[Debian-med-packaging] Bug#1049789: mira: Fails to build binary packages again after successful build
Lucas Nussbaum
lucas at debian.org
Wed Aug 16 09:26:38 BST 2023
Source: mira
Version: 4.9.6-10
Severity: minor
Tags: trixie sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-binary-20230816 ftbfs-binary-after-build
User: debian-qa at lists.debian.org
Usertags: qa-doublebuild
Hi,
This package fails to do build a binary-only build (not source) after a
successful build (dpkg-buildpackage ; dpkg-buildpackage -b).
This is probably a clear violation of Debian Policy section 4.9 (clean target),
but this is filed as severity:minor for now, because a discussion on
debian-devel showed that we might want to revisit the requirement of a working
'clean' target.
More information about this class of issues, included common problems and
solutions, is available at
https://wiki.debian.org/qa.debian.org/FTBFS/DoubleBuild
Relevant part of the build log:
> cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -b
> ---------------------------------------------------------------------------------------------------------------
>
> dpkg-buildpackage: info: source package mira
> dpkg-buildpackage: info: source version 4.9.6-10
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Nilesh Patra <nilesh at debian.org>
> dpkg-source --before-build .
> dpkg-buildpackage: info: host architecture amd64
> debian/rules clean
> dh clean
> rm -f debian/mira-assembler.debhelper.log debian/mira-doc.debhelper.log debian/mira-rfam-12s-rrna.debhelper.log
> debian/rules override_dh_auto_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> ( cd doc ; make clean ) || true
> make[2]: Entering directory '/<<PKGBUILDDIR>>/doc'
> Making clean in docbook
> make[3]: Entering directory '/<<PKGBUILDDIR>>/doc/docbook'
> rm -rf .libs _libs
> rm -rf *html *pdf versionfile
> rm -f *.lo
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/doc/docbook'
> make[3]: Entering directory '/<<PKGBUILDDIR>>/doc'
> rm -rf .libs _libs
> rm -f *.lo
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/doc'
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/doc'
> dh_auto_clean || true
> make -j8 distclean
> make[2]: Entering directory '/<<PKGBUILDDIR>>'
> Making distclean in man
> make[3]: Entering directory '/<<PKGBUILDDIR>>/man'
> rm -rf .libs _libs
> rm -f *.lo
> test -z "" || rm -f
> test . = "." || test -z "" || rm -f
> rm -f Makefile
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/man'
> Making distclean in src
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
> Making distclean in debuggersupport
> make[4]: Entering directory '/<<PKGBUILDDIR>>/src/debuggersupport'
> rm -rf .libs _libs
> test -z "libmiradebuggersupport.a" || rm -f libmiradebuggersupport.a
> rm -f *.o
> rm -f *.lo
> rm -f *.tab.c
> test -z "" || rm -f
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f
> rm -f ./.deps/dbgsupport.Po
> rm -f Makefile
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/debuggersupport'
> Making distclean in io
> make[4]: Entering directory '/<<PKGBUILDDIR>>/src/io'
> rm -rf .libs _libs
> rm -rf *flexer.cc *xxd.H
> test -z "libmirafio.a" || rm -f libmirafio.a
> rm -f *.o
> rm -f *.lo
> rm -f *.tab.c
> test -z "" || rm -f
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f
> rm -f ./.deps/annotationmappings.Po
> rm -f ./.deps/exp.Po
> rm -f ./.deps/exp_flexer.Po
> rm -f ./.deps/fasta.Po
> rm -f ./.deps/fastq-mira.Po
> rm -f ./.deps/generalio.Po
> rm -f ./.deps/ncbiinfoxml.Po
> rm -f ./.deps/phd.Po
> rm -f ./.deps/scf.Po
> rm -f Makefile
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/io'
> Making distclean in stdinc
> make[4]: Entering directory '/<<PKGBUILDDIR>>/src/stdinc'
> rm -rf .libs _libs
> rm -f *.lo
> test -z "" || rm -f
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f
> rm -f Makefile
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/stdinc'
> Making distclean in errorhandling
> make[4]: Entering directory '/<<PKGBUILDDIR>>/src/errorhandling'
> rm -rf .libs _libs
> test -z "libmiraerrorhandling.a" || rm -f libmiraerrorhandling.a
> rm -f *.o
> rm -f *.lo
> rm -f *.tab.c
> test -z "" || rm -f
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f
> rm -f ./.deps/errorhandling.Po
> rm -f Makefile
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/errorhandling'
> Making distclean in util
> make[4]: Entering directory '/<<PKGBUILDDIR>>/src/util'
> rm -rf .libs _libs
> test -z "libmirautil.a libmiradptools.a libmirafmttext.a" || rm -f libmirautil.a libmiradptools.a libmirafmttext.a
> rm -f *.o
> rm -f *.lo
> rm -f *.tab.c
> test -z "" || rm -f
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f
> rm -f ./.deps/dptools.Po
> rm -f ./.deps/fileanddisk.Po
> rm -f ./.deps/fmttext.Po
> rm -f ./.deps/machineinfo.Po
> rm -f ./.deps/misc.Po
> rm -f Makefile
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/util'
> Making distclean in mira
> make[4]: Entering directory '/<<PKGBUILDDIR>>/src/mira'
> rm -rf .libs _libs
> rm -rf *flexer.cc *xxd.H
> test -z "libmiraestass.a libmira.a" || rm -f libmiraestass.a libmira.a
> rm -f *.o
> rm -f *.lo
> rm -f *.tab.c
> test -z "" || rm -f
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f
> rm -f ./.deps/ads.Po
> rm -f ./.deps/adsfacts.Po
> rm -f ./.deps/align.Po
> rm -f ./.deps/assembly.Po
> rm -f ./.deps/assembly_buildcontigs.Po
> rm -f ./.deps/assembly_info.Po
> rm -f ./.deps/assembly_io.Po
> rm -f ./.deps/assembly_misc.Po
> rm -f ./.deps/assembly_output.Po
> rm -f ./.deps/assembly_pbcorrect.Po
> rm -f ./.deps/assembly_reduceskimhits.Po
> rm -f ./.deps/assembly_swalign.Po
> rm -f ./.deps/contig.Po
> rm -f ./.deps/contig_analysis.Po
> rm -f ./.deps/contig_consensus.Po
> rm -f ./.deps/contig_covanalysis.Po
> rm -f ./.deps/contig_edit.Po
> rm -f ./.deps/contig_featureinfo.Po
> rm -f ./.deps/contig_output.Po
> rm -f ./.deps/contig_pairconsistency.Po
> rm -f ./.deps/dataprocessing.Po
> rm -f ./.deps/dynamic.Po
> rm -f ./.deps/estassembly.Po
> rm -f ./.deps/gbf_parse.Po
> rm -f ./.deps/gff_parse.Po
> rm -f ./.deps/gff_save.Po
> rm -f ./.deps/hashstats.Po
> rm -f ./.deps/hashstats_sdbg.Po
> rm -f ./.deps/maf_parse.Po
> rm -f ./.deps/manifest.Po
> rm -f ./.deps/multitag.Po
> rm -f ./.deps/parameters.Po
> rm -f ./.deps/parameters_flexer.Po
> rm -f ./.deps/pcrcontainer.Po
> rm -f ./.deps/ppathfinder.Po
> rm -f ./.deps/preventinitfiasco.Po
> rm -f ./.deps/read.Po
> rm -f ./.deps/readgrouplib.Po
> rm -f ./.deps/readlotstat.Po
> rm -f ./.deps/readpool.Po
> rm -f ./.deps/readpool_io.Po
> rm -f ./.deps/sam_collect.Po
> rm -f ./.deps/scaffolder.Po
> rm -f ./.deps/seqtohash.Po
> rm -f ./.deps/simplebloomfilter.Po
> rm -f ./.deps/skim.Po
> rm -f ./.deps/skim_lowbph.Po
> rm -f ./.deps/warnings.Po
> rm -f Makefile
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/mira'
> Making distclean in caf
> make[4]: Entering directory '/<<PKGBUILDDIR>>/src/caf'
> rm -rf .libs _libs
> rm -rf *flexer.cc
> test -z "libmiracaf.a" || rm -f libmiracaf.a
> rm -f *.o
> rm -f *.lo
> rm -f *.tab.c
> test -z "" || rm -f
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f
> rm -f ./.deps/caf.Po
> rm -f ./.deps/caf_flexer.Po
> rm -f Makefile
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/caf'
> Making distclean in memorc
> make[4]: Entering directory '/<<PKGBUILDDIR>>/src/memorc'
> rm -rf .libs _libs
> test -z "libmemorc.a" || rm -f libmemorc.a
> rm -f *.o
> rm -f *.lo
> rm -f main
> rm -f *.tab.c
> test -z "" || rm -f
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f
> rm -f ./.deps/main.Po
> rm -f ./.deps/memorc.Po
> rm -f Makefile
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/memorc'
> Making distclean in modules
> make[4]: Entering directory '/<<PKGBUILDDIR>>/src/modules'
> rm -rf .libs _libs
> test -z "libmiramodules.a" || rm -f libmiramodules.a
> rm -f *.o
> rm -f *.lo
> rm -f *.tab.c
> test -z "" || rm -f
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f
> rm -f ./.deps/misc.Po
> rm -f ./.deps/mod_bait.Po
> rm -f ./.deps/mod_convert.Po
> rm -f ./.deps/mod_dbgreplay.Po
> rm -f ./.deps/mod_diff.Po
> rm -f ./.deps/mod_memestim.Po
> rm -f ./.deps/mod_mer.Po
> rm -f ./.deps/mod_mira.Po
> rm -f ./.deps/mod_scaffold.Po
> rm -f ./.deps/mod_sigconex.Po
> rm -f ./.deps/mod_tagsnp.Po
> rm -f Makefile
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/modules'
> Making distclean in support
> make[4]: Entering directory '/<<PKGBUILDDIR>>/src/support'
> rm -rf .libs _libs
> rm -f *.lo
> test -z "" || rm -f
> test . = "." || test -z "" || rm -f
> rm -f Makefile
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/support'
> Making distclean in scripts
> make[4]: Entering directory '/<<PKGBUILDDIR>>/src/scripts'
> rm -rf .libs _libs
> rm -f *.lo
> test -z "" || rm -f
> test . = "." || test -z "" || rm -f
> rm -f Makefile
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/scripts'
> Making distclean in version
> make[4]: Entering directory '/<<PKGBUILDDIR>>/src/version'
> rm -rf .libs _libs
> test -z "libmiraversion.a" || rm -f libmiraversion.a
> rm -f *.o
> rm -f *.lo
> rm -f *.tab.c
> test -z "" || rm -f
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f
> rm -f ./.deps/mversion.Po
> rm -f Makefile
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/version'
> Making distclean in progs
> make[4]: Entering directory '/<<PKGBUILDDIR>>/src/progs'
> rm -rf .libs _libs
> rm -f mira
> rm -f *.o
> rm -f miratest
> rm -f *.lo
> rm -f *.tab.c
> test -z "" || rm -f
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f
> rm -f ./.deps/compileinfo.itxt.xxd.Po
> rm -f ./.deps/mira.Po
> rm -f ./.deps/miratest.Po
> rm -f ./.deps/quirks.Po
> rm -f Makefile
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/progs'
> Making distclean in other
> make[4]: Entering directory '/<<PKGBUILDDIR>>/src/other'
> Making distclean in sls
> make[5]: Entering directory '/<<PKGBUILDDIR>>/src/other/sls'
> Making distclean in mira-createsls
> make[6]: Entering directory '/<<PKGBUILDDIR>>/src/other/sls/mira-createsls'
> Making distclean in bin
> make[7]: Entering directory '/<<PKGBUILDDIR>>/src/other/sls/mira-createsls/bin'
> rm -rf .libs _libs
> rm -f *.lo
> test -z "" || rm -f
> test . = "." || test -z "" || rm -f
> rm -f Makefile
> make[7]: Leaving directory '/<<PKGBUILDDIR>>/src/other/sls/mira-createsls/bin'
> make[7]: Entering directory '/<<PKGBUILDDIR>>/src/other/sls/mira-createsls'
> rm -rf .libs _libs
> rm -f *.lo
> test -z "" || rm -f
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f
> make[7]: Leaving directory '/<<PKGBUILDDIR>>/src/other/sls/mira-createsls'
> rm -f Makefile
> make[6]: Leaving directory '/<<PKGBUILDDIR>>/src/other/sls/mira-createsls'
> make[6]: Entering directory '/<<PKGBUILDDIR>>/src/other/sls'
> rm -rf .libs _libs
> rm -f *.lo
> test -z "" || rm -f
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f
> make[6]: Leaving directory '/<<PKGBUILDDIR>>/src/other/sls'
> rm -f Makefile
> make[5]: Leaving directory '/<<PKGBUILDDIR>>/src/other/sls'
> make[5]: Entering directory '/<<PKGBUILDDIR>>/src/other'
> rm -rf .libs _libs
> rm -f *.lo
> test -z "" || rm -f
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f
> make[5]: Leaving directory '/<<PKGBUILDDIR>>/src/other'
> rm -f Makefile
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/other'
> make[4]: Entering directory '/<<PKGBUILDDIR>>/src'
> rm -rf .libs _libs
> rm -f *.lo
> test -z "" || rm -f
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/src'
> rm -f Makefile
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
> make[3]: Entering directory '/<<PKGBUILDDIR>>'
> rm -rf .libs _libs
> find . -name "*~" -exec rm -rf {} \;
> rm -f *.lo
> test -z "" || rm -f
> rm -f libtool config.lt
> test . = "." || test -z "" || rm -f
> find . -name ".pure" -exec rm -rf {} \;
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> rm -f cscope.out cscope.in.out cscope.po.out cscope.files
> find . -name "*.o" -exec rm {} \;
> find . -name "*.a" -exec rm {} \;
> find . -name "bla_*" -exec rm {} \;
> find . -name "bin.*" -exec rm {} \;
> find . -name "log.*" -exec rm {} \;
> find . -name "*.bak" -exec rm {} \;
> find . -name "ttt*" -exec rm {} \;
> find . -name "TTT*" -exec rm {} \;
> find . -name "core" -exec rm {} \;
> find . -name "*.flex.C" -exec rm {} \;
> find . -name "*flexer.cc" -exec rm {} \;
> find . -type d -name "*.dSYM" -exec rm -rf {} \;
> make -C distribution clean
> find . -name ".deps" -exec rm -rf {} \;
> make[4]: Entering directory '/<<PKGBUILDDIR>>'
> make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
> rm -rf mira_`../build-aux/git-version-gen isshort ../.tarball-version`_linux-gnu_x86_64_dynamic *.tar *.gz
> rm -rf OSXstatlibs OSXstatlibs_bach
> rm -rf m4
> rm -rf Makefile Makefile.in aclocal.m4 config.status config.h config.h.in config.log configure autom4te.cache config.guess config.sub missing libtool
> rm -rf config
> rm -rf mira_*
> rm -rf 3rdparty*
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/distribution'
> make -C doc clean
> make[4]: Entering directory '/<<PKGBUILDDIR>>'
> make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
> cd .. && make am--refresh
> make[5]: Entering directory '/<<PKGBUILDDIR>>'
> make[5]: *** No rule to make target 'am--refresh'. Stop.
> make[5]: Leaving directory '/<<PKGBUILDDIR>>'
> make[4]: *** [Makefile:366: ../aclocal.m4] Error 2
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/doc'
> make[3]: *** [Makefile:887: clean-local] Error 2
> make[3]: Leaving directory '/<<PKGBUILDDIR>>'
> make[2]: *** [Makefile:416: distclean-recursive] Error 1
> make[2]: Leaving directory '/<<PKGBUILDDIR>>'
> dh_auto_clean: error: make -j8 distclean returned exit code 2
> find * -name Makefile -exec rm '{}' ';'
> find * -name '*.xxd.H' -exec rm '{}' ';'
> find * -name '*.par.H' -exec rm '{}' ';'
> find * -name 'compileinfo.*' -exec rm '{}' ';'
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> dh_autoreconf_clean
> rm -f -- ./install-sh ./m4/ltsugar.m4 ./m4/lt\~obsolete.m4 ./m4/ltversion.m4 ./m4/libtool.m4 ./m4/ltoptions.m4 ./aclocal.m4 ./INSTALL ./autom4te.cache/requests ./autom4te.cache/traces.2 ./autom4te.cache/output.2 ./autom4te.cache/output.3 ./autom4te.cache/output.1 ./autom4te.cache/traces.1 ./autom4te.cache/traces.3 ./autom4te.cache/output.0 ./autom4te.cache/traces.0 ./Makefile.in ./compile ./ltmain.sh ./man/Makefile.in ./configure ./src/memorc/Makefile.in ./src/version/Makefile.in ./src/progs/Makefile.in ./src/caf/Makefile.in ./src/io/Makefile.in ./src/Makefile.in ./src/support/Makefile.in ./src/modules/Makefile.in ./src/errorhandling/Makefile.in ./src/other/sls/Makefile.in ./src/other/sls/mira-createsls/Makefile.in ./src/other/sls/mira-createsls/bin/Makefile.in ./src/other/Makefile.in ./src/scripts/Makefile.in
> ./src/stdinc/Makefile.in ./src/debuggersupport/Makefile.in ./src/mira/Makefile.in ./src/util/Makefile.in ./mkinstalldirs ./distribution/Makefile.in ./depcomp ./configure\~ ./doc/docbook/Makefile.in ./doc/Makefile.in ./ylwrap ./missing
> rm -f debian/autoreconf.before debian/autoreconf.after
> dh_clean
> rm -f debian/debhelper-build-stamp
> cp -an --reflink=auto debian/.debhelper/bucket/files/9be3de218833c076786b919dc34aab691611f4cd73316e7705f2673e2c41921b debian/.debhelper/bucket/files/9be3de218833c076786b919dc34aab691611f4cd73316e7705f2673e2c41921b.tmp
> mv debian/.debhelper/bucket/files/9be3de218833c076786b919dc34aab691611f4cd73316e7705f2673e2c41921b.tmp config.guess
> cp -an --reflink=auto debian/.debhelper/bucket/files/e308ae7f7f524bd790f8d4457c7c0a30f8403ffff4dd0b7d4388daca24275db4 debian/.debhelper/bucket/files/e308ae7f7f524bd790f8d4457c7c0a30f8403ffff4dd0b7d4388daca24275db4.tmp
> mv debian/.debhelper/bucket/files/e308ae7f7f524bd790f8d4457c7c0a30f8403ffff4dd0b7d4388daca24275db4.tmp config.sub
> rm -f debian/.debhelper/bucket/index
> rm -rf debian/.debhelper/
> rm -f -- debian/mira-assembler.substvars debian/mira-rfam-12s-rrna.substvars debian/mira-doc.substvars ./src/io/so.obo.xxd debian/files
> rm -fr -- debian/mira-assembler/ debian/tmp/ debian/mira-rfam-12s-rrna/ debian/mira-doc/
> find . \( \( \
> \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
> \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
> -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
> -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
> -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
> \) -exec rm -f {} + \) -o \
> \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
> debian/rules binary
> dh binary
> dh_update_autotools_config
> cp -an --reflink=auto config.guess debian/.debhelper/bucket/files/9be3de218833c076786b919dc34aab691611f4cd73316e7705f2673e2c41921b.tmp
> mv debian/.debhelper/bucket/files/9be3de218833c076786b919dc34aab691611f4cd73316e7705f2673e2c41921b.tmp debian/.debhelper/bucket/files/9be3de218833c076786b919dc34aab691611f4cd73316e7705f2673e2c41921b
> cp -f /usr/share/misc/config.guess ./config.guess
> cp -an --reflink=auto config.sub debian/.debhelper/bucket/files/e308ae7f7f524bd790f8d4457c7c0a30f8403ffff4dd0b7d4388daca24275db4.tmp
> mv debian/.debhelper/bucket/files/e308ae7f7f524bd790f8d4457c7c0a30f8403ffff4dd0b7d4388daca24275db4.tmp debian/.debhelper/bucket/files/e308ae7f7f524bd790f8d4457c7c0a30f8403ffff4dd0b7d4388daca24275db4
> cp -f /usr/share/misc/config.sub ./config.sub
> dh_autoreconf
> find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p
> " > debian/autoreconf.before
> grep -q ^XDT_ configure.ac
> autoreconf -f -i
> aclocal: warning: couldn't open directory 'm4': No such file or directory
> libtoolize: putting auxiliary files in '.'.
> libtoolize: copying file './ltmain.sh'
> libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'.
> libtoolize: copying file 'm4/libtool.m4'
> libtoolize: copying file 'm4/ltoptions.m4'
> libtoolize: copying file 'm4/ltsugar.m4'
> libtoolize: copying file 'm4/ltversion.m4'
> libtoolize: copying file 'm4/lt~obsolete.m4'
> configure.ac:38: warning: The macro `AC_HELP_STRING' is obsolete.
> configure.ac:38: You should run autoupdate.
> ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
> configure.ac:38: the top level
> configure.ac:46: warning: The macro `AC_HELP_STRING' is obsolete.
> configure.ac:46: You should run autoupdate.
> ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
> configure.ac:46: the top level
> configure.ac:190: warning: The macro `AC_HELP_STRING' is obsolete.
> configure.ac:190: You should run autoupdate.
> ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
> configure.ac:190: the top level
> configure.ac:328: warning: The macro `AC_TRY_COMPILE' is obsolete.
> configure.ac:328: You should run autoupdate.
> ./lib/autoconf/general.m4:2847: AC_TRY_COMPILE is expanded from...
> configure.ac:328: the top level
> configure.ac:419: warning: The macro `AC_HELP_STRING' is obsolete.
> configure.ac:419: You should run autoupdate.
> ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
> configure.ac:419: the top level
> configure.ac:423: warning: The macro `AC_HELP_STRING' is obsolete.
> configure.ac:423: You should run autoupdate.
> ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
> configure.ac:423: the top level
> configure.ac:663: warning: AC_PROG_LEX without either yywrap or noyywrap is obsolete
> ./lib/autoconf/programs.m4:716: _AC_PROG_LEX is expanded from...
> ./lib/autoconf/programs.m4:709: AC_PROG_LEX is expanded from...
> configure.ac:663: the top level
> configure.ac:670: warning: The macro `AC_HEADER_STDC' is obsolete.
> configure.ac:670: You should run autoupdate.
> ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from...
> configure.ac:670: the top level
> configure.ac:715: warning: The macro `AC_TRY_LINK' is obsolete.
> configure.ac:715: You should run autoupdate.
> ./lib/autoconf/general.m4:2920: AC_TRY_LINK is expanded from...
> lib/m4sugar/m4sh.m4:692: _AS_IF_ELSE is expanded from...
> lib/m4sugar/m4sh.m4:699: AS_IF is expanded from...
> ./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from...
> ./lib/autoconf/general.m4:2270: AC_CACHE_CHECK is expanded from...
> configure.ac:702: SUDO_FUNC_ISBLANK is expanded from...
> configure.ac:715: the top level
> configure.ac:1045: warning: The macro `AC_LANG_C' is obsolete.
> configure.ac:1045: You should run autoupdate.
> ./lib/autoconf/c.m4:72: AC_LANG_C is expanded from...
> configure.ac:1045: the top level
> configure.ac:1134: warning: The macro `AC_HELP_STRING' is obsolete.
> configure.ac:1134: You should run autoupdate.
> ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
> configure.ac:1134: the top level
> configure.ac:1143: warning: The macro `AC_HELP_STRING' is obsolete.
> configure.ac:1143: You should run autoupdate.
> ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
> configure.ac:1143: the top level
> configure.ac:1154: warning: The macro `AC_HELP_STRING' is obsolete.
> configure.ac:1154: You should run autoupdate.
> ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
> configure.ac:1154: the top level
> configure.ac:1197: warning: The macro `AC_HELP_STRING' is obsolete.
> configure.ac:1197: You should run autoupdate.
> ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
> configure.ac:1197: the top level
> configure.ac:1248: warning: The macro `AC_HELP_STRING' is obsolete.
> configure.ac:1248: You should run autoupdate.
> ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
> configure.ac:1248: the top level
> configure.ac:1347: warning: The macro `AC_HELP_STRING' is obsolete.
> configure.ac:1347: You should run autoupdate.
> ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
> configure.ac:1347: the top level
> configure.ac:1366: warning: The macro `AC_HELP_STRING' is obsolete.
> configure.ac:1366: You should run autoupdate.
> ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
> configure.ac:1366: the top level
> configure.ac:1383: warning: The macro `AC_HELP_STRING' is obsolete.
> configure.ac:1383: You should run autoupdate.
> ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
> configure.ac:1383: the top level
> configure.ac:1401: warning: The macro `AC_HELP_STRING' is obsolete.
> configure.ac:1401: You should run autoupdate.
> ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
> configure.ac:1401: the top level
> configure.ac:1417: warning: The macro `AC_HELP_STRING' is obsolete.
> configure.ac:1417: You should run autoupdate.
> ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
> configure.ac:1417: the top level
> configure.ac:1428: warning: The macro `AC_HELP_STRING' is obsolete.
> configure.ac:1428: You should run autoupdate.
> ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from...
> configure.ac:1428: the top level
> configure.ac:1466: warning: AC_OUTPUT should be used without arguments.
> configure.ac:1466: You should run autoupdate.
> configure.ac:103: installing './compile'
> configure.ac:9: installing './install-sh'
> configure.ac:9: installing './missing'
> Makefile.am: installing './INSTALL'
> doc/docbook/Makefile.am:22: warning: '%'-style pattern rules are a GNU make extension
> src/caf/Makefile.am: installing './depcomp'
> configure.ac: installing './ylwrap'
> src/io/Makefile.am:12: warning: '%'-style pattern rules are a GNU make extension
> src/mira/Makefile.am:10: warning: '%'-style pattern rules are a GNU make extension
> find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p
> " > debian/autoreconf.after
> debian/rules override_dh_auto_configure
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_auto_configure -- --with-boost-libdir=/usr/lib/x86_64-linux-gnu --with-boost=/usr
> ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-boost-libdir=/usr/lib/x86_64-linux-gnu --with-boost=/usr
> checking for a BSD-compatible install... /usr/bin/install -c
> checking whether build environment is sane... yes
> checking for a race-free mkdir -p... /bin/mkdir -p
> checking for gawk... no
> checking for mawk... mawk
> checking whether make sets $(MAKE)... yes
> checking whether make supports nested variables... yes
> checking whether UID '1001' is supported by ustar format... yes
> checking whether GID '1001' 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
>
> +++++++++++++++++++++++++++++++++++++
> systemuname: Linux
> CFLAGS now: -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include
> CXXFLAGS now: -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include
> LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib
> +++++++++++++++++++++++++++++++++++++
> checking for gcc... gcc
> checking whether the C compiler works... yes
> checking for C compiler default output file name... a.out
> checking for suffix of executables...
> checking whether we are cross compiling... no
> checking for suffix of object files... o
> checking whether the compiler supports GNU C... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to enable C11 features... none needed
> checking whether gcc understands -c and -o together... yes
> checking whether make supports the include directive... yes (GNU style)
> checking dependency style of gcc... none
> checking for g++... g++
> checking whether the compiler supports GNU C++... yes
> checking whether g++ accepts -g... yes
> checking for g++ option to enable C++11 features... none needed
> checking dependency style of g++... none
> checking for OpenMP flag of C compiler... -fopenmp
> Rescuing C++ flags for OpenMP
> +++++++++++++++++++++++++++++++++++++
> OpenMP CFLAGS: -fopenmp
> OpenMP CXXFLAGS: -fopenmp
> +++++++++++++++++++++++++++++++++++++
>
> +++++++++++++++++++++++++++++++++++++
> systemuname: Linux
> CFLAGS now: -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include
> CXXFLAGS now: -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include
> LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib
> +++++++++++++++++++++++++++++++++++++
> checking for stdio.h... yes
> checking for stdlib.h... yes
> checking for string.h... yes
> checking for inttypes.h... yes
> checking for stdint.h... yes
> checking for strings.h... yes
> checking for sys/stat.h... yes
> checking for sys/types.h... yes
> checking for unistd.h... yes
> checking for int64_t... yes
>
> +++++++++++++++++++++++++++++++++++++
> CFLAGS now: -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include
> CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include
> LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib
> +++++++++++++++++++++++++++++++++++++
> checking whether long has 64bit... yes
> checking whether enabling 64bit compilation support... yes
> checking build system type... x86_64-pc-linux-gnu
> checking for compiler optimisation settings... -O3 -funroll-loops
>
> +++++++++++++++++++++++++++++++++++++
> CFLAGS now: -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops
> CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops
> LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib
> +++++++++++++++++++++++++++++++++++++
> checking host system type... x86_64-pc-linux-gnu
> checking how to print strings... printf
> checking for a sed that does not truncate output... (cached) /bin/sed
> checking for grep that handles long lines and -e... /bin/grep
> checking for egrep... /bin/grep -E
> checking for fgrep... /bin/grep -F
> checking for ld used by gcc... /usr/bin/ld
> checking if the linker (/usr/bin/ld) is GNU ld... yes
> checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
> checking the name lister (/usr/bin/nm -B) interface... BSD nm
> checking whether ln -s works... yes
> checking the maximum length of command line arguments... 1572864
> checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
> checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop
> checking for /usr/bin/ld option to reload object files... -r
> checking for file... file
> checking for objdump... objdump
> checking how to recognize dependent libraries... pass_all
> checking for dlltool... no
> checking how to associate runtime and link libraries... printf %s\n
> checking for ar... ar
> checking for archiver @FILE support... @
> checking for strip... strip
> checking for ranlib... ranlib
> checking command to parse /usr/bin/nm -B output from gcc object... ok
> checking for sysroot... no
> checking for a working dd... /bin/dd
> checking how to truncate binary pipes... /bin/dd bs=4096 count=1
> checking for mt... no
> checking if : is a manifest tool... no
> checking for dlfcn.h... yes
> checking for objdir... .libs
> checking if gcc supports -fno-rtti -fno-exceptions... no
> checking for gcc option to produce PIC... -fPIC -DPIC
> checking if gcc PIC flag -fPIC -DPIC works... yes
> checking if gcc static flag -static works... yes
> checking if gcc supports -c -o file.o... yes
> checking if gcc supports -c -o file.o... (cached) yes
> checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
> checking whether -lc should be explicitly linked in... no
> checking dynamic linker characteristics... GNU/Linux ld.so
> checking how to hardcode library paths into programs... immediate
> checking whether stripping libraries is possible... yes
> checking if libtool supports shared libraries... yes
> checking whether to build shared libraries... yes
> checking whether to build static libraries... yes
> checking how to run the C++ preprocessor... g++ -E
> checking for ld used by g++... /usr/bin/ld -m elf_x86_64
> checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
> checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
> checking for g++ option to produce PIC... -fPIC -DPIC
> checking if g++ PIC flag -fPIC -DPIC works... yes
> checking if g++ static flag -static works... yes
> checking if g++ supports -c -o file.o... yes
> checking if g++ supports -c -o file.o... (cached) yes
> checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
> checking dynamic linker characteristics... (cached) GNU/Linux ld.so
> checking how to hardcode library paths into programs... immediate
> checking whether make sets $(MAKE)... (cached) yes
> checking whether ln -s works... yes
> checking for flex... yes
> checking for flex... flex
> checking for lex output file root... lex.yy
> checking for lex library... none needed
> checking for library containing yywrap... -ll
> checking whether yytext is a pointer... yes
> checking for flex++... yes
> checking for xxd... yes
> checking for egrep... (cached) /bin/grep -E
> checking for _Bool... yes
> checking for stdbool.h that conforms to C99... yes
> checking for an ANSI C-conforming const... yes
> checking for inline... inline
> checking for C/C++ restrict keyword... __restrict__
> checking whether struct tm is in sys/time.h or time.h... time.h
> checking for GNU libc compatible malloc... yes
> checking for GNU libc compatible realloc... yes
> checking whether lstat correctly handles trailing slash... yes
> checking whether stat accepts an empty string... no
> checking for strftime... yes
> checking for floor... no
> checking for memset... yes
> checking for pow... no
> checking for sqrt... no
> checking for special C compiler options needed for large files... no
> checking for _FILE_OFFSET_BITS value needed for large files... no
> checking for _LARGEFILE_SOURCE value needed for large files... no
> checking for isblank... yes
>
> +++++++++++++++++++++++++++++++++++++
> CFLAGS now: -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops
> CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops
> LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib
> +++++++++++++++++++++++++++++++++++++
> checking for boostlib >= 1.48.0 (104800) includes in "/usr/include"... yes
> checking for boostlib >= 1.48.0 (104800) lib path in "/usr/lib/x86_64-linux-gnu"... yes
> checking for boostlib >= 1.48.0 (104800)... yes
>
> +++++++++++++++++++++++++++++++++++++
> BOOST_CPPFLAGS: -I/usr/include
> BOOST LDFLAGS: -L/usr/lib/x86_64-linux-gnu
> ac_boost_path:
> ac_boost_lib_path:
> CFLAGS now: -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops
> CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops
> LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib
> +++++++++++++++++++++++++++++++++++++
>
> +++++++++++++++++++++++++++++++++++++
> BOOST_CPPFLAGS: -I/usr/include
> BOOST LDFLAGS: -L/usr/lib/x86_64-linux-gnu
> CFLAGS now: -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -Wl,-rpath,
> CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops
> LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib
> +++++++++++++++++++++++++++++++++++++
> checking whether the Boost::Thread library is available... yes
> checking for exit in -lboost_thread... yes
>
> +++++++++++++++++++++++++++++++++++++
> BOOST_CPPFLAGS: -pthread -I/usr/include
> BOOST LDFLAGS: -L/usr/lib/x86_64-linux-gnu
> ac_boost_path:
> ac_boost_lib_path:
> BOOST_THREAD_LIB: -lboost_thread -lpthread
> CFLAGS now: -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -Wl,-rpath,
> CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops
> LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib
> +++++++++++++++++++++++++++++++++++++
> +++++++++++++++++++++++++++++++++++++
> BOOST_CPPFLAGS: -pthread -I/usr/include
> BOOST LDFLAGS: -L/usr/lib/x86_64-linux-gnu
> ac_boost_path:
> ac_boost_lib_path:
> BOOST_THREAD_LIB: -lboost_thread -lpthread
>
> CFLAGS now: -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -Wl,-rpath,
> CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include
> LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/x86_64-linux-gnu
> LIBS now: -lboost_thread -lpthread
> +++++++++++++++++++++++++++++++++++++
> checking whether the Boost::Regex library is available... yes
> checking for exit in -lboost_regex... yes
> +++++++++++++++++++++++++++++++++++++
> BOOST_CPPFLAGS: -pthread -I/usr/include
> BOOST LDFLAGS: -L/usr/lib/x86_64-linux-gnu
> ac_boost_path:
> ac_boost_lib_path:
> BOOST_REGEX_LIB: -lboost_regex
>
> CFLAGS now: -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -Wl,-rpath,
> CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include
> LIBS now: -lboost_thread -lpthread -lboost_regex
> +++++++++++++++++++++++++++++++++++++
> checking whether the Boost::System library is available... yes
> checking for exit in -lboost_system... yes
> +++++++++++++++++++++++++++++++++++++
> BOOST_CPPFLAGS: -pthread -I/usr/include
> BOOST LDFLAGS: -L/usr/lib/x86_64-linux-gnu
> ac_boost_path:
> ac_boost_lib_path:
> BOOST_SYSTEM_LIB: -lboost_system
>
> CFLAGS now: -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -Wl,-rpath,
> CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include
> LIBS now: -lboost_thread -lpthread -lboost_regex -lboost_system
> +++++++++++++++++++++++++++++++++++++
> checking whether the Boost::Filesystem library is available... yes
> checking for exit in -lboost_filesystem... yes
> +++++++++++++++++++++++++++++++++++++
> BOOST_CPPFLAGS: -pthread -I/usr/include
> BOOST LDFLAGS: -L/usr/lib/x86_64-linux-gnu
> ac_boost_path:
> ac_boost_lib_path:
> BOOST_FILESYSTEM_LIB: -lboost_filesystem
>
> CFLAGS now: -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -Wl,-rpath,
> CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include
> LIBS now: -lboost_thread -lpthread -lboost_regex -lboost_system -lboost_filesystem
> +++++++++++++++++++++++++++++++++++++
> checking whether the Boost::IOStreams library is available... yes
> checking for exit in -lboost_iostreams... yes
> +++++++++++++++++++++++++++++++++++++
> BOOST_CPPFLAGS: -pthread -I/usr/include
> BOOST LDFLAGS: -L/usr/lib/x86_64-linux-gnu
> ac_boost_path:
> ac_boost_lib_path:
> BOOST_IOSTREAMS_LIB: -lboost_iostreams
>
> CFLAGS now: -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -Wl,-rpath,
> CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include
> LIBS now: -lboost_thread -lpthread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams
> +++++++++++++++++++++++++++++++++++++
> checking for clock_gettime in -lrt... yes
> +++++++++++++++++++++++++++++++++++++
> Need to specifically use rt library
> LIBS now: -lboost_thread -lpthread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt
> +++++++++++++++++++++++++++++++++++++
> BOOST is through, yay.
> +++++++++++++++++++++++++++++++++++++
> CFLAGS now: -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops
> CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include
> LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/x86_64-linux-gnu
> LIBS now: -lboost_thread -lpthread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt
> +++++++++++++++++++++++++++++++++++++
> checking for Expat XML Parser headers in /usr/include... found
> checking for Expat XML Parser libraries... found
> checking for Expat XML Parser... yes
>
> +++++++++++++++++++++++++++++++++++++
> CFLAGS now: -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -I/usr/include
> CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include
> LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib
> LIBS now: -lboost_thread -lpthread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat
> +++++++++++++++++++++++++++++++++++++
> checking if zlib is wanted... yes
> checking for inflateEnd in -lz... yes
> checking for zlib.h... yes
>
> +++++++++++++++++++++++++++++++++++++
> CFLAGS now: -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -I/usr/include
> CXXFLAGS now: -DAJ_Linux64 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -pthread -I/usr/include -I/usr/include
> LDFLAGS now: -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib -L/usr/lib -L/usr/lib
> LIBS now: -lz -lboost_thread -lpthread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz
> +++++++++++++++++++++++++++++++++++++
> checking for gzoffset in -lz... yes
> checking for BZ2_bzRead in -lbz2... yes
> checking for flex version compatible with MIRA... yes
> checking for profiling settings... no
> checking for purify... no
> checking whether mira should compile in public quiet mode... yes
> checking whether mira should compile with bound tracking... yes
> checking whether mira should compile with bug tracking... yes
> checking whether mira should compile with extended bug tracking... no
> checking whether mira should compile with function trace... no
> checking that generated files are newer than configure... done
> configure: creating ./config.status
> config.status: creating Makefile
> config.status: creating src/Makefile
> config.status: creating src/other/Makefile
> config.status: creating src/other/sls/Makefile
> config.status: creating src/other/sls/mira-createsls/Makefile
> config.status: creating src/other/sls/mira-createsls/bin/Makefile
> config.status: creating src/stdinc/Makefile
> config.status: creating src/debuggersupport/Makefile
> config.status: creating src/memorc/Makefile
> config.status: creating src/errorhandling/Makefile
> config.status: creating src/util/Makefile
> config.status: creating src/io/Makefile
> config.status: creating src/mira/Makefile
> config.status: creating src/caf/Makefile
> config.status: creating src/support/Makefile
> config.status: creating src/scripts/Makefile
> config.status: creating src/modules/Makefile
> config.status: creating src/version/Makefile
> config.status: creating src/progs/Makefile
> config.status: creating man/Makefile
> config.status: creating doc/Makefile
> config.status: creating doc/docbook/Makefile
> config.status: creating distribution/Makefile
> config.status: executing depfiles commands
> config.status: executing libtool commands
>
> --------------------------------------------------------------------------------
> Summary of MIRA configuration
> --------------------------------------------------------------------------------
>
>
> Building version ................................. 4.9.6_linux-gnu_x86_64_dynamic
>
> We are building on ............................... Linux
> CPU supports 64 bit? ............................. yes
> Compiler family .................................. gcc
> Compiler optimisation flags used ................. -O3 -funroll-loops
> Do we compile in 64 bit? ......................... yes
> Building completely static? ...................... no
> BOOST expected to compile and link? .............. yes
> Have OpenMP? ..................................... yes
> Have complete zlib support? ...................... yes
>
> Can MIRA be built on this system? ................ yes
>
> Using CFLAGS : -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include -O3 -funroll-loops -I/usr/include -Werror=uninitialized -Werror=return-type -fopenmp
> Using CXXFLAGS : -DPUBLICQUIET -DAJ_Linux64 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
> Using LDFLAGS : -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib -L/usr/lib -L/usr/lib
> Using LIBS : -lz -lboost_thread -lpthread -lboost_regex -lboost_system -lboost_filesystem -lboost_iostreams -lrt -lexpat -lm -lz -lbz2
>
> Looks good, we do not expect compilation problems.
> --------------------------------------------------------------------------------
>
> Type 'make' to make the binaries
> and then 'make install' to install binaries and man pages.
> Type 'make docinstall' to install extensive documentation as HTML and PDF.
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> rm -f debian/mira-assembler.debhelper.log debian/mira-doc.debhelper.log debian/mira-rfam-12s-rrna.debhelper.log
> debian/rules override_dh_auto_build-arch
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> # some *.cc files are created by old flex version which breaks the build
> # see bug #812681
> find -name '*.ll' | sed -e 's/[.]ll$/.cc/' | xargs rm
> rm: cannot remove './src/caf/caf_flexer.cc': No such file or directory
> rm: cannot remove './src/io/exp_flexer.cc': No such file or directory
> rm: cannot remove './src/mira/parameters_flexer.cc': No such file or directory
> make[1]: *** [debian/rules:44: override_dh_auto_build-arch] Error 123
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> make: *** [debian/rules:17: binary] Error 2
> dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
>
> E: Command 'cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -b' failed to run.
The full build log is available from:
http://qa-logs.debian.net/2023/08/16/mira_4.9.6-10_unstable.log
If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.
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