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Gentoo's Bugzilla – Attachment 762088 Details for
Bug 715718
sci-biology/abyss-2.3.4 : Uncompress.cpp: error: redefinition of FILE* fopen(const char*, const char*)
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sci-biology:abyss-2.3.4:20220113-131801.log
sci-biology:abyss-2.3.4:20220113-131801.log (text/plain), 15.74 KB, created by
Toralf Förster
on 2022-01-13 13:41:48 UTC
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Description:
sci-biology:abyss-2.3.4:20220113-131801.log
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Creator:
Toralf Förster
Created:
2022-01-13 13:41:48 UTC
Size:
15.74 KB
patch
obsolete
> * Package: sci-biology/abyss-2.3.4 > * Repository: gentoo > * Maintainer: sci-biology@gentoo.org > * USE: abi_x86_64 amd64 elibc_musl kernel_linux openmp userland_GNU > * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox > >>>> Unpacking source... >>>> Unpacking abyss-2.3.4.tar.gz to /var/tmp/portage/sci-biology/abyss-2.3.4/work >>>> Source unpacked in /var/tmp/portage/sci-biology/abyss-2.3.4/work >>>> Preparing source in /var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4 ... > * Running eautoreconf in '/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4' ... > * Running 'aclocal' ... > [ ok ] > * Running 'autoconf --force' ... > [ ok ] > * Running 'autoheader' ... > [ ok ] > * Running 'automake --add-missing --copy --foreign --force-missing' ... > [ ok ] > * Running elibtoolize in: abyss-2.3.4/ >>>> Source prepared. >>>> Configuring source in /var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4 ... > * econf: updating abyss-2.3.4/config.sub with /usr/share/gnuconfig/config.sub > * econf: updating abyss-2.3.4/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 --datarootdir=/usr/share --disable-dependency-tracking --disable-silent-rules --docdir=/usr/share/doc/abyss-2.3.4 --htmldir=/usr/share/doc/abyss-2.3.4/html --libdir=/usr/lib --enable-openmp --enable-maxk=256 >checking for x86_64-gentoo-linux-musl-g++... x86_64-gentoo-linux-musl-g++ >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 x86_64-gentoo-linux-musl-g++ accepts -g... yes >checking for x86_64-gentoo-linux-musl-g++ option to enable C++11 features... none needed >checking whether x86_64-gentoo-linux-musl-g++ supports C++11 features with -std=c++11... yes >checking for a BSD-compatible install... /usr/lib/portage/python3.9/ebuild-helpers/xattr/install -c >checking whether build environment is sane... yes >checking for a race-free mkdir -p... /bin/mkdir -p >checking for gawk... gawk >checking whether make sets $(MAKE)... yes >checking whether make supports the include directive... yes (GNU style) >checking whether make supports nested variables... yes >checking whether UID '250' is supported by ustar format... yes >checking whether GID '250' is supported by ustar format... yes >checking how to create a ustar tar archive... gnutar >checking dependency style of x86_64-gentoo-linux-musl-g++ -std=c++11... none >checking for gawk... (cached) gawk >checking for x86_64-gentoo-linux-musl-gcc... x86_64-gentoo-linux-musl-gcc >checking whether the compiler supports GNU C... yes >checking whether x86_64-gentoo-linux-musl-gcc accepts -g... yes >checking for x86_64-gentoo-linux-musl-gcc option to enable C11 features... none needed >checking whether x86_64-gentoo-linux-musl-gcc understands -c and -o together... yes >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 whether the compiler supports GNU C++... (cached) yes >checking whether x86_64-gentoo-linux-musl-g++ -std=c++11 accepts -g... (cached) yes >checking for x86_64-gentoo-linux-musl-g++ -std=c++11 option to enable C++11 features... (cached) none needed >checking for x86_64-gentoo-linux-musl-ranlib... x86_64-gentoo-linux-musl-ranlib >checking for x86_64-gentoo-linux-musl-ghc... no >checking for ghc... (cached) no >./configure: line 7029: : command not found >checking for pandoc... no >checking for x86_64-gentoo-linux-musl-ar... x86_64-gentoo-linux-musl-ar >checking the archiver (x86_64-gentoo-linux-musl-ar) interface... ar >checking for stdio.h... yes >checking for stdlib.h... yes >checking for string.h... yes >checking for inttypes.h... yes >checking for stdint.h... yes >checking for strings.h... yes >checking for sys/stat.h... yes >checking for sys/types.h... yes >checking for unistd.h... yes >checking for vfork.h... no >checking for dlfcn.h... yes >checking for fcntl.h... yes >checking for float.h... yes >checking for limits.h... yes >checking for stddef.h... yes >checking for stdint.h... (cached) yes >checking for stdlib.h... (cached) yes >checking for sys/param.h... yes >checking for _Bool... yes >checking for stdbool.h that conforms to C99... yes >checking whether byte ordering is bigendian... no >checking for an ANSI C-conforming const... yes >checking for inline... inline >checking for ptrdiff_t... yes >checking for mode_t... yes >checking for pid_t... yes >checking for size_t... yes >checking for ssize_t... yes >checking for int64_t... yes >checking for uint8_t... yes >checking for uint16_t... yes >checking for uint32_t... yes >checking for uint64_t... yes >checking for std::hash<int>... yes >checking for std::tr1::hash<int>... yes >checking for std::tr1::tuple<int>... yes >checking for dup2... yes >checking for gethostname... yes >checking for getopt_long... yes >checking for getpagesize... yes >checking for memset... yes >checking for strdup... yes >checking for strerror... yes >checking for strtoul... yes >checking for fork... yes >checking for vfork... yes >checking for vprintf... yes >checking for working fork... yes >checking for working vfork... (cached) yes >checking build system type... x86_64-gentoo-linux-musl >checking host system type... x86_64-gentoo-linux-musl >checking for GNU libc compatible malloc... yes >checking for working memcmp... yes >checking for GNU libc compatible realloc... yes >checking for x86_64-gentoo-linux-musl-gcc options needed to detect all undeclared functions... none needed >checking whether HOST_NAME_MAX is declared... yes >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 for mpi.h... yes >checking for MPI_Init in -lmpi... yes >checking for sqrt in -lm... yes >checking for pow... yes >checking for sqrt... yes >checking for ceilf... yes >checking for dlsym in -ldl... yes >checking for functional... yes >checking for tr1/functional... yes >checking for boost/functional/hash.hpp... yes >checking for boost/property_map/property_map.hpp... yes >checking for google/sparse_hash_map... yes >checking for unordered_map... yes >checking for tr1/unordered_map... yes >checking for unordered_set... yes >checking for tr1/unordered_set... yes >checking for boost/unordered_set.hpp... yes >checking for sqlite3.h... yes >checking for main in -lsqlite3... yes >checking for x86_64-gentoo-linux-musl-g++ -std=c++11 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 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 vendor/gtest-1.7.0/Makefile >config.status: creating RResolver/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 vendor/Makefile >config.status: creating config.h >config.status: executing depfiles commands >>>> Source configured. >>>> Compiling source in /var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4 ... >make -j4 >make all-recursive >make[1]: Entering directory '/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4' >Making all in bin >make[2]: Entering directory '/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/bin' >make[2]: Nothing to be done for 'all'. >make[2]: Leaving directory '/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/bin' >Making all in doc >make[2]: Entering directory '/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/doc' >make[2]: Nothing to be done for 'all'. >make[2]: Leaving directory '/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/doc' >Making all in Common >make[2]: Entering directory '/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/Common' >x86_64-gentoo-linux-musl-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4 -isystem/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/boost_1_56_0 -Wall -Wextra -pipe -march=native -fno-diagnostics-color -O2 -c -o libcommon_a-ContigID.o `test -f 'ContigID.cpp' || echo './'`ContigID.cpp >x86_64-gentoo-linux-musl-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4 -isystem/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/boost_1_56_0 -Wall -Wextra -pipe -march=native -fno-diagnostics-color -O2 -c -o libcommon_a-Fcontrol.o `test -f 'Fcontrol.cpp' || echo './'`Fcontrol.cpp >x86_64-gentoo-linux-musl-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4 -isystem/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/boost_1_56_0 -Wall -Wextra -pipe -march=native -fno-diagnostics-color -O2 -c -o libcommon_a-Histogram.o `test -f 'Histogram.cpp' || echo './'`Histogram.cpp >x86_64-gentoo-linux-musl-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4 -isystem/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/boost_1_56_0 -Wall -Wextra -pipe -march=native -fno-diagnostics-color -O2 -c -o libcommon_a-Kmer.o `test -f 'Kmer.cpp' || echo './'`Kmer.cpp >x86_64-gentoo-linux-musl-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4 -isystem/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/boost_1_56_0 -Wall -Wextra -pipe -march=native -fno-diagnostics-color -O2 -c -o libcommon_a-Log.o `test -f 'Log.cpp' || echo './'`Log.cpp >x86_64-gentoo-linux-musl-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4 -isystem/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/boost_1_56_0 -Wall -Wextra -pipe -march=native -fno-diagnostics-color -O2 -c -o libcommon_a-Options.o `test -f 'Options.cpp' || echo './'`Options.cpp >x86_64-gentoo-linux-musl-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4 -isystem/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/boost_1_56_0 -Wall -Wextra -pipe -march=native -fno-diagnostics-color -O2 -c -o libcommon_a-Sequence.o `test -f 'Sequence.cpp' || echo './'`Sequence.cpp >x86_64-gentoo-linux-musl-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4 -isystem/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/boost_1_56_0 -Wall -Wextra -pipe -march=native -fno-diagnostics-color -O2 -c -o libcommon_a-SignalHandler.o `test -f 'SignalHandler.cpp' || echo './'`SignalHandler.cpp >x86_64-gentoo-linux-musl-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4 -isystem/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/boost_1_56_0 -Wall -Wextra -pipe -march=native -fno-diagnostics-color -O2 -c -o libcommon_a-Timer.o `test -f 'Timer.cpp' || echo './'`Timer.cpp >x86_64-gentoo-linux-musl-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4 -isystem/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/boost_1_56_0 -Wall -Wextra -pipe -march=native -fno-diagnostics-color -O2 -c -o libcommon_a-Uncompress.o `test -f 'Uncompress.cpp' || echo './'`Uncompress.cpp >x86_64-gentoo-linux-musl-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4 -isystem/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/boost_1_56_0 -Wall -Wextra -pipe -march=native -fno-diagnostics-color -O2 -c -o libcommon_a-city.o `test -f 'city.cc' || echo './'`city.cc >In file included from /usr/lib/gcc/x86_64-gentoo-linux-musl/11.2.1/include/g++-v11/cstdio:42, > from /usr/lib/gcc/x86_64-gentoo-linux-musl/11.2.1/include/g++-v11/ext/string_conversions.h:43, > from /usr/lib/gcc/x86_64-gentoo-linux-musl/11.2.1/include/g++-v11/bits/basic_string.h:6606, > from /usr/lib/gcc/x86_64-gentoo-linux-musl/11.2.1/include/g++-v11/string:55, > from /usr/lib/gcc/x86_64-gentoo-linux-musl/11.2.1/include/g++-v11/bits/locale_classes.h:40, > from /usr/lib/gcc/x86_64-gentoo-linux-musl/11.2.1/include/g++-v11/bits/ios_base.h:41, > from /usr/lib/gcc/x86_64-gentoo-linux-musl/11.2.1/include/g++-v11/iomanip:40, > from StringUtil.h:5, > from Uncompress.cpp:15: >Uncompress.cpp:160:7: error: redefinition of 'FILE* fopen(const char*, const char*)' > 160 | FILE *fopen64(const char *path, const char *mode) > | ^~~~~~~ >Uncompress.cpp:133:7: note: 'FILE* fopen(const char*, const char*)' previously defined here > 133 | FILE *fopen(const char *path, const char *mode) > | ^~~~~ >Uncompress.cpp:184:52: error: 'mode_t' has not been declared > 184 | typedef int (*open_t)(const char *path, int flags, mode_t mode); > | ^~~~~~ >Uncompress.cpp:189:39: error: 'mode_t' has not been declared > 189 | int open(const char *path, int flags, mode_t mode) > | ^~~~~~ >make[2]: *** [Makefile:572: libcommon_a-Uncompress.o] Error 1 >make[2]: Leaving directory '/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4/Common' >make[1]: *** [Makefile:488: all-recursive] Error 1 >make[1]: Leaving directory '/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4' >make: *** [Makefile:408: all] Error 2 > * ERROR: sci-biology/abyss-2.3.4::gentoo failed (compile phase): > * emake failed > * > * If you need support, post the output of `emerge --info '=sci-biology/abyss-2.3.4::gentoo'`, > * the complete build log and the output of `emerge -pqv '=sci-biology/abyss-2.3.4::gentoo'`. > * The complete build log is located at '/var/log/portage/sci-biology:abyss-2.3.4:20220113-131801.log'. > * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/abyss-2.3.4/temp/build.log'. > * The ebuild environment file is located at '/var/tmp/portage/sci-biology/abyss-2.3.4/temp/environment'. > * Working directory: '/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4' > * S: '/var/tmp/portage/sci-biology/abyss-2.3.4/work/abyss-2.3.4' >
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