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vezzi / FRC_align

Computes FRC from SAM/BAM file and not from afg files
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errors when installing FRC_align #11

Open binlangman opened 10 years ago

binlangman commented 10 years ago

Hi! When I have tried to install FRCcurve, I have run the following command successfully: -mkdir build

Thanks very much!

vezzi commented 10 years ago

Thanks for opening an issue. I need more information to help you.

Can you post the entire output of cmake and make and not only the error part? This will for sure help me.

What operating system are you using?

Have you installed boost libraries on your system. If you are installing it on a cluster ask your sys-admin for this.

binlangman commented 10 years ago

Hi! The entire output of cmake is as follows: -bash-3.2$ cmake ../ -- The C compiler identification is GNU 4.1.2 -- The CXX compiler identification is GNU 4.1.2 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Boost version: 1.55.0 -- Found the following Boost libraries: -- program_options -- system -- filesystem -- Configuring done -- Generating done -- Build files have been written to: /opt2/tools/FRC_align-master/build and the output of make is: -bash-3.2$ make Scanning dependencies of target BamTools [ 1%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o [ 2%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o [ 3%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/BamReader.cpp.o [ 4%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o [ 5%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o [ 7%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/SamProgram.cpp.o [ 8%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o [ 9%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o [ 10%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o [ 11%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o [ 13%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o [ 14%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o [ 15%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o [ 16%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o [ 17%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o [ 19%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o [ 20%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o [ 21%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o [ 22%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o [ 23%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o [ 25%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o [ 26%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/io/BamFtp_p.cpp.o [ 27%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/io/BamHttp_p.cpp.o [ 28%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/io/BamPipe_p.cpp.o [ 29%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o [ 30%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o [ 32%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/io/HostAddress_p.cpp.o [ 33%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/io/HostInfo_p.cpp.o [ 34%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/io/HttpHeader_p.cpp.o [ 35%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o [ 36%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o [ 38%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocket_p.cpp.o [ 39%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_p.cpp.o [ 40%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_unix_p.cpp.o [ 41%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o [ 42%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o [ 44%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o [ 45%] Building CXX object lib/bamtools/src/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o Linking CXX shared library libbamtools.so [ 45%] Built target BamTools Scanning dependencies of target FRC [ 46%] Building CXX object CMakeFiles/FRC.dir/src/FRC_align.cpp.o /opt2/tools/FRC_align-master/src/FRC_align.cpp: In function ‘void printFRCurve(std::string, int, FeatureTypes, uint64_t, FRC)’: /opt2/tools/FRC_align-master/src/FRC_align.cpp:463: 警告：当转换到 ‘uint32_t’ (从 ‘float’)时 /opt2/tools/FRC_align-master/src/FRC_align.cpp: In function ‘void computeFRC(FRC&, std::string, LibraryStatistics, int, bool, float, float)’: /opt2/tools/FRC_align-master/src/FRC_align.cpp:502: 警告：当转换到 ‘unsigned int’ (从 ‘float’)时 /opt2/tools/FRC_align-master/src/FRCalign.cpp:521: 警告：将 ‘float’ 作为实参 2 传递给 ‘void FRC::computeCEstats(Contig, unsigned int, unsigned int, float, float)’ /opt2/tools/FRC_align-master/src/FRCalign.cpp:531: 警告：将 ‘float’ 作为实参 5 传递给 ‘void FRC::computeCompressionArea(std::string, unsigned int, Contig, float, unsigned int, unsigned int)’ /opt2/tools/FRC_align-master/src/FRCalign.cpp:531: 警告：将 ‘float’ 作为实参 6 传递给 ‘void FRC::computeCompressionArea(std::string, unsigned int, Contig, float, unsigned int, unsigned int)’ /opt2/tools/FRC_align-master/src/FRCalign.cpp:532: 警告：将 ‘float’ 作为实参 5 传递给 ‘void FRC::computeStrechArea(std::string, unsigned int, Contig, float, unsigned int, unsigned int)’ /opt2/tools/FRC_align-master/src/FRCalign.cpp:532: 警告：将 ‘float’ 作为实参 6 传递给 ‘void FRC::computeStrechArea(std::string, unsigned int, Contig, float, unsigned int, unsigned int)’ /opt2/tools/FRC_align-master/src/FRCalign.cpp:541: 警告：将 ‘float’ 作为实参 5 传递给 ‘void FRC::computeCompressionArea(std::string, unsigned int, Contig, float, unsigned int, unsigned int)’ /opt2/tools/FRC_align-master/src/FRCalign.cpp:541: 警告：将 ‘float’ 作为实参 6 传递给 ‘void FRC::computeCompressionArea(std::string, unsigned int, Contig, float, unsigned int, unsigned int)’ /opt2/tools/FRC_align-master/src/FRCalign.cpp:542: 警告：将 ‘float’ 作为实参 5 传递给 ‘void FRC::computeStrechArea(std::string, unsigned int, Contig, float, unsigned int, unsigned int)’ /opt2/tools/FRC_align-master/src/FRCalign.cpp:542: 警告：将 ‘float’ 作为实参 6 传递给 ‘void FRC::computeStrechArea(std::string, unsigned int, Contig, float, unsigned int, unsigned int)’ /opt2/tools/FRC_align-master/src/FRCalign.cpp:562: 警告：将 ‘float’ 作为实参 2 传递给 ‘void FRC::computeCEstats(Contig, unsigned int, unsigned int, float, float)’ /opt2/tools/FRC_align-master/src/FRCalign.cpp:571: 警告：将 ‘float’ 作为实参 5 传递给 ‘void FRC::computeCompressionArea(std::string, unsigned int, Contig, float, unsigned int, unsigned int)’ /opt2/tools/FRC_align-master/src/FRCalign.cpp:571: 警告：将 ‘float’ 作为实参 6 传递给 ‘void FRC::computeCompressionArea(std::string, unsigned int, Contig, float, unsigned int, unsigned int)’ /opt2/tools/FRC_align-master/src/FRCalign.cpp:572: 警告：将 ‘float’ 作为实参 5 传递给 ‘void FRC::computeStrechArea(std::string, unsigned int, Contig, float, unsigned int, unsigned int)’ /opt2/tools/FRC_align-master/src/FRCalign.cpp:572: 警告：将 ‘float’ 作为实参 6 传递给 ‘void FRC::computeStrechArea(std::string, unsigned int, Contig, float, unsigned int, unsigned int)’ /opt2/tools/FRC_align-master/src/FRCalign.cpp:581: 警告：将 ‘float’ 作为实参 5 传递给 ‘void FRC::computeCompressionArea(std::string, unsigned int, Contig, float, unsigned int, unsigned int)’ /opt2/tools/FRC_align-master/src/FRCalign.cpp:581: 警告：将 ‘float’ 作为实参 6 传递给 ‘void FRC::computeCompressionArea(std::string, unsigned int, Contig, float, unsigned int, unsigned int)’ /opt2/tools/FRC_align-master/src/FRCalign.cpp:582: 警告：将 ‘float’ 作为实参 5 传递给 ‘void FRC::computeStrechArea(std::string, unsigned int, Contig, float, unsigned int, unsigned int)’ /opt2/tools/FRC_align-master/src/FRCalign.cpp:582: 警告：将 ‘float’ 作为实参 6 传递给 ‘void FRC::computeStrechArea(std::string, unsigned int, Contig, float, unsigned int, unsigned int)’ [ 47%] Building CXX object CMakeFiles/FRC.dir/src/data_structures/Contig.cpp.o /opt2/tools/FRC_align-master/src/data_structures/Contig.cpp: In member function ‘unsigned int Contig::getLowCoverageAreas(float, unsigned int, unsigned int)’: /opt2/tools/FRC_align-master/src/data_structures/Contig.cpp:255: 警告：当转换到 ‘unsigned int’ (从 ‘double’)时 /opt2/tools/FRC_align-master/src/data_structures/Contig.cpp:278: 警告：当转换到 ‘unsigned int’ (从 ‘double’)时 /opt2/tools/FRC_align-master/src/data_structures/Contig.cpp: In member function ‘unsigned int Contig::getHighCoverageAreas(float, unsigned int, unsigned int)’: /opt2/tools/FRC_align-master/src/data_structures/Contig.cpp:350: 警告：当转换到 ‘unsigned int’ (从 ‘double’)时 /opt2/tools/FRC_align-master/src/data_structures/Contig.cpp:369: 警告：当转换到 ‘unsigned int’ (从 ‘double’)时 /opt2/tools/FRC_align-master/src/data_structures/Contig.cpp: In member function ‘unsigned int Contig::getLowNormalAreas(float, unsigned int, unsigned int)’: /opt2/tools/FRC_align-master/src/data_structures/Contig.cpp:453: 警告：当转换到 ‘unsigned int’ (从 ‘double’)时 /opt2/tools/FRC_align-master/src/data_structures/Contig.cpp:472: 警告：当转换到 ‘unsigned int’ (从 ‘double’)时 /opt2/tools/FRC_align-master/src/data_structures/Contig.cpp: In member function ‘unsigned int Contig::getHighNormalAreas(float, unsigned int, unsigned int)’: /opt2/tools/FRC_align-master/src/data_structures/Contig.cpp:543: 警告：当转换到 ‘unsigned int’ (从 ‘double’)时 /opt2/tools/FRC_align-master/src/data_structures/Contig.cpp:562: 警告：当转换到 ‘unsigned int’ (从 ‘double’)时 /opt2/tools/FRC_align-master/src/data_structures/Contig.cpp: In member function ‘unsigned int Contig::getHighSingleAreas(unsigned int, unsigned int, float)’: /opt2/tools/FRC_align-master/src/data_structures/Contig.cpp:642: 警告：当转换到 ‘unsigned int’ (从 ‘double’)时 /opt2/tools/FRC_align-master/src/data_structures/Contig.cpp:662: 警告：当转换到 ‘unsigned int’ (从 ‘double’)时 /opt2/tools/FRC_align-master/src/data_structures/Contig.cpp: In member function ‘unsigned int Contig::getHighSpanningAreas(unsigned int, unsigned int, float)’: /opt2/tools/FRC_align-master/src/data_structures/Contig.cpp:740: 警告：当转换到 ‘unsigned int’ (从 ‘double’)时 /opt2/tools/FRC_align-master/src/data_structures/Contig.cpp:760: 警告：当转换到 ‘unsigned int’ (从 ‘double’)时 /opt2/tools/FRC_align-master/src/data_structures/Contig.cpp: In member function ‘unsigned int Contig::getHighOutieAreas(unsigned int, unsigned int, float)’: /opt2/tools/FRC_align-master/src/data_structures/Contig.cpp:843: 警告：当转换到 ‘unsigned int’ (从 ‘double’)时 /opt2/tools/FRC_align-master/src/data_structures/Contig.cpp:863: 警告：当转换到 ‘unsigned int’ (从 ‘double’)时 /opt2/tools/FRC_align-master/src/data_structures/Contig.cpp: In member function ‘unsigned int Contig::getCompressionAreas(float, float, float, unsigned int, unsigned int)’: /opt2/tools/FRC_align-master/src/data_structures/Contig.cpp:966: 警告：当转换到 ‘unsigned int’ (从 ‘double’)时 /opt2/tools/FRC_align-master/src/data_structures/Contig.cpp:986: 警告：当转换到 ‘unsigned int’ (从 ‘double’)时 /opt2/tools/FRC_align-master/src/data_structures/Contig.cpp: In member function ‘unsigned int Contig::getExpansionAreas(float, float, float, unsigned int, unsigned int)’: /opt2/tools/FRC_align-master/src/data_structures/Contig.cpp:1082: 警告：当转换到 ‘unsigned int’ (从 ‘double’)时 /opt2/tools/FRC_align-master/src/data_structures/Contig.cpp:1105: 警告：当转换到 ‘unsigned int’ (从 ‘double’)时 [ 48%] Building CXX object CMakeFiles/FRC.dir/src/data_structures/Features.cpp.o [ 50%] Building CXX object CMakeFiles/FRC.dir/src/data_structures/FRC.cpp.o /opt2/tools/FRC_align-master/src/data_structures/FRC.cpp: In member function ‘void contigFeatures::printFeatures(std::ofstream&)’: /opt2/tools/FRC_align-master/src/data_structures/FRC.cpp:563: 警告：当转换到 ‘unsigned int’ (从 ‘double’)时 Linking CXX executable ../bin/FRC /usr/local/lib/libboost_program_options.so: undefined reference to std::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const*, long)@GLIBCXX_3.4.9' /usr/local/lib/libboost_program_options.so: undefined reference tostd::ctype::_M_widen_init() const@GLIBCXX_3.4.11' collect2: ld return 1 make[2]: * [../bin/FRC] error 1 make[1]: * [CMakeFiles/FRC.dir/all] error 2 make: *\ [all] error 2. I'v installed FRCcurve on the server of my laboratory, and information about the operating system I'm using is Linux version 2.6.18-128.el5 (mockbuild@builder10.centos.org) (gcc version 4.1.2 20080704 (Red Hat 4.1.2-44)).

Thanks very much!

vezzi commented 10 years ago

The problem is here (as expected)

Linking CXX executable ../bin/FRC
/usr/local/lib/libboost_program_options.so: undefined reference to std::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const*, long)@GLIBCXX_3.4.9' /usr/local/lib/libboost_program_options.so: undefined reference tostd::ctype::_M_widen_init() const@GLIBCXX_3.4.11'

you need to send this error to your system administrator and ask him/her to install FRCurve. The problem here is that either the libboost_program_option is not installed on your system or it is not in a standard place.

Remove libboost dependencies is on the top of my TODO list for what concerns this tool. Libboost is an extremely useful library but it creates too often troubles in installation.