Does rmats-turbo work on mac OS？

[linyibin123]

I tried to install and run, but failed.

The following is the error message for the operation $ ./build_rmats
cd bamtools; mkdir -p build; cd build; cmake ..; make; CMake Warning (dev) at CMakeLists.txt:9 (project): cmake_minimum_required() should be called prior to this top-level project() call. Please see the cmake-commands(7) manual for usage documentation of both commands. This warning is for project developers. Use -Wno-dev to suppress it.

CMake Error at /opt/homebrew/Cellar/cmake/3.29.2/share/cmake/Modules/CMakeDetermineCXXCompiler.cmake:48 (message): Could not find compiler set in environment variable CXX:

/usr/local/bin/g++.

Call Stack (most recent call first): CMakeLists.txt:9 (project)

CMake Error: CMAKE_CXX_COMPILER not set, after EnableLanguage -- Configuring incomplete, errors occurred! make[1]: No targets specified and no makefile found. Stop. make: [build] Error 2 (base)

[EricKutschera]

I think the build should work on mac. The error above is:

Could not find compiler set in environment variable CXX:
/usr/local/bin/g++.

That seems to be saying that you have this environment variable set: CXX=/usr/local/bin/g++ but actually /usr/local/bin/g++ isn't found. Does ls -l /usr/local/bin/g++ work?

The build will set CXX unless you set that variable yourself: https://github.com/Xinglab/rmats-turbo/blob/v4.3.0/build_rmats#L79 If you do have g++ installed and know the path then you can run export CXX=/path/to/your/g++ before running the build

Also there is an osx bioconda package for rmats-turbo that you could try instead of building from source: https://anaconda.org/bioconda/rmats

conda install -c conda-forge -c bioconda rmats=4.3.0

[linyibin123]

Thank you for your reply.

I try to rebuild, but another problem happened.

yibinlin @ yibindeMacBook-Pro in ~/rmats_turbo_v4_3_0 [18:14:38]

$ ./build_rmats

cd bamtools; mkdir -p build; cd build; cmake ..; make; CMake Warning (dev) at CMakeLists.txt:9 (project): cmake_minimum_required() should be called prior to this top-level project() call. Please see the cmake-commands(7) manual for usage documentation of both commands. This warning is for project developers. Use -Wno-dev to suppress it.

-- The C compiler identification is AppleClang 15.0.0.15000309 -- The CXX compiler identification is AppleClang 15.0.0.15000309 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /opt/homebrew/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Deprecation Warning at CMakeLists.txt:12 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake.

Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions.

-- Configuring done (0.5s) CMake Warning (dev): Policy CMP0042 is not set: MACOSX_RPATH is enabled by default. Run "cmake --help-policy CMP0042" for policy details. Use the cmake_policy command to set the policy and suppress this warning.

MACOSX_RPATH is not specified for the following targets:

BamTools

This warning is for project developers. Use -Wno-dev to suppress it.

-- Generating done (0.0s) -- Build files have been written to: /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/build [ 0%] Built target SharedHeaders [ 0%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamAlignment.cpp:10: In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamAlignment.h:15: /Users/yibinlin/rmats_turbo_v4_3_0/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;

/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamAlignment.cpp:10:
/Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamAlignment.h:581:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]
    int elementLength = 0;
        ^
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamMultiReader.cpp:15:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamMultiReader.h:14:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamReader.h:14:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamAlignment.h:15:
/Users/yibinlin/rmats_turbo_v4_3_0/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;
           ~~~~~~~~     ^~~
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamMultiReader.cpp:15:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamMultiReader.h:14:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamReader.h:14:
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamReader.cpp:10:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamReader.h:14:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamAlignment.h:15:
/Users/yibinlin/rmats_turbo_v4_3_0/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;
           ~~~~~~~~     ^~~
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamReader.cpp:10:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamReader.h:14:
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamWriter.cpp:10:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamAlignment.h:15:
/Users/yibinlin/rmats_turbo_v4_3_0/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;
           ~~~~~~~~     ^~~
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamWriter.cpp:10:
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/internal/bam/BamHeader_p.cpp:11:
/Users/yibinlin/rmats_turbo_v4_3_0/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;
           ~~~~~~~~     ^~~
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/internal/bam/BamMultiReader_p.cpp:10:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamAlignment.h:15:
/Users/yibinlin/rmats_turbo_v4_3_0/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;
           ~~~~~~~~     ^~~
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/internal/bam/BamMultiReader_p.cpp:10:
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/internal/bam/BamRandomAccessController_p.cpp:12:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/internal/bam/BamReader_p.h:23:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamAlignment.h:15:
/Users/yibinlin/rmats_turbo_v4_3_0/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;
           ~~~~~~~~     ^~~
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/internal/bam/BamRandomAccessController_p.cpp:12:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/internal/bam/BamReader_p.h:23:
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/internal/bam/BamReader_p.cpp:10:
/Users/yibinlin/rmats_turbo_v4_3_0/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;
           ~~~~~~~~     ^~~
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/internal/bam/BamReader_p.cpp:11:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamReader.h:14:
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/internal/bam/BamWriter_p.cpp:10:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamAlignment.h:15:
/Users/yibinlin/rmats_turbo_v4_3_0/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;
           ~~~~~~~~     ^~~
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/internal/bam/BamWriter_p.cpp:10:
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamAlignment.h:15:
/Users/yibinlin/rmats_turbo_v4_3_0/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;
           ~~~~~~~~     ^~~
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10:
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:10:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamAlignment.h:15:
/Users/yibinlin/rmats_turbo_v4_3_0/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;
           ~~~~~~~~     ^~~
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:10:
/Users/yibinlin/rmats_turbo_v4_3_0/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
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[ 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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/internal/io/BgzfStream_p.cpp:13:
/Users/yibinlin/rmats_turbo_v4_3_0/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;
           ~~~~~~~~     ^~~
/Users/yibinlin/rmats_turbo_v4_3_0/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
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[ 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 /Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamAlignment.cpp:10:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamAlignment.h:15:
/Users/yibinlin/rmats_turbo_v4_3_0/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;
           ~~~~~~~~     ^~~
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamAlignment.cpp:10:
/Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamAlignment.h:581:9: warning: variable 'elementLength' set but not used [-Wunused-but-set-variable]
    int elementLength = 0;
        ^
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamMultiReader.cpp:15:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamMultiReader.h:14:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamReader.h:14:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamAlignment.h:15:
/Users/yibinlin/rmats_turbo_v4_3_0/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;
           ~~~~~~~~     ^~~
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamMultiReader.cpp:15:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamMultiReader.h:14:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamReader.h:14:
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamReader.cpp:10:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamReader.h:14:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamAlignment.h:15:
/Users/yibinlin/rmats_turbo_v4_3_0/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;
           ~~~~~~~~     ^~~
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamReader.cpp:10:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamReader.h:14:
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamWriter.cpp:10:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamAlignment.h:15:
/Users/yibinlin/rmats_turbo_v4_3_0/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;
           ~~~~~~~~     ^~~
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamWriter.cpp:10:
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/internal/bam/BamHeader_p.cpp:11:
/Users/yibinlin/rmats_turbo_v4_3_0/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;
           ~~~~~~~~     ^~~
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/internal/bam/BamMultiReader_p.cpp:10:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamAlignment.h:15:
/Users/yibinlin/rmats_turbo_v4_3_0/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;
           ~~~~~~~~     ^~~
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/internal/bam/BamMultiReader_p.cpp:10:
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/internal/bam/BamRandomAccessController_p.cpp:12:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/internal/bam/BamReader_p.h:23:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamAlignment.h:15:
/Users/yibinlin/rmats_turbo_v4_3_0/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;
           ~~~~~~~~     ^~~
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/internal/bam/BamRandomAccessController_p.cpp:12:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/internal/bam/BamReader_p.h:23:
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/internal/bam/BamReader_p.cpp:10:
/Users/yibinlin/rmats_turbo_v4_3_0/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;
           ~~~~~~~~     ^~~
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/internal/bam/BamReader_p.cpp:11:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamReader.h:14:
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/internal/bam/BamWriter_p.cpp:10:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamAlignment.h:15:
/Users/yibinlin/rmats_turbo_v4_3_0/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;
           ~~~~~~~~     ^~~
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/internal/bam/BamWriter_p.cpp:10:
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamAlignment.h:15:
/Users/yibinlin/rmats_turbo_v4_3_0/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;
           ~~~~~~~~     ^~~
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/internal/index/BamStandardIndex_p.cpp:10:
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:10:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamAlignment.h:15:
/Users/yibinlin/rmats_turbo_v4_3_0/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;
           ~~~~~~~~     ^~~
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/internal/index/BamToolsIndex_p.cpp:10:
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/internal/io/BgzfStream_p.cpp:13:
/Users/yibinlin/rmats_turbo_v4_3_0/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;
           ~~~~~~~~     ^~~
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/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
/Users/yibinlin/rmats_turbo_v4_3_0/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  &&  
                            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
/Users/yibinlin/rmats_turbo_v4_3_0/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/MacOSX14.4.sdk/usr/include/stdio.h:180:1: 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/MacOSX14.4.sdk/usr/include/sys/cdefs.h:218:48: 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
/Users/yibinlin/rmats_turbo_v4_3_0/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/MacOSX14.4.sdk/usr/include/stdio.h:180:1: 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/MacOSX14.4.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg'
        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
                                                      ^
1 warning generated.
[ 80%] Linking CXX static library /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/lib/libjsoncpp.a
[ 80%] Built target jsoncpp
[ 81%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_fasta.cpp.o
/Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/utils/bamtools_fasta.cpp:165:9: warning: variable 'currentId' set but not used [-Wunused-but-set-variable]
    int currentId   = 0;
        ^
1 warning generated.
[ 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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/utils/bamtools_pileup_engine.cpp:10:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/utils/bamtools_pileup_engine.h:15:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamAlignment.h:15:
/Users/yibinlin/rmats_turbo_v4_3_0/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;
           ~~~~~~~~     ^~~
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/utils/bamtools_pileup_engine.cpp:10:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/utils/bamtools_pileup_engine.h:15:
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/utils/bamtools_utilities.cpp:10:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamMultiReader.h:14:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamReader.h:14:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamAlignment.h:15:
/Users/yibinlin/rmats_turbo_v4_3_0/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;
           ~~~~~~~~     ^~~
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/utils/bamtools_utilities.cpp:10:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamMultiReader.h:14:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamReader.h:14:
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/toolkit/bamtools_convert.cpp:12:
/Users/yibinlin/rmats_turbo_v4_3_0/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;
           ~~~~~~~~     ^~~
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/toolkit/bamtools_convert.cpp:13:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamMultiReader.h:14:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamReader.h:14:
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/toolkit/bamtools_count.cpp:12:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamAlgorithms.h:15:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/algorithms/Sort.h:15:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamAlignment.h:15:
/Users/yibinlin/rmats_turbo_v4_3_0/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;
           ~~~~~~~~     ^~~
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/toolkit/bamtools_count.cpp:12:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamAlgorithms.h:15:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/algorithms/Sort.h:15:
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/toolkit/bamtools_coverage.cpp:12:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamReader.h:14:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamAlignment.h:15:
/Users/yibinlin/rmats_turbo_v4_3_0/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;
           ~~~~~~~~     ^~~
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/toolkit/bamtools_coverage.cpp:12:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamReader.h:14:
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/toolkit/bamtools_filter.cpp:12:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamMultiReader.h:14:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamReader.h:14:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamAlignment.h:15:
/Users/yibinlin/rmats_turbo_v4_3_0/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;
           ~~~~~~~~     ^~~
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/toolkit/bamtools_filter.cpp:12:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamMultiReader.h:14:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamReader.h:14:
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/toolkit/bamtools_header.cpp:13:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamMultiReader.h:14:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamReader.h:14:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamAlignment.h:15:
/Users/yibinlin/rmats_turbo_v4_3_0/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;
           ~~~~~~~~     ^~~
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/toolkit/bamtools_header.cpp:13:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamMultiReader.h:14:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamReader.h:14:
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/toolkit/bamtools_index.cpp:12:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamReader.h:14:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamAlignment.h:15:
/Users/yibinlin/rmats_turbo_v4_3_0/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;
           ~~~~~~~~     ^~~
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/toolkit/bamtools_index.cpp:12:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamReader.h:14:
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/toolkit/bamtools_merge.cpp:12:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamMultiReader.h:14:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamReader.h:14:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamAlignment.h:15:
/Users/yibinlin/rmats_turbo_v4_3_0/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;
           ~~~~~~~~     ^~~
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/toolkit/bamtools_merge.cpp:12:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamMultiReader.h:14:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamReader.h:14:
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/toolkit/bamtools_random.cpp:12:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamMultiReader.h:14:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamReader.h:14:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamAlignment.h:15:
/Users/yibinlin/rmats_turbo_v4_3_0/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;
           ~~~~~~~~     ^~~
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/toolkit/bamtools_random.cpp:12:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamMultiReader.h:14:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamReader.h:14:
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/toolkit/bamtools_resolve.cpp:12:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamReader.h:14:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamAlignment.h:15:
/Users/yibinlin/rmats_turbo_v4_3_0/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;
           ~~~~~~~~     ^~~
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/toolkit/bamtools_resolve.cpp:12:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamReader.h:14:
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/toolkit/bamtools_revert.cpp:12:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamReader.h:14:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamAlignment.h:15:
/Users/yibinlin/rmats_turbo_v4_3_0/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;
           ~~~~~~~~     ^~~
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/toolkit/bamtools_revert.cpp:12:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamReader.h:14:
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/toolkit/bamtools_sort.cpp:13:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamMultiReader.h:14:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamReader.h:14:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamAlignment.h:15:
/Users/yibinlin/rmats_turbo_v4_3_0/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;
           ~~~~~~~~     ^~~
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/toolkit/bamtools_sort.cpp:13:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamMultiReader.h:14:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamReader.h:14:
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/toolkit/bamtools_split.cpp:13:
/Users/yibinlin/rmats_turbo_v4_3_0/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;
           ~~~~~~~~     ^~~
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/toolkit/bamtools_split.cpp:14:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamReader.h:14:
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/toolkit/bamtools_stats.cpp:12:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamMultiReader.h:14:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamReader.h:14:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamAlignment.h:15:
/Users/yibinlin/rmats_turbo_v4_3_0/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;
           ~~~~~~~~     ^~~
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/toolkit/bamtools_stats.cpp:12:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamMultiReader.h:14:
In file included from /Users/yibinlin/rmats_turbo_v4_3_0/bamtools/src/api/BamReader.h:14:
/Users/yibinlin/rmats_turbo_v4_3_0/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 /Users/yibinlin/rmats_turbo_v4_3_0/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
/opt/homebrew/bin/gfortran -c -O2  -c -o lbfgsb.o lbfgsb.f
/opt/homebrew/bin/gfortran -c -O2  -c -o linpack.o linpack.f
/opt/homebrew/bin/gfortran -c -O2  -c -o timer.o timer.f
/opt/homebrew/bin/gcc -I/opt/homebrew/Cellar/gsl/2.7.1/include -Wall -O2 -msse2 -funroll-loops -fopenmp -o rMATSexe src/main.c src/myfunc.c src/util.c lbfgs_scipy/lbfgsb.o lbfgs_scipy/linpack.o lbfgs_scipy/timer.o -L/opt/homebrew/Cellar/gsl/2.7.1/lib -lgsl -lgslcblas -lm -lgfortran -lgsl -lgslcblas -lgomp -lblas -llapack
clang: error: unsupported option '-fopenmp'
clang: error: unsupported option '-fopenmp'
clang: error: unsupported option '-fopenmp'
clang: error: unsupported option '-fopenmp'
make[1]: *** [rMATSexe] Error 1
make: *** [build] Error 2
(base) 

[EricKutschera]

Most of that output is from warnings which can be ignored. The error is: clang: error: unsupported option '-fopenmp'

The build finds /opt/homebrew/bin/gcc and /Library/Developer/CommandLineTools/usr/bin/g++, but it says that those are actually AppleClang 15.0.0.15000309

This post (https://github.com/Xinglab/rmats-turbo/issues/305#issuecomment-1630895121) looks like an osx build. The solution in that case was to install a specific version of gcc with homebrew and then export CC=gcc-13. They also had to remove -msse2 from https://github.com/Xinglab/rmats-turbo/blob/v4.3.0/rMATS_C/Makefile#L13

This post was similar: https://groups.google.com/g/rmats-user-group/c/m44b0hAL6Kw

If you change compilers you need to remove old build results or start from a fresh copy of the code to avoid mixing output from different compiler versions