Failure building bayeswave on linux with libtool-2.4.6
In trying to build bayeswave on linux with conda build
I am getting errors. The buil environment is as follows:
The following NEW packages will be INSTALLED:
autoconf: 2.69-pl526h470a237_9 conda-forge
binutils_impl_linux-64: 2.31.1-h6176602_1 conda-forge
binutils_linux-64: 2.31.1-h6176602_6
gcc_impl_linux-64: 7.3.0-habb00fd_1 conda-forge
gcc_linux-64: 7.3.0-h553295d_6 conda-forge
libgcc-ng: 7.3.0-hdf63c60_0 conda-forge
libstdcxx-ng: 7.3.0-hdf63c60_0 conda-forge
libtool: 2.4.6-h14c3975_1002 conda-forge
m4: 1.4.18-h14c3975_1001 conda-forge
make: 4.2.1-h14c3975_2004 conda-forge
perl: 5.26.2-h14c3975_1001 conda-forge
pkg-config: 0.29.2-h14c3975_1004 conda-forge
Configure reports this:
autoreconf: Entering directory `.'
autoreconf: configure.ac: not using Gettext
autoreconf: running: aclocal --force
autoreconf: configure.ac: tracing
autoreconf: configure.ac: creating directory build-aux
autoreconf: running: libtoolize --copy --force
libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'build-aux'.
libtoolize: copying file 'build-aux/ltmain.sh'
libtoolize: You should add the contents of the following files to 'aclocal.m4':
libtoolize: '$BUILD_PREFIX/share/aclocal/libtool.m4'
libtoolize: '$BUILD_PREFIX/share/aclocal/ltoptions.m4'
libtoolize: '$BUILD_PREFIX/share/aclocal/ltversion.m4'
libtoolize: Consider adding 'AC_CONFIG_MACRO_DIRS([m4])' to configure.ac,
libtoolize: and rerunning libtoolize and aclocal.
libtoolize: Consider adding '-I m4' to ACLOCAL_AMFLAGS in Makefile.am.
autoreconf: running: /scratch/spxdmm/conda-bld/bayeswave_1549032869325/_build_env/bin/autoconf --force
autoreconf: configure.ac: not using Autoheader
autoreconf: running: automake --add-missing --copy --force-missing
configure.ac:27: installing 'build-aux/config.guess'
configure.ac:27: installing 'build-aux/config.sub'
configure.ac:13: installing 'build-aux/install-sh'
configure.ac:13: installing 'build-aux/missing'
Makefile.am: installing './INSTALL'
Makefile.am: installing 'build-aux/depcomp'
Makefile.am:3: warning: 'LDFLAGS' is a user variable, you should not override it;
Makefile.am:3: use 'AM_LDFLAGS' instead
autoreconf: Leaving directory `.'
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether make supports nested variables... (cached) yes
checking whether to enable maintainer-specific portions of Makefiles... yes
checking for gcc... $BUILD_PREFIX/bin/x86_64-conda_cos6-linux-gnu-cc
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 we are using the GNU C compiler... yes
checking whether $BUILD_PREFIX/bin/x86_64-conda_cos6-linux-gnu-cc accepts -g... yes
checking for $BUILD_PREFIX/bin/x86_64-conda_cos6-linux-gnu-cc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of $BUILD_PREFIX/bin/x86_64-conda_cos6-linux-gnu-cc... gcc3
checking for $BUILD_PREFIX/bin/x86_64-conda_cos6-linux-gnu-cc option to accept ISO C99... none needed
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by $BUILD_PREFIX/bin/x86_64-conda_cos6-linux-gnu-cc... $BUILD_PREFIX/bin/x86_64-conda_cos6-linux-gnu-ld
checking if the linker ($BUILD_PREFIX/bin/x86_64-conda_cos6-linux-gnu-ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... $BUILD_PREFIX/bin/x86_64-conda_cos6-linux-gnu-nm
checking the name lister ($BUILD_PREFIX/bin/x86_64-conda_cos6-linux-gnu-nm) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1966080
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for $BUILD_PREFIX/bin/x86_64-conda_cos6-linux-gnu-ld option to reload object files... -r
checking for objdump... $BUILD_PREFIX/bin/x86_64-conda_cos6-linux-gnu-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 archiver @FILE support... @
checking for strip... $BUILD_PREFIX/bin/x86_64-conda_cos6-linux-gnu-strip
checking for ranlib... $BUILD_PREFIX/bin/x86_64-conda_cos6-linux-gnu-ranlib
checking command to parse $BUILD_PREFIX/bin/x86_64-conda_cos6-linux-gnu-nm output from $BUILD_PREFIX/bin/x86_64-conda_cos6-linux-gnu-cc object... ok
checking for sysroot... no
checking for mt... no
checking if : is a manifest tool... no
checking how to run the C preprocessor... $BUILD_PREFIX/bin/x86_64-conda_cos6-linux-gnu-cpp
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if $BUILD_PREFIX/bin/x86_64-conda_cos6-linux-gnu-cc supports -fno-rtti -fno-exceptions... no
checking for $BUILD_PREFIX/bin/x86_64-conda_cos6-linux-gnu-cc option to produce PIC... -fPIC -DPIC
checking if $BUILD_PREFIX/bin/x86_64-conda_cos6-linux-gnu-cc PIC flag -fPIC -DPIC works... yes
checking if $BUILD_PREFIX/bin/x86_64-conda_cos6-linux-gnu-cc static flag -static works... yes
checking if $BUILD_PREFIX/bin/x86_64-conda_cos6-linux-gnu-cc supports -c -o file.o... yes
checking if $BUILD_PREFIX/bin/x86_64-conda_cos6-linux-gnu-cc supports -c -o file.o... (cached) yes
checking whether the $BUILD_PREFIX/bin/x86_64-conda_cos6-linux-gnu-cc linker ($BUILD_PREFIX/bin/x86_64-conda_cos6-linux-gnu-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 for pkg-config...
checking for pkg-config... $BUILD_PREFIX/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for LAL... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: executing depfiles commands
config.status: executing libtool commands
And then make
reports this at the end:
libtool: Version mismatch error. This is libtool 2.4.6, but the
libtool: definition of this LT_INIT comes from libtool 2.4.2.
libtool: You should recreate aclocal.m4 with macros from libtool 2.4.6
libtool: and run autoconf again.
libtool: Version mismatch error. This is libtool 2.4.6, but the
libtool: definition of this LT_INIT comes from libtool 2.4.2.
libtool: You should recreate aclocal.m4 with macros from libtool 2.4.6
libtool: and run autoconf again.
make: *** [Makefile:591: BayesWaveModel.lo] Error 63
make: *** Waiting for unfinished jobs....
make: *** [Makefile:591: BayesWaveLikelihood.lo] Error 63
libtool: Version mismatch error. This is libtool 2.4.6, but the
libtool: definition of this LT_INIT comes from libtool 2.4.2.
libtool: You should recreate aclocal.m4 with macros from libtool 2.4.6
libtool: and run autoconf again.
make: *** [Makefile:591: BayesWaveProposal.lo] Error 63
libtool: Version mismatch error. This is libtool 2.4.6, but the
libtool: definition of this LT_INIT comes from libtool 2.4.2.
libtool: You should recreate aclocal.m4 with macros from libtool 2.4.6
libtool: and run autoconf again.
make: *** [Makefile:591: BayesWaveMCMC.lo] Error 63
libtool: Version mismatch error. This is libtool 2.4.6, but the
libtool: definition of this LT_INIT comes from libtool 2.4.2.
libtool: You should recreate aclocal.m4 with macros from libtool 2.4.6
libtool: and run autoconf again.
make: *** [Makefile:591: BayesWavePrior.lo] Error 63
libtool: Version mismatch error. This is libtool 2.4.6, but the
libtool: definition of this LT_INIT comes from libtool 2.4.2.
libtool: You should recreate aclocal.m4 with macros from libtool 2.4.6
libtool: and run autoconf again.
make: *** [Makefile:591: BayesWaveIO.lo] Error 63
libtool: Version mismatch error. This is libtool 2.4.6, but the
libtool: definition of this LT_INIT comes from libtool 2.4.2.
libtool: You should recreate aclocal.m4 with macros from libtool 2.4.6
libtool: and run autoconf again.
make: *** [Makefile:591: BayesLine.lo] Error 63
libtool: Version mismatch error. This is libtool 2.4.6, but the
libtool: definition of this LT_INIT comes from libtool 2.4.2.
libtool: You should recreate aclocal.m4 with macros from libtool 2.4.6
libtool: and run autoconf again.
make: *** [Makefile:591: BayesWaveWavelet.lo] Error 63
libtool: Version mismatch error. This is libtool 2.4.6, but the
libtool: definition of this LT_INIT comes from libtool 2.4.2.
libtool: You should recreate aclocal.m4 with macros from libtool 2.4.6
libtool: and run autoconf again.
libtool: Version mismatch error. This is libtool 2.4.6, but the
libtool: definition of this LT_INIT comes from libtool 2.4.2.
libtool: You should recreate aclocal.m4 with macros from libtool 2.4.6
libtool: and run autoconf again.
make: *** [Makefile:591: BayesWaveEvidence.lo] Error 63
make: *** [Makefile:591: BayesWaveMath.lo] Error 63
Traceback (most recent call last):
File "/home/spxdmm/opt/miniconda3/bin/conda-build", line 11, in <module>
sys.exit(main())
File "/home/spxdmm/opt/miniconda3/lib/python3.7/site-packages/conda_build/cli/main_build.py", line 456, in main
execute(sys.argv[1:])
File "/home/spxdmm/opt/miniconda3/lib/python3.7/site-packages/conda_build/cli/main_build.py", line 447, in execute
verify=args.verify, variants=args.variants)
File "/home/spxdmm/opt/miniconda3/lib/python3.7/site-packages/conda_build/api.py", line 208, in build
notest=notest, need_source_download=need_source_download, variants=variants)
File "/home/spxdmm/opt/miniconda3/lib/python3.7/site-packages/conda_build/build.py", line 2314, in build_tree
notest=notest,
File "/home/spxdmm/opt/miniconda3/lib/python3.7/site-packages/conda_build/build.py", line 1477, in build
cwd=src_dir, stats=build_stats)
File "/home/spxdmm/opt/miniconda3/lib/python3.7/site-packages/conda_build/utils.py", line 374, in check_call_env
return _func_defaulting_env_to_os_environ('call', *popenargs, **kwargs)
File "/home/spxdmm/opt/miniconda3/lib/python3.7/site-packages/conda_build/utils.py", line 354, in _func_defaulting_env_to_os_environ
raise subprocess.CalledProcessError(proc.returncode, _args)
subprocess.CalledProcessError: Command '['/bin/bash', '-e', '/scratch/spxdmm/conda-bld/bayeswave_1549033343924/work/conda_build.sh']' returned non-zero exit status 2.