[Debian-med-packaging] Bug#1049739: mrbayes: Fails to build binary packages again after successful build
Lucas Nussbaum
lucas at debian.org
Wed Aug 16 08:42:50 BST 2023
Source: mrbayes
Version: 3.2.7a-6
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 mrbayes
> dpkg-buildpackage: info: source version 3.2.7a-6
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Andreas Tille <tille at debian.org>
> dpkg-source --before-build .
> dpkg-buildpackage: info: host architecture amd64
> debian/rules clean
> dh clean
> dh_auto_clean
> make -j8 distclean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> Making distclean in src
> make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
> test -z "mb" || rm -f mb
> rm -f *.o
> rm -f *.tab.c
> test -z "" || rm -f
> rm -f config.h stamp-h1
> test . = "." || test -z "" || rm -f
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> rm -f ./.deps/mb-bayes.Po
> rm -f ./.deps/mb-best.Po
> rm -f ./.deps/mb-command.Po
> rm -f ./.deps/mb-likelihood.Po
> rm -f ./.deps/mb-mbbeagle.Po
> rm -f ./.deps/mb-mcmc.Po
> rm -f ./.deps/mb-model.Po
> rm -f ./.deps/mb-proposal.Po
> rm -f ./.deps/mb-sumpt.Po
> rm -f ./.deps/mb-utils.Po
> rm -f Makefile
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
> Making distclean in doc
> make[2]: Entering directory '/<<PKGBUILDDIR>>/doc'
> Making distclean in manual
> make[3]: Entering directory '/<<PKGBUILDDIR>>/doc/manual'
> test -z "Manual_MrBayes_v3.2.aux Manual_MrBayes_v3.2.bbl Manual_MrBayes_v3.2.blg Manual_MrBayes_v3.2.log Manual_MrBayes_v3.2.toc" || rm -f Manual_MrBayes_v3.2.aux Manual_MrBayes_v3.2.bbl Manual_MrBayes_v3.2.blg Manual_MrBayes_v3.2.log Manual_MrBayes_v3.2.toc
> test -z "" || rm -f
> test . = "." || test -z "" || rm -f
> test -z "Manual_MrBayes_v3.2.pdf" || rm -f Manual_MrBayes_v3.2.pdf
> rm -f Makefile
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/doc/manual'
> Making distclean in tutorial
> make[3]: Entering directory '/<<PKGBUILDDIR>>/doc/tutorial'
> test -z "MBDating.aux MBDating.bbl MBDating.blg MBDating.log MBDating.out" || rm -f MBDating.aux MBDating.bbl MBDating.blg MBDating.log MBDating.out
> test -z "" || rm -f
> test . = "." || test -z "" || rm -f
> test -z "MBDating.pdf" || rm -f MBDating.pdf
> rm -f Makefile
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/doc/tutorial'
> make[3]: Entering directory '/<<PKGBUILDDIR>>/doc'
> test -z "" || rm -f
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/doc'
> rm -f Makefile
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/doc'
> Making distclean in examples
> make[2]: Entering directory '/<<PKGBUILDDIR>>/examples'
> test -z "" || rm -f
> test . = "." || test -z "" || rm -f
> rm -f Makefile
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/examples'
> make[2]: Entering directory '/<<PKGBUILDDIR>>'
> test -z "" || rm -f
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f
> rm -f cscope.out cscope.in.out cscope.po.out cscope.files
> make[2]: Leaving directory '/<<PKGBUILDDIR>>'
> rm -f config.status config.cache config.log configure.lineno config.status.lineno
> rm -f Makefile
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> dh_autoreconf_clean
> dh_clean
> debian/rules binary
> dh binary
> dh_update_autotools_config
> dh_autoreconf
> configure.ac:112: installing 'am-aux/compile'
> configure.ac:10: installing 'am-aux/install-sh'
> configure.ac:10: installing 'am-aux/missing'
> src/Makefile.am: installing 'am-aux/depcomp'
> debian/rules override_dh_auto_configure
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_auto_configure -- --with-beagle=/usr --enable-mpi=yes --enable-debug=yes
> ./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-beagle=/usr --enable-mpi=yes --enable-debug=yes
> 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 to enable maintainer-specific portions of Makefiles... no
> checking build system type... x86_64-pc-linux-gnu
> checking host system type... x86_64-pc-linux-gnu
> checking for pkg-config... /usr/bin/pkg-config
> checking pkg-config is at least version 0.9.0... yes
> checking for pdflatex... no
> checking for bibtex... no
> configure: WARNING: pdflatex or bibtex is missing, documentation will not be rebuilt
> checking whether make supports the include directive... yes (GNU style)
> checking whether to compile using MPI... no
> 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... unsupported
> checking for gcc option to enable C99 features... none needed
> checking whether gcc understands -c and -o together... yes
> checking dependency style of gcc... none
> checking for sqrt in -lm... yes
> 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
> configure: Trying to locate Beagle (hmsbeagle-1) in '/usr'
> checking for libhmsbeagle/beagle.h... yes
> checking for beagleCreateInstance in -lhmsbeagle... yes
> configure: Found Beagle in '/usr'
> checking for beagleSetCPUThreadCount in -lhmsbeagle... yes
> configure: Using BEAGLE_CFLAGS="-I/usr/include/libhmsbeagle-1 -pthread"
> configure: Using BEAGLE_LIBS="-L/usr/lib -lhmsbeagle"
> checking for a readline compatible library... -lreadline
> checking for readline.h... no
> checking for readline/readline.h... yes
> checking whether readline supports history... yes
> checking for history.h... no
> checking for readline/history.h... yes
> checking for float.h... yes
> checking for limits.h... yes
> checking for memory.h... yes
> checking for stdlib.h... (cached) yes
> checking for string.h... (cached) yes
> checking for size_t... yes
> checking for _Bool... yes
> checking for stdbool.h that conforms to C99... yes
> checking for C compiler vendor... gnu
> checking for a sed that does not truncate output... /bin/sed
> checking for C compiler version... 13.2.0
> checking CFLAGS for most reasonable warnings... -Wall
> checking for floor... yes
> checking for memset... yes
> checking for pow... yes
> checking for sqrt... yes
> checking for strchr... yes
> checking that generated files are newer than configure... done
> configure: creating ./config.status
> config.status: creating Makefile
> config.status: creating doc/Makefile
> config.status: creating doc/manual/Makefile
> config.status: creating doc/tutorial/Makefile
> config.status: creating examples/Makefile
> config.status: creating src/Makefile
> config.status: creating src/config.h
> config.status: executing depfiles commands
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> debian/rules override_dh_auto_build
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> # build mb-mpi (from initial config)
> LIBS="-Wl,--as-needed" dh_auto_build
> make -j8
> make[2]: Entering directory '/<<PKGBUILDDIR>>'
> Making all in src
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
> make all-am
> make[4]: Entering directory '/<<PKGBUILDDIR>>/src'
> gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-bayes.o `test -f 'bayes.c' || echo './'`bayes.c
> gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-best.o `test -f 'best.c' || echo './'`best.c
> gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-command.o `test -f 'command.c' || echo './'`command.c
> gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-likelihood.o `test -f 'likelihood.c' || echo './'`likelihood.c
> gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-mbbeagle.o `test -f 'mbbeagle.c' || echo './'`mbbeagle.c
> gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-mcmc.o `test -f 'mcmc.c' || echo './'`mcmc.c
> gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-model.o `test -f 'model.c' || echo './'`model.c
> gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-proposal.o `test -f 'proposal.c' || echo './'`proposal.c
> gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-sumpt.o `test -f 'sumpt.c' || echo './'`sumpt.c
> gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-utils.o `test -f 'utils.c' || echo './'`utils.c
> mbbeagle.c: In function ‘TreeLikelihood_BeagleMultiPartition’:
> mbbeagle.c:2618:33: warning: ‘nStates’ may be used uninitialized [-Wmaybe-uninitialized]
> 2618 | int i, j, d, c = 0, nStates, beagleReturn, site, dIndex, divisionOffset;
> | ^~~~~~~
> sumpt.c: In function ‘DoSump’:
> sumpt.c:335:5: warning: ‘__builtin_strncpy’ output may be truncated copying 90 bytes from a string of length 119 [-Wstringop-truncation]
> 335 | strncpy (temp, sumpParams.sumpOutfile, 90);
> | ^
> In file included from /usr/include/string.h:535,
> from /usr/include/memory.h:29,
> from bayes.h:31,
> from utils.c:38:
> In function ‘strncpy’,
> inlined from ‘CopyResults’ at utils.c:311:9:
> /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: ‘__builtin_strncpy’ accessing between 0 and 2147483647 bytes at offsets [-2147483636, 2147483649] and 0 may overlap up to 11 bytes at offset [0, 10] [-Wrestrict]
> 95 | return __builtin___strncpy_chk (__dest, __src, __len,
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 96 | __glibc_objsize (__dest));
> | ~~~~~~~~~~~~~~~~~~~~~~~~~
> In function ‘strncpy’,
> inlined from ‘CopyProcessSsFile’ at utils.c:350:9:
> /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: ‘__builtin_strncpy’ accessing between 0 and 2147483647 bytes at offsets [-2147483636, 2147483649] and 0 may overlap up to 11 bytes at offset [0, 10] [-Wrestrict]
> 95 | return __builtin___strncpy_chk (__dest, __src, __len,
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 96 | __glibc_objsize (__dest));
> | ~~~~~~~~~~~~~~~~~~~~~~~~~
> In function ‘strncpy’,
> inlined from ‘CopyTreeResults’ at utils.c:422:9:
> /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: ‘__builtin_strncpy’ accessing between 0 and 2147483647 bytes at offsets [-2147483636, 2147483649] and 0 may overlap up to 11 bytes at offset [0, 10] [-Wrestrict]
> 95 | return __builtin___strncpy_chk (__dest, __src, __len,
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 96 | __glibc_objsize (__dest));
> | ~~~~~~~~~~~~~~~~~~~~~~~~~
> sumpt.c: In function ‘DoCompRefTree’:
> sumpt.c:4612:40: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 7 and 126 [-Wformat-overflow=]
> 4612 | sprintf (inRefName, "%s.run%d.t", comptreeParams.comptFileName2, n+1);
> | ^~
> sumpt.c:4612:33: note: directive argument in the range [1, 2147483647]
> 4612 | sprintf (inRefName, "%s.run%d.t", comptreeParams.comptFileName2, n+1);
> | ^~~~~~~~~~~~
> In file included from /usr/include/stdio.h:906,
> from bayes.h:32,
> from sumpt.c:38:
> In function ‘sprintf’,
> inlined from ‘DoCompRefTree’ at sumpt.c:4612:13:
> /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 8 and 136 bytes into a destination of size 130
> 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 31 | __glibc_objsize (__s), __fmt,
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 32 | __va_arg_pack ());
> | ~~~~~~~~~~~~~~~~~
> In function ‘sprintf’,
> inlined from ‘ShowConTree’ at sumpt.c:8173:21:
> /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: warning: ‘__builtin_sprintf’ argument 3 may overlap destination object ‘printLine’ [-Wrestrict]
> 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 31 | __glibc_objsize (__s), __fmt,
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 32 | __va_arg_pack ());
> | ~~~~~~~~~~~~~~~~~
> sumpt.c: In function ‘DoSumt’:
> sumpt.c:4958:39: warning: ‘.run’ directive writing 4 bytes into a region of size between 1 and 120 [-Wformat-overflow=]
> 4958 | sprintf (tempName, "%s.run%d.t", fileName, sumtParams.runId+1);
> | ^~~~
> sumpt.c:4958:36: note: directive argument in the range [-2147483647, 2147483647]
> 4958 | sprintf (tempName, "%s.run%d.t", fileName, sumtParams.runId+1);
> | ^~~~~~~~~~~~
> In function ‘sprintf’,
> inlined from ‘DoSumt’ at sumpt.c:4958:17:
> /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 8 and 137 bytes into a destination of size 120
> 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 31 | __glibc_objsize (__s), __fmt,
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 32 | __va_arg_pack ());
> | ~~~~~~~~~~~~~~~~~
> sumpt.c: In function ‘DoSumt’:
> sumpt.c:4956:39: warning: ‘.t’ directive writing 2 bytes into a region of size between 1 and 120 [-Wformat-overflow=]
> 4956 | sprintf (tempName, "%s.t", fileName);
> | ^~
> In function ‘sprintf’,
> inlined from ‘DoSumt’ at sumpt.c:4956:17:
> /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 3 and 122 bytes into a destination of size 120
> 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 31 | __glibc_objsize (__s), __fmt,
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 32 | __va_arg_pack ());
> | ~~~~~~~~~~~~~~~~~
> mcmc.c: In function ‘ReopenMBPrintFiles’:
> mcmc.c:15467:50: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 2 and 110 [-Wformat-overflow=]
> 15467 | sprintf (fileName, "%s.tree%d.run%d.t", localFileName, i+1, n+1);
> | ^~
> mcmc.c:15467:36: note: directive argument in the range [1, 2147483647]
> 15467 | sprintf (fileName, "%s.tree%d.run%d.t", localFileName, i+1, n+1);
> | ^~~~~~~~~~~~~~~~~~~
> In file included from /usr/include/stdio.h:906,
> from bayes.h:32,
> from mcmc.c:45:
> In function ‘sprintf’,
> inlined from ‘ReopenMBPrintFiles’ at mcmc.c:15467:17:
> /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 14 and 131 bytes into a destination of size 120
> 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 31 | __glibc_objsize (__s), __fmt,
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 32 | __va_arg_pack ());
> | ~~~~~~~~~~~~~~~~~
> command.c: In function ‘DoExecute’:
> command.c:3560:5: warning: ‘__builtin_strncpy’ output may be truncated copying 98 bytes from a string of length 99 [-Wstringop-truncation]
> 3560 | strncpy (exeFileName, inputFileName, 98);
> | ^
> mcmc.c: In function ‘RunChain’:
> mcmc.c:17362:46: warning: ‘.ss’ directive writing 3 bytes into a region of size between 1 and 220 [-Wformat-overflow=]
> 17362 | sprintf (bkupFileName,"%s.ss%d", ckpFileName,chainParams.numStepsSS-stepIndexSS);
> | ^~~
> In function ‘sprintf’,
> inlined from ‘RunChain’ at mcmc.c:17362:21:
> /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 5 and 234 bytes into a destination of size 220
> 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 31 | __glibc_objsize (__s), __fmt,
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 32 | __va_arg_pack ());
> | ~~~~~~~~~~~~~~~~~
> model.c: In function ‘SetModelParams’:
> model.c:19111:48: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
> 19111 | sprintf (tempMult, "g_m{%d}", i+1);
> | ^
> In file included from /usr/include/stdio.h:906,
> from bayes.h:32,
> from model.c:38:
> In function ‘sprintf’,
> inlined from ‘SetModelParams’ at model.c:19111:21:
> /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 7 and 16 bytes into a destination of size 15
> 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 31 | __glibc_objsize (__s), __fmt,
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 32 | __va_arg_pack ());
> | ~~~~~~~~~~~~~~~~~
> gcc -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o mb mb-bayes.o mb-best.o mb-command.o mb-likelihood.o mb-mbbeagle.o mb-mcmc.o mb-model.o mb-proposal.o mb-sumpt.o mb-utils.o -L/usr/lib -lhmsbeagle -lm -lreadline
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/src'
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
> Making all in doc
> make[3]: Entering directory '/<<PKGBUILDDIR>>/doc'
> Making all in manual
> make[4]: Entering directory '/<<PKGBUILDDIR>>/doc/manual'
> echo 'Can not build the manual PDF since LaTeX was not detected' >&2
> Can not build the manual PDF since LaTeX was not detected
> exit 0
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/doc/manual'
> Making all in tutorial
> make[4]: Entering directory '/<<PKGBUILDDIR>>/doc/tutorial'
> echo 'Can not build the tutorial PDF since LaTeX was not detected' >&2
> Can not build the tutorial PDF since LaTeX was not detected
> exit 0
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/doc/tutorial'
> make[4]: Entering directory '/<<PKGBUILDDIR>>/doc'
> make[4]: Nothing to be done for 'all-am'.
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/doc'
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/doc'
> Making all in examples
> make[3]: Entering directory '/<<PKGBUILDDIR>>/examples'
> make[3]: Nothing to be done for 'all'.
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/examples'
> make[3]: Entering directory '/<<PKGBUILDDIR>>'
> make[3]: Nothing to be done for 'all-am'.
> make[3]: Leaving directory '/<<PKGBUILDDIR>>'
> make[2]: Leaving directory '/<<PKGBUILDDIR>>'
> mv src/mb ./mb-mpi
> # Now - build mb
> ( cd src ; make clean )
> make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
> test -z "mb" || rm -f mb
> rm -f *.o
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
> dh_auto_configure -- --with-beagle=/usr --enable-mpi=no --enable-debug=yes
> ./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-beagle=/usr --enable-mpi=no --enable-debug=yes
> 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 to enable maintainer-specific portions of Makefiles... no
> checking build system type... x86_64-pc-linux-gnu
> checking host system type... x86_64-pc-linux-gnu
> checking for pkg-config... /usr/bin/pkg-config
> checking pkg-config is at least version 0.9.0... yes
> checking for pdflatex... no
> checking for bibtex... no
> configure: WARNING: pdflatex or bibtex is missing, documentation will not be rebuilt
> checking whether make supports the include directive... yes (GNU style)
> checking whether to compile using MPI... no
> 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... unsupported
> checking for gcc option to enable C99 features... none needed
> checking whether gcc understands -c and -o together... yes
> checking dependency style of gcc... none
> checking for sqrt in -lm... yes
> 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
> configure: Trying to locate Beagle (hmsbeagle-1) in '/usr'
> checking for libhmsbeagle/beagle.h... yes
> checking for beagleCreateInstance in -lhmsbeagle... yes
> configure: Found Beagle in '/usr'
> checking for beagleSetCPUThreadCount in -lhmsbeagle... yes
> configure: Using BEAGLE_CFLAGS="-I/usr/include/libhmsbeagle-1 -pthread"
> configure: Using BEAGLE_LIBS="-L/usr/lib -lhmsbeagle"
> checking for a readline compatible library... -lreadline
> checking for readline.h... no
> checking for readline/readline.h... yes
> checking whether readline supports history... yes
> checking for history.h... no
> checking for readline/history.h... yes
> checking for float.h... yes
> checking for limits.h... yes
> checking for memory.h... yes
> checking for stdlib.h... (cached) yes
> checking for string.h... (cached) yes
> checking for size_t... yes
> checking for _Bool... yes
> checking for stdbool.h that conforms to C99... yes
> checking for C compiler vendor... gnu
> checking for a sed that does not truncate output... /bin/sed
> checking for C compiler version... 13.2.0
> checking CFLAGS for most reasonable warnings... -Wall
> checking for floor... yes
> checking for memset... yes
> checking for pow... yes
> checking for sqrt... yes
> checking for strchr... yes
> checking that generated files are newer than configure... done
> configure: creating ./config.status
> config.status: creating Makefile
> config.status: creating doc/Makefile
> config.status: creating doc/manual/Makefile
> config.status: creating doc/tutorial/Makefile
> config.status: creating examples/Makefile
> config.status: creating src/Makefile
> config.status: creating src/config.h
> config.status: src/config.h is unchanged
> config.status: executing depfiles commands
> LIBS="-Wl,--as-needed" dh_auto_build
> make -j8
> make[2]: Entering directory '/<<PKGBUILDDIR>>'
> Making all in src
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
> make all-am
> make[4]: Entering directory '/<<PKGBUILDDIR>>/src'
> gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-bayes.o `test -f 'bayes.c' || echo './'`bayes.c
> gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-best.o `test -f 'best.c' || echo './'`best.c
> gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-command.o `test -f 'command.c' || echo './'`command.c
> gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-likelihood.o `test -f 'likelihood.c' || echo './'`likelihood.c
> gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-mbbeagle.o `test -f 'mbbeagle.c' || echo './'`mbbeagle.c
> gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-mcmc.o `test -f 'mcmc.c' || echo './'`mcmc.c
> gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-model.o `test -f 'model.c' || echo './'`model.c
> gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-proposal.o `test -f 'proposal.c' || echo './'`proposal.c
> gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-sumpt.o `test -f 'sumpt.c' || echo './'`sumpt.c
> gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mb-utils.o `test -f 'utils.c' || echo './'`utils.c
> mbbeagle.c: In function ‘TreeLikelihood_BeagleMultiPartition’:
> mbbeagle.c:2618:33: warning: ‘nStates’ may be used uninitialized [-Wmaybe-uninitialized]
> 2618 | int i, j, d, c = 0, nStates, beagleReturn, site, dIndex, divisionOffset;
> | ^~~~~~~
> sumpt.c: In function ‘DoSump’:
> sumpt.c:335:5: warning: ‘__builtin_strncpy’ output may be truncated copying 90 bytes from a string of length 119 [-Wstringop-truncation]
> 335 | strncpy (temp, sumpParams.sumpOutfile, 90);
> | ^
> In file included from /usr/include/string.h:535,
> from /usr/include/memory.h:29,
> from bayes.h:31,
> from utils.c:38:
> In function ‘strncpy’,
> inlined from ‘CopyResults’ at utils.c:311:9:
> /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: ‘__builtin_strncpy’ accessing between 0 and 2147483647 bytes at offsets [-2147483636, 2147483649] and 0 may overlap up to 11 bytes at offset [0, 10] [-Wrestrict]
> 95 | return __builtin___strncpy_chk (__dest, __src, __len,
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 96 | __glibc_objsize (__dest));
> | ~~~~~~~~~~~~~~~~~~~~~~~~~
> In function ‘strncpy’,
> inlined from ‘CopyProcessSsFile’ at utils.c:350:9:
> /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: ‘__builtin_strncpy’ accessing between 0 and 2147483647 bytes at offsets [-2147483636, 2147483649] and 0 may overlap up to 11 bytes at offset [0, 10] [-Wrestrict]
> 95 | return __builtin___strncpy_chk (__dest, __src, __len,
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 96 | __glibc_objsize (__dest));
> | ~~~~~~~~~~~~~~~~~~~~~~~~~
> In function ‘strncpy’,
> inlined from ‘CopyTreeResults’ at utils.c:422:9:
> /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: ‘__builtin_strncpy’ accessing between 0 and 2147483647 bytes at offsets [-2147483636, 2147483649] and 0 may overlap up to 11 bytes at offset [0, 10] [-Wrestrict]
> 95 | return __builtin___strncpy_chk (__dest, __src, __len,
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 96 | __glibc_objsize (__dest));
> | ~~~~~~~~~~~~~~~~~~~~~~~~~
> sumpt.c: In function ‘DoCompRefTree’:
> sumpt.c:4612:40: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 7 and 126 [-Wformat-overflow=]
> 4612 | sprintf (inRefName, "%s.run%d.t", comptreeParams.comptFileName2, n+1);
> | ^~
> sumpt.c:4612:33: note: directive argument in the range [1, 2147483647]
> 4612 | sprintf (inRefName, "%s.run%d.t", comptreeParams.comptFileName2, n+1);
> | ^~~~~~~~~~~~
> In file included from /usr/include/stdio.h:906,
> from bayes.h:32,
> from sumpt.c:38:
> In function ‘sprintf’,
> inlined from ‘DoCompRefTree’ at sumpt.c:4612:13:
> /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 8 and 136 bytes into a destination of size 130
> 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 31 | __glibc_objsize (__s), __fmt,
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 32 | __va_arg_pack ());
> | ~~~~~~~~~~~~~~~~~
> In function ‘sprintf’,
> inlined from ‘ShowConTree’ at sumpt.c:8173:21:
> /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: warning: ‘__builtin_sprintf’ argument 3 may overlap destination object ‘printLine’ [-Wrestrict]
> 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 31 | __glibc_objsize (__s), __fmt,
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 32 | __va_arg_pack ());
> | ~~~~~~~~~~~~~~~~~
> sumpt.c: In function ‘DoSumt’:
> sumpt.c:4958:39: warning: ‘.run’ directive writing 4 bytes into a region of size between 1 and 120 [-Wformat-overflow=]
> 4958 | sprintf (tempName, "%s.run%d.t", fileName, sumtParams.runId+1);
> | ^~~~
> sumpt.c:4958:36: note: directive argument in the range [-2147483647, 2147483647]
> 4958 | sprintf (tempName, "%s.run%d.t", fileName, sumtParams.runId+1);
> | ^~~~~~~~~~~~
> In function ‘sprintf’,
> inlined from ‘DoSumt’ at sumpt.c:4958:17:
> /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 8 and 137 bytes into a destination of size 120
> 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 31 | __glibc_objsize (__s), __fmt,
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 32 | __va_arg_pack ());
> | ~~~~~~~~~~~~~~~~~
> sumpt.c: In function ‘DoSumt’:
> sumpt.c:4956:39: warning: ‘.t’ directive writing 2 bytes into a region of size between 1 and 120 [-Wformat-overflow=]
> 4956 | sprintf (tempName, "%s.t", fileName);
> | ^~
> In function ‘sprintf’,
> inlined from ‘DoSumt’ at sumpt.c:4956:17:
> /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 3 and 122 bytes into a destination of size 120
> 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 31 | __glibc_objsize (__s), __fmt,
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 32 | __va_arg_pack ());
> | ~~~~~~~~~~~~~~~~~
> mcmc.c: In function ‘ReopenMBPrintFiles’:
> mcmc.c:15467:50: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 2 and 110 [-Wformat-overflow=]
> 15467 | sprintf (fileName, "%s.tree%d.run%d.t", localFileName, i+1, n+1);
> | ^~
> mcmc.c:15467:36: note: directive argument in the range [1, 2147483647]
> 15467 | sprintf (fileName, "%s.tree%d.run%d.t", localFileName, i+1, n+1);
> | ^~~~~~~~~~~~~~~~~~~
> In file included from /usr/include/stdio.h:906,
> from bayes.h:32,
> from mcmc.c:45:
> In function ‘sprintf’,
> inlined from ‘ReopenMBPrintFiles’ at mcmc.c:15467:17:
> /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 14 and 131 bytes into a destination of size 120
> 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 31 | __glibc_objsize (__s), __fmt,
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 32 | __va_arg_pack ());
> | ~~~~~~~~~~~~~~~~~
> command.c: In function ‘DoExecute’:
> command.c:3560:5: warning: ‘__builtin_strncpy’ output may be truncated copying 98 bytes from a string of length 99 [-Wstringop-truncation]
> 3560 | strncpy (exeFileName, inputFileName, 98);
> | ^
> mcmc.c: In function ‘RunChain’:
> mcmc.c:17362:46: warning: ‘.ss’ directive writing 3 bytes into a region of size between 1 and 220 [-Wformat-overflow=]
> 17362 | sprintf (bkupFileName,"%s.ss%d", ckpFileName,chainParams.numStepsSS-stepIndexSS);
> | ^~~
> In function ‘sprintf’,
> inlined from ‘RunChain’ at mcmc.c:17362:21:
> /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 5 and 234 bytes into a destination of size 220
> 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 31 | __glibc_objsize (__s), __fmt,
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 32 | __va_arg_pack ());
> | ~~~~~~~~~~~~~~~~~
> model.c: In function ‘SetModelParams’:
> model.c:19111:48: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
> 19111 | sprintf (tempMult, "g_m{%d}", i+1);
> | ^
> In file included from /usr/include/stdio.h:906,
> from bayes.h:32,
> from model.c:38:
> In function ‘sprintf’,
> inlined from ‘SetModelParams’ at model.c:19111:21:
> /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 7 and 16 bytes into a destination of size 15
> 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 31 | __glibc_objsize (__s), __fmt,
> | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 32 | __va_arg_pack ());
> | ~~~~~~~~~~~~~~~~~
> gcc -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o mb mb-bayes.o mb-best.o mb-command.o mb-likelihood.o mb-mbbeagle.o mb-mcmc.o mb-model.o mb-proposal.o mb-sumpt.o mb-utils.o -L/usr/lib -lhmsbeagle -lm -lreadline
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/src'
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
> Making all in doc
> make[3]: Entering directory '/<<PKGBUILDDIR>>/doc'
> Making all in manual
> make[4]: Entering directory '/<<PKGBUILDDIR>>/doc/manual'
> echo 'Can not build the manual PDF since LaTeX was not detected' >&2
> Can not build the manual PDF since LaTeX was not detected
> exit 0
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/doc/manual'
> Making all in tutorial
> make[4]: Entering directory '/<<PKGBUILDDIR>>/doc/tutorial'
> echo 'Can not build the tutorial PDF since LaTeX was not detected' >&2
> Can not build the tutorial PDF since LaTeX was not detected
> exit 0
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/doc/tutorial'
> make[4]: Entering directory '/<<PKGBUILDDIR>>/doc'
> make[4]: Nothing to be done for 'all-am'.
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/doc'
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/doc'
> Making all in examples
> make[3]: Entering directory '/<<PKGBUILDDIR>>/examples'
> make[3]: Nothing to be done for 'all'.
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/examples'
> make[3]: Entering directory '/<<PKGBUILDDIR>>'
> make[3]: Nothing to be done for 'all-am'.
> make[3]: Leaving directory '/<<PKGBUILDDIR>>'
> make[2]: Leaving directory '/<<PKGBUILDDIR>>'
> mv src/mb .
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> dh_auto_test
> make -j8 check "TESTSUITEFLAGS=-j8 --verbose" VERBOSE=1
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> Making check in src
> make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
> gcc -I/usr/include/libhmsbeagle-1 -pthread -Wall -g -std=c99 -pedantic -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o mb mb-bayes.o mb-best.o mb-command.o mb-likelihood.o mb-mbbeagle.o mb-mcmc.o mb-model.o mb-proposal.o mb-sumpt.o mb-utils.o -L/usr/lib -lhmsbeagle -lm -lreadline
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
> Making check in doc
> make[2]: Entering directory '/<<PKGBUILDDIR>>/doc'
> Making check in manual
> make[3]: Entering directory '/<<PKGBUILDDIR>>/doc/manual'
> echo 'Can not build the manual PDF since LaTeX was not detected' >&2
> Can not build the manual PDF since LaTeX was not detected
> exit 0
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/doc/manual'
> Making check in tutorial
> make[3]: Entering directory '/<<PKGBUILDDIR>>/doc/tutorial'
> echo 'Can not build the tutorial PDF since LaTeX was not detected' >&2
> Can not build the tutorial PDF since LaTeX was not detected
> exit 0
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/doc/tutorial'
> make[3]: Entering directory '/<<PKGBUILDDIR>>/doc'
> make[3]: Nothing to be done for 'check-am'.
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/doc'
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/doc'
> Making check in examples
> make[2]: Entering directory '/<<PKGBUILDDIR>>/examples'
> make[2]: Nothing to be done for 'check'.
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/examples'
> make[2]: Entering directory '/<<PKGBUILDDIR>>'
> make[2]: Nothing to be done for 'check-am'.
> make[2]: Leaving directory '/<<PKGBUILDDIR>>'
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> create-stamp debian/debhelper-build-stamp
> dh_prep
> dh_auto_install
> make -j8 install DESTDIR=/<<PKGBUILDDIR>>/debian/tmp AM_UPDATE_INFO_DIR=no
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> Making install in src
> make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
> make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
> make[3]: Nothing to be done for 'install-data-am'.
> /bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
> /usr/bin/install -c mb '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
> Making install in doc
> make[2]: Entering directory '/<<PKGBUILDDIR>>/doc'
> Making install in manual
> make[3]: Entering directory '/<<PKGBUILDDIR>>/doc/manual'
> echo 'Can not build the manual PDF since LaTeX was not detected' >&2
> Can not build the manual PDF since LaTeX was not detected
> exit 0
> make[4]: Entering directory '/<<PKGBUILDDIR>>/doc/manual'
> make[4]: Nothing to be done for 'install-exec-am'.
> echo 'Can not build the manual PDF since LaTeX was not detected' >&2
> Can not build the manual PDF since LaTeX was not detected
> exit 0
> /bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/share/doc/mrbayes'
> /usr/bin/install -c -m 644 ./Manual_MrBayes_v3.2.pdf '/<<PKGBUILDDIR>>/debian/tmp/usr/share/doc/mrbayes'
> /usr/bin/install: cannot stat './Manual_MrBayes_v3.2.pdf': No such file or directory
> make[4]: *** [Makefile:304: install-dist_pdfDATA] Error 1
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/doc/manual'
> make[3]: *** [Makefile:375: install-am] Error 2
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/doc/manual'
> make[2]: *** [Makefile:329: install-recursive] Error 1
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/doc'
> make[1]: *** [Makefile:413: install-recursive] Error 1
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> dh_auto_install: error: make -j8 install DESTDIR=/<<PKGBUILDDIR>>/debian/tmp AM_UPDATE_INFO_DIR=no returned exit code 2
> make: *** [debian/rules:12: binary] Error 25
> 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/mrbayes_3.2.7a-6_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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