sci-biology:goby-cpp-2.0.1:20160608-180617.log

sci-biology:goby-cpp-2.0.1:20160608-180617.log (text/plain), 20.13 KB, created by Toralf Förster on 2016-06-08 18:11:12 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_beta2/work/protobuf-3.0.0-beta-2/src/google/protobuf/compiler/parser.cc:547] No syntax specified for the proto file. 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_beta2/work/protobuf-3.0.0-beta-2/src/google/protobuf/compiler/parser.cc:547] No syntax specified for the proto file. 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
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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
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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
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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
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checking for /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files... -r
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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
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checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E
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checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
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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
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checking size of unsigned long... 8
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checking fcntl.h usability... yes
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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
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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
/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.pb.lo `test -f 'goby/Alignments.pb.cc' || echo '/var/tmp/portage/sci-biology/goby-cpp-2.0.1/work/2.0.1/cpp/src/'`goby/Alignments.pb.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.pb.cc  -fPIC -DPIC -o .libs/Alignments.pb.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 common.lo `test -f 'goby/common.cc' || echo '/var/tmp/portage/sci-biology/goby-cpp-2.0.1/work/2.0.1/cpp/src/'`goby/common.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/common.cc  -fPIC -DPIC -o .libs/common.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 Reads.lo `test -f 'goby/Reads.cc' || echo '/var/tmp/portage/sci-biology/goby-cpp-2.0.1/work/2.0.1/cpp/src/'`goby/Reads.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/Reads.cc  -fPIC -DPIC -o .libs/Reads.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 Reads.pb.lo `test -f 'goby/Reads.pb.cc' || echo '/var/tmp/portage/sci-biology/goby-cpp-2.0.1/work/2.0.1/cpp/src/'`goby/Reads.pb.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/Reads.pb.cc  -fPIC -DPIC -o .libs/Reads.pb.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 TooManyHits.lo `test -f 'goby/TooManyHits.cc' || echo '/var/tmp/portage/sci-biology/goby-cpp-2.0.1/work/2.0.1/cpp/src/'`goby/TooManyHits.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/TooManyHits.cc  -fPIC -DPIC -o .libs/TooManyHits.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 C_Gsnap.lo `test -f 'goby/C_Gsnap.cc' || echo '/var/tmp/portage/sci-biology/goby-cpp-2.0.1/work/2.0.1/cpp/src/'`goby/C_Gsnap.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/C_Gsnap.cc  -fPIC -DPIC -o .libs/C_Gsnap.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 C_Reads.lo `test -f 'goby/C_Reads.cc' || echo '/var/tmp/portage/sci-biology/goby-cpp-2.0.1/work/2.0.1/cpp/src/'`goby/C_Reads.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/C_Reads.cc  -fPIC -DPIC -o .libs/C_Reads.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 C_Alignments.lo `test -f 'goby/C_Alignments.cc' || echo '/var/tmp/portage/sci-biology/goby-cpp-2.0.1/work/2.0.1/cpp/src/'`goby/C_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/C_Alignments.cc  -fPIC -DPIC -o .libs/C_Alignments.o
/bin/sh ../libtool  --tag=CXX   --mode=link x86_64-pc-linux-gnu-g++ -pthread      -march=native -O2 -pipe -version-info 1:0:0 -export-dynamic  -Wl,-O1 -Wl,--as-needed -o libgoby.la -rpath /usr/lib64 ICBFileInputStream.lo Alignments.lo Alignments.pb.lo common.lo Reads.lo Reads.pb.lo TooManyHits.lo C_Gsnap.lo C_Reads.lo C_Alignments.lo -lprotobuf -pthread  -lpthread   -lpcrecpp   
libtool: link: x86_64-pc-linux-gnu-g++  -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/../../../../lib64/crti.o /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/crtbeginS.o  .libs/ICBFileInputStream.o .libs/Alignments.o .libs/Alignments.pb.o .libs/common.o .libs/Reads.o .libs/Reads.pb.o .libs/TooManyHits.o .libs/C_Gsnap.o .libs/C_Reads.o .libs/C_Alignments.o   -Wl,--as-needed /usr/lib64/libprotobuf.so -lz -lpthread -lpcrecpp -L/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0 -L/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/crtendS.o /usr/lib/gcc/x86_64-pc-linux-gnu/5.3.0/../../../../lib64/crtn.o  -pthread -march=native -O2 -Wl,-O1 -pthread   -pthread -Wl,-soname -Wl,libgoby.so.1 -o .libs/libgoby.so.1.0.0
libtool: link: (cd ".libs" && rm -f "libgoby.so.1" && ln -s "libgoby.so.1.0.0" "libgoby.so.1")
libtool: link: (cd ".libs" && rm -f "libgoby.so" && ln -s "libgoby.so.1.0.0" "libgoby.so")
libtool: link: ( cd ".libs" && rm -f "libgoby.la" && ln -s "../libgoby.la" "libgoby.la" )
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 GobyAlignmentStats.o /var/tmp/portage/sci-biology/goby-cpp-2.0.1/work/2.0.1/cpp/src/GobyAlignmentStats.cc
/bin/sh ../libtool  --tag=CXX   --mode=link x86_64-pc-linux-gnu-g++ -pthread      -march=native -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o GobyAlignmentStats GobyAlignmentStats.o libgoby.la     
libtool: link: x86_64-pc-linux-gnu-g++ -pthread -march=native -O2 -pipe -Wl,-O1 -o .libs/GobyAlignmentStats GobyAlignmentStats.o  -Wl,--as-needed ./.libs/libgoby.so /usr/lib64/libprotobuf.so -lz -lpthread -lpcrecpp -pthread
./.libs/libgoby.so: undefined reference to `pcrecpp::RE::Init(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, pcrecpp::RE_Options const*)'
collect2: error: ld returned 1 exit status
make[3]: *** [Makefile:600: GobyAlignmentStats] 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-2.0.1:20160608-180617.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'