Source: mrbayes Version: 3.2.7a-6 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 mrbayes > dpkg-buildpackage: info: source version 3.2.7a-6 > dpkg-buildpackage: info: source distribution unstable > dpkg-buildpackage: info: source changed by Andreas Tille <[email protected]> > 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 âTreeLikelihood_BeagleMultiPartitionâ: > mbbeagle.c:2618:33: warning: ânStatesâ may be used uninitialized > [-Wmaybe-uninitialized] > 2618 | int i, j, d, c = 0, nStates, beagleReturn, site, dIndex, > divisionOffset; > | ^~~~~~~ > sumpt.c: In function âDoSumpâ: > sumpt.c:335:5: warning: â__builtin_strncpyâ 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 âstrncpyâ, > inlined from âCopyResultsâ at utils.c:311:9: > /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: > â__builtin_strncpyâ 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 âstrncpyâ, > inlined from âCopyProcessSsFileâ at utils.c:350:9: > /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: > â__builtin_strncpyâ 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 âstrncpyâ, > inlined from âCopyTreeResultsâ at utils.c:422:9: > /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: > â__builtin_strncpyâ 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 âDoCompRefTreeâ: > sumpt.c:4612:40: warning: â%dâ 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 âsprintfâ, > inlined from âDoCompRefTreeâ at sumpt.c:4612:13: > /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: > â__builtin___sprintf_chkâ 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 âsprintfâ, > inlined from âShowConTreeâ at sumpt.c:8173:21: > /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: warning: > â__builtin_sprintfâ argument 3 may overlap destination object > âprintLineâ [-Wrestrict] > 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > 31 | __glibc_objsize (__s), __fmt, > | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > 32 | __va_arg_pack ()); > | ~~~~~~~~~~~~~~~~~ > sumpt.c: In function âDoSumtâ: > sumpt.c:4958:39: warning: â.runâ 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 âsprintfâ, > inlined from âDoSumtâ at sumpt.c:4958:17: > /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: > â__builtin___sprintf_chkâ 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 âDoSumtâ: > sumpt.c:4956:39: warning: â.tâ directive writing 2 bytes into a region of > size between 1 and 120 [-Wformat-overflow=] > 4956 | sprintf (tempName, "%s.t", fileName); > | ^~ > In function âsprintfâ, > inlined from âDoSumtâ at sumpt.c:4956:17: > /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: > â__builtin___sprintf_chkâ 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 âReopenMBPrintFilesâ: > mcmc.c:15467:50: warning: â%dâ 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 âsprintfâ, > inlined from âReopenMBPrintFilesâ at mcmc.c:15467:17: > /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: > â__builtin___sprintf_chkâ 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 âDoExecuteâ: > command.c:3560:5: warning: â__builtin_strncpyâ output may be truncated > copying 98 bytes from a string of length 99 [-Wstringop-truncation] > 3560 | strncpy (exeFileName, inputFileName, 98); > | ^ > mcmc.c: In function âRunChainâ: > mcmc.c:17362:46: warning: â.ssâ 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 âsprintfâ, > inlined from âRunChainâ at mcmc.c:17362:21: > /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: > â__builtin___sprintf_chkâ 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 âSetModelParamsâ: > model.c:19111:48: warning: â__builtin___sprintf_chkâ 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 âsprintfâ, > inlined from âSetModelParamsâ at model.c:19111:21: > /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: > â__builtin___sprintf_chkâ 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 âTreeLikelihood_BeagleMultiPartitionâ: > mbbeagle.c:2618:33: warning: ânStatesâ may be used uninitialized > [-Wmaybe-uninitialized] > 2618 | int i, j, d, c = 0, nStates, beagleReturn, site, dIndex, > divisionOffset; > | ^~~~~~~ > sumpt.c: In function âDoSumpâ: > sumpt.c:335:5: warning: â__builtin_strncpyâ 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 âstrncpyâ, > inlined from âCopyResultsâ at utils.c:311:9: > /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: > â__builtin_strncpyâ 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 âstrncpyâ, > inlined from âCopyProcessSsFileâ at utils.c:350:9: > /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: > â__builtin_strncpyâ 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 âstrncpyâ, > inlined from âCopyTreeResultsâ at utils.c:422:9: > /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: > â__builtin_strncpyâ 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 âDoCompRefTreeâ: > sumpt.c:4612:40: warning: â%dâ 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 âsprintfâ, > inlined from âDoCompRefTreeâ at sumpt.c:4612:13: > /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: > â__builtin___sprintf_chkâ 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 âsprintfâ, > inlined from âShowConTreeâ at sumpt.c:8173:21: > /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: warning: > â__builtin_sprintfâ argument 3 may overlap destination object > âprintLineâ [-Wrestrict] > 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > 31 | __glibc_objsize (__s), __fmt, > | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > 32 | __va_arg_pack ()); > | ~~~~~~~~~~~~~~~~~ > sumpt.c: In function âDoSumtâ: > sumpt.c:4958:39: warning: â.runâ 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 âsprintfâ, > inlined from âDoSumtâ at sumpt.c:4958:17: > /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: > â__builtin___sprintf_chkâ 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 âDoSumtâ: > sumpt.c:4956:39: warning: â.tâ directive writing 2 bytes into a region of > size between 1 and 120 [-Wformat-overflow=] > 4956 | sprintf (tempName, "%s.t", fileName); > | ^~ > In function âsprintfâ, > inlined from âDoSumtâ at sumpt.c:4956:17: > /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: > â__builtin___sprintf_chkâ 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 âReopenMBPrintFilesâ: > mcmc.c:15467:50: warning: â%dâ 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 âsprintfâ, > inlined from âReopenMBPrintFilesâ at mcmc.c:15467:17: > /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: > â__builtin___sprintf_chkâ 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 âDoExecuteâ: > command.c:3560:5: warning: â__builtin_strncpyâ output may be truncated > copying 98 bytes from a string of length 99 [-Wstringop-truncation] > 3560 | strncpy (exeFileName, inputFileName, 98); > | ^ > mcmc.c: In function âRunChainâ: > mcmc.c:17362:46: warning: â.ssâ 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 âsprintfâ, > inlined from âRunChainâ at mcmc.c:17362:21: > /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: > â__builtin___sprintf_chkâ 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 âSetModelParamsâ: > model.c:19111:48: warning: â__builtin___sprintf_chkâ 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 âsprintfâ, > inlined from âSetModelParamsâ at model.c:19111:21: > /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: > â__builtin___sprintf_chkâ 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.
