sci-biology:express-1.5.1:20170223-123807.log

sci-biology:express-1.5.1:20170223-123807.log (text/plain), 14.82 KB, created by Toralf Förster on 2017-02-23 12:47:37 UTC

 * Package:    sci-biology/express-1.5.1
 * 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 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
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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
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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.)
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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".
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Scanning dependencies of target express
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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 Target*>*) 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<BiasBoss>&) 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<BiasBoss>’ 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<BiasBoss>&) 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<BiasBoss>’ 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'