build.log

file_823894.txt (text/plain), 18.16 KB, created by Sam James on 2021-11-16 03:08:57 UTC

 * Package:    sci-chemistry/dssp-3.0.11
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_32 elibc_glibc kernel_linux userland_GNU x86
 * FEATURES:   network-sandbox preserve-libs sandbox test userpriv usersandbox
>>> Unpacking source...
>>> Unpacking dssp-3.0.11.tar.gz to /var/tmp/portage/sci-chemistry/dssp-3.0.11/work
>>> Source unpacked in /var/tmp/portage/sci-chemistry/dssp-3.0.11/work
>>> Preparing source in /var/tmp/portage/sci-chemistry/dssp-3.0.11/work/hssp-3.0.11 ...
 * Running eautoreconf in '/var/tmp/portage/sci-chemistry/dssp-3.0.11/work/hssp-3.0.11' ...
 * Running 'aclocal' ...
 [ ok ]
 * Running 'autoconf --force' ...
 [ ok ]
 * Running 'autoheader' ...
 [ ok ]
 * Running 'automake --add-missing --copy --force-missing' ...
 [ ok ]
 * Running elibtoolize in: hssp-3.0.11/
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-chemistry/dssp-3.0.11/work/hssp-3.0.11 ...
 * econf: updating hssp-3.0.11/config.sub with /usr/share/gnuconfig/config.sub
 * econf: updating hssp-3.0.11/config.guess with /usr/share/gnuconfig/config.guess
./configure --prefix=/usr --build=i686-pc-linux-gnu --host=i686-pc-linux-gnu --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/dssp-3.0.11 --htmldir=/usr/share/doc/dssp-3.0.11/html --libdir=/usr/lib
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 nested variables... yes
checking for i686-pc-linux-gnu-g++... i686-pc-linux-gnu-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 i686-pc-linux-gnu-g++ accepts -g... yes
checking for i686-pc-linux-gnu-g++ option to enable C++11 features... none needed
checking whether make supports the include directive... yes (GNU style)
checking dependency style of i686-pc-linux-gnu-g++... none
checking for i686-pc-linux-gnu-gcc... i686-pc-linux-gnu-gcc
checking whether the compiler supports GNU C... yes
checking whether i686-pc-linux-gnu-gcc accepts -g... yes
checking for i686-pc-linux-gnu-gcc option to enable C11 features... none needed
checking whether i686-pc-linux-gnu-gcc understands -c and -o together... yes
checking dependency style of i686-pc-linux-gnu-gcc... none
checking for perl... perl
checking for cppcheck... no
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking for boostlib >= 1.48... yes
checking whether the Boost::Date_Time library is available... yes
checking for exit in -lboost_date_time-mt... yes
checking whether the Boost::Filesystem library is available... yes
checking for exit in -lboost_filesystem... yes
checking whether the Boost::IOStreams library is available... yes
checking for exit in -lboost_iostreams-mt... yes
checking whether the Boost::Program_Options library is available... yes
checking for exit in -lboost_program_options-mt... yes
checking whether the Boost::Regex library is available... yes
checking for exit in -lboost_regex-mt... yes
checking whether the Boost::System library is available... yes
checking for exit in -lboost_system... yes
checking whether the Boost::Thread library is available... yes
checking for exit in -lboost_thread... yes
checking whether the Boost::Unit_Test_Framework library is available... yes
checking for main in -lzeep... no
configure: WARNING: libzeep not found - fetch-dbrefs is disabled in mkhssp
./configure: line 7814: test: : integer expression expected
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 bzlib.h... yes
checking for main in -lbz2... yes
checking for zlib.h... yes
checking for main in -lz... yes
checking for sys/ioctl.h... yes
checking for termios.h... yes
checking for _Bool... yes
checking for stdbool.h that conforms to C99... yes
checking for inline... inline
checking for int16_t... yes
checking for int32_t... yes
checking for int64_t... yes
checking for int8_t... yes
checking for size_t... yes
checking for uint16_t... yes
checking for uint32_t... yes
checking for uint64_t... yes
checking for uint8_t... yes
checking for error_at_line... yes
checking for pid_t... yes
checking for fork... yes
checking for vfork... yes
checking for working fork... yes
checking for working vfork... (cached) yes
checking for dup2... yes
checking for floor... no
checking for pow... no
checking for socket... yes
checking for sqrt... no
checking for strchr... yes
checking for strerror... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
config.status: executing depfiles commands
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-chemistry/dssp-3.0.11/work/hssp-3.0.11 ...
make -j9 -l9 
perl mtrx/mkmat_h.pl mtrx/
make  all-am
make[1]: Entering directory '/var/tmp/portage/sci-chemistry/dssp-3.0.11/work/hssp-3.0.11'
i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Wno-reorder -pthread -I/usr/include   -I./src/   -O2 -march=i686 -pipe -fdiagnostics-color=always -frecord-gcc-switches -c -o tests/test_readpdb.o tests/test_readpdb.cpp
i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Wno-reorder -pthread -I/usr/include   -I./src/   -O2 -march=i686 -pipe -fdiagnostics-color=always -frecord-gcc-switches -c -o src/structure.o src/structure.cpp
In file included from /usr/include/boost/math/tools/cxx03_warn.hpp:9,
                 from /usr/include/boost/math/quaternion.hpp:28,
                 from src/primitives-3d.h:16,
                 from src/structure.h:11,
                 from src/structure.cpp:9:
/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Wno-reorder -pthread -I/usr/include   -I./src/   -O2 -march=i686 -pipe -fdiagnostics-color=always -frecord-gcc-switches -c -o src/utils.o src/utils.cpp
In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
                 from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23,
                 from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
                 from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42,
                 from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
                 from /usr/include/boost/smart_ptr/shared_ptr.hpp:29,
                 from /usr/include/boost/shared_ptr.hpp:17,
                 from /usr/include/boost/format/alt_sstream.hpp:22,
                 from /usr/include/boost/format/internals.hpp:24,
                 from /usr/include/boost/format.hpp:38,
                 from src/utils.h:15,
                 from src/utils.cpp:7:
/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Wno-reorder -pthread -I/usr/include   -I./src/   -O2 -march=i686 -pipe -fdiagnostics-color=always -frecord-gcc-switches -c -o src/blast.o src/blast.cpp
i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Wno-reorder -pthread -I/usr/include   -I./src/   -O2 -march=i686 -pipe -fdiagnostics-color=always -frecord-gcc-switches -c -o src/fasta.o src/fasta.cpp
i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Wno-reorder -pthread -I/usr/include   -I./src/   -O2 -march=i686 -pipe -fdiagnostics-color=always -frecord-gcc-switches -c -o src/hssp-nt.o src/hssp-nt.cpp
i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Wno-reorder -pthread -I/usr/include   -I./src/   -O2 -march=i686 -pipe -fdiagnostics-color=always -frecord-gcc-switches -c -o src/matrix.o src/matrix.cpp
In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
                 from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23,
                 from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
                 from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42,
                 from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
                 from /usr/include/boost/smart_ptr/shared_ptr.hpp:29,
                 from /usr/include/boost/shared_ptr.hpp:17,
                 from /usr/include/boost/format/alt_sstream.hpp:22,
                 from /usr/include/boost/format/internals.hpp:24,
                 from /usr/include/boost/format.hpp:38,
                 from src/utils.h:15,
                 from src/matrix.cpp:12:
/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Wno-reorder -pthread -I/usr/include   -I./src/   -O2 -march=i686 -pipe -fdiagnostics-color=always -frecord-gcc-switches -c -o src/mkhssp.o src/mkhssp.cpp
i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Wno-reorder -pthread -I/usr/include   -I./src/   -O2 -march=i686 -pipe -fdiagnostics-color=always -frecord-gcc-switches -c -o src/progress.o src/progress.cpp
In file included from /usr/include/boost/bind.hpp:30,
                 from src/progress.cpp:19:
/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Wno-reorder -pthread -I/usr/include   -I./src/   -O2 -march=i686 -pipe -fdiagnostics-color=always -frecord-gcc-switches -c -o src/hssp-convert-3to1.o src/hssp-convert-3to1.cpp
i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Wno-reorder -pthread -I/usr/include   -I./src/   -O2 -march=i686 -pipe -fdiagnostics-color=always -frecord-gcc-switches -c -o src/hsspconv.o src/hsspconv.cpp
i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Wno-reorder -pthread -I/usr/include   -I./src/   -O2 -march=i686 -pipe -fdiagnostics-color=always -frecord-gcc-switches -c -o src/primitives-3d.o src/primitives-3d.cpp
i686-pc-linux-gnu-g++  -O2 -march=i686 -pipe -fdiagnostics-color=always -frecord-gcc-switches -L/usr/lib   -O2 -march=i686 -pipe -fdiagnostics-color=always -frecord-gcc-switches -Wl,--defsym=__gentoo_check_ldflags__=0 -Wl,-O1 -Wl,--as-needed -o hsspconv src/hssp-convert-3to1.o src/hsspconv.o src/utils.o -lboost_date_time-mt -lboost_filesystem -lboost_iostreams-mt -lboost_program_options-mt -lboost_regex-mt -lboost_system -lboost_thread -lpthread 
i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Wno-reorder -pthread -I/usr/include   -I./src/   -O2 -march=i686 -pipe -fdiagnostics-color=always -frecord-gcc-switches -c -o src/mkdssp.o src/mkdssp.cpp
i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Wno-reorder -pthread -I/usr/include   -I./src/   -O2 -march=i686 -pipe -fdiagnostics-color=always -frecord-gcc-switches -c -o src/mas.o src/mas.cpp
i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Wno-reorder -pthread -I/usr/include   -I./src/   -O2 -march=i686 -pipe -fdiagnostics-color=always -frecord-gcc-switches -c -o src/iocif.o src/iocif.cpp
i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Wno-reorder -pthread -I/usr/include   -I./src/   -O2 -march=i686 -pipe -fdiagnostics-color=always -frecord-gcc-switches -c -o src/dssp.o src/dssp.cpp
In file included from /usr/include/boost/math/tools/cxx03_warn.hpp:9,
                 from /usr/include/boost/math/quaternion.hpp:28,
                 from src/primitives-3d.h:16,
                 from src/structure.h:11,
                 from src/dssp.cpp:14:
/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
i686-pc-linux-gnu-g++  -O2 -march=i686 -pipe -fdiagnostics-color=always -frecord-gcc-switches -L/usr/lib   -O2 -march=i686 -pipe -fdiagnostics-color=always -frecord-gcc-switches -Wl,--defsym=__gentoo_check_ldflags__=0 -Wl,-O1 -Wl,--as-needed -o test_readpdb src/fasta.o src/iocif.o src/mas.o src/primitives-3d.o src/structure.o src/utils.o tests/test_readpdb.o -lboost_date_time-mt -lboost_filesystem -lboost_iostreams-mt -lboost_program_options-mt -lboost_regex-mt -lboost_system -lboost_thread -lpthread -lboost_unit_test_framework-mt 
i686-pc-linux-gnu-g++  -O2 -march=i686 -pipe -fdiagnostics-color=always -frecord-gcc-switches -L/usr/lib   -O2 -march=i686 -pipe -fdiagnostics-color=always -frecord-gcc-switches -Wl,--defsym=__gentoo_check_ldflags__=0 -Wl,-O1 -Wl,--as-needed -o mkhssp src/blast.o src/dssp.o src/fasta.o src/hssp-nt.o src/iocif.o src/mas.o src/matrix.o src/mkhssp.o src/primitives-3d.o src/progress.o src/structure.o src/utils.o  -lboost_date_time-mt -lboost_filesystem -lboost_iostreams-mt -lboost_program_options-mt -lboost_regex-mt -lboost_system -lboost_thread -lpthread -lboost_timer  
i686-pc-linux-gnu-g++  -O2 -march=i686 -pipe -fdiagnostics-color=always -frecord-gcc-switches -L/usr/lib   -O2 -march=i686 -pipe -fdiagnostics-color=always -frecord-gcc-switches -Wl,--defsym=__gentoo_check_ldflags__=0 -Wl,-O1 -Wl,--as-needed -o mkdssp src/dssp.o src/iocif.o src/mas.o src/mkdssp.o src/primitives-3d.o src/structure.o src/utils.o -lboost_date_time-mt -lboost_filesystem -lboost_iostreams-mt -lboost_program_options-mt -lboost_regex-mt -lboost_system -lboost_thread -lpthread 
i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Wno-reorder -pthread -I/usr/include   -I./src/   -O2 -march=i686 -pipe -fdiagnostics-color=always -frecord-gcc-switches -c -o tests/test_conv.o tests/test_conv.cpp
i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I.  -std=c++11 -pedantic -Wall -Wno-reorder -pthread -I/usr/include   -I./src/   -O2 -march=i686 -pipe -fdiagnostics-color=always -frecord-gcc-switches -c -o tests/test_fasta.o tests/test_fasta.cpp
i686-pc-linux-gnu-g++  -O2 -march=i686 -pipe -fdiagnostics-color=always -frecord-gcc-switches -L/usr/lib   -O2 -march=i686 -pipe -fdiagnostics-color=always -frecord-gcc-switches -Wl,--defsym=__gentoo_check_ldflags__=0 -Wl,-O1 -Wl,--as-needed -o test_conv src/hssp-convert-3to1.o src/utils.o src/mas.o tests/test_conv.o -lboost_date_time-mt -lboost_filesystem -lboost_iostreams-mt -lboost_program_options-mt -lboost_regex-mt -lboost_system -lboost_thread -lpthread -lboost_unit_test_framework-mt 
i686-pc-linux-gnu-g++  -O2 -march=i686 -pipe -fdiagnostics-color=always -frecord-gcc-switches -L/usr/lib   -O2 -march=i686 -pipe -fdiagnostics-color=always -frecord-gcc-switches -Wl,--defsym=__gentoo_check_ldflags__=0 -Wl,-O1 -Wl,--as-needed -o test_fasta src/fasta.o src/iocif.o src/mas.o src/primitives-3d.o src/structure.o src/utils.o tests/test_fasta.o -lboost_date_time-mt -lboost_filesystem -lboost_iostreams-mt -lboost_program_options-mt -lboost_regex-mt -lboost_system -lboost_thread -lpthread -lboost_unit_test_framework-mt 
make[1]: Leaving directory '/var/tmp/portage/sci-chemistry/dssp-3.0.11/work/hssp-3.0.11'
>>> Source compiled.
>>> Test phase: sci-chemistry/dssp-3.0.11
make -j9 -l9   check
yes --quiet --enable=style ./src ./test
yes: unrecognized option '--quiet'
Try 'yes --help' for more information.
make: *** [Makefile:1118: cppcheck] Error 1
 * ERROR: sci-chemistry/dssp-3.0.11::gentoo failed (test phase):
 *   Make check failed. See above for details.
 * 
 * Call stack:
 *            ebuild.sh, line  127:  Called src_test
 *          environment, line 1579:  Called default
 *   phase-functions.sh, line  858:  Called default_src_test
 *   phase-functions.sh, line  887:  Called __eapi0_src_test
 *     phase-helpers.sh, line  809:  Called die
 * The specific snippet of code:
 *   		$emake_cmd ${internal_opts} check || \
 *   			die "Make check failed. See above for details."
 * 
 * If you need support, post the output of `emerge --info '=sci-chemistry/dssp-3.0.11::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-chemistry/dssp-3.0.11::gentoo'`.
 * The complete build log is located at '/var/tmp/portage/sci-chemistry/dssp-3.0.11/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/dssp-3.0.11/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-chemistry/dssp-3.0.11/work/hssp-3.0.11'
 * S: '/var/tmp/portage/sci-chemistry/dssp-3.0.11/work/hssp-3.0.11'