sci-biology:goby-cpp-2.0.1:20161013-095220.log

sci-biology:goby-cpp-2.0.1:20161013-095220.log (text/plain), 13.10 KB, created by Toralf Förster on 2016-10-13 14:52:36 UTC

 * Package:    sci-biology/goby-cpp-2.0.1
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU
 * FEATURES:   preserve-libs sandbox userpriv usersandbox
>>> Unpacking source...
>>> Unpacking goby_2.0.1-cpp.zip to /var/tmp/portage/sci-biology/goby-cpp-2.0.1/work
>>> Source unpacked in /var/tmp/portage/sci-biology/goby-cpp-2.0.1/work
>>> Preparing source in /var/tmp/portage/sci-biology/goby-cpp-2.0.1/work/2.0.1/cpp ...
[libprotobuf WARNING /var/tmp/portage/dev-libs/protobuf-3.0.0_beta3_p1/work/protobuf-3.0.0-beta-3.1/src/google/protobuf/compiler/parser.cc:547] No syntax specified for the proto file: Alignments.proto. Please use 'syntax = "proto2";' or 'syntax = "proto3";' to specify a syntax version. (Defaulted to proto2 syntax.)
[libprotobuf WARNING /var/tmp/portage/dev-libs/protobuf-3.0.0_beta3_p1/work/protobuf-3.0.0-beta-3.1/src/google/protobuf/compiler/parser.cc:547] No syntax specified for the proto file: Reads.proto. Please use 'syntax = "proto2";' or 'syntax = "proto3";' to specify a syntax version. (Defaulted to proto2 syntax.)
 * Applying goby-cpp-2.0.1-underlinking.patch ...
 [ ok ]
 * Running eautoreconf in '/var/tmp/portage/sci-biology/goby-cpp-2.0.1/work/2.0.1/cpp' ...
 * Running libtoolize --install --copy --force --automake ...
 [ ok ]
 * Running aclocal -I m4 ...
 [ ok ]
 * Running autoconf --force ...
 [ ok ]
 * Running autoheader ...
 [ ok ]
 * Running automake --add-missing --copy --foreign --force-missing ...
 [ ok ]
 * Running elibtoolize in: 2.0.1/cpp/
 *   Applying portage/1.2.0 patch ...
 *   Applying sed/1.5.6 patch ...
 *   Applying as-needed/2.4.3 patch ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/goby-cpp-2.0.1/work/2.0.1/cpp ...
>>> Working in BUILD_DIR: "/var/tmp/portage/sci-biology/goby-cpp-2.0.1/work/goby-cpp-2.0.1_build"
 * econf: updating 2.0.1/cpp/config.sub with /usr/share/gnuconfig/config.sub
 * econf: updating 2.0.1/cpp/config.guess with /usr/share/gnuconfig/config.guess
/var/tmp/portage/sci-biology/goby-cpp-2.0.1/work/2.0.1/cpp/configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-dependency-tracking --disable-silent-rules --libdir=/usr/lib64 --docdir=/usr/share/doc/goby-cpp-2.0.1 --enable-shared --disable-static
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking target system type... x86_64-pc-linux-gnu
checking for a BSD-compatible install... /usr/lib/portage/python3.4/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 x86_64-pc-linux-gnu-g++... x86_64-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 we are using the GNU C++ compiler... yes
checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of x86_64-pc-linux-gnu-g++... none
checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
checking whether we are using the GNU C compiler... yes
checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes
checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed
checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... yes
checking dependency style of x86_64-pc-linux-gnu-gcc... none
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by x86_64-pc-linux-gnu-gcc... /usr/x86_64-pc-linux-gnu/bin/ld
checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/x86_64-pc-linux-gnu-nm -B
checking the name lister (/usr/bin/x86_64-pc-linux-gnu-nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files... -r
checking for x86_64-pc-linux-gnu-objdump... x86_64-pc-linux-gnu-objdump
checking how to recognize dependent libraries... pass_all
checking for x86_64-pc-linux-gnu-dlltool... no
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for x86_64-pc-linux-gnu-ar... x86_64-pc-linux-gnu-ar
checking for archiver @FILE support... @
checking for x86_64-pc-linux-gnu-strip... x86_64-pc-linux-gnu-strip
checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib
checking command to parse /usr/bin/x86_64-pc-linux-gnu-nm -B output from x86_64-pc-linux-gnu-gcc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for x86_64-pc-linux-gnu-mt... no
checking for mt... mt
checking if mt is a manifest tool... no
checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E
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 x86_64-pc-linux-gnu-gcc supports -fno-rtti -fno-exceptions... no
checking for x86_64-pc-linux-gnu-gcc option to produce PIC... -fPIC -DPIC
checking if x86_64-pc-linux-gnu-gcc PIC flag -fPIC -DPIC works... yes
checking if x86_64-pc-linux-gnu-gcc static flag -static works... yes
checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... yes
checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... (cached) yes
checking whether the x86_64-pc-linux-gnu-gcc linker (/usr/x86_64-pc-linux-gnu/bin/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... no
checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E
checking for ld used by x86_64-pc-linux-gnu-g++... /usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64
checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for x86_64-pc-linux-gnu-g++ option to produce PIC... -fPIC -DPIC
checking if x86_64-pc-linux-gnu-g++ PIC flag -fPIC -DPIC works... yes
checking if x86_64-pc-linux-gnu-g++ static flag -static works... yes
checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... yes
checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... (cached) yes
checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for stdbool.h that conforms to C99... no
checking for _Bool... no
checking for ANSI C header files... (cached) yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for off_t... yes
checking for size_t... yes
checking size of unsigned long... 8
checking size of unsigned long long... 8
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking for getcwd... yes
checking for memset... yes
checking for putenv... yes
checking for realpath... yes
checking for setenv... yes
checking for strerror... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking whether lstat correctly handles trailing slash... yes
checking whether stat accepts an empty string... no
checking whether lstat correctly handles trailing slash... (cached) yes
checking for x86_64-pc-linux-gnu-pkg-config... /usr/bin/x86_64-pc-linux-gnu-pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for PROTOBUF... yes
checking for LIBPCRECPP... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating goby.pc
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/goby-cpp-2.0.1/work/2.0.1/cpp ...
>>> Working in BUILD_DIR: "/var/tmp/portage/sci-biology/goby-cpp-2.0.1/work/goby-cpp-2.0.1_build"
make -j1 
make  all-recursive
make[1]: Entering directory '/var/tmp/portage/sci-biology/goby-cpp-2.0.1/work/goby-cpp-2.0.1_build'
Making all in .
make[2]: Entering directory '/var/tmp/portage/sci-biology/goby-cpp-2.0.1/work/goby-cpp-2.0.1_build'
make[2]: Leaving directory '/var/tmp/portage/sci-biology/goby-cpp-2.0.1/work/goby-cpp-2.0.1_build'
Making all in src
make[2]: Entering directory '/var/tmp/portage/sci-biology/goby-cpp-2.0.1/work/goby-cpp-2.0.1_build/src'
echo '#define BUILD_TIMESTAMP "'`date "+%G%m%d%k%M%S"  | sed 's/ //g'`'"' > /var/tmp/portage/sci-biology/goby-cpp-2.0.1/work/2.0.1/cpp/src/goby/timestamp.h
make  all-am
make[3]: Entering directory '/var/tmp/portage/sci-biology/goby-cpp-2.0.1/work/goby-cpp-2.0.1_build/src'
/bin/sh ../libtool  --tag=CXX   --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/var/tmp/portage/sci-biology/goby-cpp-2.0.1/work/2.0.1/cpp/src -I..    -pthread   -march=native -O2 -pipe -c -o ICBFileInputStream.lo `test -f 'goby/ICBFileInputStream.cc' || echo '/var/tmp/portage/sci-biology/goby-cpp-2.0.1/work/2.0.1/cpp/src/'`goby/ICBFileInputStream.cc
libtool: compile:  x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/var/tmp/portage/sci-biology/goby-cpp-2.0.1/work/2.0.1/cpp/src -I.. -pthread -march=native -O2 -pipe -c /var/tmp/portage/sci-biology/goby-cpp-2.0.1/work/2.0.1/cpp/src/goby/ICBFileInputStream.cc  -fPIC -DPIC -o .libs/ICBFileInputStream.o
/bin/sh ../libtool  --tag=CXX   --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/var/tmp/portage/sci-biology/goby-cpp-2.0.1/work/2.0.1/cpp/src -I..    -pthread   -march=native -O2 -pipe -c -o Alignments.lo `test -f 'goby/Alignments.cc' || echo '/var/tmp/portage/sci-biology/goby-cpp-2.0.1/work/2.0.1/cpp/src/'`goby/Alignments.cc
libtool: compile:  x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I/var/tmp/portage/sci-biology/goby-cpp-2.0.1/work/2.0.1/cpp/src -I.. -pthread -march=native -O2 -pipe -c /var/tmp/portage/sci-biology/goby-cpp-2.0.1/work/2.0.1/cpp/src/goby/Alignments.cc  -fPIC -DPIC -o .libs/Alignments.o
/var/tmp/portage/sci-biology/goby-cpp-2.0.1/work/2.0.1/cpp/src/goby/Alignments.cc:31:44: fatal error: google/protobuf/io/gzip_stream.h: No such file or directory
 #include <google/protobuf/io/gzip_stream.h>
                                            ^
compilation terminated.
make[3]: *** [Makefile:695: Alignments.lo] Error 1
make[3]: Leaving directory '/var/tmp/portage/sci-biology/goby-cpp-2.0.1/work/goby-cpp-2.0.1_build/src'
make[2]: *** [Makefile:473: all] Error 2
make[2]: Leaving directory '/var/tmp/portage/sci-biology/goby-cpp-2.0.1/work/goby-cpp-2.0.1_build/src'
make[1]: *** [Makefile:494: all-recursive] Error 1
make[1]: Leaving directory '/var/tmp/portage/sci-biology/goby-cpp-2.0.1/work/goby-cpp-2.0.1_build'
make: *** [Makefile:403: all] Error 2
 * ERROR: sci-biology/goby-cpp-2.0.1::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/goby-cpp-2.0.1::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/goby-cpp-2.0.1::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-biology:goby-cpp-2.0.1:20161013-095220.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/goby-cpp-2.0.1/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/goby-cpp-2.0.1/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/goby-cpp-2.0.1/work/goby-cpp-2.0.1_build'
 * S: '/var/tmp/portage/sci-biology/goby-cpp-2.0.1/work/2.0.1/cpp'