Problem with installing rMAT on macOS Ventura 13.1. Apple M2 chip

[Babak Loghmani]

Dear all, 

I am trying to instal rMAT on my macOS Ventura 13.1 using an Apple M2 chip. I get plenty of warnings and errors during the installation and I have no clue how to fix them. I am posting all the warnings and errors here. It would be nice if you can help me to fix them. I Sorry for the very long content:

-- Generating done

-- Build files have been written to: /Applications/rmats_turbo_v4_1_2/bamtools/build

[ 0%] Built target SharedHeaders

[ 0%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.cpp:10:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:15:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]

const char GZIP_ID2 = 139;

~~~~~~~~ ^~~

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]

const char OS_UNKNOWN = 255;

~~~~~~~~~~ ^~~

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.cpp:10:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:581:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]

int elementLength = 0;

^

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.cpp:848:18: warning: variable 'newTagDataLength' set but not used [-Wunused-but-set-variable]

unsigned int newTagDataLength = 0;

^

4 warnings generated.

[ 1%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamMultiReader.cpp:15:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamMultiReader.h:14:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamReader.h:14:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:15:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]

const char GZIP_ID2 = 139;

~~~~~~~~ ^~~

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]

const char OS_UNKNOWN = 255;

~~~~~~~~~~ ^~~

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamMultiReader.cpp:15:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamMultiReader.h:14:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamReader.h:14:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:581:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]

int elementLength = 0;

^

3 warnings generated.

[ 2%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamReader.cpp.o

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamReader.cpp:10:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamReader.h:14:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:15:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]

const char GZIP_ID2 = 139;

~~~~~~~~ ^~~

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]

const char OS_UNKNOWN = 255;

~~~~~~~~~~ ^~~

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamReader.cpp:10:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamReader.h:14:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:581:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]

int elementLength = 0;

^

3 warnings generated.

[ 3%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamWriter.cpp:10:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:15:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]

const char GZIP_ID2 = 139;

~~~~~~~~ ^~~

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]

const char OS_UNKNOWN = 255;

~~~~~~~~~~ ^~~

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamWriter.cpp:10:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:581:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]

int elementLength = 0;

^

3 warnings generated.

[ 4%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o

[ 5%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamProgram.cpp.o

[ 6%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o

[ 7%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o

[ 8%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o

[ 9%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o

[ 10%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o

[ 11%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/internal/bam/BamHeader_p.cpp:11:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]

const char GZIP_ID2 = 139;

~~~~~~~~ ^~~

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]

const char OS_UNKNOWN = 255;

~~~~~~~~~~ ^~~

2 warnings generated.

[ 12%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/internal/bam/BamMultiReader_p.cpp:10:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:15:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]

const char GZIP_ID2 = 139;

~~~~~~~~ ^~~

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]

const char OS_UNKNOWN = 255;

~~~~~~~~~~ ^~~

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/internal/bam/BamMultiReader_p.cpp:10:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:581:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]

int elementLength = 0;

^

3 warnings generated.

[ 13%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/internal/bam/BamRandomAccessController_p.cpp:12:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/internal/bam/BamReader_p.h:23:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:15:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]

const char GZIP_ID2 = 139;

~~~~~~~~ ^~~

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]

const char OS_UNKNOWN = 255;

~~~~~~~~~~ ^~~

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/internal/bam/BamRandomAccessController_p.cpp:12:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/internal/bam/BamReader_p.h:23:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:581:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]

int elementLength = 0;

^

3 warnings generated.

[ 14%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/internal/bam/BamReader_p.cpp:10:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]

const char GZIP_ID2 = 139;

~~~~~~~~ ^~~

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]

const char OS_UNKNOWN = 255;

~~~~~~~~~~ ^~~

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/internal/bam/BamReader_p.cpp:11:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamReader.h:14:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:581:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]

int elementLength = 0;

^

3 warnings generated.

[ 15%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/internal/bam/BamWriter_p.cpp:10:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:15:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]

const char GZIP_ID2 = 139;

~~~~~~~~ ^~~

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]

const char OS_UNKNOWN = 255;

~~~~~~~~~~ ^~~

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/internal/bam/BamWriter_p.cpp:10:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:581:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]

int elementLength = 0;

^

3 warnings generated.

[ 16%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o

[ 17%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:15:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]

const char GZIP_ID2 = 139;

~~~~~~~~ ^~~

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]

const char OS_UNKNOWN = 255;

~~~~~~~~~~ ^~~

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:581:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]

int elementLength = 0;

^

3 warnings generated.

[ 18%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:10:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:15:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]

const char GZIP_ID2 = 139;

~~~~~~~~ ^~~

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]

const char OS_UNKNOWN = 255;

~~~~~~~~~~ ^~~

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:10:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:581:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]

int elementLength = 0;

^

3 warnings generated.

[ 19%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o

[ 20%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o

[ 21%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamFtp_p.cpp.o

[ 22%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamHttp_p.cpp.o

[ 23%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamPipe_p.cpp.o

[ 24%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/internal/io/BgzfStream_p.cpp:13:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]

const char GZIP_ID2 = 139;

~~~~~~~~ ^~~

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]

const char OS_UNKNOWN = 255;

~~~~~~~~~~ ^~~

2 warnings generated.

[ 25%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o

[ 26%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HostAddress_p.cpp.o

[ 27%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HostInfo_p.cpp.o

[ 28%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HttpHeader_p.cpp.o

[ 29%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o

[ 30%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o

[ 31%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocket_p.cpp.o

[ 32%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_p.cpp.o

[ 33%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_unix_p.cpp.o

[ 34%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o

[ 35%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o

[ 36%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o

[ 37%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o

[ 38%] Linking CXX shared library /Applications/rmats_turbo_v4_1_2/bamtools/lib/libbamtools.dylib

[ 38%] Built target BamTools

[ 39%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamAlignment.cpp.o

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.cpp:10:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:15:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]

const char GZIP_ID2 = 139;

~~~~~~~~ ^~~

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]

const char OS_UNKNOWN = 255;

~~~~~~~~~~ ^~~

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.cpp:10:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:581:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]

int elementLength = 0;

^

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.cpp:848:18: warning: variable 'newTagDataLength' set but not used [-Wunused-but-set-variable]

unsigned int newTagDataLength = 0;

^

4 warnings generated.

[ 40%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamMultiReader.cpp.o

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamMultiReader.cpp:15:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamMultiReader.h:14:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamReader.h:14:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:15:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]

const char GZIP_ID2 = 139;

~~~~~~~~ ^~~

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]

const char OS_UNKNOWN = 255;

~~~~~~~~~~ ^~~

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamMultiReader.cpp:15:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamMultiReader.h:14:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamReader.h:14:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:581:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]

int elementLength = 0;

^

3 warnings generated.

[ 41%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamReader.cpp.o

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamReader.cpp:10:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamReader.h:14:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:15:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]

const char GZIP_ID2 = 139;

~~~~~~~~ ^~~

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]

const char OS_UNKNOWN = 255;

~~~~~~~~~~ ^~~

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamReader.cpp:10:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamReader.h:14:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:581:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]

int elementLength = 0;

^

3 warnings generated.

[ 42%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamWriter.cpp.o

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamWriter.cpp:10:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:15:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]

const char GZIP_ID2 = 139;

~~~~~~~~ ^~~

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]

const char OS_UNKNOWN = 255;

~~~~~~~~~~ ^~~

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamWriter.cpp:10:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:581:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]

int elementLength = 0;

^

3 warnings generated.

[ 43%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamHeader.cpp.o

[ 44%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamProgram.cpp.o

[ 45%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamProgramChain.cpp.o

[ 46%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamReadGroup.cpp.o

[ 47%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamReadGroupDictionary.cpp.o

[ 48%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamSequence.cpp.o

[ 49%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamSequenceDictionary.cpp.o

[ 50%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamHeader_p.cpp.o

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/internal/bam/BamHeader_p.cpp:11:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]

const char GZIP_ID2 = 139;

~~~~~~~~ ^~~

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]

const char OS_UNKNOWN = 255;

~~~~~~~~~~ ^~~

2 warnings generated.

[ 50%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamMultiReader_p.cpp.o

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/internal/bam/BamMultiReader_p.cpp:10:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:15:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]

const char GZIP_ID2 = 139;

~~~~~~~~ ^~~

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]

const char OS_UNKNOWN = 255;

~~~~~~~~~~ ^~~

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/internal/bam/BamMultiReader_p.cpp:10:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:581:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]

int elementLength = 0;

^

3 warnings generated.

[ 51%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamRandomAccessController_p.cpp.o

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/internal/bam/BamRandomAccessController_p.cpp:12:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/internal/bam/BamReader_p.h:23:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:15:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]

const char GZIP_ID2 = 139;

~~~~~~~~ ^~~

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]

const char OS_UNKNOWN = 255;

~~~~~~~~~~ ^~~

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/internal/bam/BamRandomAccessController_p.cpp:12:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/internal/bam/BamReader_p.h:23:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:581:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]

int elementLength = 0;

^

3 warnings generated.

[ 52%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamReader_p.cpp.o

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/internal/bam/BamReader_p.cpp:10:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]

const char GZIP_ID2 = 139;

~~~~~~~~ ^~~

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]

const char OS_UNKNOWN = 255;

~~~~~~~~~~ ^~~

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/internal/bam/BamReader_p.cpp:11:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamReader.h:14:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:581:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]

int elementLength = 0;

^

3 warnings generated.

[ 53%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamWriter_p.cpp.o

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/internal/bam/BamWriter_p.cpp:10:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:15:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]

const char GZIP_ID2 = 139;

~~~~~~~~ ^~~

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]

const char OS_UNKNOWN = 255;

~~~~~~~~~~ ^~~

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/internal/bam/BamWriter_p.cpp:10:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:581:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]

int elementLength = 0;

^

3 warnings generated.

[ 54%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamIndexFactory_p.cpp.o

[ 55%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamStandardIndex_p.cpp.o

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:15:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]

const char GZIP_ID2 = 139;

~~~~~~~~ ^~~

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]

const char OS_UNKNOWN = 255;

~~~~~~~~~~ ^~~

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:581:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]

int elementLength = 0;

^

3 warnings generated.

[ 56%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamToolsIndex_p.cpp.o

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:10:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:15:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]

const char GZIP_ID2 = 139;

~~~~~~~~ ^~~

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]

const char OS_UNKNOWN = 255;

~~~~~~~~~~ ^~~

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:10:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:581:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]

int elementLength = 0;

^

3 warnings generated.

[ 57%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamDeviceFactory_p.cpp.o

[ 58%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamFile_p.cpp.o

[ 59%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamFtp_p.cpp.o

[ 60%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamHttp_p.cpp.o

[ 61%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamPipe_p.cpp.o

[ 62%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BgzfStream_p.cpp.o

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/internal/io/BgzfStream_p.cpp:13:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]

const char GZIP_ID2 = 139;

~~~~~~~~ ^~~

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]

const char OS_UNKNOWN = 255;

~~~~~~~~~~ ^~~

2 warnings generated.

[ 63%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/ByteArray_p.cpp.o

[ 64%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HostAddress_p.cpp.o

[ 65%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HostInfo_p.cpp.o

[ 66%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HttpHeader_p.cpp.o

[ 67%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/ILocalIODevice_p.cpp.o

[ 68%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/RollingBuffer_p.cpp.o

[ 69%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocket_p.cpp.o

[ 70%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_p.cpp.o

[ 71%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_unix_p.cpp.o

[ 72%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamFormatParser_p.cpp.o

[ 73%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamFormatPrinter_p.cpp.o

[ 74%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamHeaderValidator_p.cpp.o

[ 75%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/utils/BamException_p.cpp.o

[ 76%] Linking CXX static library /Applications/rmats_turbo_v4_1_2/bamtools/lib/libbamtools.a

[ 76%] Built target BamTools-static

[ 76%] Built target APIHeaders

[ 76%] Built target AlgorithmsHeaders

[ 77%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_reader.cpp.o

/Applications/rmats_turbo_v4_1_2/bamtools/src/third_party/jsoncpp/json_reader.cpp:536:65: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]

bool badTokenType = ( token.type_ == tokenArraySeparator &&

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~

/Applications/rmats_turbo_v4_1_2/bamtools/src/third_party/jsoncpp/json_reader.cpp:837:4: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]

sprintf( buffer, "Line %d, Column %d", line, column );

^

/Library/Developer/CommandLineTools/SDKs/MacOSX13.1.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here

__deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")

^

/Library/Developer/CommandLineTools/SDKs/MacOSX13.1.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'

#define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))

^

2 warnings generated.

[ 78%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_value.cpp.o

[ 79%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_writer.cpp.o

/Applications/rmats_turbo_v4_1_2/bamtools/src/third_party/jsoncpp/json_writer.cpp:62:4: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]

sprintf(buffer, "%#.16g", value);

^

/Library/Developer/CommandLineTools/SDKs/MacOSX13.1.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here

__deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")

^

/Library/Developer/CommandLineTools/SDKs/MacOSX13.1.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'

#define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))

^

1 warning generated.

[ 80%] Linking CXX static library /Applications/rmats_turbo_v4_1_2/bamtools/lib/libjsoncpp.a

[ 80%] Built target jsoncpp

[ 81%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_fasta.cpp.o

[ 82%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_options.cpp.o

[ 83%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_pileup_engine.cpp.o

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/utils/bamtools_pileup_engine.cpp:10:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/utils/bamtools_pileup_engine.h:15:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:15:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]

const char GZIP_ID2 = 139;

~~~~~~~~ ^~~

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]

const char OS_UNKNOWN = 255;

~~~~~~~~~~ ^~~

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/utils/bamtools_pileup_engine.cpp:10:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/utils/bamtools_pileup_engine.h:15:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:581:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]

int elementLength = 0;

^

3 warnings generated.

[ 84%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_utilities.cpp.o

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/utils/bamtools_utilities.cpp:10:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamMultiReader.h:14:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamReader.h:14:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:15:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]

const char GZIP_ID2 = 139;

~~~~~~~~ ^~~

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]

const char OS_UNKNOWN = 255;

~~~~~~~~~~ ^~~

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/utils/bamtools_utilities.cpp:10:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamMultiReader.h:14:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamReader.h:14:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:581:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]

int elementLength = 0;

^

3 warnings generated.

[ 85%] Linking CXX static library /Applications/rmats_turbo_v4_1_2/bamtools/lib/libbamtools-utils.a

[ 85%] Built target BamTools-utils

[ 86%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_convert.cpp.o

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/toolkit/bamtools_convert.cpp:12:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]

const char GZIP_ID2 = 139;

~~~~~~~~ ^~~

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]

const char OS_UNKNOWN = 255;

~~~~~~~~~~ ^~~

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/toolkit/bamtools_convert.cpp:13:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamMultiReader.h:14:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamReader.h:14:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:581:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]

int elementLength = 0;

^

3 warnings generated.

[ 87%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_count.cpp.o

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/toolkit/bamtools_count.cpp:12:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlgorithms.h:15:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/algorithms/Sort.h:15:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:15:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]

const char GZIP_ID2 = 139;

~~~~~~~~ ^~~

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]

const char OS_UNKNOWN = 255;

~~~~~~~~~~ ^~~

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/toolkit/bamtools_count.cpp:12:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlgorithms.h:15:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/algorithms/Sort.h:15:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:581:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]

int elementLength = 0;

^

3 warnings generated.

[ 88%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_coverage.cpp.o

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/toolkit/bamtools_coverage.cpp:12:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamReader.h:14:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:15:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]

const char GZIP_ID2 = 139;

~~~~~~~~ ^~~

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]

const char OS_UNKNOWN = 255;

~~~~~~~~~~ ^~~

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/toolkit/bamtools_coverage.cpp:12:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamReader.h:14:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:581:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]

int elementLength = 0;

^

3 warnings generated.

[ 89%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_filter.cpp.o

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/toolkit/bamtools_filter.cpp:12:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamMultiReader.h:14:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamReader.h:14:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:15:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]

const char GZIP_ID2 = 139;

~~~~~~~~ ^~~

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]

const char OS_UNKNOWN = 255;

~~~~~~~~~~ ^~~

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/toolkit/bamtools_filter.cpp:12:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamMultiReader.h:14:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamReader.h:14:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:581:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]

int elementLength = 0;

^

3 warnings generated.

[ 90%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_header.cpp.o

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/toolkit/bamtools_header.cpp:13:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamMultiReader.h:14:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamReader.h:14:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:15:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]

const char GZIP_ID2 = 139;

~~~~~~~~ ^~~

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]

const char OS_UNKNOWN = 255;

~~~~~~~~~~ ^~~

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/toolkit/bamtools_header.cpp:13:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamMultiReader.h:14:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamReader.h:14:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:581:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]

int elementLength = 0;

^

3 warnings generated.

[ 91%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_index.cpp.o

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/toolkit/bamtools_index.cpp:12:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamReader.h:14:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:15:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]

const char GZIP_ID2 = 139;

~~~~~~~~ ^~~

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]

const char OS_UNKNOWN = 255;

~~~~~~~~~~ ^~~

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/toolkit/bamtools_index.cpp:12:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamReader.h:14:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:581:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]

int elementLength = 0;

^

3 warnings generated.

[ 92%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_merge.cpp.o

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/toolkit/bamtools_merge.cpp:12:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamMultiReader.h:14:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamReader.h:14:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:15:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]

const char GZIP_ID2 = 139;

~~~~~~~~ ^~~

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]

const char OS_UNKNOWN = 255;

~~~~~~~~~~ ^~~

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/toolkit/bamtools_merge.cpp:12:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamMultiReader.h:14:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamReader.h:14:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:581:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]

int elementLength = 0;

^

3 warnings generated.

[ 93%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/toolkit/bamtools_random.cpp:12:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamMultiReader.h:14:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamReader.h:14:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:15:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]

const char GZIP_ID2 = 139;

~~~~~~~~ ^~~

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]

const char OS_UNKNOWN = 255;

~~~~~~~~~~ ^~~

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/toolkit/bamtools_random.cpp:12:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamMultiReader.h:14:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamReader.h:14:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:581:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]

int elementLength = 0;

^

3 warnings generated.

[ 94%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/toolkit/bamtools_resolve.cpp:12:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamReader.h:14:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:15:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]

const char GZIP_ID2 = 139;

~~~~~~~~ ^~~

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]

const char OS_UNKNOWN = 255;

~~~~~~~~~~ ^~~

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/toolkit/bamtools_resolve.cpp:12:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamReader.h:14:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:581:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]

int elementLength = 0;

^

3 warnings generated.

[ 95%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_revert.cpp.o

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/toolkit/bamtools_revert.cpp:12:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamReader.h:14:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:15:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]

const char GZIP_ID2 = 139;

~~~~~~~~ ^~~

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]

const char OS_UNKNOWN = 255;

~~~~~~~~~~ ^~~

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/toolkit/bamtools_revert.cpp:12:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamReader.h:14:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:581:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]

int elementLength = 0;

^

3 warnings generated.

[ 96%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_sort.cpp.o

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/toolkit/bamtools_sort.cpp:13:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamMultiReader.h:14:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamReader.h:14:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:15:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]

const char GZIP_ID2 = 139;

~~~~~~~~ ^~~

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]

const char OS_UNKNOWN = 255;

~~~~~~~~~~ ^~~

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/toolkit/bamtools_sort.cpp:13:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamMultiReader.h:14:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamReader.h:14:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:581:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]

int elementLength = 0;

^

3 warnings generated.

[ 97%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_split.cpp.o

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/toolkit/bamtools_split.cpp:13:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]

const char GZIP_ID2 = 139;

~~~~~~~~ ^~~

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]

const char OS_UNKNOWN = 255;

~~~~~~~~~~ ^~~

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/toolkit/bamtools_split.cpp:14:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamReader.h:14:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:581:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]

int elementLength = 0;

^

3 warnings generated.

[ 98%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_stats.cpp.o

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/toolkit/bamtools_stats.cpp:12:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamMultiReader.h:14:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamReader.h:14:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:15:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:129:25: warning: implicit conversion from 'int' to 'const char' changes value from 139 to -117 [-Wconstant-conversion]

const char GZIP_ID2 = 139;

~~~~~~~~ ^~~

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamConstants.h:132:25: warning: implicit conversion from 'int' to 'const char' changes value from 255 to -1 [-Wconstant-conversion]

const char OS_UNKNOWN = 255;

~~~~~~~~~~ ^~~

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/toolkit/bamtools_stats.cpp:12:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamMultiReader.h:14:

In file included from /Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamReader.h:14:

/Applications/rmats_turbo_v4_1_2/bamtools/src/api/BamAlignment.h:581:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]

int elementLength = 0;

^

3 warnings generated.

[ 99%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools.cpp.o

[100%] Linking CXX executable /Applications/rmats_turbo_v4_1_2/bamtools/bin/bamtools

[100%] Built target bamtools_cmd

# rm -f to ignore nonexistent files since *.dylib will only exist for mac

cd bamtools/lib; rm -f *.so *.so.* *.dylib

cd rMATS_C; make;

cd lbfgs_scipy && make

f77 -c -O2 -c -o lbfgsb.o lbfgsb.f

make[2]: f77: No such file or directory

make[2]: *** [lbfgsb.o] Error 1

make[1]: *** [lbfgs_scipy/lbfgsb.o] Error 2

make: *** [build] Error 2

[kutsc...@gmail.com]

It looks like everything is a warning (not an error) up to:

make[2]: f77: No such file or directory

See this post with a similar error message: https://github.com/Xinglab/rmats-turbo/issues/103
The build is trying to use f77 as the fortran compiler. If you have gfortran installed you can tell the build where to find it with:
export FC="/path/to/gfortran"

Eric

[Babak Loghmani]

thanks a lot. This issue was solved after following the link. Now I get another error:

clang: error: unsupported option '-fopenmp'

I followed the instruction here:

https://github.com/jts/nanopolish/issues/789#issuecomment-641655404

but that also results in an error:

gcc-12: error: unrecognized command-line option '-msse2'

That would be great if you can help me by this issue. 

I am using Apple M2 chip, macOS Ventura 13.1

Best,

Babak

[kutsc...@gmail.com]

For: gcc-12: error: unrecognized command-line option '-msse2'

It seems like that error comes from this line: https://github.com/Xinglab/rmats-turbo/blob/v4.1.2/rMATS_C/Makefile#L13

I think you should be able to just delete -msse2 from that line and run the build again. The -msse2 flag is telling the compiler that it should try some system specific instructions to optimize the code. Without that flag the compiler should just choose instructions that are appropriate for your system

Eric

[Babak Loghmani]

I tried that as well but that also results in the following error, when I run make CXX=g++-12 CC=gcc-12:

src/main.c:7:10: fatal error: gsl/gsl_cdf.h: No such file or directory

    7 | #include <gsl/gsl_cdf.h>

      |          ^~~~~~~~~~~~~~~

compilation terminated.

src/myfunc.c:4:10: fatal error: gsl/gsl_cdf.h: No such file or directory

    4 | #include <gsl/gsl_cdf.h>

      |          ^~~~~~~~~~~~~~~

compilation terminated.

src/util.c:6:10: fatal error: gsl/gsl_vector.h: No such file or directory

    6 | #include <gsl/gsl_vector.h>

      |          ^~~~~~~~~~~~~~~~~~

compilation terminated.

make[1]: *** [rMATSexe] Error 1

[kutsc...@gmail.com]

Those errors look like the build didn't find GSL. If you run with ./build_rmats it will try to set flags using gsl-config: https://github.com/Xinglab/rmats-turbo/blob/v4.1.2/build_rmats#L68

It looks like you're running the command without ./build_rmats:

make CXX=g++-12 CC=gcc-12

You could try editing the make command in build_rmats to match the one that you're using. That way it should still set the GSL flags. There's also a place in setup_environment.sh for setting CXX and CC. Setting those CXX and CC lines should have the same effect as editing the make command: https://github.com/Xinglab/rmats-turbo/blob/v4.1.2/setup_environment.sh#L28

Eric

[Babak Loghmani]

As I mentioned above, I tried  ./build_rmats, but that would give the 

clang: error: unsupported option '-fopenmp'

error. that is why I tried make CXX=g++-12 CC=gcc-12. 

If I comment out -fopenmp from the make file and run ./build_rmats, I will get the following errors:

src/myfunc.c:17:8: error: unknown type name 'clock_t'

extern clock_t dur;

       ^

1 error generated.

src/util.c:7:10: fatal error: 'omp.h' file not found

#include <omp.h>

P.S: I let these two lines, export CC="$(which gcc)" || return 1 and export CXX="$(which g++)" || return 1 to execute in the setup_environment.sh, so that gcc and g++ are automatically set, and it seems to work fine.

[kutsc...@gmail.com]

Did it work when you set CC and CXX from setup_environment.sh? If not then you could try setting the specific versions instead of which gcc and which g++:

export CC="gcc-12" || return 1
export CXX="g++-12" || return 1

-fopenmp needs to be kept in for the build to work

Eric

[Babak Loghmani]

I dont get any error for CC and CXX, so I think it works fine.

The problem now is fopenmp. when running ./build_rmats, it gives:

clang: error: unsupported option '-fopenmp'

Best,

Babak

[kutsc...@gmail.com]

That is the error you resolved before by using gcc-12 and g++-12. The error shows that it is using clang and not gcc-12. Did you try:

export CC="gcc-12" || return 1
export CXX="g++-12" || return 1

Eric

[Babak Loghmani]

I used these two lines and now the  ./build_rmats runs with no error. But when I run: python rmats.py {arguments},  I get the following error:

Traceback (most recent call last):

  File "/Applications/rmats_turbo_v4_1_2/rmats.py", line 19, in <module>

    from rmatspipeline import run_pipe

ImportError: dlopen(/Applications/rmats_turbo_v4_1_2/rmatspipeline.cpython-39-darwin.so, 0x0002): symbol not found in flat namespace '__ZN8BamTools9BamReader4OpenERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE'

I went through this issue https://github.com/Xinglab/rmats-turbo/issues/21 and found that it comes from the  fact that rmatspipeline might use a different compiler from the bamtools. My bamtool compilers are:

CC='gcc-12'

CXX='g++-12'

and the rmatspipeline, I think is using gcc-12 according to this line:

creating build/temp.macosx-11.1-arm64-cpython-39/rmatspipeline

gcc-12 -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/homebrew/anaconda3/include -arch arm64 -I/opt/homebrew/anaconda3/include -fPIC -O2 -isystem /opt/homebrew/anaconda3/include -arch arm64 -I/Applications/rmats_turbo_v4_1_2/bamtools/include -I/opt/homebrew/anaconda3/include/python3.9 -c rmatspipeline/rmatspipeline.cpp -o build/temp.macosx-11.1-arm64-cpython-39/rmatspipeline/rmatspipeline.o -O3 -funroll-loops -std=c++11 -fopenmp -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -w -Wl,-static

I tried to modify some arguments in the L11 of this file:

https://github.com/Xinglab/rmats-turbo/blob/master/rMATS_pipeline/setup.py#L11

but it did not solve the problem and raised more issues.

Best,

Babak

[kutsc...@gmail.com]

As you mentioned, that error can happen when bamtools and rmatspipeline were built with different compilers. I think in this case bamtools was built before you changed the build scripts to use gcc-12 and g++-12. Even though later runs of the build show gcc-12 and g++-12 being used for bamtools and rmatspipeline, actually the old build results that used clang are probably still being kept. I think you'll need to either remove the bamtools build results:
bamtools/bin/
bamtools/build/
bamtools/include/
bamtools/lib/

Or just start from a clean copy of the source code and run the build with gcc-12 and g++-12

Eric

[Babak Loghmani]

Thanks a lot. Starting a clean copy worked fine and installed with no error.

Thank you very much for the support.

Babak