembly_misc.C:475:119: required from here +assembly_misc.C:376:17: warning: use of an operand of type 'bool' in 'operator++' is deprecated [-Wdeprecated] +assembly_misc.C: In instantiation of 'void Assembly::priv_phahelper(const string&, const string&, uint32, bool, int32, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string) [with TVHASH_T = VLuint<512>; std::__cxx11::string = std::__cxx11::basic_string; uint32 = unsigned int; int32 = int]': +assembly_misc.C:477:119: required from here +assembly_misc.C:376:17: warning: use of an operand of type 'bool' in 'operator++' is deprecated [-Wdeprecated] +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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 +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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 +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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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_pbcorrect.C:59: warning: "CEBUG" redefined + #define CEBUG(bla) { if(docebug) {cout << bla; cout.flush();}} + +assembly_pbcorrect.C:45: note: this is the location of the previous definition + #define CEBUG(bla) + +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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 assembly_reduceskimhits.C:1111: warning: "CEBUG" redefined #define CEBUG(bla) {cout << bla; cout.flush();} @@ -1822,75 +1890,17 @@ assembly_reduceskimhits.C:2808: note: this is the location of the previous definition #define CEBUG(bla) {cout << bla; cout.flush();} -assembly_misc.C:1871: warning: "CEBUG" redefined - #define CEBUG(bla) {cout << bla; cout.flush();} - -assembly_misc.C:55: note: this is the location of the previous definition - #define CEBUG(bla) - -assembly_misc.C:1905: warning: "CEBUG" redefined - #define CEBUG(bla) - -assembly_misc.C:1871: note: this is the location of the previous definition - #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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 -read.C: In member function 'void Read::dumpAsReadname(std::ostream&)': -read.C:1242:23: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=] - sprintf(buffer, "%x", this) ; - ^~~~ -read.C: In member function 'void Read::dumpAsFASTA(std::ostream&, bool, bool, bool)': -read.C:1273:23: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=] - sprintf(buffer, "%x", this) ; - ^~~~ -read.C: In member function 'void Read::dumpAsFASTQ(std::ostream&, bool, bool, bool)': -read.C:1357:23: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=] - sprintf(buffer, "%x", this) ; - ^~~~ -read.C: In member function 'void Read::dumpAsFASTAQual(std::ostream&, bool, bool, bool)': -read.C:1458:23: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=] - sprintf(buffer, "%x", this) ; - ^~~~ -read.C: In member function 'void Read::dumpAsCAF(std::ostream&)': -read.C:1530:23: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=] - sprintf(buffer, "%x", this) ; - ^~~~ -read.C: In member function 'void Read::dumpAsMAF(std::ostream&)': -read.C:1945:23: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'Read*' [-Wformat=] - sprintf(buffer, "%x", this) ; - ^~~~ -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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 -assembly_misc.C: In member function 'void Assembly::priv_phahelper(const string&, const string&, uint32, bool, int32, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string)': -assembly_misc.C:376:17: warning: use of an operand of type 'bool' in 'operator++' is deprecated [-Wdeprecated] - countedthisseq++; - ^~ -assembly_misc.C: In instantiation of 'void Assembly::priv_phahelper(const string&, const string&, uint32, bool, int32, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string) [with TVHASH_T = long long unsigned int; std::__cxx11::string = std::__cxx11::basic_string; uint32 = unsigned int; int32 = int]': -assembly_misc.C:471:118: required from here -assembly_misc.C:376:17: warning: use of an operand of type 'bool' in 'operator++' is deprecated [-Wdeprecated] - countedthisseq++; - ~~~~~~~~~~~~~~^~ -assembly_misc.C: In instantiation of 'void Assembly::priv_phahelper(const string&, const string&, uint32, bool, int32, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string) [with TVHASH_T = VLuint<128>; std::__cxx11::string = std::__cxx11::basic_string; uint32 = unsigned int; int32 = int]': -assembly_misc.C:473:119: required from here -assembly_misc.C:376:17: warning: use of an operand of type 'bool' in 'operator++' is deprecated [-Wdeprecated] -assembly_misc.C: In instantiation of 'void Assembly::priv_phahelper(const string&, const string&, uint32, bool, int32, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string) [with TVHASH_T = VLuint<256>; std::__cxx11::string = std::__cxx11::basic_string; uint32 = unsigned int; int32 = int]': -assembly_misc.C:475:119: required from here -assembly_misc.C:376:17: warning: use of an operand of type 'bool' in 'operator++' is deprecated [-Wdeprecated] -assembly_misc.C: In instantiation of 'void Assembly::priv_phahelper(const string&, const string&, uint32, bool, int32, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string) [with TVHASH_T = VLuint<512>; std::__cxx11::string = std::__cxx11::basic_string; uint32 = unsigned int; int32 = int]': -assembly_misc.C:477:119: required from here -assembly_misc.C:376:17: warning: use of an operand of type 'bool' in 'operator++' is deprecated [-Wdeprecated] 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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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: warning: "CEBUGF2" redefined #define CEBUGF2 contig_featureinfo.C:473: note: this is the location of the previous definition #define CEBUGF2(bla) -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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 -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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 contig_pairconsistency.C:313: warning: "CEBUG" redefined #define CEBUG(bla) @@ -1909,12 +1919,14 @@ contig_pairconsistency.C:315: note: this is the location of the previous definition #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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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_save.o gff_save.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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 +/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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 @@ -1937,9 +1949,9 @@ 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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 cru libmiraestass.a estassembly.o +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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 ar: `u' modifier ignored since `D' is the default (see `U') 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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 rm -f libmira.a ar cru libmira.a hashstats_sdbg.o hashstats.o skim.o assembly.o contig.o read.o contig_analysis.o ads.o adsfacts.o align.o assembly_info.o assembly_buildcontigs.o assembly_io.o assembly_misc.o assembly_output.o assembly_pbcorrect.o assembly_reduceskimhits.o assembly_swalign.o contig_consensus.o contig_covanalysis.o contig_edit.o contig_featureinfo.o contig_output.o contig_pairconsistency.o dataprocessing.o dynamic.o gbf_parse.o gff_parse.o gff_save.o maf_parse.o manifest.o multitag.o parameters_flexer.o parameters.o pcrcontainer.o ppathfinder.o preventinitfiasco.o readgrouplib.o readlotstat.o readpool.o readpool_io.o sam_collect.o scaffolder.o seqtohash.o simplebloomfilter.o skim_lowbph.o warnings.o ar: `u' modifier ignored since `D' is the default (see `U') @@ -1949,7 +1961,7 @@ Making all in caf make[5]: Entering directory '/build/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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 rm -f libmiracaf.a ar cru libmiracaf.a caf.o caf_flexer.o @@ -1999,7 +2011,7 @@ ar cru libmemorc.a memorc.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libmemorc.a -/bin/bash ../../libtool --tag=CXX --mode=link g++ -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 -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/i386-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/mira-4.9.6/src/memorc' Making all in modules @@ -2056,9 +2068,9 @@ 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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 miratest.o miratest.C 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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-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++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 -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/i386-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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-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++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 -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/i386-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/mira-4.9.6/src/progs' make[5]: Leaving directory '/build/mira-4.9.6/src/progs' @@ -2098,14 +2110,14 @@ debian/rules override_dh_auto_build-indep make[1]: Entering directory '/build/mira-4.9.6' dh_auto_build --sourcedir=doc - cd doc && make -j18 "INSTALL=install --strip-program=true" + cd doc && make -j10 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/mira-4.9.6/doc' Making all in docbook make[3]: Entering directory '/build/mira-4.9.6/doc/docbook' Making versionfile Making .html out of _part.xml chap_bitsandpieces_part.html -Making .html out of _part.xml chap_est_part.html Making .html out of _part.xml chap_mirautils_part.html +Making .html out of _part.xml chap_est_part.html Making .html out of _part.xml chap_faq_part.html Making .html out of _part.xml chap_hard_part.html Making .html out of _part.xml chap_logfiles_part.html @@ -2114,15 +2126,6 @@ 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 -xsltproc --nonet --xinclude --output DefinitiveGuideToMIRA.html ../../doc/docbook/book.xsl ../../doc/docbook/book_definitiveguide.xml -xsltproc --nonet --xinclude --output 3rdparty_MIRA.html ../../doc/docbook/book.xsl ../../doc/docbook/book_3rdparty.xml -dblatex --xslt-opts=--nonet --output=DefinitiveGuideToMIRA.pdf ../../doc/docbook/book_definitiveguide.xml -Build the book set list... -dblatex --xslt-opts=--nonet --output=3rdparty_MIRA.pdf ../../doc/docbook/book_3rdparty.xml 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. @@ -2147,8 +2150,17 @@ 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". -Build the book set list... +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 Element emph in namespace '' encountered in note, but no template matches. +Making .html out of _part.xml chap_preface_part.html +xsltproc --nonet --xinclude --output DefinitiveGuideToMIRA.html ../../doc/docbook/book.xsl ../../doc/docbook/book_definitiveguide.xml +xsltproc --nonet --xinclude --output 3rdparty_MIRA.html ../../doc/docbook/book.xsl ../../doc/docbook/book_3rdparty.xml +dblatex --xslt-opts=--nonet --output=DefinitiveGuideToMIRA.pdf ../../doc/docbook/book_definitiveguide.xml +dblatex --xslt-opts=--nonet --output=3rdparty_MIRA.pdf ../../doc/docbook/book_3rdparty.xml +Build the book set list... +Build the book set list... Build the listings... XSLT stylesheets DocBook - LaTeX 2e (0.3.10) =================================================== @@ -2156,9 +2168,9 @@ No template matches year in copyright. No template matches holder in copyright. Build book_3rdparty.pdf -'3rdparty_MIRA.pdf' successfully built Element emph in namespace '' encountered in note, but no template matches. Build the listings... +'3rdparty_MIRA.pdf' successfully built XSLT stylesheets DocBook - LaTeX 2e (0.3.10) =================================================== No template matches copyright in chapterinfo. @@ -2415,9 +2427,9 @@ make[6]: Entering directory '/build/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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-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++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 -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/i386-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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-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++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 -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/i386-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/mira-4.9.6/src/progs' make[5]: Leaving directory '/build/mira-4.9.6/src/progs' @@ -2579,14 +2591,14 @@ make[6]: Entering directory '/build/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 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -D_FILE_OFFSET_BITS=64 -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-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++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 -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/i386-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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-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/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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/i386-linux-gnu -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/i386-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++ -pthread -I/usr/include -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/build/mira-4.9.6=. -fstack-protector-strong -Wformat -Werror=format-security -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 -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/i386-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/mira-4.9.6/src/progs' Making .C out of .xxd compileinfo.itxt /bin/mkdir -p '/build/mira-4.9.6/debian/mira-assembler/usr/bin' - /bin/bash ../../libtool --mode=install /usr/bin/install -c mira '/build/mira-4.9.6/debian/mira-assembler/usr/bin' + /bin/sh ../../libtool --mode=install /usr/bin/install -c mira '/build/mira-4.9.6/debian/mira-assembler/usr/bin' libtool: install: /usr/bin/install -c mira /build/mira-4.9.6/debian/mira-assembler/usr/bin/mira make install-exec-hook make[8]: Entering directory '/build/mira-4.9.6/src/progs' @@ -2702,114 +2714,114 @@ install -p -m0644 src/mira/CHANGES.txt debian/mira-doc/usr/share/doc/mira-doc/changelog make[1]: Leaving directory '/build/mira-4.9.6' dh_installman - man -l --recode UTF-8 ./debian/mira-assembler/usr/share/man/man1/miradiff.1 > debian/mira-assembler/usr/share/man/man1/miradiff.1.dh-new - man -l --recode UTF-8 ./debian/mira-assembler/usr/share/man/man1/mirabait.1 > debian/mira-assembler/usr/share/man/man1/mirabait.1.dh-new - man -l --recode UTF-8 ./debian/mira-assembler/usr/share/man/man1/miraconvert.1 > debian/mira-assembler/usr/share/man/man1/miraconvert.1.dh-new man -l --recode UTF-8 ./debian/mira-assembler/usr/share/man/man1/mira.1 > debian/mira-assembler/usr/share/man/man1/mira.1.dh-new - man -l --recode UTF-8 ./debian/mira-assembler/usr/share/man/man1/miramer.1 > debian/mira-assembler/usr/share/man/man1/miramer.1.dh-new + man -l --recode UTF-8 ./debian/mira-assembler/usr/share/man/man1/miraconvert.1 > debian/mira-assembler/usr/share/man/man1/miraconvert.1.dh-new man -l --recode UTF-8 ./debian/mira-assembler/usr/share/man/man1/miramem.1 > debian/mira-assembler/usr/share/man/man1/miramem.1.dh-new + man -l --recode UTF-8 ./debian/mira-assembler/usr/share/man/man1/mirabait.1 > debian/mira-assembler/usr/share/man/man1/mirabait.1.dh-new + man -l --recode UTF-8 ./debian/mira-assembler/usr/share/man/man1/miramer.1 > debian/mira-assembler/usr/share/man/man1/miramer.1.dh-new + man -l --recode UTF-8 ./debian/mira-assembler/usr/share/man/man1/miradiff.1 > debian/mira-assembler/usr/share/man/man1/miradiff.1.dh-new + 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/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/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/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/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/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/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/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/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 -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/miraconvert - ln -s mira debian/mira-assembler/usr/bin/miraconvert - 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/miramem + ln -s mira debian/mira-assembler/usr/bin/miramem + rm -f debian/mira-assembler/usr/bin/miraconvert + ln -s mira debian/mira-assembler/usr/bin/miraconvert + rm -f debian/mira-assembler/usr/bin/miramer + ln -s mira debian/mira-assembler/usr/bin/miramer dh_strip_nondeterminism Using 1537388009 as canonical time Normalizing debian/mira-rfam-12s-rrna/usr/share/mira/rfam_rrna-21-12.sls.gz using File::StripNondeterminism::handlers::gzip Using 1537388009 as canonical time - 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/sxa_sroc_lenski1.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/ion_dh10bdirdepindel.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/454_autoedit2.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/iontor_indelhpexample.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/ion_dh10bgoodB13.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_unsc_ggc3_lenski.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/srmc_in_454sxahyb_lastpass1.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/results_mira2other.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/gcb99_edit.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/454_stacks_join.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_xmastree_lenski1.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/gcb99_replocator.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_unsc_ggcxg1_lenski.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/pb_elasticdarkinserts04.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/images/warning.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/sxa_gcbias_comp20082009.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_gcbias_nobias2008.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_gcbias_bias2009.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/haf2_end_nomoredata.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_wrmcsrmc_hiding_lenski1.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_unsc_ggc4_lenski.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/sxa_unsc_ggc2_lenski.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/results_miraconvert.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/454_autoedit2.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_bias2009.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_xmastree_lenski2.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/ion_dh10bdirdepindel.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/454_stacks_join.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/san_autoedit1.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_sroc_lenski2.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/haf2_haf5_clearshortrepeat.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/srmc_in_454sxahyb_lastpass2.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/sxa_cer_reads1.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/haf5_haf2_contigcoverage.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/haf5_haf2_contigcoverage_ovals.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/sxa_xmastree_lenski1.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/haf_danger_join_notok.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/iontor_indelhpexample.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/srmc_in_454sxahyb_1stpass.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/images/warning.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_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/pb_elasticdarkinserts03.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/gcb99_replocator.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 dh_compress cd debian/mira-assembler - cd debian/mira-rfam-12s-rrna cd debian/mira-doc + cd debian/mira-rfam-12s-rrna 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-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-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-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/mira-4.9.6' cd '/build/mira-4.9.6' cd '/build/mira-4.9.6' dh_fixperms find debian/mira-assembler -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 - find debian/mira-rfam-12s-rrna -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/mira-doc -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 + find debian/mira-rfam-12s-rrna -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 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-assembler ! -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-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-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 d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/mira-rfam-12s-rrna -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/mira-doc/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 @@ -2819,12 +2831,12 @@ find debian/mira-assembler/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing dh_strip - install -d debian/.debhelper/mira-assembler/dbgsym-root/usr/lib/debug/.build-id/3a - objcopy --only-keep-debug --compress-debug-sections debian/mira-assembler/usr/bin/mira debian/.debhelper/mira-assembler/dbgsym-root/usr/lib/debug/.build-id/3a/0d1165fcdd189240b67fe9a7f815a922af0c65.debug - chmod 0644 -- debian/.debhelper/mira-assembler/dbgsym-root/usr/lib/debug/.build-id/3a/0d1165fcdd189240b67fe9a7f815a922af0c65.debug - chown 0:0 -- debian/.debhelper/mira-assembler/dbgsym-root/usr/lib/debug/.build-id/3a/0d1165fcdd189240b67fe9a7f815a922af0c65.debug + install -d debian/.debhelper/mira-assembler/dbgsym-root/usr/lib/debug/.build-id/c2 + objcopy --only-keep-debug --compress-debug-sections debian/mira-assembler/usr/bin/mira debian/.debhelper/mira-assembler/dbgsym-root/usr/lib/debug/.build-id/c2/e67943279f54d61104a429db5fb707c4ac38d9.debug + chmod 0644 -- debian/.debhelper/mira-assembler/dbgsym-root/usr/lib/debug/.build-id/c2/e67943279f54d61104a429db5fb707c4ac38d9.debug + chown 0:0 -- debian/.debhelper/mira-assembler/dbgsym-root/usr/lib/debug/.build-id/c2/e67943279f54d61104a429db5fb707c4ac38d9.debug strip --remove-section=.comment --remove-section=.note debian/mira-assembler/usr/bin/mira - objcopy --add-gnu-debuglink debian/.debhelper/mira-assembler/dbgsym-root/usr/lib/debug/.build-id/3a/0d1165fcdd189240b67fe9a7f815a922af0c65.debug debian/mira-assembler/usr/bin/mira + objcopy --add-gnu-debuglink debian/.debhelper/mira-assembler/dbgsym-root/usr/lib/debug/.build-id/c2/e67943279f54d61104a429db5fb707c4ac38d9.debug debian/mira-assembler/usr/bin/mira install -d debian/.debhelper/mira-assembler/dbgsym-root/usr/share/doc ln -s mira-assembler debian/.debhelper/mira-assembler/dbgsym-root/usr/share/doc/mira-assembler-dbgsym dh_makeshlibs @@ -2856,27 +2868,27 @@ echo misc:Depends= >> debian/mira-assembler.substvars echo misc:Pre-Depends= >> debian/mira-assembler.substvars install -d debian/.debhelper/mira-assembler/dbgsym-root/DEBIAN - dpkg-gencontrol -pmira-assembler -ldebian/changelog -Tdebian/mira-assembler.substvars -Pdebian/.debhelper/mira-assembler/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -DPackage=mira-assembler-dbgsym "-DDepends=mira-assembler (= \${binary:Version})" "-DDescription=debug symbols for mira-assembler" -DBuild-Ids=3a0d1165fcdd189240b67fe9a7f815a922af0c65 -DSection=debug -UMulti-Arch -UReplaces -UBreaks + dpkg-gencontrol -pmira-assembler -ldebian/changelog -Tdebian/mira-assembler.substvars -Pdebian/.debhelper/mira-assembler/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -DPackage=mira-assembler-dbgsym "-DDepends=mira-assembler (= \${binary:Version})" "-DDescription=debug symbols for mira-assembler" -DBuild-Ids=c2e67943279f54d61104a429db5fb707c4ac38d9 -DSection=debug -UMulti-Arch -UReplaces -UBreaks + chmod 0644 -- debian/.debhelper/mira-assembler/dbgsym-root/DEBIAN/control + chown 0:0 -- debian/.debhelper/mira-assembler/dbgsym-root/DEBIAN/control + dpkg-gencontrol -pmira-assembler -ldebian/changelog -Tdebian/mira-assembler.substvars -Pdebian/mira-assembler -UMulti-Arch chmod 0644 -- debian/mira-rfam-12s-rrna/DEBIAN/control chown 0:0 -- debian/mira-rfam-12s-rrna/DEBIAN/control chmod 0644 -- debian/mira-doc/DEBIAN/control chown 0:0 -- debian/mira-doc/DEBIAN/control - chmod 0644 -- debian/.debhelper/mira-assembler/dbgsym-root/DEBIAN/control - chown 0:0 -- debian/.debhelper/mira-assembler/dbgsym-root/DEBIAN/control - dpkg-gencontrol -pmira-assembler -ldebian/changelog -Tdebian/mira-assembler.substvars -Pdebian/mira-assembler -UMulti-Arch chmod 0644 -- debian/mira-assembler/DEBIAN/control chown 0:0 -- debian/mira-assembler/DEBIAN/control dh_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-assembler >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums - chmod 0644 -- debian/mira-doc/DEBIAN/md5sums - chown 0:0 -- debian/mira-doc/DEBIAN/md5sums chmod 0644 -- debian/mira-assembler/DEBIAN/md5sums chown 0:0 -- debian/mira-assembler/DEBIAN/md5sums - cd debian/.debhelper/mira-assembler/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/mira-rfam-12s-rrna/DEBIAN/md5sums chown 0:0 -- debian/mira-rfam-12s-rrna/DEBIAN/md5sums + cd debian/.debhelper/mira-assembler/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums + chmod 0644 -- debian/mira-doc/DEBIAN/md5sums + chown 0:0 -- debian/mira-doc/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/mira-assembler/dbgsym-root/DEBIAN/md5sums chown 0:0 -- debian/.debhelper/mira-assembler/dbgsym-root/DEBIAN/md5sums rm -f debian/mira-assembler.debhelper.log debian/mira-doc.debhelper.log debian/mira-rfam-12s-rrna.debhelper.log @@ -2887,10 +2899,10 @@ dpkg-deb -Z xz --build debian/.debhelper/mira-assembler/dbgsym-root .. dpkg-deb -Z xz --build debian/mira-rfam-12s-rrna .. dpkg-deb -Z xz --build debian/mira-doc .. -dpkg-deb: building package 'mira-rfam-12s-rrna' in '../mira-rfam-12s-rrna_4.9.6-4_all.deb'. dpkg-deb: building package 'mira-assembler' in '../mira-assembler_4.9.6-4_i386.deb'. -dpkg-deb: building package 'mira-doc' in '../mira-doc_4.9.6-4_all.deb'. dpkg-deb: building package 'mira-assembler-dbgsym' in '../mira-assembler-dbgsym_4.9.6-4_i386.deb'. +dpkg-deb: building package 'mira-doc' in '../mira-doc_4.9.6-4_all.deb'. +dpkg-deb: building package 'mira-rfam-12s-rrna' in '../mira-rfam-12s-rrna_4.9.6-4_all.deb'. make[1]: Leaving directory '/build/mira-4.9.6' dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../mira_4.9.6-4_i386.changes @@ -2898,12 +2910,14 @@ dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/30754/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/30754/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/41223 and its subdirectories -I: Current time: Sun May 30 15:48:41 -12 2021 -I: pbuilder-time-stamp: 1622432921 +I: removing directory /srv/workspace/pbuilder/30754 and its subdirectories +I: Current time: Tue Apr 28 11:52:26 +14 2020 +I: pbuilder-time-stamp: 1588024346