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A collection of easyconfig files that describe which software to build using which build options with EasyBuild.
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Failing to install ExomeDepth extension in R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb #15771

Closed VictorGoitea closed 1 year ago

VictorGoitea commented 2 years ago

Hi, I was trying to install R-bundle-Bioconductor-3.15 but I could not make it to work the extension ExomeDepth. It is failing with the same error message open here: https://github.com/vplagnol/ExomeDepth/issues/46.

Do you think it is a dependency with some link to OS files that it is necessary to rebuild? If so, by any chance you can telll which one by looking at this error log? Otherwise, can you tell me how I can skip this extension and continue with the others? By the way I was using --rebuild --skip options already.

== 2022-06-26 19:15:01,135 build_log.py:265 INFO        ... (took 13 secs)
== 2022-06-26 19:15:01,135 easyblock.py:1773 INFO Starting extension ExomeDepth
== 2022-06-26 19:15:01,135 build_log.py:265 INFO installing extension ExomeDepth 1.1.15 (332/341)...
== 2022-06-26 19:15:01,455 modules.py:626 INFO Checking whether foss/2021b exists...
== 2022-06-26 19:15:01,455 modules.py:633 INFO Module foss/2021b not found in list of available modules, checking via 'module show'...
== 2022-06-26 19:15:01,455 modules.py:654 INFO Result for existence check of foss/2021b module: True
== 2022-06-26 19:15:01,457 toolchain.py:760 INFO List of toolchain dependency modules and toolchain definition match!
== 2022-06-26 19:15:01,459 compiler.py:361 INFO _set_optimal_architecture: using march=native as optarch for x86_64.
== 2022-06-26 19:15:01,468 variables.py:201 WARNING flags_for_subdirs: directory /work/easybuild/software/ScaLAPACK/2.1.0-gompi-2021b-fb/include was not found
== 2022-06-26 19:15:01,471 environment.py:91 INFO Environment variable BLAS_INC_DIR set to /work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/include/flexiblas (previous value: '/work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/include/flexiblas')
== 2022-06-26 19:15:01,472 environment.py:91 INFO Environment variable EBVARBLAS_INC_DIR set to /work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/include/flexiblas (previous value: '/work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/include/flexiblas')
== 2022-06-26 19:15:01,472 environment.py:91 INFO Environment variable BLAS_LAPACK_INC_DIR set to /work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/include/flexiblas (previous value: '/work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/include/flexiblas')
== 2022-06-26 19:15:01,472 environment.py:91 INFO Environment variable EBVARBLAS_LAPACK_INC_DIR set to /work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/include/flexiblas (previous value: '/work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/include/flexiblas')
== 2022-06-26 19:15:01,472 environment.py:91 INFO Environment variable BLAS_LAPACK_LIB_DIR set to /work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/lib (previous value: '/work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/lib')
== 2022-06-26 19:15:01,472 environment.py:91 INFO Environment variable EBVARBLAS_LAPACK_LIB_DIR set to /work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/lib (previous value: '/work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/lib')
== 2022-06-26 19:15:01,472 environment.py:91 INFO Environment variable BLAS_LAPACK_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previous value: 'libflexiblas.so,libgfortran.so')
== 2022-06-26 19:15:01,472 environment.py:91 INFO Environment variable EBVARBLAS_LAPACK_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previous value: 'libflexiblas.so,libgfortran.so')
== 2022-06-26 19:15:01,472 environment.py:91 INFO Environment variable BLAS_LAPACK_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previous value: 'libflexiblas.a,libgfortran.a')
== 2022-06-26 19:15:01,472 environment.py:91 INFO Environment variable EBVARBLAS_LAPACK_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previous value: 'libflexiblas.a,libgfortran.a')
== 2022-06-26 19:15:01,472 environment.py:91 INFO Environment variable BLAS_LAPACK_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previous value: 'libflexiblas.so,libgfortran.so')
== 2022-06-26 19:15:01,472 environment.py:91 INFO Environment variable EBVARBLAS_LAPACK_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previous value: 'libflexiblas.so,libgfortran.so')
== 2022-06-26 19:15:01,472 environment.py:91 INFO Environment variable BLAS_LAPACK_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previous value: 'libflexiblas.a,libgfortran.a')
== 2022-06-26 19:15:01,473 environment.py:91 INFO Environment variable EBVARBLAS_LAPACK_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previous value: 'libflexiblas.a,libgfortran.a')
== 2022-06-26 19:15:01,473 environment.py:91 INFO Environment variable BLAS_LIB_DIR set to /work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/lib (previous value: '/work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/lib')
== 2022-06-26 19:15:01,473 environment.py:91 INFO Environment variable EBVARBLAS_LIB_DIR set to /work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/lib (previous value: '/work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/lib')
== 2022-06-26 19:15:01,473 environment.py:91 INFO Environment variable BLAS_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previous value: 'libflexiblas.so,libgfortran.so')
== 2022-06-26 19:15:01,473 environment.py:91 INFO Environment variable EBVARBLAS_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previous value: 'libflexiblas.so,libgfortran.so')
== 2022-06-26 19:15:01,473 environment.py:91 INFO Environment variable BLAS_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previous value: 'libflexiblas.a,libgfortran.a')
== 2022-06-26 19:15:01,473 environment.py:91 INFO Environment variable EBVARBLAS_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previous value: 'libflexiblas.a,libgfortran.a')
== 2022-06-26 19:15:01,473 environment.py:91 INFO Environment variable BLAS_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previous value: 'libflexiblas.so,libgfortran.so')
== 2022-06-26 19:15:01,473 environment.py:91 INFO Environment variable EBVARBLAS_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previous value: 'libflexiblas.so,libgfortran.so')
== 2022-06-26 19:15:01,473 environment.py:91 INFO Environment variable BLAS_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previous value: 'libflexiblas.a,libgfortran.a')
== 2022-06-26 19:15:01,473 environment.py:91 INFO Environment variable EBVARBLAS_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previous value: 'libflexiblas.a,libgfortran.a')
== 2022-06-26 19:15:01,473 environment.py:91 INFO Environment variable CC set to gcc (previous value: 'gcc')
== 2022-06-26 19:15:01,473 environment.py:91 INFO Environment variable EBVARCC set to gcc (previous value: 'gcc')
== 2022-06-26 19:15:01,473 environment.py:91 INFO Environment variable CFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno')
== 2022-06-26 19:15:01,474 environment.py:91 INFO Environment variable EBVARCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno')
== 2022-06-26 19:15:01,474 environment.py:91 INFO Environment variable CPPFLAGS set to -I/work/easybuild/software/FFTW/3.3.10-gompi-2021b/include -I/work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/include -I/work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/include/flexiblas (previous value: '-I/work/easybuild/software/FFTW/3.3.10-gompi-2021b/include -I/work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/include -I/work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/include/flexiblas')
== 2022-06-26 19:15:01,474 environment.py:91 INFO Environment variable EBVARCPPFLAGS set to -I/work/easybuild/software/FFTW/3.3.10-gompi-2021b/include -I/work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/include -I/work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/include/flexiblas (previous value: '-I/work/easybuild/software/FFTW/3.3.10-gompi-2021b/include -I/work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/include -I/work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/include/flexiblas')
== 2022-06-26 19:15:01,474 environment.py:91 INFO Environment variable CXX set to g++ (previous value: 'g++')
== 2022-06-26 19:15:01,474 environment.py:91 INFO Environment variable EBVARCXX set to g++ (previous value: 'g++')
== 2022-06-26 19:15:01,474 environment.py:91 INFO Environment variable CXXFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno')
== 2022-06-26 19:15:01,474 environment.py:91 INFO Environment variable EBVARCXXFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno')
== 2022-06-26 19:15:01,474 environment.py:91 INFO Environment variable F77 set to gfortran (previous value: 'gfortran')
== 2022-06-26 19:15:01,474 environment.py:91 INFO Environment variable EBVARF77 set to gfortran (previous value: 'gfortran')
== 2022-06-26 19:15:01,474 environment.py:91 INFO Environment variable F90 set to gfortran (previous value: 'gfortran')
== 2022-06-26 19:15:01,474 environment.py:91 INFO Environment variable EBVARF90 set to gfortran (previous value: 'gfortran')
== 2022-06-26 19:15:01,474 environment.py:91 INFO Environment variable F90FLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno')
== 2022-06-26 19:15:01,474 environment.py:91 INFO Environment variable EBVARF90FLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno')
== 2022-06-26 19:15:01,474 environment.py:91 INFO Environment variable FC set to gfortran (previous value: 'gfortran')
== 2022-06-26 19:15:01,475 environment.py:91 INFO Environment variable EBVARFC set to gfortran (previous value: 'gfortran')
== 2022-06-26 19:15:01,475 environment.py:91 INFO Environment variable FCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno')
== 2022-06-26 19:15:01,475 environment.py:91 INFO Environment variable EBVARFCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno')
== 2022-06-26 19:15:01,475 environment.py:91 INFO Environment variable FFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno')
== 2022-06-26 19:15:01,475 environment.py:91 INFO Environment variable EBVARFFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno')
== 2022-06-26 19:15:01,475 environment.py:91 INFO Environment variable FFTW_INC_DIR set to /work/easybuild/software/FFTW/3.3.10-gompi-2021b/include (previous value: '/work/easybuild/software/FFTW/3.3.10-gompi-2021b/include')
== 2022-06-26 19:15:01,475 environment.py:91 INFO Environment variable EBVARFFTW_INC_DIR set to /work/easybuild/software/FFTW/3.3.10-gompi-2021b/include (previous value: '/work/easybuild/software/FFTW/3.3.10-gompi-2021b/include')
== 2022-06-26 19:15:01,475 environment.py:91 INFO Environment variable FFTW_LIB_DIR set to /work/easybuild/software/FFTW/3.3.10-gompi-2021b/lib (previous value: '/work/easybuild/software/FFTW/3.3.10-gompi-2021b/lib')
== 2022-06-26 19:15:01,475 environment.py:91 INFO Environment variable EBVARFFTW_LIB_DIR set to /work/easybuild/software/FFTW/3.3.10-gompi-2021b/lib (previous value: '/work/easybuild/software/FFTW/3.3.10-gompi-2021b/lib')
== 2022-06-26 19:15:01,475 environment.py:91 INFO Environment variable FFTW_SHARED_LIBS set to libfftw3.so (previous value: 'libfftw3.so')
== 2022-06-26 19:15:01,475 environment.py:91 INFO Environment variable EBVARFFTW_SHARED_LIBS set to libfftw3.so (previous value: 'libfftw3.so')
== 2022-06-26 19:15:01,475 environment.py:91 INFO Environment variable FFTW_SHARED_LIBS_MT set to libfftw3.so,libpthread.so (previous value: 'libfftw3.so,libpthread.so')
== 2022-06-26 19:15:01,475 environment.py:91 INFO Environment variable EBVARFFTW_SHARED_LIBS_MT set to libfftw3.so,libpthread.so (previous value: 'libfftw3.so,libpthread.so')
== 2022-06-26 19:15:01,475 environment.py:91 INFO Environment variable FFTW_STATIC_LIBS set to libfftw3.a (previous value: 'libfftw3.a')
== 2022-06-26 19:15:01,476 environment.py:91 INFO Environment variable EBVARFFTW_STATIC_LIBS set to libfftw3.a (previous value: 'libfftw3.a')
== 2022-06-26 19:15:01,476 environment.py:91 INFO Environment variable FFTW_STATIC_LIBS_MT set to libfftw3.a,libpthread.a (previous value: 'libfftw3.a,libpthread.a')
== 2022-06-26 19:15:01,476 environment.py:91 INFO Environment variable EBVARFFTW_STATIC_LIBS_MT set to libfftw3.a,libpthread.a (previous value: 'libfftw3.a,libpthread.a')
== 2022-06-26 19:15:01,476 environment.py:91 INFO Environment variable FFT_INC_DIR set to /work/easybuild/software/FFTW/3.3.10-gompi-2021b/include (previous value: '/work/easybuild/software/FFTW/3.3.10-gompi-2021b/include')
== 2022-06-26 19:15:01,476 environment.py:91 INFO Environment variable EBVARFFT_INC_DIR set to /work/easybuild/software/FFTW/3.3.10-gompi-2021b/include (previous value: '/work/easybuild/software/FFTW/3.3.10-gompi-2021b/include')
== 2022-06-26 19:15:01,476 environment.py:91 INFO Environment variable FFT_LIB_DIR set to /work/easybuild/software/FFTW/3.3.10-gompi-2021b/lib (previous value: '/work/easybuild/software/FFTW/3.3.10-gompi-2021b/lib')
== 2022-06-26 19:15:01,476 environment.py:91 INFO Environment variable EBVARFFT_LIB_DIR set to /work/easybuild/software/FFTW/3.3.10-gompi-2021b/lib (previous value: '/work/easybuild/software/FFTW/3.3.10-gompi-2021b/lib')
== 2022-06-26 19:15:01,476 environment.py:91 INFO Environment variable FFT_SHARED_LIBS set to libfftw3.so (previous value: 'libfftw3.so')
== 2022-06-26 19:15:01,476 environment.py:91 INFO Environment variable EBVARFFT_SHARED_LIBS set to libfftw3.so (previous value: 'libfftw3.so')
== 2022-06-26 19:15:01,476 environment.py:91 INFO Environment variable FFT_SHARED_LIBS_MT set to libfftw3.so,libpthread.so (previous value: 'libfftw3.so,libpthread.so')
== 2022-06-26 19:15:01,476 environment.py:91 INFO Environment variable EBVARFFT_SHARED_LIBS_MT set to libfftw3.so,libpthread.so (previous value: 'libfftw3.so,libpthread.so')
== 2022-06-26 19:15:01,476 environment.py:91 INFO Environment variable FFT_STATIC_LIBS set to libfftw3.a (previous value: 'libfftw3.a')
== 2022-06-26 19:15:01,476 environment.py:91 INFO Environment variable EBVARFFT_STATIC_LIBS set to libfftw3.a (previous value: 'libfftw3.a')
== 2022-06-26 19:15:01,476 environment.py:91 INFO Environment variable FFT_STATIC_LIBS_MT set to libfftw3.a,libpthread.a (previous value: 'libfftw3.a,libpthread.a')
== 2022-06-26 19:15:01,477 environment.py:91 INFO Environment variable EBVARFFT_STATIC_LIBS_MT set to libfftw3.a,libpthread.a (previous value: 'libfftw3.a,libpthread.a')
== 2022-06-26 19:15:01,477 environment.py:91 INFO Environment variable FLIBS set to -lgfortran (previous value: '-lgfortran')
== 2022-06-26 19:15:01,477 environment.py:91 INFO Environment variable EBVARFLIBS set to -lgfortran (previous value: '-lgfortran')
== 2022-06-26 19:15:01,477 environment.py:91 INFO Environment variable LAPACK_INC_DIR set to /work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/include/flexiblas (previous value: '/work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/include/flexiblas')
== 2022-06-26 19:15:01,477 environment.py:91 INFO Environment variable EBVARLAPACK_INC_DIR set to /work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/include/flexiblas (previous value: '/work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/include/flexiblas')
== 2022-06-26 19:15:01,477 environment.py:91 INFO Environment variable LAPACK_LIB_DIR set to /work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/lib (previous value: '/work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/lib')
== 2022-06-26 19:15:01,477 environment.py:91 INFO Environment variable EBVARLAPACK_LIB_DIR set to /work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/lib (previous value: '/work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/lib')
== 2022-06-26 19:15:01,477 environment.py:91 INFO Environment variable LAPACK_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previous value: 'libflexiblas.so,libgfortran.so')
== 2022-06-26 19:15:01,477 environment.py:91 INFO Environment variable EBVARLAPACK_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previous value: 'libflexiblas.so,libgfortran.so')
== 2022-06-26 19:15:01,477 environment.py:91 INFO Environment variable LAPACK_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previous value: 'libflexiblas.a,libgfortran.a')
== 2022-06-26 19:15:01,477 environment.py:91 INFO Environment variable EBVARLAPACK_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previous value: 'libflexiblas.a,libgfortran.a')
== 2022-06-26 19:15:01,477 environment.py:91 INFO Environment variable LAPACK_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previous value: 'libflexiblas.so,libgfortran.so')
== 2022-06-26 19:15:01,477 environment.py:91 INFO Environment variable EBVARLAPACK_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previous value: 'libflexiblas.so,libgfortran.so')
== 2022-06-26 19:15:01,477 environment.py:91 INFO Environment variable LAPACK_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previous value: 'libflexiblas.a,libgfortran.a')
== 2022-06-26 19:15:01,478 environment.py:91 INFO Environment variable EBVARLAPACK_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previous value: 'libflexiblas.a,libgfortran.a')
== 2022-06-26 19:15:01,478 environment.py:91 INFO Environment variable LDFLAGS set to -L/work/easybuild/software/FFTW/3.3.10-gompi-2021b/lib64 -L/work/easybuild/software/FFTW/3.3.10-gompi-2021b/lib -L/work/easybuild/software/ScaLAPACK/2.1.0-gompi-2021b-fb/lib64 -L/work/easybuild/software/ScaLAPACK/2.1.0-gompi-2021b-fb/lib -L/work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/lib64 -L/work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/lib -L/work/easybuild/software/GCCcore/11.2.0/lib64 -L/work/easybuild/software/GCCcore/11.2.0/lib (previous value: '-L/work/easybuild/software/FFTW/3.3.10-gompi-2021b/lib64 -L/work/easybuild/software/FFTW/3.3.10-gompi-2021b/lib -L/work/easybuild/software/ScaLAPACK/2.1.0-gompi-2021b-fb/lib64 -L/work/easybuild/software/ScaLAPACK/2.1.0-gompi-2021b-fb/lib -L/work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/lib64 -L/work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/lib -L/work/easybuild/software/GCCcore/11.2.0/lib64 -L/work/easybuild/software/GCCcore/11.2.0/lib')
== 2022-06-26 19:15:01,478 environment.py:91 INFO Environment variable EBVARLDFLAGS set to -L/work/easybuild/software/FFTW/3.3.10-gompi-2021b/lib64 -L/work/easybuild/software/FFTW/3.3.10-gompi-2021b/lib -L/work/easybuild/software/ScaLAPACK/2.1.0-gompi-2021b-fb/lib64 -L/work/easybuild/software/ScaLAPACK/2.1.0-gompi-2021b-fb/lib -L/work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/lib64 -L/work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/lib -L/work/easybuild/software/GCCcore/11.2.0/lib64 -L/work/easybuild/software/GCCcore/11.2.0/lib (previous value: '-L/work/easybuild/software/FFTW/3.3.10-gompi-2021b/lib64 -L/work/easybuild/software/FFTW/3.3.10-gompi-2021b/lib -L/work/easybuild/software/ScaLAPACK/2.1.0-gompi-2021b-fb/lib64 -L/work/easybuild/software/ScaLAPACK/2.1.0-gompi-2021b-fb/lib -L/work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/lib64 -L/work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/lib -L/work/easybuild/software/GCCcore/11.2.0/lib64 -L/work/easybuild/software/GCCcore/11.2.0/lib')
== 2022-06-26 19:15:01,478 environment.py:91 INFO Environment variable LIBBLAS set to -lflexiblas -lgfortran (previous value: '-lflexiblas -lgfortran')
== 2022-06-26 19:15:01,478 environment.py:91 INFO Environment variable EBVARLIBBLAS set to -lflexiblas -lgfortran (previous value: '-lflexiblas -lgfortran')
== 2022-06-26 19:15:01,478 environment.py:91 INFO Environment variable LIBBLAS_MT set to -lflexiblas -lgfortran (previous value: '-lflexiblas -lgfortran')
== 2022-06-26 19:15:01,478 environment.py:91 INFO Environment variable EBVARLIBBLAS_MT set to -lflexiblas -lgfortran (previous value: '-lflexiblas -lgfortran')
== 2022-06-26 19:15:01,478 environment.py:91 INFO Environment variable LIBFFT set to -lfftw3 (previous value: '-lfftw3')
== 2022-06-26 19:15:01,478 environment.py:91 INFO Environment variable EBVARLIBFFT set to -lfftw3 (previous value: '-lfftw3')
== 2022-06-26 19:15:01,478 environment.py:91 INFO Environment variable LIBFFT_MT set to -lfftw3 -lpthread (previous value: '-lfftw3 -lpthread')
== 2022-06-26 19:15:01,478 environment.py:91 INFO Environment variable EBVARLIBFFT_MT set to -lfftw3 -lpthread (previous value: '-lfftw3 -lpthread')
== 2022-06-26 19:15:01,478 environment.py:91 INFO Environment variable LIBLAPACK set to -lflexiblas -lgfortran (previous value: '-lflexiblas -lgfortran')
== 2022-06-26 19:15:01,479 environment.py:91 INFO Environment variable EBVARLIBLAPACK set to -lflexiblas -lgfortran (previous value: '-lflexiblas -lgfortran')
== 2022-06-26 19:15:01,479 environment.py:91 INFO Environment variable LIBLAPACK_MT set to -lflexiblas -lgfortran (previous value: '-lflexiblas -lgfortran')
== 2022-06-26 19:15:01,479 environment.py:91 INFO Environment variable EBVARLIBLAPACK_MT set to -lflexiblas -lgfortran (previous value: '-lflexiblas -lgfortran')
== 2022-06-26 19:15:01,479 environment.py:91 INFO Environment variable LIBLAPACK_MT_ONLY set to -lflexiblas -lgfortran (previous value: '-lflexiblas -lgfortran')
== 2022-06-26 19:15:01,479 environment.py:91 INFO Environment variable EBVARLIBLAPACK_MT_ONLY set to -lflexiblas -lgfortran (previous value: '-lflexiblas -lgfortran')
== 2022-06-26 19:15:01,479 environment.py:91 INFO Environment variable LIBLAPACK_ONLY set to -lflexiblas -lgfortran (previous value: '-lflexiblas -lgfortran')
== 2022-06-26 19:15:01,479 environment.py:91 INFO Environment variable EBVARLIBLAPACK_ONLY set to -lflexiblas -lgfortran (previous value: '-lflexiblas -lgfortran')
== 2022-06-26 19:15:01,479 environment.py:91 INFO Environment variable LIBS set to -lm -lpthread (previous value: '-lm -lpthread')
== 2022-06-26 19:15:01,479 environment.py:91 INFO Environment variable EBVARLIBS set to -lm -lpthread (previous value: '-lm -lpthread')
== 2022-06-26 19:15:01,479 environment.py:91 INFO Environment variable LIBSCALAPACK set to -lscalapack -lflexiblas -lgfortran (previous value: '-lscalapack -lflexiblas -lgfortran')
== 2022-06-26 19:15:01,479 environment.py:91 INFO Environment variable EBVARLIBSCALAPACK set to -lscalapack -lflexiblas -lgfortran (previous value: '-lscalapack -lflexiblas -lgfortran')
== 2022-06-26 19:15:01,479 environment.py:91 INFO Environment variable LIBSCALAPACK_MT set to -lscalapack -lflexiblas -lpthread -lgfortran (previous value: '-lscalapack -lflexiblas -lpthread -lgfortran')
== 2022-06-26 19:15:01,479 environment.py:91 INFO Environment variable EBVARLIBSCALAPACK_MT set to -lscalapack -lflexiblas -lpthread -lgfortran (previous value: '-lscalapack -lflexiblas -lpthread -lgfortran')
== 2022-06-26 19:15:01,480 environment.py:91 INFO Environment variable LIBSCALAPACK_MT_ONLY set to -lscalapack -lgfortran (previous value: '-lscalapack -lgfortran')
== 2022-06-26 19:15:01,480 environment.py:91 INFO Environment variable EBVARLIBSCALAPACK_MT_ONLY set to -lscalapack -lgfortran (previous value: '-lscalapack -lgfortran')
== 2022-06-26 19:15:01,480 environment.py:91 INFO Environment variable LIBSCALAPACK_ONLY set to -lscalapack -lgfortran (previous value: '-lscalapack -lgfortran')
== 2022-06-26 19:15:01,480 environment.py:91 INFO Environment variable EBVARLIBSCALAPACK_ONLY set to -lscalapack -lgfortran (previous value: '-lscalapack -lgfortran')
== 2022-06-26 19:15:01,480 environment.py:91 INFO Environment variable MPICC set to mpicc (previous value: 'mpicc')
== 2022-06-26 19:15:01,480 environment.py:91 INFO Environment variable EBVARMPICC set to mpicc (previous value: 'mpicc')
== 2022-06-26 19:15:01,480 environment.py:91 INFO Environment variable MPICXX set to mpicxx (previous value: 'mpicxx')
== 2022-06-26 19:15:01,480 environment.py:91 INFO Environment variable EBVARMPICXX set to mpicxx (previous value: 'mpicxx')
== 2022-06-26 19:15:01,480 environment.py:91 INFO Environment variable MPIF77 set to mpifort (previous value: 'mpifort')
== 2022-06-26 19:15:01,480 environment.py:91 INFO Environment variable EBVARMPIF77 set to mpifort (previous value: 'mpifort')
== 2022-06-26 19:15:01,480 environment.py:91 INFO Environment variable MPIF90 set to mpifort (previous value: 'mpifort')
== 2022-06-26 19:15:01,480 environment.py:91 INFO Environment variable EBVARMPIF90 set to mpifort (previous value: 'mpifort')
== 2022-06-26 19:15:01,480 environment.py:91 INFO Environment variable MPIFC set to mpifort (previous value: 'mpifort')
== 2022-06-26 19:15:01,481 environment.py:91 INFO Environment variable EBVARMPIFC set to mpifort (previous value: 'mpifort')
== 2022-06-26 19:15:01,481 environment.py:91 INFO Environment variable MPI_INC_DIR set to /work/easybuild/software/OpenMPI/4.1.1-GCC-11.2.0/include (previous value: '/work/easybuild/software/OpenMPI/4.1.1-GCC-11.2.0/include')
== 2022-06-26 19:15:01,481 environment.py:91 INFO Environment variable EBVARMPI_INC_DIR set to /work/easybuild/software/OpenMPI/4.1.1-GCC-11.2.0/include (previous value: '/work/easybuild/software/OpenMPI/4.1.1-GCC-11.2.0/include')
== 2022-06-26 19:15:01,481 environment.py:91 INFO Environment variable MPI_LIB_DIR set to /work/easybuild/software/OpenMPI/4.1.1-GCC-11.2.0/lib64 (previous value: '/work/easybuild/software/OpenMPI/4.1.1-GCC-11.2.0/lib64')
== 2022-06-26 19:15:01,481 environment.py:91 INFO Environment variable EBVARMPI_LIB_DIR set to /work/easybuild/software/OpenMPI/4.1.1-GCC-11.2.0/lib64 (previous value: '/work/easybuild/software/OpenMPI/4.1.1-GCC-11.2.0/lib64')
== 2022-06-26 19:15:01,481 environment.py:91 INFO Environment variable MPI_LIB_SHARED set to /work/easybuild/software/OpenMPI/4.1.1-GCC-11.2.0/lib64/libmpi.so (previous value: '/work/easybuild/software/OpenMPI/4.1.1-GCC-11.2.0/lib64/libmpi.so')
== 2022-06-26 19:15:01,481 environment.py:91 INFO Environment variable EBVARMPI_LIB_SHARED set to /work/easybuild/software/OpenMPI/4.1.1-GCC-11.2.0/lib64/libmpi.so (previous value: '/work/easybuild/software/OpenMPI/4.1.1-GCC-11.2.0/lib64/libmpi.so')
== 2022-06-26 19:15:01,481 environment.py:91 INFO Environment variable MPI_LIB_STATIC set to  (previous value: '')
== 2022-06-26 19:15:01,481 environment.py:91 INFO Environment variable EBVARMPI_LIB_STATIC set to  (previous value: '')
== 2022-06-26 19:15:01,481 environment.py:91 INFO Environment variable OMPI_CC set to gcc (previous value: 'gcc')
== 2022-06-26 19:15:01,481 environment.py:91 INFO Environment variable EBVAROMPI_CC set to gcc (previous value: 'gcc')
== 2022-06-26 19:15:01,481 environment.py:91 INFO Environment variable OMPI_CXX set to g++ (previous value: 'g++')
== 2022-06-26 19:15:01,482 environment.py:91 INFO Environment variable EBVAROMPI_CXX set to g++ (previous value: 'g++')
== 2022-06-26 19:15:01,482 environment.py:91 INFO Environment variable OMPI_F77 set to gfortran (previous value: 'gfortran')
== 2022-06-26 19:15:01,482 environment.py:91 INFO Environment variable EBVAROMPI_F77 set to gfortran (previous value: 'gfortran')
== 2022-06-26 19:15:01,482 environment.py:91 INFO Environment variable OMPI_F90 set to gfortran (previous value: 'gfortran')
== 2022-06-26 19:15:01,482 environment.py:91 INFO Environment variable EBVAROMPI_F90 set to gfortran (previous value: 'gfortran')
== 2022-06-26 19:15:01,482 environment.py:91 INFO Environment variable OMPI_FC set to gfortran (previous value: 'gfortran')
== 2022-06-26 19:15:01,482 environment.py:91 INFO Environment variable EBVAROMPI_FC set to gfortran (previous value: 'gfortran')
== 2022-06-26 19:15:01,482 environment.py:91 INFO Environment variable OPTFLAGS set to -O2 -ftree-vectorize -march=native (previous value: '-O2 -ftree-vectorize -march=native')
== 2022-06-26 19:15:01,482 environment.py:91 INFO Environment variable EBVAROPTFLAGS set to -O2 -ftree-vectorize -march=native (previous value: '-O2 -ftree-vectorize -march=native')
== 2022-06-26 19:15:01,482 environment.py:91 INFO Environment variable PRECFLAGS set to -fno-math-errno (previous value: '-fno-math-errno')
== 2022-06-26 19:15:01,482 environment.py:91 INFO Environment variable EBVARPRECFLAGS set to -fno-math-errno (previous value: '-fno-math-errno')
== 2022-06-26 19:15:01,482 environment.py:91 INFO Environment variable SCALAPACK_INC_DIR set to  (previous value: '')
== 2022-06-26 19:15:01,482 environment.py:91 INFO Environment variable EBVARSCALAPACK_INC_DIR set to  (previous value: '')
== 2022-06-26 19:15:01,483 environment.py:91 INFO Environment variable SCALAPACK_LIB_DIR set to /work/easybuild/software/ScaLAPACK/2.1.0-gompi-2021b-fb/lib (previous value: '/work/easybuild/software/ScaLAPACK/2.1.0-gompi-2021b-fb/lib')
== 2022-06-26 19:15:01,483 environment.py:91 INFO Environment variable EBVARSCALAPACK_LIB_DIR set to /work/easybuild/software/ScaLAPACK/2.1.0-gompi-2021b-fb/lib (previous value: '/work/easybuild/software/ScaLAPACK/2.1.0-gompi-2021b-fb/lib')
== 2022-06-26 19:15:01,483 environment.py:91 INFO Environment variable SCALAPACK_MT_SHARED_LIBS set to libscalapack.so,libflexiblas.so,libgfortran.so,libpthread.so (previous value: 'libscalapack.so,libflexiblas.so,libgfortran.so,libpthread.so')
== 2022-06-26 19:15:01,483 environment.py:91 INFO Environment variable EBVARSCALAPACK_MT_SHARED_LIBS set to libscalapack.so,libflexiblas.so,libgfortran.so,libpthread.so (previous value: 'libscalapack.so,libflexiblas.so,libgfortran.so,libpthread.so')
== 2022-06-26 19:15:01,483 environment.py:91 INFO Environment variable SCALAPACK_MT_STATIC_LIBS set to libscalapack.a,libflexiblas.a,libgfortran.a,libpthread.a (previous value: 'libscalapack.a,libflexiblas.a,libgfortran.a,libpthread.a')
== 2022-06-26 19:15:01,483 environment.py:91 INFO Environment variable EBVARSCALAPACK_MT_STATIC_LIBS set to libscalapack.a,libflexiblas.a,libgfortran.a,libpthread.a (previous value: 'libscalapack.a,libflexiblas.a,libgfortran.a,libpthread.a')
== 2022-06-26 19:15:01,483 environment.py:91 INFO Environment variable SCALAPACK_SHARED_LIBS set to libscalapack.so,libflexiblas.so,libgfortran.so (previous value: 'libscalapack.so,libflexiblas.so,libgfortran.so')
== 2022-06-26 19:15:01,483 environment.py:91 INFO Environment variable EBVARSCALAPACK_SHARED_LIBS set to libscalapack.so,libflexiblas.so,libgfortran.so (previous value: 'libscalapack.so,libflexiblas.so,libgfortran.so')
== 2022-06-26 19:15:01,483 environment.py:91 INFO Environment variable SCALAPACK_STATIC_LIBS set to libscalapack.a,libflexiblas.a,libgfortran.a (previous value: 'libscalapack.a,libflexiblas.a,libgfortran.a')
== 2022-06-26 19:15:01,483 environment.py:91 INFO Environment variable EBVARSCALAPACK_STATIC_LIBS set to libscalapack.a,libflexiblas.a,libgfortran.a (previous value: 'libscalapack.a,libflexiblas.a,libgfortran.a')
== 2022-06-26 19:15:01,483 filetools.py:1882 INFO Creating directory /home/ucloud/.local/easybuild/build/RbundleBioconductor/3.15/foss-2021b-R-4.2.0/ExomeDepth (parents: True, set_gid: False, sticky: False)
== 2022-06-26 19:15:01,484 run.py:233 INFO running cmd: tar xzf /home/ucloud/.local/easybuild/sources/r/R-bundle-Bioconductor/extensions/ExomeDepth_1.1.15.tar.gz 
== 2022-06-26 19:15:01,575 run.py:233 INFO running cmd:  R CMD INSTALL /home/ucloud/.local/easybuild/build/RbundleBioconductor/3.15/foss-2021b-R-4.2.0/ExomeDepth/ExomeDepth   --library=/work/easybuild/software/R-bundle-Bioconductor/3.15-foss-2021b-R-4.2.0/ --no-clean-on-error  
== 2022-06-26 19:15:03,347 build_log.py:169 ERROR EasyBuild crashed with an error (at easybuild/software/EasyBuild/4.5.5/lib/python3.10/site-packages/easybuild/base/exceptions.py:124 in __init__): cmd " R CMD INSTALL /home/ucloud/.local/easybuild/build/RbundleBioconductor/3.15/foss-2021b-R-4.2.0/ExomeDepth/ExomeDepth   --library=/work/easybuild/software/R-bundle-Bioconductor/3.15-foss-2021b-R-4.2.0/ --no-clean-on-error " exited with exit code 1 and output:
* installing *source* package ExomeDepth ...
** package ExomeDepth successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++14 -I"/work/easybuild/software/R/4.2.0-foss-2021b/lib/R/include" -DNDEBUG   -I/work/easybuild/software/OpenSSL/1.1/include -I/work/easybuild/software/libgit2/1.1.1-GCCcore-11.2.0/include -I/work/easybuild/software/MPFR/4.1.0-GCCcore-11.2.0/include -I/work/easybuild/software/GDAL/3.3.2-foss-2021b/include -I/work/easybuild/software/nodejs/14.17.6-GCCcore-11.2.0/include -I/work/easybuild/software/GLPK/5.0-GCCcore-11.2.0/include -I/work/easybuild/software/ImageMagick/7.1.0-4-GCCcore-11.2.0/include -I/work/easybuild/software/GSL/2.7-GCC-11.2.0/include -I/work/easybuild/software/UDUNITS/2.2.28-GCCcore-11.2.0/include -I/work/easybuild/software/HDF5/1.12.1-gompi-2021b/include -I/work/easybuild/software/ICU/69.1-GCCcore-11.2.0/include -I/work/easybuild/software/libsndfile/1.0.31-GCCcore-11.2.0/include -I/work/easybuild/software/FFTW/3.3.10-gompi-2021b/include -I/work/easybuild/software/NLopt/2.7.0-GCCcore-11.2.0/include -I/work/easybuild/software/GMP/6.2.1-GCCcore-11.2.0/include -I/work/easybuild/software/libxml2/2.9.10-GCCcore-11.2.0/include -I/work/easybuild/software/cURL/7.78.0-GCCcore-11.2.0/include -I/work/easybuild/software/Tk/8.6.11-GCCcore-11.2.0/include -I/work/easybuild/software/Java/11.0.2/include -I/work/easybuild/software/LibTIFF/4.3.0-GCCcore-11.2.0/include -I/work/easybuild/software/libjpeg-turbo/2.0.6-GCCcore-11.2.0/include -I/work/easybuild/software/libpng/1.6.37-GCCcore-11.2.0/include -I/work/easybuild/software/PCRE2/10.37-GCCcore-11.2.0/include -I/work/easybuild/software/SQLite/3.36-GCCcore-11.2.0/include -I/work/easybuild/software/zlib/1.2.11-GCCcore-11.2.0/include -I/work/easybuild/software/XZ/5.2.5-GCCcore-11.2.0/include -I/work/easybuild/software/bzip2/1.0.8-GCCcore-11.2.0/include -I/work/easybuild/software/ncurses/6.2-GCCcore-11.2.0/include -I/work/easybuild/software/libreadline/8.1-GCCcore-11.2.0/include -I/work/easybuild/software/cairo/1.16.0-GCCcore-11.2.0/include -I/work/easybuild/software/libGLU/9.0.2-GCCcore-11.2.0/include -I/work/easybuild/software/Mesa/21.1.7-GCCcore-11.2.0/include -I/work/easybuild/software/X11/20210802-GCCcore-11.2.0/include -I/work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/include -I/work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/include/flexiblas   -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c CNV_estimate.cpp -o CNV_estimate.o
gcc -I"/work/easybuild/software/R/4.2.0-foss-2021b/lib/R/include" -DNDEBUG   -I/work/easybuild/software/OpenSSL/1.1/include -I/work/easybuild/software/libgit2/1.1.1-GCCcore-11.2.0/include -I/work/easybuild/software/MPFR/4.1.0-GCCcore-11.2.0/include -I/work/easybuild/software/GDAL/3.3.2-foss-2021b/include -I/work/easybuild/software/nodejs/14.17.6-GCCcore-11.2.0/include -I/work/easybuild/software/GLPK/5.0-GCCcore-11.2.0/include -I/work/easybuild/software/ImageMagick/7.1.0-4-GCCcore-11.2.0/include -I/work/easybuild/software/GSL/2.7-GCC-11.2.0/include -I/work/easybuild/software/UDUNITS/2.2.28-GCCcore-11.2.0/include -I/work/easybuild/software/HDF5/1.12.1-gompi-2021b/include -I/work/easybuild/software/ICU/69.1-GCCcore-11.2.0/include -I/work/easybuild/software/libsndfile/1.0.31-GCCcore-11.2.0/include -I/work/easybuild/software/FFTW/3.3.10-gompi-2021b/include -I/work/easybuild/software/NLopt/2.7.0-GCCcore-11.2.0/include -I/work/easybuild/software/GMP/6.2.1-GCCcore-11.2.0/include -I/work/easybuild/software/libxml2/2.9.10-GCCcore-11.2.0/include -I/work/easybuild/software/cURL/7.78.0-GCCcore-11.2.0/include -I/work/easybuild/software/Tk/8.6.11-GCCcore-11.2.0/include -I/work/easybuild/software/Java/11.0.2/include -I/work/easybuild/software/LibTIFF/4.3.0-GCCcore-11.2.0/include -I/work/easybuild/software/libjpeg-turbo/2.0.6-GCCcore-11.2.0/include -I/work/easybuild/software/libpng/1.6.37-GCCcore-11.2.0/include -I/work/easybuild/software/PCRE2/10.37-GCCcore-11.2.0/include -I/work/easybuild/software/SQLite/3.36-GCCcore-11.2.0/include -I/work/easybuild/software/zlib/1.2.11-GCCcore-11.2.0/include -I/work/easybuild/software/XZ/5.2.5-GCCcore-11.2.0/include -I/work/easybuild/software/bzip2/1.0.8-GCCcore-11.2.0/include -I/work/easybuild/software/ncurses/6.2-GCCcore-11.2.0/include -I/work/easybuild/software/libreadline/8.1-GCCcore-11.2.0/include -I/work/easybuild/software/cairo/1.16.0-GCCcore-11.2.0/include -I/work/easybuild/software/libGLU/9.0.2-GCCcore-11.2.0/include -I/work/easybuild/software/Mesa/21.1.7-GCCcore-11.2.0/include -I/work/easybuild/software/X11/20210802-GCCcore-11.2.0/include -I/work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/include -I/work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/include/flexiblas   -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c ExomeDepth_init.c -o ExomeDepth_init.o
gcc -I"/work/easybuild/software/R/4.2.0-foss-2021b/lib/R/include" -DNDEBUG   -I/work/easybuild/software/OpenSSL/1.1/include -I/work/easybuild/software/libgit2/1.1.1-GCCcore-11.2.0/include -I/work/easybuild/software/MPFR/4.1.0-GCCcore-11.2.0/include -I/work/easybuild/software/GDAL/3.3.2-foss-2021b/include -I/work/easybuild/software/nodejs/14.17.6-GCCcore-11.2.0/include -I/work/easybuild/software/GLPK/5.0-GCCcore-11.2.0/include -I/work/easybuild/software/ImageMagick/7.1.0-4-GCCcore-11.2.0/include -I/work/easybuild/software/GSL/2.7-GCC-11.2.0/include -I/work/easybuild/software/UDUNITS/2.2.28-GCCcore-11.2.0/include -I/work/easybuild/software/HDF5/1.12.1-gompi-2021b/include -I/work/easybuild/software/ICU/69.1-GCCcore-11.2.0/include -I/work/easybuild/software/libsndfile/1.0.31-GCCcore-11.2.0/include -I/work/easybuild/software/FFTW/3.3.10-gompi-2021b/include -I/work/easybuild/software/NLopt/2.7.0-GCCcore-11.2.0/include -I/work/easybuild/software/GMP/6.2.1-GCCcore-11.2.0/include -I/work/easybuild/software/libxml2/2.9.10-GCCcore-11.2.0/include -I/work/easybuild/software/cURL/7.78.0-GCCcore-11.2.0/include -I/work/easybuild/software/Tk/8.6.11-GCCcore-11.2.0/include -I/work/easybuild/software/Java/11.0.2/include -I/work/easybuild/software/LibTIFF/4.3.0-GCCcore-11.2.0/include -I/work/easybuild/software/libjpeg-turbo/2.0.6-GCCcore-11.2.0/include -I/work/easybuild/software/libpng/1.6.37-GCCcore-11.2.0/include -I/work/easybuild/software/PCRE2/10.37-GCCcore-11.2.0/include -I/work/easybuild/software/SQLite/3.36-GCCcore-11.2.0/include -I/work/easybuild/software/zlib/1.2.11-GCCcore-11.2.0/include -I/work/easybuild/software/XZ/5.2.5-GCCcore-11.2.0/include -I/work/easybuild/software/bzip2/1.0.8-GCCcore-11.2.0/include -I/work/easybuild/software/ncurses/6.2-GCCcore-11.2.0/include -I/work/easybuild/software/libreadline/8.1-GCCcore-11.2.0/include -I/work/easybuild/software/cairo/1.16.0-GCCcore-11.2.0/include -I/work/easybuild/software/libGLU/9.0.2-GCCcore-11.2.0/include -I/work/easybuild/software/Mesa/21.1.7-GCCcore-11.2.0/include -I/work/easybuild/software/X11/20210802-GCCcore-11.2.0/include -I/work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/include -I/work/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/include/flexiblas   -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c VP_gamma.c -o VP_gamma.o
In file included from gsl_math.h:22,
                 from VP_gamma.c:23:
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:85:1: error: expected ; before extern
   85 | __MATHCALL_VEC (acosh,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:87:1: error: expected ; before extern
   87 | __MATHCALL_VEC (asinh,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:89:1: error: expected ; before extern
   89 | __MATHCALL_VEC (atanh,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:119:1: error: expected ; before extern
  119 | __MATHCALL_VEC (expm1,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:122:1: error: expected ; before extern
  122 | __MATHCALL_VEC (log1p,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:147:1: error: expected ; before extern
  147 | __MATHCALL_VEC (hypot,, (_Mdouble_ __x, _Mdouble_ __y));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:85:1: error: expected ; before extern
   85 | __MATHCALL_VEC (acosh,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:87:1: error: expected ; before extern
   87 | __MATHCALL_VEC (asinh,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:89:1: error: expected ; before extern
   89 | __MATHCALL_VEC (atanh,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:119:1: error: expected ; before extern
  119 | __MATHCALL_VEC (expm1,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:122:1: error: expected ; before extern
  122 | __MATHCALL_VEC (log1p,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:147:1: error: expected ; before extern
  147 | __MATHCALL_VEC (hypot,, (_Mdouble_ __x, _Mdouble_ __y));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:85:1: error: expected ; before extern
   85 | __MATHCALL_VEC (acosh,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:87:1: error: expected ; before extern
   87 | __MATHCALL_VEC (asinh,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:89:1: error: expected ; before extern
   89 | __MATHCALL_VEC (atanh,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:119:1: error: expected ; before extern
  119 | __MATHCALL_VEC (expm1,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:122:1: error: expected ; before extern
  122 | __MATHCALL_VEC (log1p,, (_Mdouble_ __x));
      | ^~~~~~~~~~~~~~
/usr/include/x86_64-linux-gnu/bits/mathcalls.h:147:1: error: expected ; before extern
  147 | __MATHCALL_VEC (hypot,, (_Mdouble_ __x, _Mdouble_ __y));
      | ^~~~~~~~~~~~~~
make: *** [/work/easybuild/software/R/4.2.0-foss-2021b/lib64/R/etc/Makeconf:168: VP_gamma.o] Error 1
ERROR: compilation failed for package ExomeDepth
 (at easybuild/software/EasyBuild/4.5.5/lib/python3.10/site-packages/easybuild/tools/run.py:618 in parse_cmd_output)
== 2022-06-26 19:15:03,348 build_log.py:265 INFO        ... (took 2 secs)
== 2022-06-26 19:15:03,349 build_log.py:265 INFO ... (took 3 hours 20 mins 20 secs)
== 2022-06-26 19:15:03,349 filetools.py:1983 INFO Removing lock /work/easybuild/software/.locks/_work_easybuild_software_R-bundle-Bioconductor_3.15-foss-2021b-R-4.2.0.lock...
== 2022-06-26 19:15:03,354 filetools.py:382 INFO Path /work/easybuild/software/.locks/_work_easybuild_software_R-bundle-Bioconductor_3.15-foss-2021b-R-4.2.0.lock successfully removed.
== 2022-06-26 19:15:03,354 filetools.py:1987 INFO Lock removed: /work/easybuild/software/.locks/_work_easybuild_software_R-bundle-Bioconductor_3.15-foss-2021b-R-4.2.0.lock
== 2022-06-26 19:15:03,354 easyblock.py:4079 WARNING build failed (first 300 chars): cmd " R CMD INSTALL /home/ucloud/.local/easybuild/build/RbundleBioconductor/3.15/foss-2021b-R-4.2.0/ExomeDepth/ExomeDepth   --library=/work/easybuild/software/R-bundle-Bioconductor/3.15-foss-2021b-R-4.2.0/ --no-clean-on-error " exited with exit code 1 and output:
* installing *source* package ExomeD
== 2022-06-26 19:15:03,355 easyblock.py:318 INFO Closing log for application name R-bundle-Bioconductor version 3.15
boegel commented 2 years ago

@VictorGoitea Can you share the output of eb --show-config and eb --show-system-info? It's quite strange you're seeing this, while others are not...

VictorGoitea commented 2 years ago

@boegel Here it is:

System information (j-80093-job-0):

* OS:
  -> name: Ubuntu
  -> type: Linux
  -> version: 22.04
  -> platform name: x86_64-unknown-linux

* CPU:
  -> vendor: Intel
  -> architecture: x86_64
  -> family: Intel
  -> arch name: UNKNOWN (archspec is not installed?)
  -> model: Intel(R) Xeon(R) Gold 6130 CPU @ 2.10GHz
  -> speed: 1000.045
  -> cores: 64
  -> features: 3dnowprefetch,abm,acpi,adx,aes,aperfmperf,apic,arat,arch_perfmon,art,avx,avx2,avx512bw,avx512cd,avx512dq,avx512f,avx512vl,bmi1,bmi2,bts,cat_l3,cdp_l3,clflush,clflushopt,clwb,cmov,constant_tsc,cpuid,cpuid_fault,cqm,cqm_llc,cqm_mbm_local,cqm_mbm_total,cqm_occup_llc,cx16,cx8,dca,de,ds_cpl,dtes64,dtherm,dts,epb,ept,ept_ad,erms,est,f16c,flexpriority,flush_l1d,fma,fpu,fsgsbase,fxsr,hle,ht,ibpb,ibrs,ida,intel_ppin,intel_pt,invpcid,invpcid_single,lahf_lm,lm,mba,mca,mce,md_clear,mmx,monitor,movbe,mpx,msr,mtrr,nonstop_tsc,nopl,nx,ospke,pae,pat,pbe,pcid,pclmulqdq,pdcm,pdpe1gb,pebs,pge,pku,pln,pni,popcnt,pse,pse36,pti,pts,rdrand,rdseed,rdt_a,rdtscp,rep_good,rtm,sdbg,sep,smap,smep,smx,ss,ssbd,sse,sse2,sse4_1,sse4_2,ssse3,stibp,syscall,tm,tm2,tpr_shadow,tsc,tsc_adjust,tsc_deadline_timer,vme,vmx,vnmi,vpid,x2apic,xgetbv1,xsave,xsavec,xsaveopt,xsaves,xtopology,xtpr

* software:
  -> glibc version: 2.35
  -> Python binary: /usr/bin/python3
  -> Python version: 3.10.4
Luis-WP-Arge commented 2 years ago

Is there some update in this issue? I'm facing the same problem.

branfosj commented 1 year ago

In #16492 we removed ExomeDepth from recent R-bundle-Bioconductor easyconfigs, so I'll go ahead and close this issue.

However, I suspect the issue is the includes in https://github.com/vplagnol/ExomeDepth/blob/master/src/Makefile and that changing the /usr parts in:

INCLUDES= -I. -I$(RDIST)/include -I/usr/lib64/R/include -I/usr/share/R/include/

and also

CFLAGS= -L/usr/local/lib -pthread -fPIC -Wall $(OPT) $(PROF) $(DEB) $(INCLUDES) -lgsl -lblas -static

would solve the issue seen here.