Your message dated Tue, 06 Feb 2024 11:19:17 +0000
with message-id <[email protected]>
and subject line Bug#1049789: fixed in mira 4.9.6-11
has caused the Debian Bug report #1049789,
regarding mira: Fails to build binary packages again after successful build
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
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--
1049789: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1049789
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: mira
Version: 4.9.6-10
Severity: minor
Tags: trixie sid ftbfs
User: [email protected]
Usertags: ftbfs-binary-20230816 ftbfs-binary-after-build
User: [email protected]
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 <[email protected]>
> 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.
--- End Message ---
--- Begin Message ---
Source: mira
Source-Version: 4.9.6-11
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
mira, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated mira package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Tue, 06 Feb 2024 11:41:10 +0100
Source: mira
Architecture: source
Version: 4.9.6-11
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Closes: 1045311 1049789
Changes:
mira (4.9.6-11) unstable; urgency=medium
.
* Do not fail when attempting to remove not exiting files
Closes: #1049789
* Fix clean target
Closes: #1045311
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