* Package: sci-biology/express-1.5.1 * Repository: gentoo * Maintainer: sci-biology@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU * FEATURES: preserve-libs sandbox userpriv usersandbox >>> Unpacking source... >>> Unpacking express-1.5.1-src.tgz to /var/tmp/portage/sci-biology/express-1.5.1/work >>> Source unpacked in /var/tmp/portage/sci-biology/express-1.5.1/work >>> Preparing source in /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1-src ... * Applying express-1.5.1-buildsystem.patch ... [ ok ] >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1-src ... >>> Working in BUILD_DIR: "/var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build" cmake --no-warn-unused-cli -C /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build/gentoo_common_config.cmake -G Unix Makefiles -DCMAKE_INSTALL_PREFIX=/usr -DBAMTOOLS_INCLUDE=/usr/include/bamtools -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_INSTALL_DO_STRIP=OFF -DCMAKE_USER_MAKE_RULES_OVERRIDE=/var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build/gentoo_rules.cmake -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build/gentoo_toolchain.cmake /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1-src Not searching for unused variables given on the command line. loading initial cache file /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build/gentoo_common_config.cmake -- The C compiler identification is GNU 6.3.0 -- The CXX compiler identification is GNU 6.3.0 -- Check for working C compiler: /usr/bin/x86_64-pc-linux-gnu-gcc -- Check for working C compiler: /usr/bin/x86_64-pc-linux-gnu-gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/x86_64-pc-linux-gnu-g++ -- Check for working CXX compiler: /usr/bin/x86_64-pc-linux-gnu-g++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Boost version: 1.63.0 -- Found the following Boost libraries: -- thread -- system -- filesystem -- program_options -- date_time -- chrono -- atomic -- Found GPERFTOOLS_TCMALLOC: /usr/lib64/libtcmalloc.so -- Found Protobuf: /usr/lib64/libprotobuf.so;-lpthread (found version "3.1.0") -- Found ZLIB: /usr/lib64/libz.so (found version "1.2.11") -- <<< Gentoo configuration >>> Build type Gentoo Install path /usr Compiler flags: C -O2 -pipe -march=native -Wall C++ -Werror=terminate -O2 -pipe -march=native Linker flags: Executable -Wl,-O1 -Wl,--as-needed Module -Wl,-O1 -Wl,--as-needed Shared -Wl,-O1 -Wl,--as-needed -- Configuring done -- Generating done -- Build files have been written to: /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1-src ... >>> Working in BUILD_DIR: "/var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build" make -j1 VERBOSE=1 /usr/bin/cmake -H/var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1-src -B/var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build/CMakeFiles /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[1]: Entering directory '/var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build' make -f src/CMakeFiles/express.dir/build.make src/CMakeFiles/express.dir/depend make[2]: Entering directory '/var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build' [ 5%] Running C++ protocol buffer compiler on /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1-src/src/targets.proto cd /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build/src && /usr/bin/protoc --cpp_out /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build/src -I /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1-src/src /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1-src/src/targets.proto [libprotobuf WARNING /var/tmp/portage/dev-libs/protobuf-3.1.0/work/protobuf-3.1.0/src/google/protobuf/compiler/parser.cc:546] No syntax specified for the proto file: targets.proto. Please use 'syntax = "proto2";' or 'syntax = "proto3";' to specify a syntax version. (Defaulted to proto2 syntax.) [ 11%] Running C++ protocol buffer compiler on /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1-src/src/alignments.proto cd /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build/src && /usr/bin/protoc --cpp_out /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build/src -I /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1-src/src /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1-src/src/alignments.proto [libprotobuf WARNING /var/tmp/portage/dev-libs/protobuf-3.1.0/work/protobuf-3.1.0/src/google/protobuf/compiler/parser.cc:546] 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.) cd /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1-src /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1-src/src /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build/src /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build/src/CMakeFiles/express.dir/DependInfo.cmake Dependee "/var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build/src/CMakeFiles/express.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build/src/CMakeFiles/express.dir/depend.internal". Dependee "/var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build/src/CMakeFiles/express.dir/depend.internal". Scanning dependencies of target express make[2]: Leaving directory '/var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build' make -f src/CMakeFiles/express.dir/build.make src/CMakeFiles/express.dir/build make[2]: Entering directory '/var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build' [ 16%] Building CXX object src/CMakeFiles/express.dir/biascorrection.cpp.o cd /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build/src && /usr/bin/x86_64-pc-linux-gnu-g++ -I/usr/include/bamtools -DNDEBUG -Werror=terminate -O2 -pipe -march=native -o CMakeFiles/express.dir/biascorrection.cpp.o -c /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1-src/src/biascorrection.cpp [ 22%] Building CXX object src/CMakeFiles/express.dir/bundles.cpp.o cd /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build/src && /usr/bin/x86_64-pc-linux-gnu-g++ -I/usr/include/bamtools -DNDEBUG -Werror=terminate -O2 -pipe -march=native -o CMakeFiles/express.dir/bundles.cpp.o -c /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1-src/src/bundles.cpp [ 27%] Building CXX object src/CMakeFiles/express.dir/directiondetector.cpp.o cd /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build/src && /usr/bin/x86_64-pc-linux-gnu-g++ -I/usr/include/bamtools -DNDEBUG -Werror=terminate -O2 -pipe -march=native -o CMakeFiles/express.dir/directiondetector.cpp.o -c /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1-src/src/directiondetector.cpp [ 33%] Building CXX object src/CMakeFiles/express.dir/fragments.cpp.o cd /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build/src && /usr/bin/x86_64-pc-linux-gnu-g++ -I/usr/include/bamtools -DNDEBUG -Werror=terminate -O2 -pipe -march=native -o CMakeFiles/express.dir/fragments.cpp.o -c /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1-src/src/fragments.cpp [ 38%] Building CXX object src/CMakeFiles/express.dir/lengthdistribution.cpp.o cd /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build/src && /usr/bin/x86_64-pc-linux-gnu-g++ -I/usr/include/bamtools -DNDEBUG -Werror=terminate -O2 -pipe -march=native -o CMakeFiles/express.dir/lengthdistribution.cpp.o -c /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1-src/src/lengthdistribution.cpp [ 44%] Building CXX object src/CMakeFiles/express.dir/main.cpp.o cd /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build/src && /usr/bin/x86_64-pc-linux-gnu-g++ -I/usr/include/bamtools -DNDEBUG -Werror=terminate -O2 -pipe -march=native -o CMakeFiles/express.dir/main.cpp.o -c /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1-src/src/main.cpp [ 50%] Building CXX object src/CMakeFiles/express.dir/mapparser.cpp.o cd /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build/src && /usr/bin/x86_64-pc-linux-gnu-g++ -I/usr/include/bamtools -DNDEBUG -Werror=terminate -O2 -pipe -march=native -o CMakeFiles/express.dir/mapparser.cpp.o -c /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1-src/src/mapparser.cpp [ 55%] Building CXX object src/CMakeFiles/express.dir/markovmodel.cpp.o cd /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build/src && /usr/bin/x86_64-pc-linux-gnu-g++ -I/usr/include/bamtools -DNDEBUG -Werror=terminate -O2 -pipe -march=native -o CMakeFiles/express.dir/markovmodel.cpp.o -c /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1-src/src/markovmodel.cpp [ 61%] Building CXX object src/CMakeFiles/express.dir/mismatchmodel.cpp.o cd /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build/src && /usr/bin/x86_64-pc-linux-gnu-g++ -I/usr/include/bamtools -DNDEBUG -Werror=terminate -O2 -pipe -march=native -o CMakeFiles/express.dir/mismatchmodel.cpp.o -c /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1-src/src/mismatchmodel.cpp [ 66%] Building CXX object src/CMakeFiles/express.dir/robertsfilter.cpp.o cd /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build/src && /usr/bin/x86_64-pc-linux-gnu-g++ -I/usr/include/bamtools -DNDEBUG -Werror=terminate -O2 -pipe -march=native -o CMakeFiles/express.dir/robertsfilter.cpp.o -c /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1-src/src/robertsfilter.cpp [ 72%] Building CXX object src/CMakeFiles/express.dir/sequence.cpp.o cd /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build/src && /usr/bin/x86_64-pc-linux-gnu-g++ -I/usr/include/bamtools -DNDEBUG -Werror=terminate -O2 -pipe -march=native -o CMakeFiles/express.dir/sequence.cpp.o -c /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1-src/src/sequence.cpp [ 77%] Building CXX object src/CMakeFiles/express.dir/targets.cpp.o cd /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build/src && /usr/bin/x86_64-pc-linux-gnu-g++ -I/usr/include/bamtools -DNDEBUG -Werror=terminate -O2 -pipe -march=native -o CMakeFiles/express.dir/targets.cpp.o -c /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1-src/src/targets.cpp /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1-src/src/targets.cpp: In member function ‘double Target::sample_likelihood(bool, const std::vector*) const’: /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1-src/src/targets.cpp:116:62: error: no matching function for call to ‘Target::cached_effective_length(const boost::shared_ptr&) const’ double tot_eff_len = cached_effective_length(lib.bias_table); ^ In file included from /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1-src/src/targets.cpp:10:0: /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1-src/src/targets.h:399:10: note: candidate: double Target::cached_effective_length(bool) const double cached_effective_length(bool with_bias=true) const; ^~~~~~~~~~~~~~~~~~~~~~~ /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1-src/src/targets.h:399:10: note: no known conversion for argument 1 from ‘const boost::shared_ptr’ to ‘bool’ /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1-src/src/targets.cpp:121:77: error: no matching function for call to ‘Target::cached_effective_length(const boost::shared_ptr&) const’ neighbor->cached_effective_length(lib.bias_table)); ^ In file included from /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1-src/src/targets.cpp:10:0: /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1-src/src/targets.h:399:10: note: candidate: double Target::cached_effective_length(bool) const double cached_effective_length(bool with_bias=true) const; ^~~~~~~~~~~~~~~~~~~~~~~ /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1-src/src/targets.h:399:10: note: no known conversion for argument 1 from ‘const boost::shared_ptr’ to ‘bool’ make[2]: *** [src/CMakeFiles/express.dir/build.make:343: src/CMakeFiles/express.dir/targets.cpp.o] Error 1 make[2]: Leaving directory '/var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build' make[1]: *** [CMakeFiles/Makefile2:86: src/CMakeFiles/express.dir/all] Error 2 make[1]: Leaving directory '/var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build' make: *** [Makefile:128: all] Error 2 * ERROR: sci-biology/express-1.5.1::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-biology/express-1.5.1::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-biology/express-1.5.1::gentoo'`. * The complete build log is located at '/var/log/portage/sci-biology:express-1.5.1:20170223-123807.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/express-1.5.1/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/express-1.5.1/temp/environment'. * Working directory: '/var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build' * S: '/var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1-src'