sci-biology:express-1.5.1:20230822-015010.log

sci-biology:express-1.5.1:20230822-015010.log (text/plain), 18.56 KB, created by Toralf Förster on 2023-08-22 11:26:02 UTC

 * Package:    sci-biology/express-1.5.1:0
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux
 * FEATURES:   network-sandbox 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 ...
 * Source directory (CMAKE_USE_DIR): "/var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1-src"
 * Build directory  (BUILD_DIR):     "/var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build"
 * Applying express-1.5.1-buildsystem.patch ...
 [ ok ]
 * Applying express-1.5.1-gcc6.patch ...
 [ ok ]
 * Hardcoded definition(s) removed in CMakeLists.txt:
 *  set(CMAKE_BUILD_TYPE Release)
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1-src ...
 * Source directory (CMAKE_USE_DIR): "/var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1-src"
 * Build directory  (BUILD_DIR):     "/var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build"
cmake -C /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build/gentoo_common_config.cmake -G Ninja -DCMAKE_INSTALL_PREFIX=/usr -DBAMTOOLS_INCLUDE=/usr/include/bamtools -DCMAKE_BUILD_TYPE=Gentoo -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
loading initial cache file /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build/gentoo_common_config.cmake
CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required):
  Compatibility with CMake < 3.5 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.


-- The C compiler identification is GNU 13.2.0
-- The CXX compiler identification is GNU 13.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/x86_64-pc-linux-gnu-gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/x86_64-pc-linux-gnu-g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found Boost: /usr/lib64/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.39") found components: thread system filesystem program_options date_time 
-- Found GPERFTOOLS_TCMALLOC: /usr/lib64/libtcmalloc.so
-- Found Protobuf: /usr/lib64/libprotobuf.so (found version "4.23.3") 
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.13")  
-- <<< Gentoo configuration >>>
Build type      Gentoo
Install path    /usr
Compiler flags:
C               -O2 -pipe -march=native -fno-diagnostics-color
C++             -O2 -pipe -march=native -fno-diagnostics-color
Linker flags:
Executable      -Wl,-O1 -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,--defsym=__gentoo_check_ldflags__=0
Module          -Wl,-O1 -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,--defsym=__gentoo_check_ldflags__=0
Shared          -Wl,-O1 -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,--defsym=__gentoo_check_ldflags__=0

-- Configuring done (1.3s)
-- Generating done (0.0s)
-- 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 ...
 * Source directory (CMAKE_USE_DIR): "/var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1-src"
 * Build directory  (BUILD_DIR):     "/var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build"
ninja -v -j5 -l0
[1/18] 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
[2/18] 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
[3/18] /usr/bin/x86_64-pc-linux-gnu-g++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_DATE_TIME_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -I/usr/include/bamtools  -O2 -pipe -march=native -fno-diagnostics-color -fno-diagnostics-color -MD -MT src/CMakeFiles/express.dir/directiondetector.cpp.o -MF src/CMakeFiles/express.dir/directiondetector.cpp.o.d -o src/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
[4/18] /usr/bin/x86_64-pc-linux-gnu-g++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_DATE_TIME_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -I/usr/include/bamtools  -O2 -pipe -march=native -fno-diagnostics-color -fno-diagnostics-color -MD -MT src/CMakeFiles/express.dir/fragments.cpp.o -MF src/CMakeFiles/express.dir/fragments.cpp.o.d -o src/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
[5/18] /usr/bin/x86_64-pc-linux-gnu-g++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_DATE_TIME_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -I/usr/include/bamtools  -O2 -pipe -march=native -fno-diagnostics-color -fno-diagnostics-color -MD -MT src/CMakeFiles/express.dir/bundles.cpp.o -MF src/CMakeFiles/express.dir/bundles.cpp.o.d -o src/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
[6/18] /usr/bin/x86_64-pc-linux-gnu-g++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_DATE_TIME_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -I/usr/include/bamtools  -O2 -pipe -march=native -fno-diagnostics-color -fno-diagnostics-color -MD -MT src/CMakeFiles/express.dir/biascorrection.cpp.o -MF src/CMakeFiles/express.dir/biascorrection.cpp.o.d -o src/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
[7/18] /usr/bin/x86_64-pc-linux-gnu-g++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_DATE_TIME_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -I/usr/include/bamtools  -O2 -pipe -march=native -fno-diagnostics-color -fno-diagnostics-color -MD -MT src/CMakeFiles/express.dir/lengthdistribution.cpp.o -MF src/CMakeFiles/express.dir/lengthdistribution.cpp.o.d -o src/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
[8/18] /usr/bin/x86_64-pc-linux-gnu-g++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_DATE_TIME_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -I/usr/include/bamtools  -O2 -pipe -march=native -fno-diagnostics-color -fno-diagnostics-color -MD -MT src/CMakeFiles/express.dir/robertsfilter.cpp.o -MF src/CMakeFiles/express.dir/robertsfilter.cpp.o.d -o src/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
[9/18] /usr/bin/x86_64-pc-linux-gnu-g++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_DATE_TIME_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -I/usr/include/bamtools  -O2 -pipe -march=native -fno-diagnostics-color -fno-diagnostics-color -MD -MT src/CMakeFiles/express.dir/markovmodel.cpp.o -MF src/CMakeFiles/express.dir/markovmodel.cpp.o.d -o src/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
[10/18] /usr/bin/x86_64-pc-linux-gnu-g++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_DATE_TIME_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -I/usr/include/bamtools  -O2 -pipe -march=native -fno-diagnostics-color -fno-diagnostics-color -MD -MT src/CMakeFiles/express.dir/mapparser.cpp.o -MF src/CMakeFiles/express.dir/mapparser.cpp.o.d -o src/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
[11/18] /usr/bin/x86_64-pc-linux-gnu-g++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_DATE_TIME_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -I/usr/include/bamtools  -O2 -pipe -march=native -fno-diagnostics-color -fno-diagnostics-color -MD -MT src/CMakeFiles/express.dir/mismatchmodel.cpp.o -MF src/CMakeFiles/express.dir/mismatchmodel.cpp.o.d -o src/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
[12/18] /usr/bin/x86_64-pc-linux-gnu-g++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_DATE_TIME_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -I/usr/include/bamtools  -O2 -pipe -march=native -fno-diagnostics-color -fno-diagnostics-color -MD -MT src/CMakeFiles/express.dir/sequence.cpp.o -MF src/CMakeFiles/express.dir/sequence.cpp.o.d -o src/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
[13/18] /usr/bin/x86_64-pc-linux-gnu-g++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_DATE_TIME_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -I/usr/include/bamtools  -O2 -pipe -march=native -fno-diagnostics-color -fno-diagnostics-color -MD -MT src/CMakeFiles/express.dir/alignments.pb.cc.o -MF src/CMakeFiles/express.dir/alignments.pb.cc.o.d -o src/CMakeFiles/express.dir/alignments.pb.cc.o -c /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build/src/alignments.pb.cc
[14/18] /usr/bin/x86_64-pc-linux-gnu-g++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_DATE_TIME_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -I/usr/include/bamtools  -O2 -pipe -march=native -fno-diagnostics-color -fno-diagnostics-color -MD -MT src/CMakeFiles/express.dir/main.cpp.o -MF src/CMakeFiles/express.dir/main.cpp.o.d -o src/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
[15/18] /usr/bin/x86_64-pc-linux-gnu-g++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_DATE_TIME_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -I/usr/include/bamtools  -O2 -pipe -march=native -fno-diagnostics-color -fno-diagnostics-color -MD -MT src/CMakeFiles/express.dir/threadsafety.cpp.o -MF src/CMakeFiles/express.dir/threadsafety.cpp.o.d -o src/CMakeFiles/express.dir/threadsafety.cpp.o -c /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1-src/src/threadsafety.cpp
[16/18] /usr/bin/x86_64-pc-linux-gnu-g++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_DATE_TIME_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -I/usr/include/bamtools  -O2 -pipe -march=native -fno-diagnostics-color -fno-diagnostics-color -MD -MT src/CMakeFiles/express.dir/targets.cpp.o -MF src/CMakeFiles/express.dir/targets.cpp.o.d -o src/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
[17/18] /usr/bin/x86_64-pc-linux-gnu-g++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_DATE_TIME_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -I/usr/include/bamtools  -O2 -pipe -march=native -fno-diagnostics-color -fno-diagnostics-color -MD -MT src/CMakeFiles/express.dir/targets.pb.cc.o -MF src/CMakeFiles/express.dir/targets.pb.cc.o.d -o src/CMakeFiles/express.dir/targets.pb.cc.o -c /var/tmp/portage/sci-biology/express-1.5.1/work/express-1.5.1_build/src/targets.pb.cc
[18/18] : && /usr/bin/x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -fno-diagnostics-color -Wl,-O1 -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,--defsym=__gentoo_check_ldflags__=0    -rdynamic src/CMakeFiles/express.dir/biascorrection.cpp.o src/CMakeFiles/express.dir/bundles.cpp.o src/CMakeFiles/express.dir/directiondetector.cpp.o src/CMakeFiles/express.dir/fragments.cpp.o src/CMakeFiles/express.dir/lengthdistribution.cpp.o src/CMakeFiles/express.dir/main.cpp.o src/CMakeFiles/express.dir/mapparser.cpp.o src/CMakeFiles/express.dir/markovmodel.cpp.o src/CMakeFiles/express.dir/mismatchmodel.cpp.o src/CMakeFiles/express.dir/robertsfilter.cpp.o src/CMakeFiles/express.dir/sequence.cpp.o src/CMakeFiles/express.dir/targets.cpp.o src/CMakeFiles/express.dir/threadsafety.cpp.o src/CMakeFiles/express.dir/alignments.pb.cc.o src/CMakeFiles/express.dir/targets.pb.cc.o -o src/express  /usr/lib64/libboost_thread.so.1.83.0  /usr/lib64/libboost_system.so.1.83.0  /usr/lib64/libboost_filesystem.so.1.83.0  /usr/lib64/libboost_program_options.so.1.83.0  /usr/lib64/libboost_date_time.so.1.83.0  -lz  -lbamtools  -lpthread  -lprotobuf  /usr/lib64/libboost_atomic.so.1.83.0 && :
FAILED: src/express 
: && /usr/bin/x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -fno-diagnostics-color -Wl,-O1 -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,--defsym=__gentoo_check_ldflags__=0    -rdynamic src/CMakeFiles/express.dir/biascorrection.cpp.o src/CMakeFiles/express.dir/bundles.cpp.o src/CMakeFiles/express.dir/directiondetector.cpp.o src/CMakeFiles/express.dir/fragments.cpp.o src/CMakeFiles/express.dir/lengthdistribution.cpp.o src/CMakeFiles/express.dir/main.cpp.o src/CMakeFiles/express.dir/mapparser.cpp.o src/CMakeFiles/express.dir/markovmodel.cpp.o src/CMakeFiles/express.dir/mismatchmodel.cpp.o src/CMakeFiles/express.dir/robertsfilter.cpp.o src/CMakeFiles/express.dir/sequence.cpp.o src/CMakeFiles/express.dir/targets.cpp.o src/CMakeFiles/express.dir/threadsafety.cpp.o src/CMakeFiles/express.dir/alignments.pb.cc.o src/CMakeFiles/express.dir/targets.pb.cc.o -o src/express  /usr/lib64/libboost_thread.so.1.83.0  /usr/lib64/libboost_system.so.1.83.0  /usr/lib64/libboost_filesystem.so.1.83.0  /usr/lib64/libboost_program_options.so.1.83.0  /usr/lib64/libboost_date_time.so.1.83.0  -lz  -lbamtools  -lpthread  -lprotobuf  /usr/lib64/libboost_atomic.so.1.83.0 && :
/usr/libexec/gcc/x86_64-pc-linux-gnu/ld: src/CMakeFiles/express.dir/alignments.pb.cc.o: undefined reference to symbol '_ZN4absl12lts_2023012512log_internal17MakeCheckOpStringIllEEPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEET_T0_PKc'
/usr/libexec/gcc/x86_64-pc-linux-gnu/ld: /usr/lib/gcc/x86_64-pc-linux-gnu/13/../../../../lib64/libabsl_log_internal_check_op.so.2301.0.0: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
ninja: build stopped: subcommand failed.
 * ERROR: sci-biology/express-1.5.1::gentoo failed (compile phase):
 *   ninja -v -j5 -l0 failed
 * 
 * Call stack:
 *     ebuild.sh, line  136:  Called src_compile
 *   environment, line 2249:  Called cmake_src_compile
 *   environment, line  951:  Called cmake_build
 *   environment, line  917:  Called eninja
 *   environment, line 1384:  Called die
 * The specific snippet of code:
 *       "$@" || die -n "${*} 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-1.5.1:20230822-015010.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'