sci-biology:abyss-2.0.3:20200401-070520.log

sci-biology:abyss-2.0.3:20200401-070520.log (text/plain), 16.51 KB, created by Toralf Förster on 2020-04-01 07:15:19 UTC

 * Package:    sci-biology/abyss-2.0.3
 * Repository: gentoo
 * Maintainer: [e-mail] [e-mail]
 * USE:        abi_x86_64 amd64 elibc_musl kernel_linux mpi openmp userland_GNU
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox
>>> Unpacking source...
>>> Unpacking abyss-2.0.3.tar.gz to /var/tmp/portage/sci-biology/abyss-2.0.3/work
>>> Source unpacked in /var/tmp/portage/sci-biology/abyss-2.0.3/work
>>> Preparing source in /var/tmp/portage/sci-biology/abyss-2.0.3/work/abyss-2.0.3 ...
 * Running eautoreconf in '/var/tmp/portage/sci-biology/abyss-2.0.3/work/abyss-2.0.3' ...
 * Running aclocal ...
 [ ok ]
 * Running autoconf --force ...
 [ ok ]
 * Running autoheader ...
 [ ok ]
 * Running automake --add-missing --copy --foreign --force-missing ...
 [ ok ]
 * Running elibtoolize in: abyss-2.0.3/
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/abyss-2.0.3/work/abyss-2.0.3 ...
 * econf: updating abyss-2.0.3/config.sub with /usr/share/gnuconfig/config.sub
 * econf: updating abyss-2.0.3/config.guess with /usr/share/gnuconfig/config.guess
./configure --prefix=/usr --build=x86_64-gentoo-linux-musl --host=x86_64-gentoo-linux-musl --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-dependency-tracking --disable-silent-rules --docdir=/usr/share/doc/abyss-2.0.3 --htmldir=/usr/share/doc/abyss-2.0.3/html --libdir=/usr/lib --enable-openmp
checking for a BSD-compatible install... /usr/lib/portage/python3.6/ebuild-helpers/xattr/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gawk... (cached) gawk
checking for x86_64-gentoo-linux-musl-gcc... x86_64-gentoo-linux-musl-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 we are using the GNU C compiler... yes
checking whether x86_64-gentoo-linux-musl-gcc accepts -g... yes
checking for x86_64-gentoo-linux-musl-gcc option to accept ISO C89... none needed
checking whether x86_64-gentoo-linux-musl-gcc understands -c and -o together... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of x86_64-gentoo-linux-musl-gcc... none
checking how to run the C preprocessor... x86_64-gentoo-linux-musl-gcc -E
checking for x86_64-gentoo-linux-musl-g++... x86_64-gentoo-linux-musl-g++
checking whether we are using the GNU C++ compiler... yes
checking whether x86_64-gentoo-linux-musl-g++ accepts -g... yes
checking dependency style of x86_64-gentoo-linux-musl-g++... none
checking for x86_64-gentoo-linux-musl-ranlib... x86_64-gentoo-linux-musl-ranlib
checking for x86_64-gentoo-linux-musl-ghc... no
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./configure: line 5208: : command not found
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checking for ANSI C header files... yes
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checking float.h usability... yes
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checking limits.h usability... yes
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checking for stdbool.h that conforms to C99... yes
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checking for inline... inline
checking for ptrdiff_t... yes
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checking vfork.h usability... no
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checking for fork... yes
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checking for working fork... yes
checking for working vfork... (cached) yes
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checking for GNU libc compatible malloc... yes
checking for working memcmp... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for vprintf... yes
checking for _doprnt... no
checking whether HOST_NAME_MAX is declared... yes
checking build system type... x86_64-gentoo-linux-musl
checking host system type... x86_64-gentoo-linux-musl
checking if compiler needs -Werror to reject unknown flags... no
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
checking for PTHREAD_PRIO_INHERIT... yes
checking mpi.h usability... yes
checking mpi.h presence... yes
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checking for MPI_Init in -lmpi... yes
checking for sqrt in -lm... yes
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checking how to run the C++ preprocessor... x86_64-gentoo-linux-musl-g++ -E
checking functional usability... yes
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checking boost/functional/hash.hpp usability... yes
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checking boost/property_map/property_map.hpp usability... yes
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checking google/sparse_hash_map usability... yes
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checking sqlite3.h usability... yes
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checking for main in -lsqlite3... yes
checking for x86_64-gentoo-linux-musl-g++ option to support OpenMP... -fopenmp
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating ABYSS/Makefile
config.status: creating Align/Makefile
config.status: creating Assembly/Makefile
config.status: creating Common/Makefile
config.status: creating DataLayer/Makefile
config.status: creating FMIndex/Makefile
config.status: creating Graph/Makefile
config.status: creating Parallel/Makefile
config.status: creating bin/Makefile
config.status: creating doc/Makefile
config.status: creating dialign/Makefile
config.status: creating kmerprint/Makefile
config.status: creating AdjList/Makefile
config.status: creating Konnector/Makefile
config.status: creating DAssembler/Makefile
config.status: creating DistanceEst/Makefile
config.status: creating Layout/Makefile
config.status: creating Map/Makefile
config.status: creating Misc/Makefile
config.status: creating Overlap/Makefile
config.status: creating PopBubbles/Makefile
config.status: creating Scaffold/Makefile
config.status: creating SimpleGraph/Makefile
config.status: creating MergePaths/Makefile
config.status: creating KAligner/Makefile
config.status: creating PairedDBG/Makefile
config.status: creating ParseAligns/Makefile
config.status: creating PathOverlap/Makefile
config.status: creating Consensus/Makefile
config.status: creating FilterGraph/Makefile
config.status: creating GapFiller/Makefile
config.status: creating Sealer/Makefile
config.status: creating lib/gtest-1.7.0/Makefile
config.status: creating Unittest/Makefile
config.status: creating LogKmerCount/Makefile
config.status: creating Bloom/Makefile
config.status: creating BloomDBG/Makefile
config.status: creating DataBase/Makefile
config.status: creating lib/bloomfilter/Makefile
config.status: creating lib/rolling-hash/Makefile
config.status: creating config.h
config.status: executing depfiles commands
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/abyss-2.0.3/work/abyss-2.0.3 ...
make -j1 
make  all-recursive
make[1]: Entering directory '/var/tmp/portage/sci-biology/abyss-2.0.3/work/abyss-2.0.3'
Making all in bin
make[2]: Entering directory '/var/tmp/portage/sci-biology/abyss-2.0.3/work/abyss-2.0.3/bin'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/var/tmp/portage/sci-biology/abyss-2.0.3/work/abyss-2.0.3/bin'
Making all in doc
make[2]: Entering directory '/var/tmp/portage/sci-biology/abyss-2.0.3/work/abyss-2.0.3/doc'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/var/tmp/portage/sci-biology/abyss-2.0.3/work/abyss-2.0.3/doc'
Making all in Common
make[2]: Entering directory '/var/tmp/portage/sci-biology/abyss-2.0.3/work/abyss-2.0.3/Common'
x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I/var/tmp/portage/sci-biology/abyss-2.0.3/work/abyss-2.0.3      -isystem/var/tmp/portage/sci-biology/abyss-2.0.3/work/abyss-2.0.3/boost_1_56_0 -Wall -Wextra -O2 -pipe -march=native -c -o libcommon_a-ContigID.o `test -f 'ContigID.cpp' || echo './'`ContigID.cpp
x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I/var/tmp/portage/sci-biology/abyss-2.0.3/work/abyss-2.0.3      -isystem/var/tmp/portage/sci-biology/abyss-2.0.3/work/abyss-2.0.3/boost_1_56_0 -Wall -Wextra -O2 -pipe -march=native -c -o libcommon_a-Fcontrol.o `test -f 'Fcontrol.cpp' || echo './'`Fcontrol.cpp
x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I/var/tmp/portage/sci-biology/abyss-2.0.3/work/abyss-2.0.3      -isystem/var/tmp/portage/sci-biology/abyss-2.0.3/work/abyss-2.0.3/boost_1_56_0 -Wall -Wextra -O2 -pipe -march=native -c -o libcommon_a-Histogram.o `test -f 'Histogram.cpp' || echo './'`Histogram.cpp
x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I/var/tmp/portage/sci-biology/abyss-2.0.3/work/abyss-2.0.3      -isystem/var/tmp/portage/sci-biology/abyss-2.0.3/work/abyss-2.0.3/boost_1_56_0 -Wall -Wextra -O2 -pipe -march=native -c -o libcommon_a-Kmer.o `test -f 'Kmer.cpp' || echo './'`Kmer.cpp
x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I/var/tmp/portage/sci-biology/abyss-2.0.3/work/abyss-2.0.3      -isystem/var/tmp/portage/sci-biology/abyss-2.0.3/work/abyss-2.0.3/boost_1_56_0 -Wall -Wextra -O2 -pipe -march=native -c -o libcommon_a-Log.o `test -f 'Log.cpp' || echo './'`Log.cpp
x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I/var/tmp/portage/sci-biology/abyss-2.0.3/work/abyss-2.0.3      -isystem/var/tmp/portage/sci-biology/abyss-2.0.3/work/abyss-2.0.3/boost_1_56_0 -Wall -Wextra -O2 -pipe -march=native -c -o libcommon_a-Options.o `test -f 'Options.cpp' || echo './'`Options.cpp
x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I/var/tmp/portage/sci-biology/abyss-2.0.3/work/abyss-2.0.3      -isystem/var/tmp/portage/sci-biology/abyss-2.0.3/work/abyss-2.0.3/boost_1_56_0 -Wall -Wextra -O2 -pipe -march=native -c -o libcommon_a-Sequence.o `test -f 'Sequence.cpp' || echo './'`Sequence.cpp
x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I/var/tmp/portage/sci-biology/abyss-2.0.3/work/abyss-2.0.3      -isystem/var/tmp/portage/sci-biology/abyss-2.0.3/work/abyss-2.0.3/boost_1_56_0 -Wall -Wextra -O2 -pipe -march=native -c -o libcommon_a-SignalHandler.o `test -f 'SignalHandler.cpp' || echo './'`SignalHandler.cpp
x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I/var/tmp/portage/sci-biology/abyss-2.0.3/work/abyss-2.0.3      -isystem/var/tmp/portage/sci-biology/abyss-2.0.3/work/abyss-2.0.3/boost_1_56_0 -Wall -Wextra -O2 -pipe -march=native -c -o libcommon_a-Timer.o `test -f 'Timer.cpp' || echo './'`Timer.cpp
x86_64-gentoo-linux-musl-g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I/var/tmp/portage/sci-biology/abyss-2.0.3/work/abyss-2.0.3      -isystem/var/tmp/portage/sci-biology/abyss-2.0.3/work/abyss-2.0.3/boost_1_56_0 -Wall -Wextra -O2 -pipe -march=native -c -o libcommon_a-Uncompress.o `test -f 'Uncompress.cpp' || echo './'`Uncompress.cpp
Uncompress.cpp: In function ‘int uncompress(const char*)’:
Uncompress.cpp:99:39: warning: missing sentinel in function call [-Wformat=]
   99 |    execlp(arg0, arg0, arg1, path, NULL);
      |                                       ^
Uncompress.cpp:101:45: warning: missing sentinel in function call [-Wformat=]
  101 |    execlp(arg0, arg0, arg1, arg2, path, NULL);
      |                                             ^
In file included from /usr/lib/gcc/x86_64-gentoo-linux-musl/9.3.0/include/g++-v9/cstdio:42,
                 from /usr/lib/gcc/x86_64-gentoo-linux-musl/9.3.0/include/g++-v9/ext/string_conversions.h:43,
                 from /usr/lib/gcc/x86_64-gentoo-linux-musl/9.3.0/include/g++-v9/bits/basic_string.h:6493,
                 from /usr/lib/gcc/x86_64-gentoo-linux-musl/9.3.0/include/g++-v9/string:55,
                 from /usr/lib/gcc/x86_64-gentoo-linux-musl/9.3.0/include/g++-v9/bits/locale_classes.h:40,
                 from /usr/lib/gcc/x86_64-gentoo-linux-musl/9.3.0/include/g++-v9/bits/ios_base.h:41,
                 from /usr/lib/gcc/x86_64-gentoo-linux-musl/9.3.0/include/g++-v9/iomanip:40,
                 from StringUtil.h:5,
                 from Uncompress.cpp:15:
Uncompress.cpp: At global scope:
Uncompress.cpp:157:7: error: redefinition of ‘FILE* fopen(const char*, const char*)’
  157 | FILE *fopen64(const char *path, const char *mode)
      |       ^~~~~~~
Uncompress.cpp:130:7: note: ‘FILE* fopen(const char*, const char*)’ previously defined here
  130 | FILE *fopen(const char *path, const char *mode)
      |       ^~~~~
Uncompress.cpp:181:52: error: ‘mode_t’ has not been declared
  181 | typedef int (*open_t)(const char *path, int flags, mode_t mode);
      |                                                    ^~~~~~
Uncompress.cpp:186:39: error: ‘mode_t’ has not been declared
  186 | int open(const char *path, int flags, mode_t mode)
      |                                       ^~~~~~
make[2]: *** [Makefile:570: libcommon_a-Uncompress.o] Error 1
make[2]: Leaving directory '/var/tmp/portage/sci-biology/abyss-2.0.3/work/abyss-2.0.3/Common'
make[1]: *** [Makefile:486: all-recursive] Error 1
make[1]: Leaving directory '/var/tmp/portage/sci-biology/abyss-2.0.3/work/abyss-2.0.3'
make: *** [Makefile:406: all] Error 2
 * ERROR: sci-biology/abyss-2.0.3::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/abyss-2.0.3::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/abyss-2.0.3::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-biology:abyss-2.0.3:20200401-070520.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/abyss-2.0.3/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/abyss-2.0.3/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/abyss-2.0.3/work/abyss-2.0.3'
 * S: '/var/tmp/portage/sci-biology/abyss-2.0.3/work/abyss-2.0.3'