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Gentoo's Bugzilla – Attachment 464870 Details for
Bug 610692
sci-biology/express-1.5.1 : /.../targets.cpp:116:62: error: no matching function for call to ‘Target::cached_effective_length(const boost::shared_ptr<BiasBoss>&) const’
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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
(
hide
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Description:
sci-biology:express-1.5.1:20170223-123807.log
Filename:
MIME Type:
Creator:
Toralf Förster
Created:
2017-02-23 12:47:37 UTC
Size:
14.82 KB
patch
obsolete
> * 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 âdouble Target::sample_likelihood(bool, const std::vector<const Target*>*) constâ: >/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 âTarget::cached_effective_length(const boost::shared_ptr<BiasBoss>&) constâ > 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 âconst boost::shared_ptr<BiasBoss>â to âboolâ >/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 âTarget::cached_effective_length(const boost::shared_ptr<BiasBoss>&) constâ > 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 âconst boost::shared_ptr<BiasBoss>â to âboolâ >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'
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