build.log

build.log (text/plain), 11.68 KB, created by Sergey Popov on 2014-01-23 13:12:33 UTC

 * Package:    sci-biology/express-0.9.5
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux multilib userland_GNU
 * FEATURES:   ccache preserve-libs sandbox splitdebug userpriv usersandbox
>>> Unpacking source...
>>> Unpacking express-0.9.5-src.tgz to /var/tmp/portage/sci-biology/express-0.9.5/work
>>> Source unpacked in /var/tmp/portage/sci-biology/express-0.9.5/work
>>> Preparing source in /var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5-src ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5-src ...
>>> Working in BUILD_DIR: "/var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5_build"
cmake --no-warn-unused-cli -C /var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5_build/gentoo_common_config.cmake -G Unix Makefiles -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_INSTALL_DO_STRIP=OFF -DCMAKE_USER_MAKE_RULES_OVERRIDE=/var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5_build/gentoo_rules.cmake  /var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5-src/src
Not searching for unused variables given on the command line.
loading initial cache file /var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5_build/gentoo_common_config.cmake
-- The C compiler identification is GNU 4.7.3
-- The CXX compiler identification is GNU 4.7.3
-- Check for working C compiler: /usr/lib64/ccache/bin/x86_64-pc-linux-gnu-gcc
-- Check for working C compiler: /usr/lib64/ccache/bin/x86_64-pc-linux-gnu-gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/lib64/ccache/bin/x86_64-pc-linux-gnu-g++
-- Check for working CXX compiler: /usr/lib64/ccache/bin/x86_64-pc-linux-gnu-g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Boost version: 1.52.0
-- Found the following Boost libraries:
--   filesystem
--   program_options
--   thread
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.8") 
-- <<< Gentoo configuration >>>
Build type      Gentoo
Install path    /usr
Compiler flags:
C               -O2 -pipe 
C++             -O2 -pipe 
Linker flags:
Executable       -Wl,--hash-style=gnu -Wl,-O1 -Wl,--as-needed
Module           -Wl,--hash-style=gnu -Wl,-O1 -Wl,--as-needed
Shared           -Wl,--hash-style=gnu -Wl,-O1 -Wl,--as-needed

CMake Warning (dev) in CMakeLists.txt:
  No cmake_minimum_required command is present.  A line of code such as

    cmake_minimum_required(VERSION 2.8)

  should be added at the top of the file.  The version specified may be lower
  if you wish to support older CMake versions for this project.  For more
  information run "cmake --help-policy CMP0000".
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Configuring done
-- Generating done
-- Build files have been written to: /var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5_build
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5-src ...
>>> Working in BUILD_DIR: "/var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5_build"
make -j9 VERBOSE=1 
/usr/bin/cmake -H/var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5-src/src -B/var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5_build --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5_build/CMakeFiles /var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5_build/CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[1]: Entering directory `/var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5_build'
make -f CMakeFiles/express.dir/build.make CMakeFiles/express.dir/depend
make[2]: Entering directory `/var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5_build'
cd /var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5-src/src /var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5-src/src /var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5_build /var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5_build /var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5_build/CMakeFiles/express.dir/DependInfo.cmake
Dependee "/var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5_build/CMakeFiles/express.dir/DependInfo.cmake" is newer than depender "/var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5_build/CMakeFiles/express.dir/depend.internal".
Dependee "/var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5_build/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5_build/CMakeFiles/express.dir/depend.internal".
Scanning dependencies of target express
make[2]: Leaving directory `/var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5_build'
make -f CMakeFiles/express.dir/build.make CMakeFiles/express.dir/build
make[2]: Entering directory `/var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5_build'
/usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5_build/CMakeFiles 1
/usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5_build/CMakeFiles 2
/usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5_build/CMakeFiles 3
/usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5_build/CMakeFiles 4
/usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5_build/CMakeFiles 5
[  9%] [ 18%] [ 27%] [ 36%] /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5_build/CMakeFiles 6
[ 45%] Building CXX object CMakeFiles/express.dir/transcripts.o
Building CXX object CMakeFiles/express.dir/sequence.o
Building CXX object CMakeFiles/express.dir/mismatchmodel.o
Building CXX object CMakeFiles/express.dir/markovmodel.o
Building CXX object CMakeFiles/express.dir/mapparser.o
/usr/lib64/ccache/bin/x86_64-pc-linux-gnu-g++    -DNDEBUG -O2 -pipe  -I/usr/include/bamtools    -o CMakeFiles/express.dir/transcripts.o -c /var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5-src/src/transcripts.cpp
[ 54%] /usr/lib64/ccache/bin/x86_64-pc-linux-gnu-g++    -DNDEBUG -O2 -pipe  -I/usr/include/bamtools    -o CMakeFiles/express.dir/sequence.o -c /var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5-src/src/sequence.cpp
/usr/lib64/ccache/bin/x86_64-pc-linux-gnu-g++    -DNDEBUG -O2 -pipe  -I/usr/include/bamtools    -o CMakeFiles/express.dir/mismatchmodel.o -c /var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5-src/src/mismatchmodel.cpp
/usr/lib64/ccache/bin/x86_64-pc-linux-gnu-g++    -DNDEBUG -O2 -pipe  -I/usr/include/bamtools    -o CMakeFiles/express.dir/markovmodel.o -c /var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5-src/src/markovmodel.cpp
/usr/lib64/ccache/bin/x86_64-pc-linux-gnu-g++    -DNDEBUG -O2 -pipe  -I/usr/include/bamtools    -o CMakeFiles/express.dir/mapparser.o -c /var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5-src/src/mapparser.cpp
/usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5_build/CMakeFiles 7
Building CXX object CMakeFiles/express.dir/main.o
/usr/lib64/ccache/bin/x86_64-pc-linux-gnu-g++    -DNDEBUG -O2 -pipe  -I/usr/include/bamtools    -o CMakeFiles/express.dir/main.o -c /var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5-src/src/main.cpp
[ 63%] /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5_build/CMakeFiles 8
Building CXX object CMakeFiles/express.dir/frequencymatrix.o
/usr/lib64/ccache/bin/x86_64-pc-linux-gnu-g++    -DNDEBUG -O2 -pipe  -I/usr/include/bamtools    -o CMakeFiles/express.dir/frequencymatrix.o -c /var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5-src/src/frequencymatrix.cpp
[ 72%] /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5_build/CMakeFiles 9
Building CXX object CMakeFiles/express.dir/fragments.o
/usr/lib64/ccache/bin/x86_64-pc-linux-gnu-g++    -DNDEBUG -O2 -pipe  -I/usr/include/bamtools    -o CMakeFiles/express.dir/fragments.o -c /var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5-src/src/fragments.cpp
[ 81%] /usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5_build/CMakeFiles 10
Building CXX object CMakeFiles/express.dir/fld.o
/usr/lib64/ccache/bin/x86_64-pc-linux-gnu-g++    -DNDEBUG -O2 -pipe  -I/usr/include/bamtools    -o CMakeFiles/express.dir/fld.o -c /var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5-src/src/fld.cpp
[ 90%] Building CXX object CMakeFiles/express.dir/bundles.o
/usr/lib64/ccache/bin/x86_64-pc-linux-gnu-g++    -DNDEBUG -O2 -pipe  -I/usr/include/bamtools    -o CMakeFiles/express.dir/bundles.o -c /var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5-src/src/bundles.cpp
/usr/bin/cmake -E cmake_progress_report /var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5_build/CMakeFiles 11
[100%] Building CXX object CMakeFiles/express.dir/biascorrection.o
/usr/lib64/ccache/bin/x86_64-pc-linux-gnu-g++    -DNDEBUG -O2 -pipe  -I/usr/include/bamtools    -o CMakeFiles/express.dir/biascorrection.o -c /var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5-src/src/biascorrection.cpp
Linking CXX executable express
/usr/bin/cmake -E cmake_link_script CMakeFiles/express.dir/link.txt --verbose=1
/usr/lib64/ccache/bin/x86_64-pc-linux-gnu-g++   -O2 -pipe    -Wl,--hash-style=gnu -Wl,-O1 -Wl,--as-needed CMakeFiles/express.dir/transcripts.o CMakeFiles/express.dir/sequence.o CMakeFiles/express.dir/mismatchmodel.o CMakeFiles/express.dir/markovmodel.o CMakeFiles/express.dir/mapparser.o CMakeFiles/express.dir/main.o CMakeFiles/express.dir/frequencymatrix.o CMakeFiles/express.dir/fragments.o CMakeFiles/express.dir/fld.o CMakeFiles/express.dir/bundles.o CMakeFiles/express.dir/biascorrection.o  -o express -rdynamic -lboost_filesystem-mt -lboost_program_options-mt -lboost_thread-mt -lz -lbamtools -lpthread 
/usr/lib/gcc/x86_64-pc-linux-gnu/4.7.3/../../../../x86_64-pc-linux-gnu/bin/ld: CMakeFiles/express.dir/transcripts.o: undefined reference to symbol '_ZN5boost6system15system_categoryEv'
/usr/lib/gcc/x86_64-pc-linux-gnu/4.7.3/../../../../x86_64-pc-linux-gnu/bin/ld: note: '_ZN5boost6system15system_categoryEv' is defined in DSO /usr/lib64/libboost_system.so.1.52.0 so try adding it to the linker command line
/usr/lib64/libboost_system.so.1.52.0: could not read symbols: Invalid operation
collect2: error: ld returned 1 exit status
make[2]: *** [express] Error 1
make[2]: Leaving directory `/var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5_build'
make[1]: *** [CMakeFiles/express.dir/all] Error 2
make[1]: Leaving directory `/var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5_build'
make: *** [all] Error 2
 * ERROR: sci-biology/express-0.9.5::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/express-0.9.5::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/express-0.9.5::gentoo'`.
 * The complete build log is located at '/var/tmp/portage/sci-biology/express-0.9.5/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/express-0.9.5/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5_build'
 * S: '/var/tmp/portage/sci-biology/express-0.9.5/work/express-0.9.5-src'