Created
August 26, 2016 14:16
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(partial) EasyBuild log for failed build of /tmp/eb-oCWEht/files_pr3317/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb (PR #3317)
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| == 2016-08-26 16:16:14,436 environment.py:97 INFO Environment variable EBVARFFT_STATIC_LIBS_MT set to libfftw3.a,libpthread.a (previously undefined) | |
| == 2016-08-26 16:16:14,436 toolchain.py:742 DEBUG _setenv_variables: setting environment variable FLIBS to -lgfortran | |
| == 2016-08-26 16:16:14,436 environment.py:97 INFO Environment variable FLIBS set to -lgfortran (previously undefined) | |
| == 2016-08-26 16:16:14,437 environment.py:97 INFO Environment variable EBVARFLIBS set to -lgfortran (previously undefined) | |
| == 2016-08-26 16:16:14,437 toolchain.py:742 DEBUG _setenv_variables: setting environment variable LAPACK_INC_DIR to /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/OpenBLAS/0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0/include | |
| == 2016-08-26 16:16:14,437 environment.py:97 INFO Environment variable LAPACK_INC_DIR set to /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/OpenBLAS/0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0/include (previously undefined) | |
| == 2016-08-26 16:16:14,437 environment.py:97 INFO Environment variable EBVARLAPACK_INC_DIR set to /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/OpenBLAS/0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0/include (previously undefined) | |
| == 2016-08-26 16:16:14,437 toolchain.py:742 DEBUG _setenv_variables: setting environment variable LAPACK_LIB_DIR to /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/OpenBLAS/0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0/lib | |
| == 2016-08-26 16:16:14,438 environment.py:97 INFO Environment variable LAPACK_LIB_DIR set to /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/OpenBLAS/0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0/lib (previously undefined) | |
| == 2016-08-26 16:16:14,438 environment.py:97 INFO Environment variable EBVARLAPACK_LIB_DIR set to /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/OpenBLAS/0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0/lib (previously undefined) | |
| == 2016-08-26 16:16:14,438 toolchain.py:742 DEBUG _setenv_variables: setting environment variable LAPACK_MT_STATIC_LIBS to libopenblas.a,libgfortran.a | |
| == 2016-08-26 16:16:14,438 environment.py:97 INFO Environment variable LAPACK_MT_STATIC_LIBS set to libopenblas.a,libgfortran.a (previously undefined) | |
| == 2016-08-26 16:16:14,438 environment.py:97 INFO Environment variable EBVARLAPACK_MT_STATIC_LIBS set to libopenblas.a,libgfortran.a (previously undefined) | |
| == 2016-08-26 16:16:14,438 toolchain.py:742 DEBUG _setenv_variables: setting environment variable LAPACK_STATIC_LIBS to libopenblas.a,libgfortran.a | |
| == 2016-08-26 16:16:14,439 environment.py:97 INFO Environment variable LAPACK_STATIC_LIBS set to libopenblas.a,libgfortran.a (previously undefined) | |
| == 2016-08-26 16:16:14,439 environment.py:97 INFO Environment variable EBVARLAPACK_STATIC_LIBS set to libopenblas.a,libgfortran.a (previously undefined) | |
| == 2016-08-26 16:16:14,439 toolchain.py:742 DEBUG _setenv_variables: setting environment variable LDFLAGS to -L/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/GCCcore/4.9.3/lib64 -L/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/GCCcore/4.9.3/lib -L/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/OpenBLAS/0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0/lib -L/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/ScaLAPACK/2.0.2-gompi-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0/lib -L/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/FFTW/3.3.4-gompi-2016a/lib -L/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/Perl/5.22.1-foss-2016a/lib -L/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/libpsortb/1.0-foss-2016a/lib64 -L/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/BioPerl/1.6.924-foss-2016a-Perl-5.22.1/lib | |
| == 2016-08-26 16:16:14,439 environment.py:97 INFO Environment variable LDFLAGS set to -L/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/GCCcore/4.9.3/lib64 -L/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/GCCcore/4.9.3/lib -L/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/OpenBLAS/0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0/lib -L/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/ScaLAPACK/2.0.2-gompi-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0/lib -L/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/FFTW/3.3.4-gompi-2016a/lib -L/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/Perl/5.22.1-foss-2016a/lib -L/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/libpsortb/1.0-foss-2016a/lib64 -L/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/BioPerl/1.6.924-foss-2016a-Perl-5.22.1/lib (previously undefined) | |
| == 2016-08-26 16:16:14,439 environment.py:97 INFO Environment variable EBVARLDFLAGS set to -L/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/GCCcore/4.9.3/lib64 -L/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/GCCcore/4.9.3/lib -L/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/OpenBLAS/0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0/lib -L/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/ScaLAPACK/2.0.2-gompi-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0/lib -L/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/FFTW/3.3.4-gompi-2016a/lib -L/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/Perl/5.22.1-foss-2016a/lib -L/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/libpsortb/1.0-foss-2016a/lib64 -L/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/BioPerl/1.6.924-foss-2016a-Perl-5.22.1/lib (previously undefined) | |
| == 2016-08-26 16:16:14,440 toolchain.py:742 DEBUG _setenv_variables: setting environment variable LIBBLAS to -lopenblas -lgfortran | |
| == 2016-08-26 16:16:14,440 environment.py:97 INFO Environment variable LIBBLAS set to -lopenblas -lgfortran (previously undefined) | |
| == 2016-08-26 16:16:14,440 environment.py:97 INFO Environment variable EBVARLIBBLAS set to -lopenblas -lgfortran (previously undefined) | |
| == 2016-08-26 16:16:14,440 toolchain.py:742 DEBUG _setenv_variables: setting environment variable LIBBLAS_MT to -lopenblas -lgfortran | |
| == 2016-08-26 16:16:14,440 environment.py:97 INFO Environment variable LIBBLAS_MT set to -lopenblas -lgfortran (previously undefined) | |
| == 2016-08-26 16:16:14,441 environment.py:97 INFO Environment variable EBVARLIBBLAS_MT set to -lopenblas -lgfortran (previously undefined) | |
| == 2016-08-26 16:16:14,441 toolchain.py:742 DEBUG _setenv_variables: setting environment variable LIBFFT to -lfftw3 | |
| == 2016-08-26 16:16:14,441 environment.py:97 INFO Environment variable LIBFFT set to -lfftw3 (previously undefined) | |
| == 2016-08-26 16:16:14,441 environment.py:97 INFO Environment variable EBVARLIBFFT set to -lfftw3 (previously undefined) | |
| == 2016-08-26 16:16:14,441 toolchain.py:742 DEBUG _setenv_variables: setting environment variable LIBFFT_MT to -lfftw3 -lpthread | |
| == 2016-08-26 16:16:14,442 environment.py:97 INFO Environment variable LIBFFT_MT set to -lfftw3 -lpthread (previously undefined) | |
| == 2016-08-26 16:16:14,442 environment.py:97 INFO Environment variable EBVARLIBFFT_MT set to -lfftw3 -lpthread (previously undefined) | |
| == 2016-08-26 16:16:14,442 toolchain.py:742 DEBUG _setenv_variables: setting environment variable LIBLAPACK to -lopenblas -lgfortran | |
| == 2016-08-26 16:16:14,442 environment.py:97 INFO Environment variable LIBLAPACK set to -lopenblas -lgfortran (previously undefined) | |
| == 2016-08-26 16:16:14,442 environment.py:97 INFO Environment variable EBVARLIBLAPACK set to -lopenblas -lgfortran (previously undefined) | |
| == 2016-08-26 16:16:14,442 toolchain.py:742 DEBUG _setenv_variables: setting environment variable LIBLAPACK_MT to -lopenblas -lgfortran | |
| == 2016-08-26 16:16:14,443 environment.py:97 INFO Environment variable LIBLAPACK_MT set to -lopenblas -lgfortran (previously undefined) | |
| == 2016-08-26 16:16:14,443 environment.py:97 INFO Environment variable EBVARLIBLAPACK_MT set to -lopenblas -lgfortran (previously undefined) | |
| == 2016-08-26 16:16:14,443 toolchain.py:742 DEBUG _setenv_variables: setting environment variable LIBLAPACK_MT_ONLY to -lopenblas -lgfortran | |
| == 2016-08-26 16:16:14,443 environment.py:97 INFO Environment variable LIBLAPACK_MT_ONLY set to -lopenblas -lgfortran (previously undefined) | |
| == 2016-08-26 16:16:14,443 environment.py:97 INFO Environment variable EBVARLIBLAPACK_MT_ONLY set to -lopenblas -lgfortran (previously undefined) | |
| == 2016-08-26 16:16:14,444 toolchain.py:742 DEBUG _setenv_variables: setting environment variable LIBLAPACK_ONLY to -lopenblas -lgfortran | |
| == 2016-08-26 16:16:14,444 environment.py:97 INFO Environment variable LIBLAPACK_ONLY set to -lopenblas -lgfortran (previously undefined) | |
| == 2016-08-26 16:16:14,444 environment.py:97 INFO Environment variable EBVARLIBLAPACK_ONLY set to -lopenblas -lgfortran (previously undefined) | |
| == 2016-08-26 16:16:14,444 toolchain.py:742 DEBUG _setenv_variables: setting environment variable LIBS to -lm -lpthread | |
| == 2016-08-26 16:16:14,444 environment.py:97 INFO Environment variable LIBS set to -lm -lpthread (previously undefined) | |
| == 2016-08-26 16:16:14,445 environment.py:97 INFO Environment variable EBVARLIBS set to -lm -lpthread (previously undefined) | |
| == 2016-08-26 16:16:14,445 toolchain.py:742 DEBUG _setenv_variables: setting environment variable LIBSCALAPACK to -lscalapack -lopenblas -lgfortran | |
| == 2016-08-26 16:16:14,445 environment.py:97 INFO Environment variable LIBSCALAPACK set to -lscalapack -lopenblas -lgfortran (previously undefined) | |
| == 2016-08-26 16:16:14,445 environment.py:97 INFO Environment variable EBVARLIBSCALAPACK set to -lscalapack -lopenblas -lgfortran (previously undefined) | |
| == 2016-08-26 16:16:14,445 toolchain.py:742 DEBUG _setenv_variables: setting environment variable LIBSCALAPACK_MT to -lscalapack -lopenblas -lpthread -lgfortran | |
| == 2016-08-26 16:16:14,445 environment.py:97 INFO Environment variable LIBSCALAPACK_MT set to -lscalapack -lopenblas -lpthread -lgfortran (previously undefined) | |
| == 2016-08-26 16:16:14,446 environment.py:97 INFO Environment variable EBVARLIBSCALAPACK_MT set to -lscalapack -lopenblas -lpthread -lgfortran (previously undefined) | |
| == 2016-08-26 16:16:14,446 toolchain.py:742 DEBUG _setenv_variables: setting environment variable LIBSCALAPACK_MT_ONLY to -lscalapack -lgfortran | |
| == 2016-08-26 16:16:14,446 environment.py:97 INFO Environment variable LIBSCALAPACK_MT_ONLY set to -lscalapack -lgfortran (previously undefined) | |
| == 2016-08-26 16:16:14,446 environment.py:97 INFO Environment variable EBVARLIBSCALAPACK_MT_ONLY set to -lscalapack -lgfortran (previously undefined) | |
| == 2016-08-26 16:16:14,446 toolchain.py:742 DEBUG _setenv_variables: setting environment variable LIBSCALAPACK_ONLY to -lscalapack -lgfortran | |
| == 2016-08-26 16:16:14,447 environment.py:97 INFO Environment variable LIBSCALAPACK_ONLY set to -lscalapack -lgfortran (previously undefined) | |
| == 2016-08-26 16:16:14,447 environment.py:97 INFO Environment variable EBVARLIBSCALAPACK_ONLY set to -lscalapack -lgfortran (previously undefined) | |
| == 2016-08-26 16:16:14,447 toolchain.py:742 DEBUG _setenv_variables: setting environment variable MPICC to mpicc | |
| == 2016-08-26 16:16:14,447 environment.py:97 INFO Environment variable MPICC set to mpicc (previously undefined) | |
| == 2016-08-26 16:16:14,447 environment.py:97 INFO Environment variable EBVARMPICC set to mpicc (previously undefined) | |
| == 2016-08-26 16:16:14,448 toolchain.py:742 DEBUG _setenv_variables: setting environment variable MPICXX to mpicxx | |
| == 2016-08-26 16:16:14,448 environment.py:97 INFO Environment variable MPICXX set to mpicxx (previously undefined) | |
| == 2016-08-26 16:16:14,448 environment.py:97 INFO Environment variable EBVARMPICXX set to mpicxx (previously undefined) | |
| == 2016-08-26 16:16:14,448 toolchain.py:742 DEBUG _setenv_variables: setting environment variable MPIF77 to mpifort | |
| == 2016-08-26 16:16:14,448 environment.py:97 INFO Environment variable MPIF77 set to mpifort (previously undefined) | |
| == 2016-08-26 16:16:14,449 environment.py:97 INFO Environment variable EBVARMPIF77 set to mpifort (previously undefined) | |
| == 2016-08-26 16:16:14,449 toolchain.py:742 DEBUG _setenv_variables: setting environment variable MPIF90 to mpifort | |
| == 2016-08-26 16:16:14,449 environment.py:97 INFO Environment variable MPIF90 set to mpifort (previously undefined) | |
| == 2016-08-26 16:16:14,449 environment.py:97 INFO Environment variable EBVARMPIF90 set to mpifort (previously undefined) | |
| == 2016-08-26 16:16:14,449 toolchain.py:742 DEBUG _setenv_variables: setting environment variable MPIFC to mpifort | |
| == 2016-08-26 16:16:14,449 environment.py:97 INFO Environment variable MPIFC set to mpifort (previously undefined) | |
| == 2016-08-26 16:16:14,450 environment.py:97 INFO Environment variable EBVARMPIFC set to mpifort (previously undefined) | |
| == 2016-08-26 16:16:14,450 toolchain.py:742 DEBUG _setenv_variables: setting environment variable MPI_INC_DIR to /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/OpenMPI/1.10.2-GCC-4.9.3-2.25/include | |
| == 2016-08-26 16:16:14,450 environment.py:97 INFO Environment variable MPI_INC_DIR set to /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/OpenMPI/1.10.2-GCC-4.9.3-2.25/include (previously undefined) | |
| == 2016-08-26 16:16:14,450 environment.py:97 INFO Environment variable EBVARMPI_INC_DIR set to /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/OpenMPI/1.10.2-GCC-4.9.3-2.25/include (previously undefined) | |
| == 2016-08-26 16:16:14,450 toolchain.py:742 DEBUG _setenv_variables: setting environment variable MPI_LIB_DIR to /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/OpenMPI/1.10.2-GCC-4.9.3-2.25/lib | |
| == 2016-08-26 16:16:14,451 environment.py:97 INFO Environment variable MPI_LIB_DIR set to /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/OpenMPI/1.10.2-GCC-4.9.3-2.25/lib (previously undefined) | |
| == 2016-08-26 16:16:14,451 environment.py:97 INFO Environment variable EBVARMPI_LIB_DIR set to /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/OpenMPI/1.10.2-GCC-4.9.3-2.25/lib (previously undefined) | |
| == 2016-08-26 16:16:14,451 toolchain.py:742 DEBUG _setenv_variables: setting environment variable MPI_LIB_SHARED to /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/OpenMPI/1.10.2-GCC-4.9.3-2.25/lib/libmpi.so | |
| == 2016-08-26 16:16:14,451 environment.py:97 INFO Environment variable MPI_LIB_SHARED set to /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/OpenMPI/1.10.2-GCC-4.9.3-2.25/lib/libmpi.so (previously undefined) | |
| == 2016-08-26 16:16:14,451 environment.py:97 INFO Environment variable EBVARMPI_LIB_SHARED set to /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/OpenMPI/1.10.2-GCC-4.9.3-2.25/lib/libmpi.so (previously undefined) | |
| == 2016-08-26 16:16:14,452 toolchain.py:742 DEBUG _setenv_variables: setting environment variable MPI_LIB_STATIC to | |
| == 2016-08-26 16:16:14,452 environment.py:97 INFO Environment variable MPI_LIB_STATIC set to (previously undefined) | |
| == 2016-08-26 16:16:14,452 environment.py:97 INFO Environment variable EBVARMPI_LIB_STATIC set to (previously undefined) | |
| == 2016-08-26 16:16:14,452 toolchain.py:742 DEBUG _setenv_variables: setting environment variable OMPI_CC to gcc | |
| == 2016-08-26 16:16:14,452 environment.py:97 INFO Environment variable OMPI_CC set to gcc (previously undefined) | |
| == 2016-08-26 16:16:14,453 environment.py:97 INFO Environment variable EBVAROMPI_CC set to gcc (previously undefined) | |
| == 2016-08-26 16:16:14,453 toolchain.py:742 DEBUG _setenv_variables: setting environment variable OMPI_CXX to g++ | |
| == 2016-08-26 16:16:14,453 environment.py:97 INFO Environment variable OMPI_CXX set to g++ (previously undefined) | |
| == 2016-08-26 16:16:14,453 environment.py:97 INFO Environment variable EBVAROMPI_CXX set to g++ (previously undefined) | |
| == 2016-08-26 16:16:14,453 toolchain.py:742 DEBUG _setenv_variables: setting environment variable OMPI_F77 to gfortran | |
| == 2016-08-26 16:16:14,453 environment.py:97 INFO Environment variable OMPI_F77 set to gfortran (previously undefined) | |
| == 2016-08-26 16:16:14,454 environment.py:97 INFO Environment variable EBVAROMPI_F77 set to gfortran (previously undefined) | |
| == 2016-08-26 16:16:14,454 toolchain.py:742 DEBUG _setenv_variables: setting environment variable OMPI_F90 to gfortran | |
| == 2016-08-26 16:16:14,454 environment.py:97 INFO Environment variable OMPI_F90 set to gfortran (previously undefined) | |
| == 2016-08-26 16:16:14,454 environment.py:97 INFO Environment variable EBVAROMPI_F90 set to gfortran (previously undefined) | |
| == 2016-08-26 16:16:14,454 toolchain.py:742 DEBUG _setenv_variables: setting environment variable OMPI_FC to gfortran | |
| == 2016-08-26 16:16:14,455 environment.py:97 INFO Environment variable OMPI_FC set to gfortran (previously undefined) | |
| == 2016-08-26 16:16:14,455 environment.py:97 INFO Environment variable EBVAROMPI_FC set to gfortran (previously undefined) | |
| == 2016-08-26 16:16:14,455 toolchain.py:742 DEBUG _setenv_variables: setting environment variable OPTFLAGS to -O2 -march=native | |
| == 2016-08-26 16:16:14,455 environment.py:97 INFO Environment variable OPTFLAGS set to -O2 -march=native (previously undefined) | |
| == 2016-08-26 16:16:14,455 environment.py:97 INFO Environment variable EBVAROPTFLAGS set to -O2 -march=native (previously undefined) | |
| == 2016-08-26 16:16:14,456 toolchain.py:742 DEBUG _setenv_variables: setting environment variable PRECFLAGS to | |
| == 2016-08-26 16:16:14,456 environment.py:97 INFO Environment variable PRECFLAGS set to (previously undefined) | |
| == 2016-08-26 16:16:14,456 environment.py:97 INFO Environment variable EBVARPRECFLAGS set to (previously undefined) | |
| == 2016-08-26 16:16:14,456 toolchain.py:742 DEBUG _setenv_variables: setting environment variable SCALAPACK_INC_DIR to /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/ScaLAPACK/2.0.2-gompi-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0/include | |
| == 2016-08-26 16:16:14,456 environment.py:97 INFO Environment variable SCALAPACK_INC_DIR set to /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/ScaLAPACK/2.0.2-gompi-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0/include (previously undefined) | |
| == 2016-08-26 16:16:14,457 environment.py:97 INFO Environment variable EBVARSCALAPACK_INC_DIR set to /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/ScaLAPACK/2.0.2-gompi-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0/include (previously undefined) | |
| == 2016-08-26 16:16:14,457 toolchain.py:742 DEBUG _setenv_variables: setting environment variable SCALAPACK_LIB_DIR to /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/ScaLAPACK/2.0.2-gompi-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0/lib | |
| == 2016-08-26 16:16:14,457 environment.py:97 INFO Environment variable SCALAPACK_LIB_DIR set to /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/ScaLAPACK/2.0.2-gompi-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0/lib (previously undefined) | |
| == 2016-08-26 16:16:14,457 environment.py:97 INFO Environment variable EBVARSCALAPACK_LIB_DIR set to /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/ScaLAPACK/2.0.2-gompi-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0/lib (previously undefined) | |
| == 2016-08-26 16:16:14,457 toolchain.py:742 DEBUG _setenv_variables: setting environment variable SCALAPACK_MT_STATIC_LIBS to libscalapack.a,libopenblas.a,libgfortran.a,libpthread.a | |
| == 2016-08-26 16:16:14,457 environment.py:97 INFO Environment variable SCALAPACK_MT_STATIC_LIBS set to libscalapack.a,libopenblas.a,libgfortran.a,libpthread.a (previously undefined) | |
| == 2016-08-26 16:16:14,458 environment.py:97 INFO Environment variable EBVARSCALAPACK_MT_STATIC_LIBS set to libscalapack.a,libopenblas.a,libgfortran.a,libpthread.a (previously undefined) | |
| == 2016-08-26 16:16:14,458 toolchain.py:742 DEBUG _setenv_variables: setting environment variable SCALAPACK_STATIC_LIBS to libscalapack.a,libopenblas.a,libgfortran.a | |
| == 2016-08-26 16:16:14,458 environment.py:97 INFO Environment variable SCALAPACK_STATIC_LIBS set to libscalapack.a,libopenblas.a,libgfortran.a (previously undefined) | |
| == 2016-08-26 16:16:14,458 environment.py:97 INFO Environment variable EBVARSCALAPACK_STATIC_LIBS set to libscalapack.a,libopenblas.a,libgfortran.a (previously undefined) | |
| == 2016-08-26 16:16:14,459 easyblock.py:1308 INFO Using /tmp/vsc40023/easybuild_build/PSORTb/3.0.4/foss-2016a-Perl-5.22.1/bio-tools-psort-all/ as start dir | |
| == 2016-08-26 16:16:14,459 easyblock.py:1312 DEBUG Changed to real build directory /tmp/vsc40023/easybuild_build/PSORTb/3.0.4/foss-2016a-Perl-5.22.1/bio-tools-psort-all/ (start_dir) | |
| == 2016-08-26 16:16:14,459 easyblock.py:2128 DEBUG Not skipping configure step (skippable: True, skip: None, skipsteps: [], module_only: False, force: True | |
| == 2016-08-26 16:16:14,459 build_log.py:227 INFO configuring... | |
| == 2016-08-26 16:16:14,459 easyblock.py:2136 INFO Starting configure step | |
| == 2016-08-26 16:16:14,461 templates.py:151 DEBUG config: {'preinstallopts': ['', 'Extra prefix options for installation.', (3, 'build')], 'postinstallcmds': [['cp -r psort/* %(installdir)s/.'], 'Commands to run after the install step.', (3, 'build')], 'moduleloadnoconflict': [False, "Don't check for conflicts, unload other versions instead ", (8, 'modules')], 'skip': [False, 'Skip existing software', (3, 'build')], 'cleanupoldbuild': [True, 'Boolean to remove (True) or backup (False) the previous build directory with identical name or not.', (4, 'file-management')], 'installopts': ['', 'Extra options for installation', (3, 'build')], 'sources': [['bio-tools-psort-all.%(version)s.tar.gz'], 'List of source files', (3, 'build')], 'versionsuffix': ['-Perl-%(perlver)s', 'Additional suffix for software version (placed after toolchain name)', (3, 'build')], 'license_server': [None, 'License server for software', (6, 'license')], 'modaltsoftname': [None, 'Module name to use (rather than using software name', (8, 'modules')], 'keeppreviousinstall': [False, 'Boolean to keep the previous installation with identical name. Experts only!', (4, 'file-management')], 'hiddendependencies': [[], 'List of dependencies available as hidden modules', (5, 'dependencies')], 'checksums': [[], 'Checksums for sources and patches', (3, 'build')], 'keepsymlinks': [False, 'Boolean to determine whether symlinks are to be kept during copying or if the content of the files pointed to should be copied', (4, 'file-management')], 'cleanupoldinstall': [True, 'Boolean to remove (True) or backup (False) the previous install directory with identical name or not.', (4, 'file-management')], 'builddependencies': [[], 'List of build dependencies', (5, 'dependencies')], 'dontcreateinstalldir': [False, 'Boolean to create (False) or not create (True) the install directory', (4, 'file-management')], 'modextravars': [{}, 'Extra environment variables to be added to module file', (8, 'modules')], 'unpack_options': ['', 'Extra options for unpacking source', (3, 'build')], 'group': [None, 'Name of the user group for which the software should be available', (6, 'license')], 'versionprefix': ['', 'Additional prefix for software version (placed before version and toolchain name)', (3, 'build')], 'parsed': [True, 'This is a parsed easyconfig', 'HIDDEN'], 'prebuildopts': ['', 'Extra options pre-passed to build command.', (3, 'build')], 'easybuild_version': [None, 'EasyBuild-version this spec-file was written for', (3, 'build')], 'skipsteps': [[], 'Skip these steps', (3, 'build')], 'start_dir': ['/tmp/vsc40023/easybuild_build/PSORTb/3.0.4/foss-2016a-Perl-5.22.1/bio-tools-psort-all/', 'Path to start the make in. If the path is absolute, use that path. If not, this is added to the guessed path.', (4, 'file-management')], 'version': ['3.0.4', 'Version of software', (0, 'mandatory')], 'exts_filter': [None, 'Extension filter details: template for cmd and input to cmd (templates for name, version and src).', (7, 'extensions')], 'modaliases': [{}, 'Aliases to be defined in module file', (8, 'modules')], 'allow_system_deps': [[], 'Allow listed system dependencies (format: (<name>, <version>))', (5, 'dependencies')], 'osdependencies': [[], 'OS dependencies that should be present on the system', (5, 'dependencies')], 'hidden': [False, "Install module file as 'hidden' by prefixing its version with '.'", (3, 'build')], 'modluafooter': ['', 'Footer to include in generated module file (Lua syntax)', (8, 'modules')], 'homepage': ['http://psort.org/psortb/index.html', 'The homepage of the software', (0, 'mandatory')], 'buildstats': [None, 'A list of dicts with build statistics', (9, 'other')], 'license_file': [None, 'License file for software', (6, 'license')], 'tests': [[], 'List of test-scripts to run after install. A test script should return a non-zero exit status to fail', (3, 'build')], 'buildopts': ['', 'Extra options passed to make step (default already has -j X)', (3, 'build')], 'description': ['PSORTb v3.0.4 is the most precise bacterial localization prediction tool available.', 'A short description of the software', (0, 'mandatory')], 'modextrapaths': [{}, 'Extra paths to be prepended in module file', (8, 'modules')], 'exts_list': [[], 'List with extensions added to the base installation', (7, 'extensions')], 'docurls': [None, 'List of urls with documentation of the software (not necessarily on homepage)', (0, 'mandatory')], 'stop': [None, 'Keyword to halt the build process after a certain step.', (3, 'build')], 'sanity_check_commands': [[], "format: [(name, options)] e.g. [('gzip','-h')]. Using a non-tuple is equivalent to (name, '-h')", (3, 'build')], 'exts_classmap': [{}, 'Map of extension name to class for handling build and installation.', (7, 'extensions')], 'moduleforceunload': [False, 'Force unload of all modules when loading the extension', (8, 'modules')], 'dependencies': [[{'external_module_metadata': {}, 'full_mod_name': 'Perl/5.22.1-foss-2016a', 'toolchain': {'version': '2016a', 'name': 'foss'}, 'name': 'Perl', 'dummy': False, 'short_mod_name': 'Perl/5.22.1-foss-2016a', 'external_module': False, 'versionsuffix': '', 'version': '5.22.1', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}, {'external_module_metadata': {}, 'full_mod_name': 'libpsortb/1.0-foss-2016a', 'toolchain': {'version': '2016a', 'name': 'foss'}, 'name': 'libpsortb', 'dummy': False, 'short_mod_name': 'libpsortb/1.0-foss-2016a', 'external_module': False, 'versionsuffix': '', 'version': '1.0', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}, {'external_module_metadata': {}, 'full_mod_name': 'BioPerl/1.6.924-foss-2016a-Perl-5.22.1', 'toolchain': {'version': '2016a', 'name': 'foss'}, 'name': 'BioPerl', 'dummy': False, 'short_mod_name': 'BioPerl/1.6.924-foss-2016a-Perl-5.22.1', 'external_module': False, 'versionsuffix': '-Perl-5.22.1', 'version': '1.6.924', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}, {'external_module_metadata': {}, 'full_mod_name': 'BLAST/2.2.26-Linux_x86_64', 'toolchain': {'version': 'dummy', 'name': 'dummy'}, 'name': 'BLAST', 'dummy': True, 'short_mod_name': 'BLAST/2.2.26-Linux_x86_64', 'external_module': False, 'versionsuffix': '-Linux_x86_64', 'version': '2.2.26', 'toolchain_inherited': False, 'hidden': False, 'build_only': False}, {'external_module_metadata': {}, 'full_mod_name': 'pftoolsV3/20160324-foss-2016a', 'toolchain': {'version': '2016a', 'name': 'foss'}, 'name': 'pftoolsV3', 'dummy': False, 'short_mod_name': 'pftoolsV3/20160324-foss-2016a', 'external_module': False, 'versionsuffix': '', 'version': '20160324', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}], 'List of dependencies', (5, 'dependencies')], 'moduleclass': ['bio', 'Module class to be used for this software', (8, 'modules')], 'key': [None, 'Key for installing software', (6, 'license')], 'include_modpath_extensions': [True, 'Include $MODULEPATH extensions specified by module naming scheme.', (8, 'modules')], 'modtclfooter': ['', 'Footer to include in generated module file (Tcl syntax)', (8, 'modules')], 'modloadmsg': [{}, 'Message that should be printed when generated module is loaded', (8, 'modules')], 'parallel': [16, 'Degree of parallelism for e.g. make (default: based on the number of cores, active cpuset and restrictions in ulimit)', (3, 'build')], 'buildininstalldir': [False, 'Boolean to build (True) or not build (False) in the installation directory', (4, 'file-management')], 'patches': [['PSORTb-%(version)s-libpsortb.patch'], 'List of patches to apply', (3, 'build')], 'sanity_check_paths': [{'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Algorithm/HMM.pm', 'lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Bio/Tools/PSort.pm'], 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Algorithm/HMM', 'lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Bio/Tools/PSort']}, "List of files and directories to check (format: {'files':<list>, 'dirs':<list>})", (3, 'build')], 'runtest': ['test', 'Run unit tests.', (1, 'easyblock-specific')], 'onlytcmod': [False, 'Boolean/string to indicate if the toolchain should only load the environment with module (True) or also set all other variables (False) like compiler CC etc (if string: comma separated list of variables that will be ignored).', (2, 'toolchain')], 'github_account': [None, 'GitHub account name to be used to resolve template values in source URLs', (3, 'build')], 'unwanted_env_vars': [{}, "List of environment variables that shouldn't be set during build", (3, 'build')], 'name': ['PSORTb', 'Name of software', (0, 'mandatory')], 'recursive_module_unload': [False, 'Recursive unload of all dependencies when unloading module', (8, 'modules')], 'toolchain': [{'version': '2016a', 'name': 'foss'}, 'Name and version of toolchain', (0, 'mandatory')], 'preconfigopts': ['export PSORTROOT=%(installdir)s && ', 'Extra options pre-passed to configure.', (3, 'build')], 'maxparallel': [None, 'Max degree of parallelism', (3, 'build')], 'license_server_port': [None, 'Port for license server', (6, 'license')], 'exts_defaultclass': [None, 'List of module for and name of the default extension class', (7, 'extensions')], 'toolchainopts': [None, 'Extra options for compilers', (2, 'toolchain')], 'source_urls': [['http://www.psort.org/download/'], 'List of URLs for source files', (3, 'build')], 'easyblock': ['PerlModule', 'EasyBlock to use for building; if set to None, an easyblock is selected based on the software name', (3, 'build')], 'whatis': [None, 'List of brief (one line) package description entries', (8, 'modules')], 'software_license': [None, 'Software license', (0, 'mandatory')], 'options': [{'modulename': 'Bio::Tools::PSort'}, 'Dictionary with extension options.', (1, 'easyblock-specific')], 'configopts': ['', 'Extra options passed to configure (default already has --prefix)', (3, 'build')], 'software_license_urls': [None, 'List of software license locations', (0, 'mandatory')]} | |
| == 2016-08-26 16:16:14,462 templates.py:175 DEBUG version found in easyconfig is 3.0.4 | |
| == 2016-08-26 16:16:14,462 templates.py:212 DEBUG name: github_account, config: None | |
| == 2016-08-26 16:16:14,462 templates.py:212 DEBUG name: name, config: PSORTb | |
| == 2016-08-26 16:16:14,463 templates.py:212 DEBUG name: version, config: 3.0.4 | |
| == 2016-08-26 16:16:14,463 templates.py:212 DEBUG name: versionsuffix, config: -Perl-%(perlver)s | |
| == 2016-08-26 16:16:14,463 templates.py:212 DEBUG name: versionprefix, config: | |
| == 2016-08-26 16:16:14,464 templates.py:151 DEBUG config: {'preinstallopts': ['', 'Extra prefix options for installation.', (3, 'build')], 'postinstallcmds': [['cp -r psort/* %(installdir)s/.'], 'Commands to run after the install step.', (3, 'build')], 'moduleloadnoconflict': [False, "Don't check for conflicts, unload other versions instead ", (8, 'modules')], 'skip': [False, 'Skip existing software', (3, 'build')], 'cleanupoldbuild': [True, 'Boolean to remove (True) or backup (False) the previous build directory with identical name or not.', (4, 'file-management')], 'installopts': ['', 'Extra options for installation', (3, 'build')], 'sources': [['bio-tools-psort-all.%(version)s.tar.gz'], 'List of source files', (3, 'build')], 'versionsuffix': ['-Perl-%(perlver)s', 'Additional suffix for software version (placed after toolchain name)', (3, 'build')], 'license_server': [None, 'License server for software', (6, 'license')], 'modaltsoftname': [None, 'Module name to use (rather than using software name', (8, 'modules')], 'keeppreviousinstall': [False, 'Boolean to keep the previous installation with identical name. Experts only!', (4, 'file-management')], 'hiddendependencies': [[], 'List of dependencies available as hidden modules', (5, 'dependencies')], 'checksums': [[], 'Checksums for sources and patches', (3, 'build')], 'keepsymlinks': [False, 'Boolean to determine whether symlinks are to be kept during copying or if the content of the files pointed to should be copied', (4, 'file-management')], 'cleanupoldinstall': [True, 'Boolean to remove (True) or backup (False) the previous install directory with identical name or not.', (4, 'file-management')], 'builddependencies': [[], 'List of build dependencies', (5, 'dependencies')], 'dontcreateinstalldir': [False, 'Boolean to create (False) or not create (True) the install directory', (4, 'file-management')], 'modextravars': [{}, 'Extra environment variables to be added to module file', (8, 'modules')], 'unpack_options': ['', 'Extra options for unpacking source', (3, 'build')], 'group': [None, 'Name of the user group for which the software should be available', (6, 'license')], 'versionprefix': ['', 'Additional prefix for software version (placed before version and toolchain name)', (3, 'build')], 'parsed': [True, 'This is a parsed easyconfig', 'HIDDEN'], 'prebuildopts': ['', 'Extra options pre-passed to build command.', (3, 'build')], 'easybuild_version': [None, 'EasyBuild-version this spec-file was written for', (3, 'build')], 'skipsteps': [[], 'Skip these steps', (3, 'build')], 'start_dir': ['/tmp/vsc40023/easybuild_build/PSORTb/3.0.4/foss-2016a-Perl-5.22.1/bio-tools-psort-all/', 'Path to start the make in. If the path is absolute, use that path. If not, this is added to the guessed path.', (4, 'file-management')], 'version': ['3.0.4', 'Version of software', (0, 'mandatory')], 'exts_filter': [None, 'Extension filter details: template for cmd and input to cmd (templates for name, version and src).', (7, 'extensions')], 'modaliases': [{}, 'Aliases to be defined in module file', (8, 'modules')], 'allow_system_deps': [[], 'Allow listed system dependencies (format: (<name>, <version>))', (5, 'dependencies')], 'osdependencies': [[], 'OS dependencies that should be present on the system', (5, 'dependencies')], 'hidden': [False, "Install module file as 'hidden' by prefixing its version with '.'", (3, 'build')], 'modluafooter': ['', 'Footer to include in generated module file (Lua syntax)', (8, 'modules')], 'homepage': ['http://psort.org/psortb/index.html', 'The homepage of the software', (0, 'mandatory')], 'buildstats': [None, 'A list of dicts with build statistics', (9, 'other')], 'license_file': [None, 'License file for software', (6, 'license')], 'tests': [[], 'List of test-scripts to run after install. A test script should return a non-zero exit status to fail', (3, 'build')], 'buildopts': ['', 'Extra options passed to make step (default already has -j X)', (3, 'build')], 'description': ['PSORTb v3.0.4 is the most precise bacterial localization prediction tool available.', 'A short description of the software', (0, 'mandatory')], 'modextrapaths': [{}, 'Extra paths to be prepended in module file', (8, 'modules')], 'exts_list': [[], 'List with extensions added to the base installation', (7, 'extensions')], 'docurls': [None, 'List of urls with documentation of the software (not necessarily on homepage)', (0, 'mandatory')], 'stop': [None, 'Keyword to halt the build process after a certain step.', (3, 'build')], 'sanity_check_commands': [[], "format: [(name, options)] e.g. [('gzip','-h')]. Using a non-tuple is equivalent to (name, '-h')", (3, 'build')], 'exts_classmap': [{}, 'Map of extension name to class for handling build and installation.', (7, 'extensions')], 'moduleforceunload': [False, 'Force unload of all modules when loading the extension', (8, 'modules')], 'dependencies': [[{'external_module_metadata': {}, 'full_mod_name': 'Perl/5.22.1-foss-2016a', 'toolchain': {'version': '2016a', 'name': 'foss'}, 'name': 'Perl', 'dummy': False, 'short_mod_name': 'Perl/5.22.1-foss-2016a', 'external_module': False, 'versionsuffix': '', 'version': '5.22.1', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}, {'external_module_metadata': {}, 'full_mod_name': 'libpsortb/1.0-foss-2016a', 'toolchain': {'version': '2016a', 'name': 'foss'}, 'name': 'libpsortb', 'dummy': False, 'short_mod_name': 'libpsortb/1.0-foss-2016a', 'external_module': False, 'versionsuffix': '', 'version': '1.0', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}, {'external_module_metadata': {}, 'full_mod_name': 'BioPerl/1.6.924-foss-2016a-Perl-5.22.1', 'toolchain': {'version': '2016a', 'name': 'foss'}, 'name': 'BioPerl', 'dummy': False, 'short_mod_name': 'BioPerl/1.6.924-foss-2016a-Perl-5.22.1', 'external_module': False, 'versionsuffix': '-Perl-5.22.1', 'version': '1.6.924', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}, {'external_module_metadata': {}, 'full_mod_name': 'BLAST/2.2.26-Linux_x86_64', 'toolchain': {'version': 'dummy', 'name': 'dummy'}, 'name': 'BLAST', 'dummy': True, 'short_mod_name': 'BLAST/2.2.26-Linux_x86_64', 'external_module': False, 'versionsuffix': '-Linux_x86_64', 'version': '2.2.26', 'toolchain_inherited': False, 'hidden': False, 'build_only': False}, {'external_module_metadata': {}, 'full_mod_name': 'pftoolsV3/20160324-foss-2016a', 'toolchain': {'version': '2016a', 'name': 'foss'}, 'name': 'pftoolsV3', 'dummy': False, 'short_mod_name': 'pftoolsV3/20160324-foss-2016a', 'external_module': False, 'versionsuffix': '', 'version': '20160324', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}], 'List of dependencies', (5, 'dependencies')], 'moduleclass': ['bio', 'Module class to be used for this software', (8, 'modules')], 'key': [None, 'Key for installing software', (6, 'license')], 'include_modpath_extensions': [True, 'Include $MODULEPATH extensions specified by module naming scheme.', (8, 'modules')], 'modtclfooter': ['', 'Footer to include in generated module file (Tcl syntax)', (8, 'modules')], 'modloadmsg': [{}, 'Message that should be printed when generated module is loaded', (8, 'modules')], 'parallel': [16, 'Degree of parallelism for e.g. make (default: based on the number of cores, active cpuset and restrictions in ulimit)', (3, 'build')], 'buildininstalldir': [False, 'Boolean to build (True) or not build (False) in the installation directory', (4, 'file-management')], 'patches': [['PSORTb-%(version)s-libpsortb.patch'], 'List of patches to apply', (3, 'build')], 'sanity_check_paths': [{'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Algorithm/HMM.pm', 'lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Bio/Tools/PSort.pm'], 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Algorithm/HMM', 'lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Bio/Tools/PSort']}, "List of files and directories to check (format: {'files':<list>, 'dirs':<list>})", (3, 'build')], 'runtest': ['test', 'Run unit tests.', (1, 'easyblock-specific')], 'onlytcmod': [False, 'Boolean/string to indicate if the toolchain should only load the environment with module (True) or also set all other variables (False) like compiler CC etc (if string: comma separated list of variables that will be ignored).', (2, 'toolchain')], 'github_account': [None, 'GitHub account name to be used to resolve template values in source URLs', (3, 'build')], 'unwanted_env_vars': [{}, "List of environment variables that shouldn't be set during build", (3, 'build')], 'name': ['PSORTb', 'Name of software', (0, 'mandatory')], 'recursive_module_unload': [False, 'Recursive unload of all dependencies when unloading module', (8, 'modules')], 'toolchain': [{'version': '2016a', 'name': 'foss'}, 'Name and version of toolchain', (0, 'mandatory')], 'preconfigopts': ['export PSORTROOT=%(installdir)s && ', 'Extra options pre-passed to configure.', (3, 'build')], 'maxparallel': [None, 'Max degree of parallelism', (3, 'build')], 'license_server_port': [None, 'Port for license server', (6, 'license')], 'exts_defaultclass': [None, 'List of module for and name of the default extension class', (7, 'extensions')], 'toolchainopts': [None, 'Extra options for compilers', (2, 'toolchain')], 'source_urls': [['http://www.psort.org/download/'], 'List of URLs for source files', (3, 'build')], 'easyblock': ['PerlModule', 'EasyBlock to use for building; if set to None, an easyblock is selected based on the software name', (3, 'build')], 'whatis': [None, 'List of brief (one line) package description entries', (8, 'modules')], 'software_license': [None, 'Software license', (0, 'mandatory')], 'options': [{'modulename': 'Bio::Tools::PSort'}, 'Dictionary with extension options.', (1, 'easyblock-specific')], 'configopts': ['', 'Extra options passed to configure (default already has --prefix)', (3, 'build')], 'software_license_urls': [None, 'List of software license locations', (0, 'mandatory')]} | |
| == 2016-08-26 16:16:14,466 templates.py:175 DEBUG version found in easyconfig is 3.0.4 | |
| == 2016-08-26 16:16:14,466 templates.py:212 DEBUG name: github_account, config: None | |
| == 2016-08-26 16:16:14,466 templates.py:212 DEBUG name: name, config: PSORTb | |
| == 2016-08-26 16:16:14,466 templates.py:212 DEBUG name: version, config: 3.0.4 | |
| == 2016-08-26 16:16:14,466 templates.py:212 DEBUG name: versionsuffix, config: -Perl-%(perlver)s | |
| == 2016-08-26 16:16:14,466 templates.py:212 DEBUG name: versionprefix, config: | |
| == 2016-08-26 16:16:14,467 easyblock.py:2139 INFO Running method configure_step part of step configure | |
| == 2016-08-26 16:16:14,467 easyblock.py:2128 DEBUG Not skipping build step (skippable: True, skip: None, skipsteps: [], module_only: False, force: True | |
| == 2016-08-26 16:16:14,467 build_log.py:227 INFO building... | |
| == 2016-08-26 16:16:14,467 easyblock.py:2136 INFO Starting build step | |
| == 2016-08-26 16:16:14,468 templates.py:151 DEBUG config: {'preinstallopts': ['', 'Extra prefix options for installation.', (3, 'build')], 'postinstallcmds': [['cp -r psort/* %(installdir)s/.'], 'Commands to run after the install step.', (3, 'build')], 'moduleloadnoconflict': [False, "Don't check for conflicts, unload other versions instead ", (8, 'modules')], 'skip': [False, 'Skip existing software', (3, 'build')], 'cleanupoldbuild': [True, 'Boolean to remove (True) or backup (False) the previous build directory with identical name or not.', (4, 'file-management')], 'installopts': ['', 'Extra options for installation', (3, 'build')], 'sources': [['bio-tools-psort-all.%(version)s.tar.gz'], 'List of source files', (3, 'build')], 'versionsuffix': ['-Perl-%(perlver)s', 'Additional suffix for software version (placed after toolchain name)', (3, 'build')], 'license_server': [None, 'License server for software', (6, 'license')], 'modaltsoftname': [None, 'Module name to use (rather than using software name', (8, 'modules')], 'keeppreviousinstall': [False, 'Boolean to keep the previous installation with identical name. Experts only!', (4, 'file-management')], 'hiddendependencies': [[], 'List of dependencies available as hidden modules', (5, 'dependencies')], 'checksums': [[], 'Checksums for sources and patches', (3, 'build')], 'keepsymlinks': [False, 'Boolean to determine whether symlinks are to be kept during copying or if the content of the files pointed to should be copied', (4, 'file-management')], 'cleanupoldinstall': [True, 'Boolean to remove (True) or backup (False) the previous install directory with identical name or not.', (4, 'file-management')], 'builddependencies': [[], 'List of build dependencies', (5, 'dependencies')], 'dontcreateinstalldir': [False, 'Boolean to create (False) or not create (True) the install directory', (4, 'file-management')], 'modextravars': [{}, 'Extra environment variables to be added to module file', (8, 'modules')], 'unpack_options': ['', 'Extra options for unpacking source', (3, 'build')], 'group': [None, 'Name of the user group for which the software should be available', (6, 'license')], 'versionprefix': ['', 'Additional prefix for software version (placed before version and toolchain name)', (3, 'build')], 'parsed': [True, 'This is a parsed easyconfig', 'HIDDEN'], 'prebuildopts': ['', 'Extra options pre-passed to build command.', (3, 'build')], 'easybuild_version': [None, 'EasyBuild-version this spec-file was written for', (3, 'build')], 'skipsteps': [[], 'Skip these steps', (3, 'build')], 'start_dir': ['/tmp/vsc40023/easybuild_build/PSORTb/3.0.4/foss-2016a-Perl-5.22.1/bio-tools-psort-all/', 'Path to start the make in. If the path is absolute, use that path. If not, this is added to the guessed path.', (4, 'file-management')], 'version': ['3.0.4', 'Version of software', (0, 'mandatory')], 'exts_filter': [None, 'Extension filter details: template for cmd and input to cmd (templates for name, version and src).', (7, 'extensions')], 'modaliases': [{}, 'Aliases to be defined in module file', (8, 'modules')], 'allow_system_deps': [[], 'Allow listed system dependencies (format: (<name>, <version>))', (5, 'dependencies')], 'osdependencies': [[], 'OS dependencies that should be present on the system', (5, 'dependencies')], 'hidden': [False, "Install module file as 'hidden' by prefixing its version with '.'", (3, 'build')], 'modluafooter': ['', 'Footer to include in generated module file (Lua syntax)', (8, 'modules')], 'homepage': ['http://psort.org/psortb/index.html', 'The homepage of the software', (0, 'mandatory')], 'buildstats': [None, 'A list of dicts with build statistics', (9, 'other')], 'license_file': [None, 'License file for software', (6, 'license')], 'tests': [[], 'List of test-scripts to run after install. A test script should return a non-zero exit status to fail', (3, 'build')], 'buildopts': ['', 'Extra options passed to make step (default already has -j X)', (3, 'build')], 'description': ['PSORTb v3.0.4 is the most precise bacterial localization prediction tool available.', 'A short description of the software', (0, 'mandatory')], 'modextrapaths': [{}, 'Extra paths to be prepended in module file', (8, 'modules')], 'exts_list': [[], 'List with extensions added to the base installation', (7, 'extensions')], 'docurls': [None, 'List of urls with documentation of the software (not necessarily on homepage)', (0, 'mandatory')], 'stop': [None, 'Keyword to halt the build process after a certain step.', (3, 'build')], 'sanity_check_commands': [[], "format: [(name, options)] e.g. [('gzip','-h')]. Using a non-tuple is equivalent to (name, '-h')", (3, 'build')], 'exts_classmap': [{}, 'Map of extension name to class for handling build and installation.', (7, 'extensions')], 'moduleforceunload': [False, 'Force unload of all modules when loading the extension', (8, 'modules')], 'dependencies': [[{'external_module_metadata': {}, 'full_mod_name': 'Perl/5.22.1-foss-2016a', 'toolchain': {'version': '2016a', 'name': 'foss'}, 'name': 'Perl', 'dummy': False, 'short_mod_name': 'Perl/5.22.1-foss-2016a', 'external_module': False, 'versionsuffix': '', 'version': '5.22.1', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}, {'external_module_metadata': {}, 'full_mod_name': 'libpsortb/1.0-foss-2016a', 'toolchain': {'version': '2016a', 'name': 'foss'}, 'name': 'libpsortb', 'dummy': False, 'short_mod_name': 'libpsortb/1.0-foss-2016a', 'external_module': False, 'versionsuffix': '', 'version': '1.0', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}, {'external_module_metadata': {}, 'full_mod_name': 'BioPerl/1.6.924-foss-2016a-Perl-5.22.1', 'toolchain': {'version': '2016a', 'name': 'foss'}, 'name': 'BioPerl', 'dummy': False, 'short_mod_name': 'BioPerl/1.6.924-foss-2016a-Perl-5.22.1', 'external_module': False, 'versionsuffix': '-Perl-5.22.1', 'version': '1.6.924', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}, {'external_module_metadata': {}, 'full_mod_name': 'BLAST/2.2.26-Linux_x86_64', 'toolchain': {'version': 'dummy', 'name': 'dummy'}, 'name': 'BLAST', 'dummy': True, 'short_mod_name': 'BLAST/2.2.26-Linux_x86_64', 'external_module': False, 'versionsuffix': '-Linux_x86_64', 'version': '2.2.26', 'toolchain_inherited': False, 'hidden': False, 'build_only': False}, {'external_module_metadata': {}, 'full_mod_name': 'pftoolsV3/20160324-foss-2016a', 'toolchain': {'version': '2016a', 'name': 'foss'}, 'name': 'pftoolsV3', 'dummy': False, 'short_mod_name': 'pftoolsV3/20160324-foss-2016a', 'external_module': False, 'versionsuffix': '', 'version': '20160324', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}], 'List of dependencies', (5, 'dependencies')], 'moduleclass': ['bio', 'Module class to be used for this software', (8, 'modules')], 'key': [None, 'Key for installing software', (6, 'license')], 'include_modpath_extensions': [True, 'Include $MODULEPATH extensions specified by module naming scheme.', (8, 'modules')], 'modtclfooter': ['', 'Footer to include in generated module file (Tcl syntax)', (8, 'modules')], 'modloadmsg': [{}, 'Message that should be printed when generated module is loaded', (8, 'modules')], 'parallel': [16, 'Degree of parallelism for e.g. make (default: based on the number of cores, active cpuset and restrictions in ulimit)', (3, 'build')], 'buildininstalldir': [False, 'Boolean to build (True) or not build (False) in the installation directory', (4, 'file-management')], 'patches': [['PSORTb-%(version)s-libpsortb.patch'], 'List of patches to apply', (3, 'build')], 'sanity_check_paths': [{'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Algorithm/HMM.pm', 'lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Bio/Tools/PSort.pm'], 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Algorithm/HMM', 'lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Bio/Tools/PSort']}, "List of files and directories to check (format: {'files':<list>, 'dirs':<list>})", (3, 'build')], 'runtest': ['test', 'Run unit tests.', (1, 'easyblock-specific')], 'onlytcmod': [False, 'Boolean/string to indicate if the toolchain should only load the environment with module (True) or also set all other variables (False) like compiler CC etc (if string: comma separated list of variables that will be ignored).', (2, 'toolchain')], 'github_account': [None, 'GitHub account name to be used to resolve template values in source URLs', (3, 'build')], 'unwanted_env_vars': [{}, "List of environment variables that shouldn't be set during build", (3, 'build')], 'name': ['PSORTb', 'Name of software', (0, 'mandatory')], 'recursive_module_unload': [False, 'Recursive unload of all dependencies when unloading module', (8, 'modules')], 'toolchain': [{'version': '2016a', 'name': 'foss'}, 'Name and version of toolchain', (0, 'mandatory')], 'preconfigopts': ['export PSORTROOT=%(installdir)s && ', 'Extra options pre-passed to configure.', (3, 'build')], 'maxparallel': [None, 'Max degree of parallelism', (3, 'build')], 'license_server_port': [None, 'Port for license server', (6, 'license')], 'exts_defaultclass': [None, 'List of module for and name of the default extension class', (7, 'extensions')], 'toolchainopts': [None, 'Extra options for compilers', (2, 'toolchain')], 'source_urls': [['http://www.psort.org/download/'], 'List of URLs for source files', (3, 'build')], 'easyblock': ['PerlModule', 'EasyBlock to use for building; if set to None, an easyblock is selected based on the software name', (3, 'build')], 'whatis': [None, 'List of brief (one line) package description entries', (8, 'modules')], 'software_license': [None, 'Software license', (0, 'mandatory')], 'options': [{'modulename': 'Bio::Tools::PSort'}, 'Dictionary with extension options.', (1, 'easyblock-specific')], 'configopts': ['', 'Extra options passed to configure (default already has --prefix)', (3, 'build')], 'software_license_urls': [None, 'List of software license locations', (0, 'mandatory')]} | |
| == 2016-08-26 16:16:14,470 templates.py:175 DEBUG version found in easyconfig is 3.0.4 | |
| == 2016-08-26 16:16:14,470 templates.py:212 DEBUG name: github_account, config: None | |
| == 2016-08-26 16:16:14,470 templates.py:212 DEBUG name: name, config: PSORTb | |
| == 2016-08-26 16:16:14,471 templates.py:212 DEBUG name: version, config: 3.0.4 | |
| == 2016-08-26 16:16:14,471 templates.py:212 DEBUG name: versionsuffix, config: -Perl-%(perlver)s | |
| == 2016-08-26 16:16:14,471 templates.py:212 DEBUG name: versionprefix, config: | |
| == 2016-08-26 16:16:14,472 templates.py:151 DEBUG config: {'preinstallopts': ['', 'Extra prefix options for installation.', (3, 'build')], 'postinstallcmds': [['cp -r psort/* %(installdir)s/.'], 'Commands to run after the install step.', (3, 'build')], 'moduleloadnoconflict': [False, "Don't check for conflicts, unload other versions instead ", (8, 'modules')], 'skip': [False, 'Skip existing software', (3, 'build')], 'cleanupoldbuild': [True, 'Boolean to remove (True) or backup (False) the previous build directory with identical name or not.', (4, 'file-management')], 'installopts': ['', 'Extra options for installation', (3, 'build')], 'sources': [['bio-tools-psort-all.%(version)s.tar.gz'], 'List of source files', (3, 'build')], 'versionsuffix': ['-Perl-%(perlver)s', 'Additional suffix for software version (placed after toolchain name)', (3, 'build')], 'license_server': [None, 'License server for software', (6, 'license')], 'modaltsoftname': [None, 'Module name to use (rather than using software name', (8, 'modules')], 'keeppreviousinstall': [False, 'Boolean to keep the previous installation with identical name. Experts only!', (4, 'file-management')], 'hiddendependencies': [[], 'List of dependencies available as hidden modules', (5, 'dependencies')], 'checksums': [[], 'Checksums for sources and patches', (3, 'build')], 'keepsymlinks': [False, 'Boolean to determine whether symlinks are to be kept during copying or if the content of the files pointed to should be copied', (4, 'file-management')], 'cleanupoldinstall': [True, 'Boolean to remove (True) or backup (False) the previous install directory with identical name or not.', (4, 'file-management')], 'builddependencies': [[], 'List of build dependencies', (5, 'dependencies')], 'dontcreateinstalldir': [False, 'Boolean to create (False) or not create (True) the install directory', (4, 'file-management')], 'modextravars': [{}, 'Extra environment variables to be added to module file', (8, 'modules')], 'unpack_options': ['', 'Extra options for unpacking source', (3, 'build')], 'group': [None, 'Name of the user group for which the software should be available', (6, 'license')], 'versionprefix': ['', 'Additional prefix for software version (placed before version and toolchain name)', (3, 'build')], 'parsed': [True, 'This is a parsed easyconfig', 'HIDDEN'], 'prebuildopts': ['', 'Extra options pre-passed to build command.', (3, 'build')], 'easybuild_version': [None, 'EasyBuild-version this spec-file was written for', (3, 'build')], 'skipsteps': [[], 'Skip these steps', (3, 'build')], 'start_dir': ['/tmp/vsc40023/easybuild_build/PSORTb/3.0.4/foss-2016a-Perl-5.22.1/bio-tools-psort-all/', 'Path to start the make in. If the path is absolute, use that path. If not, this is added to the guessed path.', (4, 'file-management')], 'version': ['3.0.4', 'Version of software', (0, 'mandatory')], 'exts_filter': [None, 'Extension filter details: template for cmd and input to cmd (templates for name, version and src).', (7, 'extensions')], 'modaliases': [{}, 'Aliases to be defined in module file', (8, 'modules')], 'allow_system_deps': [[], 'Allow listed system dependencies (format: (<name>, <version>))', (5, 'dependencies')], 'osdependencies': [[], 'OS dependencies that should be present on the system', (5, 'dependencies')], 'hidden': [False, "Install module file as 'hidden' by prefixing its version with '.'", (3, 'build')], 'modluafooter': ['', 'Footer to include in generated module file (Lua syntax)', (8, 'modules')], 'homepage': ['http://psort.org/psortb/index.html', 'The homepage of the software', (0, 'mandatory')], 'buildstats': [None, 'A list of dicts with build statistics', (9, 'other')], 'license_file': [None, 'License file for software', (6, 'license')], 'tests': [[], 'List of test-scripts to run after install. A test script should return a non-zero exit status to fail', (3, 'build')], 'buildopts': ['', 'Extra options passed to make step (default already has -j X)', (3, 'build')], 'description': ['PSORTb v3.0.4 is the most precise bacterial localization prediction tool available.', 'A short description of the software', (0, 'mandatory')], 'modextrapaths': [{}, 'Extra paths to be prepended in module file', (8, 'modules')], 'exts_list': [[], 'List with extensions added to the base installation', (7, 'extensions')], 'docurls': [None, 'List of urls with documentation of the software (not necessarily on homepage)', (0, 'mandatory')], 'stop': [None, 'Keyword to halt the build process after a certain step.', (3, 'build')], 'sanity_check_commands': [[], "format: [(name, options)] e.g. [('gzip','-h')]. Using a non-tuple is equivalent to (name, '-h')", (3, 'build')], 'exts_classmap': [{}, 'Map of extension name to class for handling build and installation.', (7, 'extensions')], 'moduleforceunload': [False, 'Force unload of all modules when loading the extension', (8, 'modules')], 'dependencies': [[{'external_module_metadata': {}, 'full_mod_name': 'Perl/5.22.1-foss-2016a', 'toolchain': {'version': '2016a', 'name': 'foss'}, 'name': 'Perl', 'dummy': False, 'short_mod_name': 'Perl/5.22.1-foss-2016a', 'external_module': False, 'versionsuffix': '', 'version': '5.22.1', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}, {'external_module_metadata': {}, 'full_mod_name': 'libpsortb/1.0-foss-2016a', 'toolchain': {'version': '2016a', 'name': 'foss'}, 'name': 'libpsortb', 'dummy': False, 'short_mod_name': 'libpsortb/1.0-foss-2016a', 'external_module': False, 'versionsuffix': '', 'version': '1.0', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}, {'external_module_metadata': {}, 'full_mod_name': 'BioPerl/1.6.924-foss-2016a-Perl-5.22.1', 'toolchain': {'version': '2016a', 'name': 'foss'}, 'name': 'BioPerl', 'dummy': False, 'short_mod_name': 'BioPerl/1.6.924-foss-2016a-Perl-5.22.1', 'external_module': False, 'versionsuffix': '-Perl-5.22.1', 'version': '1.6.924', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}, {'external_module_metadata': {}, 'full_mod_name': 'BLAST/2.2.26-Linux_x86_64', 'toolchain': {'version': 'dummy', 'name': 'dummy'}, 'name': 'BLAST', 'dummy': True, 'short_mod_name': 'BLAST/2.2.26-Linux_x86_64', 'external_module': False, 'versionsuffix': '-Linux_x86_64', 'version': '2.2.26', 'toolchain_inherited': False, 'hidden': False, 'build_only': False}, {'external_module_metadata': {}, 'full_mod_name': 'pftoolsV3/20160324-foss-2016a', 'toolchain': {'version': '2016a', 'name': 'foss'}, 'name': 'pftoolsV3', 'dummy': False, 'short_mod_name': 'pftoolsV3/20160324-foss-2016a', 'external_module': False, 'versionsuffix': '', 'version': '20160324', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}], 'List of dependencies', (5, 'dependencies')], 'moduleclass': ['bio', 'Module class to be used for this software', (8, 'modules')], 'key': [None, 'Key for installing software', (6, 'license')], 'include_modpath_extensions': [True, 'Include $MODULEPATH extensions specified by module naming scheme.', (8, 'modules')], 'modtclfooter': ['', 'Footer to include in generated module file (Tcl syntax)', (8, 'modules')], 'modloadmsg': [{}, 'Message that should be printed when generated module is loaded', (8, 'modules')], 'parallel': [16, 'Degree of parallelism for e.g. make (default: based on the number of cores, active cpuset and restrictions in ulimit)', (3, 'build')], 'buildininstalldir': [False, 'Boolean to build (True) or not build (False) in the installation directory', (4, 'file-management')], 'patches': [['PSORTb-%(version)s-libpsortb.patch'], 'List of patches to apply', (3, 'build')], 'sanity_check_paths': [{'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Algorithm/HMM.pm', 'lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Bio/Tools/PSort.pm'], 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Algorithm/HMM', 'lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Bio/Tools/PSort']}, "List of files and directories to check (format: {'files':<list>, 'dirs':<list>})", (3, 'build')], 'runtest': ['test', 'Run unit tests.', (1, 'easyblock-specific')], 'onlytcmod': [False, 'Boolean/string to indicate if the toolchain should only load the environment with module (True) or also set all other variables (False) like compiler CC etc (if string: comma separated list of variables that will be ignored).', (2, 'toolchain')], 'github_account': [None, 'GitHub account name to be used to resolve template values in source URLs', (3, 'build')], 'unwanted_env_vars': [{}, "List of environment variables that shouldn't be set during build", (3, 'build')], 'name': ['PSORTb', 'Name of software', (0, 'mandatory')], 'recursive_module_unload': [False, 'Recursive unload of all dependencies when unloading module', (8, 'modules')], 'toolchain': [{'version': '2016a', 'name': 'foss'}, 'Name and version of toolchain', (0, 'mandatory')], 'preconfigopts': ['export PSORTROOT=%(installdir)s && ', 'Extra options pre-passed to configure.', (3, 'build')], 'maxparallel': [None, 'Max degree of parallelism', (3, 'build')], 'license_server_port': [None, 'Port for license server', (6, 'license')], 'exts_defaultclass': [None, 'List of module for and name of the default extension class', (7, 'extensions')], 'toolchainopts': [None, 'Extra options for compilers', (2, 'toolchain')], 'source_urls': [['http://www.psort.org/download/'], 'List of URLs for source files', (3, 'build')], 'easyblock': ['PerlModule', 'EasyBlock to use for building; if set to None, an easyblock is selected based on the software name', (3, 'build')], 'whatis': [None, 'List of brief (one line) package description entries', (8, 'modules')], 'software_license': [None, 'Software license', (0, 'mandatory')], 'options': [{'modulename': 'Bio::Tools::PSort'}, 'Dictionary with extension options.', (1, 'easyblock-specific')], 'configopts': ['', 'Extra options passed to configure (default already has --prefix)', (3, 'build')], 'software_license_urls': [None, 'List of software license locations', (0, 'mandatory')]} | |
| == 2016-08-26 16:16:14,473 templates.py:175 DEBUG version found in easyconfig is 3.0.4 | |
| == 2016-08-26 16:16:14,474 templates.py:212 DEBUG name: github_account, config: None | |
| == 2016-08-26 16:16:14,474 templates.py:212 DEBUG name: name, config: PSORTb | |
| == 2016-08-26 16:16:14,474 templates.py:212 DEBUG name: version, config: 3.0.4 | |
| == 2016-08-26 16:16:14,474 templates.py:212 DEBUG name: versionsuffix, config: -Perl-%(perlver)s | |
| == 2016-08-26 16:16:14,474 templates.py:212 DEBUG name: versionprefix, config: | |
| == 2016-08-26 16:16:14,475 easyblock.py:2139 INFO Running method build_step part of step build | |
| == 2016-08-26 16:16:14,475 easyblock.py:2128 DEBUG Not skipping test step (skippable: True, skip: None, skipsteps: [], module_only: False, force: True | |
| == 2016-08-26 16:16:14,475 build_log.py:227 INFO testing... | |
| == 2016-08-26 16:16:14,475 easyblock.py:2136 INFO Starting test step | |
| == 2016-08-26 16:16:14,476 templates.py:151 DEBUG config: {'preinstallopts': ['', 'Extra prefix options for installation.', (3, 'build')], 'postinstallcmds': [['cp -r psort/* %(installdir)s/.'], 'Commands to run after the install step.', (3, 'build')], 'moduleloadnoconflict': [False, "Don't check for conflicts, unload other versions instead ", (8, 'modules')], 'skip': [False, 'Skip existing software', (3, 'build')], 'cleanupoldbuild': [True, 'Boolean to remove (True) or backup (False) the previous build directory with identical name or not.', (4, 'file-management')], 'installopts': ['', 'Extra options for installation', (3, 'build')], 'sources': [['bio-tools-psort-all.%(version)s.tar.gz'], 'List of source files', (3, 'build')], 'versionsuffix': ['-Perl-%(perlver)s', 'Additional suffix for software version (placed after toolchain name)', (3, 'build')], 'license_server': [None, 'License server for software', (6, 'license')], 'modaltsoftname': [None, 'Module name to use (rather than using software name', (8, 'modules')], 'keeppreviousinstall': [False, 'Boolean to keep the previous installation with identical name. Experts only!', (4, 'file-management')], 'hiddendependencies': [[], 'List of dependencies available as hidden modules', (5, 'dependencies')], 'checksums': [[], 'Checksums for sources and patches', (3, 'build')], 'keepsymlinks': [False, 'Boolean to determine whether symlinks are to be kept during copying or if the content of the files pointed to should be copied', (4, 'file-management')], 'cleanupoldinstall': [True, 'Boolean to remove (True) or backup (False) the previous install directory with identical name or not.', (4, 'file-management')], 'builddependencies': [[], 'List of build dependencies', (5, 'dependencies')], 'dontcreateinstalldir': [False, 'Boolean to create (False) or not create (True) the install directory', (4, 'file-management')], 'modextravars': [{}, 'Extra environment variables to be added to module file', (8, 'modules')], 'unpack_options': ['', 'Extra options for unpacking source', (3, 'build')], 'group': [None, 'Name of the user group for which the software should be available', (6, 'license')], 'versionprefix': ['', 'Additional prefix for software version (placed before version and toolchain name)', (3, 'build')], 'parsed': [True, 'This is a parsed easyconfig', 'HIDDEN'], 'prebuildopts': ['', 'Extra options pre-passed to build command.', (3, 'build')], 'easybuild_version': [None, 'EasyBuild-version this spec-file was written for', (3, 'build')], 'skipsteps': [[], 'Skip these steps', (3, 'build')], 'start_dir': ['/tmp/vsc40023/easybuild_build/PSORTb/3.0.4/foss-2016a-Perl-5.22.1/bio-tools-psort-all/', 'Path to start the make in. If the path is absolute, use that path. If not, this is added to the guessed path.', (4, 'file-management')], 'version': ['3.0.4', 'Version of software', (0, 'mandatory')], 'exts_filter': [None, 'Extension filter details: template for cmd and input to cmd (templates for name, version and src).', (7, 'extensions')], 'modaliases': [{}, 'Aliases to be defined in module file', (8, 'modules')], 'allow_system_deps': [[], 'Allow listed system dependencies (format: (<name>, <version>))', (5, 'dependencies')], 'osdependencies': [[], 'OS dependencies that should be present on the system', (5, 'dependencies')], 'hidden': [False, "Install module file as 'hidden' by prefixing its version with '.'", (3, 'build')], 'modluafooter': ['', 'Footer to include in generated module file (Lua syntax)', (8, 'modules')], 'homepage': ['http://psort.org/psortb/index.html', 'The homepage of the software', (0, 'mandatory')], 'buildstats': [None, 'A list of dicts with build statistics', (9, 'other')], 'license_file': [None, 'License file for software', (6, 'license')], 'tests': [[], 'List of test-scripts to run after install. A test script should return a non-zero exit status to fail', (3, 'build')], 'buildopts': ['', 'Extra options passed to make step (default already has -j X)', (3, 'build')], 'description': ['PSORTb v3.0.4 is the most precise bacterial localization prediction tool available.', 'A short description of the software', (0, 'mandatory')], 'modextrapaths': [{}, 'Extra paths to be prepended in module file', (8, 'modules')], 'exts_list': [[], 'List with extensions added to the base installation', (7, 'extensions')], 'docurls': [None, 'List of urls with documentation of the software (not necessarily on homepage)', (0, 'mandatory')], 'stop': [None, 'Keyword to halt the build process after a certain step.', (3, 'build')], 'sanity_check_commands': [[], "format: [(name, options)] e.g. [('gzip','-h')]. Using a non-tuple is equivalent to (name, '-h')", (3, 'build')], 'exts_classmap': [{}, 'Map of extension name to class for handling build and installation.', (7, 'extensions')], 'moduleforceunload': [False, 'Force unload of all modules when loading the extension', (8, 'modules')], 'dependencies': [[{'external_module_metadata': {}, 'full_mod_name': 'Perl/5.22.1-foss-2016a', 'toolchain': {'version': '2016a', 'name': 'foss'}, 'name': 'Perl', 'dummy': False, 'short_mod_name': 'Perl/5.22.1-foss-2016a', 'external_module': False, 'versionsuffix': '', 'version': '5.22.1', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}, {'external_module_metadata': {}, 'full_mod_name': 'libpsortb/1.0-foss-2016a', 'toolchain': {'version': '2016a', 'name': 'foss'}, 'name': 'libpsortb', 'dummy': False, 'short_mod_name': 'libpsortb/1.0-foss-2016a', 'external_module': False, 'versionsuffix': '', 'version': '1.0', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}, {'external_module_metadata': {}, 'full_mod_name': 'BioPerl/1.6.924-foss-2016a-Perl-5.22.1', 'toolchain': {'version': '2016a', 'name': 'foss'}, 'name': 'BioPerl', 'dummy': False, 'short_mod_name': 'BioPerl/1.6.924-foss-2016a-Perl-5.22.1', 'external_module': False, 'versionsuffix': '-Perl-5.22.1', 'version': '1.6.924', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}, {'external_module_metadata': {}, 'full_mod_name': 'BLAST/2.2.26-Linux_x86_64', 'toolchain': {'version': 'dummy', 'name': 'dummy'}, 'name': 'BLAST', 'dummy': True, 'short_mod_name': 'BLAST/2.2.26-Linux_x86_64', 'external_module': False, 'versionsuffix': '-Linux_x86_64', 'version': '2.2.26', 'toolchain_inherited': False, 'hidden': False, 'build_only': False}, {'external_module_metadata': {}, 'full_mod_name': 'pftoolsV3/20160324-foss-2016a', 'toolchain': {'version': '2016a', 'name': 'foss'}, 'name': 'pftoolsV3', 'dummy': False, 'short_mod_name': 'pftoolsV3/20160324-foss-2016a', 'external_module': False, 'versionsuffix': '', 'version': '20160324', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}], 'List of dependencies', (5, 'dependencies')], 'moduleclass': ['bio', 'Module class to be used for this software', (8, 'modules')], 'key': [None, 'Key for installing software', (6, 'license')], 'include_modpath_extensions': [True, 'Include $MODULEPATH extensions specified by module naming scheme.', (8, 'modules')], 'modtclfooter': ['', 'Footer to include in generated module file (Tcl syntax)', (8, 'modules')], 'modloadmsg': [{}, 'Message that should be printed when generated module is loaded', (8, 'modules')], 'parallel': [16, 'Degree of parallelism for e.g. make (default: based on the number of cores, active cpuset and restrictions in ulimit)', (3, 'build')], 'buildininstalldir': [False, 'Boolean to build (True) or not build (False) in the installation directory', (4, 'file-management')], 'patches': [['PSORTb-%(version)s-libpsortb.patch'], 'List of patches to apply', (3, 'build')], 'sanity_check_paths': [{'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Algorithm/HMM.pm', 'lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Bio/Tools/PSort.pm'], 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Algorithm/HMM', 'lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Bio/Tools/PSort']}, "List of files and directories to check (format: {'files':<list>, 'dirs':<list>})", (3, 'build')], 'runtest': ['test', 'Run unit tests.', (1, 'easyblock-specific')], 'onlytcmod': [False, 'Boolean/string to indicate if the toolchain should only load the environment with module (True) or also set all other variables (False) like compiler CC etc (if string: comma separated list of variables that will be ignored).', (2, 'toolchain')], 'github_account': [None, 'GitHub account name to be used to resolve template values in source URLs', (3, 'build')], 'unwanted_env_vars': [{}, "List of environment variables that shouldn't be set during build", (3, 'build')], 'name': ['PSORTb', 'Name of software', (0, 'mandatory')], 'recursive_module_unload': [False, 'Recursive unload of all dependencies when unloading module', (8, 'modules')], 'toolchain': [{'version': '2016a', 'name': 'foss'}, 'Name and version of toolchain', (0, 'mandatory')], 'preconfigopts': ['export PSORTROOT=%(installdir)s && ', 'Extra options pre-passed to configure.', (3, 'build')], 'maxparallel': [None, 'Max degree of parallelism', (3, 'build')], 'license_server_port': [None, 'Port for license server', (6, 'license')], 'exts_defaultclass': [None, 'List of module for and name of the default extension class', (7, 'extensions')], 'toolchainopts': [None, 'Extra options for compilers', (2, 'toolchain')], 'source_urls': [['http://www.psort.org/download/'], 'List of URLs for source files', (3, 'build')], 'easyblock': ['PerlModule', 'EasyBlock to use for building; if set to None, an easyblock is selected based on the software name', (3, 'build')], 'whatis': [None, 'List of brief (one line) package description entries', (8, 'modules')], 'software_license': [None, 'Software license', (0, 'mandatory')], 'options': [{'modulename': 'Bio::Tools::PSort'}, 'Dictionary with extension options.', (1, 'easyblock-specific')], 'configopts': ['', 'Extra options passed to configure (default already has --prefix)', (3, 'build')], 'software_license_urls': [None, 'List of software license locations', (0, 'mandatory')]} | |
| == 2016-08-26 16:16:14,478 templates.py:175 DEBUG version found in easyconfig is 3.0.4 | |
| == 2016-08-26 16:16:14,478 templates.py:212 DEBUG name: github_account, config: None | |
| == 2016-08-26 16:16:14,478 templates.py:212 DEBUG name: name, config: PSORTb | |
| == 2016-08-26 16:16:14,478 templates.py:212 DEBUG name: version, config: 3.0.4 | |
| == 2016-08-26 16:16:14,479 templates.py:212 DEBUG name: versionsuffix, config: -Perl-%(perlver)s | |
| == 2016-08-26 16:16:14,479 templates.py:212 DEBUG name: versionprefix, config: | |
| == 2016-08-26 16:16:14,480 templates.py:151 DEBUG config: {'preinstallopts': ['', 'Extra prefix options for installation.', (3, 'build')], 'postinstallcmds': [['cp -r psort/* %(installdir)s/.'], 'Commands to run after the install step.', (3, 'build')], 'moduleloadnoconflict': [False, "Don't check for conflicts, unload other versions instead ", (8, 'modules')], 'skip': [False, 'Skip existing software', (3, 'build')], 'cleanupoldbuild': [True, 'Boolean to remove (True) or backup (False) the previous build directory with identical name or not.', (4, 'file-management')], 'installopts': ['', 'Extra options for installation', (3, 'build')], 'sources': [['bio-tools-psort-all.%(version)s.tar.gz'], 'List of source files', (3, 'build')], 'versionsuffix': ['-Perl-%(perlver)s', 'Additional suffix for software version (placed after toolchain name)', (3, 'build')], 'license_server': [None, 'License server for software', (6, 'license')], 'modaltsoftname': [None, 'Module name to use (rather than using software name', (8, 'modules')], 'keeppreviousinstall': [False, 'Boolean to keep the previous installation with identical name. Experts only!', (4, 'file-management')], 'hiddendependencies': [[], 'List of dependencies available as hidden modules', (5, 'dependencies')], 'checksums': [[], 'Checksums for sources and patches', (3, 'build')], 'keepsymlinks': [False, 'Boolean to determine whether symlinks are to be kept during copying or if the content of the files pointed to should be copied', (4, 'file-management')], 'cleanupoldinstall': [True, 'Boolean to remove (True) or backup (False) the previous install directory with identical name or not.', (4, 'file-management')], 'builddependencies': [[], 'List of build dependencies', (5, 'dependencies')], 'dontcreateinstalldir': [False, 'Boolean to create (False) or not create (True) the install directory', (4, 'file-management')], 'modextravars': [{}, 'Extra environment variables to be added to module file', (8, 'modules')], 'unpack_options': ['', 'Extra options for unpacking source', (3, 'build')], 'group': [None, 'Name of the user group for which the software should be available', (6, 'license')], 'versionprefix': ['', 'Additional prefix for software version (placed before version and toolchain name)', (3, 'build')], 'parsed': [True, 'This is a parsed easyconfig', 'HIDDEN'], 'prebuildopts': ['', 'Extra options pre-passed to build command.', (3, 'build')], 'easybuild_version': [None, 'EasyBuild-version this spec-file was written for', (3, 'build')], 'skipsteps': [[], 'Skip these steps', (3, 'build')], 'start_dir': ['/tmp/vsc40023/easybuild_build/PSORTb/3.0.4/foss-2016a-Perl-5.22.1/bio-tools-psort-all/', 'Path to start the make in. If the path is absolute, use that path. If not, this is added to the guessed path.', (4, 'file-management')], 'version': ['3.0.4', 'Version of software', (0, 'mandatory')], 'exts_filter': [None, 'Extension filter details: template for cmd and input to cmd (templates for name, version and src).', (7, 'extensions')], 'modaliases': [{}, 'Aliases to be defined in module file', (8, 'modules')], 'allow_system_deps': [[], 'Allow listed system dependencies (format: (<name>, <version>))', (5, 'dependencies')], 'osdependencies': [[], 'OS dependencies that should be present on the system', (5, 'dependencies')], 'hidden': [False, "Install module file as 'hidden' by prefixing its version with '.'", (3, 'build')], 'modluafooter': ['', 'Footer to include in generated module file (Lua syntax)', (8, 'modules')], 'homepage': ['http://psort.org/psortb/index.html', 'The homepage of the software', (0, 'mandatory')], 'buildstats': [None, 'A list of dicts with build statistics', (9, 'other')], 'license_file': [None, 'License file for software', (6, 'license')], 'tests': [[], 'List of test-scripts to run after install. A test script should return a non-zero exit status to fail', (3, 'build')], 'buildopts': ['', 'Extra options passed to make step (default already has -j X)', (3, 'build')], 'description': ['PSORTb v3.0.4 is the most precise bacterial localization prediction tool available.', 'A short description of the software', (0, 'mandatory')], 'modextrapaths': [{}, 'Extra paths to be prepended in module file', (8, 'modules')], 'exts_list': [[], 'List with extensions added to the base installation', (7, 'extensions')], 'docurls': [None, 'List of urls with documentation of the software (not necessarily on homepage)', (0, 'mandatory')], 'stop': [None, 'Keyword to halt the build process after a certain step.', (3, 'build')], 'sanity_check_commands': [[], "format: [(name, options)] e.g. [('gzip','-h')]. Using a non-tuple is equivalent to (name, '-h')", (3, 'build')], 'exts_classmap': [{}, 'Map of extension name to class for handling build and installation.', (7, 'extensions')], 'moduleforceunload': [False, 'Force unload of all modules when loading the extension', (8, 'modules')], 'dependencies': [[{'external_module_metadata': {}, 'full_mod_name': 'Perl/5.22.1-foss-2016a', 'toolchain': {'version': '2016a', 'name': 'foss'}, 'name': 'Perl', 'dummy': False, 'short_mod_name': 'Perl/5.22.1-foss-2016a', 'external_module': False, 'versionsuffix': '', 'version': '5.22.1', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}, {'external_module_metadata': {}, 'full_mod_name': 'libpsortb/1.0-foss-2016a', 'toolchain': {'version': '2016a', 'name': 'foss'}, 'name': 'libpsortb', 'dummy': False, 'short_mod_name': 'libpsortb/1.0-foss-2016a', 'external_module': False, 'versionsuffix': '', 'version': '1.0', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}, {'external_module_metadata': {}, 'full_mod_name': 'BioPerl/1.6.924-foss-2016a-Perl-5.22.1', 'toolchain': {'version': '2016a', 'name': 'foss'}, 'name': 'BioPerl', 'dummy': False, 'short_mod_name': 'BioPerl/1.6.924-foss-2016a-Perl-5.22.1', 'external_module': False, 'versionsuffix': '-Perl-5.22.1', 'version': '1.6.924', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}, {'external_module_metadata': {}, 'full_mod_name': 'BLAST/2.2.26-Linux_x86_64', 'toolchain': {'version': 'dummy', 'name': 'dummy'}, 'name': 'BLAST', 'dummy': True, 'short_mod_name': 'BLAST/2.2.26-Linux_x86_64', 'external_module': False, 'versionsuffix': '-Linux_x86_64', 'version': '2.2.26', 'toolchain_inherited': False, 'hidden': False, 'build_only': False}, {'external_module_metadata': {}, 'full_mod_name': 'pftoolsV3/20160324-foss-2016a', 'toolchain': {'version': '2016a', 'name': 'foss'}, 'name': 'pftoolsV3', 'dummy': False, 'short_mod_name': 'pftoolsV3/20160324-foss-2016a', 'external_module': False, 'versionsuffix': '', 'version': '20160324', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}], 'List of dependencies', (5, 'dependencies')], 'moduleclass': ['bio', 'Module class to be used for this software', (8, 'modules')], 'key': [None, 'Key for installing software', (6, 'license')], 'include_modpath_extensions': [True, 'Include $MODULEPATH extensions specified by module naming scheme.', (8, 'modules')], 'modtclfooter': ['', 'Footer to include in generated module file (Tcl syntax)', (8, 'modules')], 'modloadmsg': [{}, 'Message that should be printed when generated module is loaded', (8, 'modules')], 'parallel': [16, 'Degree of parallelism for e.g. make (default: based on the number of cores, active cpuset and restrictions in ulimit)', (3, 'build')], 'buildininstalldir': [False, 'Boolean to build (True) or not build (False) in the installation directory', (4, 'file-management')], 'patches': [['PSORTb-%(version)s-libpsortb.patch'], 'List of patches to apply', (3, 'build')], 'sanity_check_paths': [{'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Algorithm/HMM.pm', 'lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Bio/Tools/PSort.pm'], 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Algorithm/HMM', 'lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Bio/Tools/PSort']}, "List of files and directories to check (format: {'files':<list>, 'dirs':<list>})", (3, 'build')], 'runtest': ['test', 'Run unit tests.', (1, 'easyblock-specific')], 'onlytcmod': [False, 'Boolean/string to indicate if the toolchain should only load the environment with module (True) or also set all other variables (False) like compiler CC etc (if string: comma separated list of variables that will be ignored).', (2, 'toolchain')], 'github_account': [None, 'GitHub account name to be used to resolve template values in source URLs', (3, 'build')], 'unwanted_env_vars': [{}, "List of environment variables that shouldn't be set during build", (3, 'build')], 'name': ['PSORTb', 'Name of software', (0, 'mandatory')], 'recursive_module_unload': [False, 'Recursive unload of all dependencies when unloading module', (8, 'modules')], 'toolchain': [{'version': '2016a', 'name': 'foss'}, 'Name and version of toolchain', (0, 'mandatory')], 'preconfigopts': ['export PSORTROOT=%(installdir)s && ', 'Extra options pre-passed to configure.', (3, 'build')], 'maxparallel': [None, 'Max degree of parallelism', (3, 'build')], 'license_server_port': [None, 'Port for license server', (6, 'license')], 'exts_defaultclass': [None, 'List of module for and name of the default extension class', (7, 'extensions')], 'toolchainopts': [None, 'Extra options for compilers', (2, 'toolchain')], 'source_urls': [['http://www.psort.org/download/'], 'List of URLs for source files', (3, 'build')], 'easyblock': ['PerlModule', 'EasyBlock to use for building; if set to None, an easyblock is selected based on the software name', (3, 'build')], 'whatis': [None, 'List of brief (one line) package description entries', (8, 'modules')], 'software_license': [None, 'Software license', (0, 'mandatory')], 'options': [{'modulename': 'Bio::Tools::PSort'}, 'Dictionary with extension options.', (1, 'easyblock-specific')], 'configopts': ['', 'Extra options passed to configure (default already has --prefix)', (3, 'build')], 'software_license_urls': [None, 'List of software license locations', (0, 'mandatory')]} | |
| == 2016-08-26 16:16:14,481 templates.py:175 DEBUG version found in easyconfig is 3.0.4 | |
| == 2016-08-26 16:16:14,482 templates.py:212 DEBUG name: github_account, config: None | |
| == 2016-08-26 16:16:14,482 templates.py:212 DEBUG name: name, config: PSORTb | |
| == 2016-08-26 16:16:14,482 templates.py:212 DEBUG name: version, config: 3.0.4 | |
| == 2016-08-26 16:16:14,482 templates.py:212 DEBUG name: versionsuffix, config: -Perl-%(perlver)s | |
| == 2016-08-26 16:16:14,482 templates.py:212 DEBUG name: versionprefix, config: | |
| == 2016-08-26 16:16:14,483 easyblock.py:2139 INFO Running method test_step part of step test | |
| == 2016-08-26 16:16:14,483 easyblock.py:2128 DEBUG Not skipping install step (skippable: True, skip: None, skipsteps: [], module_only: False, force: True | |
| == 2016-08-26 16:16:14,483 build_log.py:227 INFO installing... | |
| == 2016-08-26 16:16:14,483 easyblock.py:2136 INFO Starting install step | |
| == 2016-08-26 16:16:14,484 templates.py:151 DEBUG config: {'preinstallopts': ['', 'Extra prefix options for installation.', (3, 'build')], 'postinstallcmds': [['cp -r psort/* %(installdir)s/.'], 'Commands to run after the install step.', (3, 'build')], 'moduleloadnoconflict': [False, "Don't check for conflicts, unload other versions instead ", (8, 'modules')], 'skip': [False, 'Skip existing software', (3, 'build')], 'cleanupoldbuild': [True, 'Boolean to remove (True) or backup (False) the previous build directory with identical name or not.', (4, 'file-management')], 'installopts': ['', 'Extra options for installation', (3, 'build')], 'sources': [['bio-tools-psort-all.%(version)s.tar.gz'], 'List of source files', (3, 'build')], 'versionsuffix': ['-Perl-%(perlver)s', 'Additional suffix for software version (placed after toolchain name)', (3, 'build')], 'license_server': [None, 'License server for software', (6, 'license')], 'modaltsoftname': [None, 'Module name to use (rather than using software name', (8, 'modules')], 'keeppreviousinstall': [False, 'Boolean to keep the previous installation with identical name. Experts only!', (4, 'file-management')], 'hiddendependencies': [[], 'List of dependencies available as hidden modules', (5, 'dependencies')], 'checksums': [[], 'Checksums for sources and patches', (3, 'build')], 'keepsymlinks': [False, 'Boolean to determine whether symlinks are to be kept during copying or if the content of the files pointed to should be copied', (4, 'file-management')], 'cleanupoldinstall': [True, 'Boolean to remove (True) or backup (False) the previous install directory with identical name or not.', (4, 'file-management')], 'builddependencies': [[], 'List of build dependencies', (5, 'dependencies')], 'dontcreateinstalldir': [False, 'Boolean to create (False) or not create (True) the install directory', (4, 'file-management')], 'modextravars': [{}, 'Extra environment variables to be added to module file', (8, 'modules')], 'unpack_options': ['', 'Extra options for unpacking source', (3, 'build')], 'group': [None, 'Name of the user group for which the software should be available', (6, 'license')], 'versionprefix': ['', 'Additional prefix for software version (placed before version and toolchain name)', (3, 'build')], 'parsed': [True, 'This is a parsed easyconfig', 'HIDDEN'], 'prebuildopts': ['', 'Extra options pre-passed to build command.', (3, 'build')], 'easybuild_version': [None, 'EasyBuild-version this spec-file was written for', (3, 'build')], 'skipsteps': [[], 'Skip these steps', (3, 'build')], 'start_dir': ['/tmp/vsc40023/easybuild_build/PSORTb/3.0.4/foss-2016a-Perl-5.22.1/bio-tools-psort-all/', 'Path to start the make in. If the path is absolute, use that path. If not, this is added to the guessed path.', (4, 'file-management')], 'version': ['3.0.4', 'Version of software', (0, 'mandatory')], 'exts_filter': [None, 'Extension filter details: template for cmd and input to cmd (templates for name, version and src).', (7, 'extensions')], 'modaliases': [{}, 'Aliases to be defined in module file', (8, 'modules')], 'allow_system_deps': [[], 'Allow listed system dependencies (format: (<name>, <version>))', (5, 'dependencies')], 'osdependencies': [[], 'OS dependencies that should be present on the system', (5, 'dependencies')], 'hidden': [False, "Install module file as 'hidden' by prefixing its version with '.'", (3, 'build')], 'modluafooter': ['', 'Footer to include in generated module file (Lua syntax)', (8, 'modules')], 'homepage': ['http://psort.org/psortb/index.html', 'The homepage of the software', (0, 'mandatory')], 'buildstats': [None, 'A list of dicts with build statistics', (9, 'other')], 'license_file': [None, 'License file for software', (6, 'license')], 'tests': [[], 'List of test-scripts to run after install. A test script should return a non-zero exit status to fail', (3, 'build')], 'buildopts': ['', 'Extra options passed to make step (default already has -j X)', (3, 'build')], 'description': ['PSORTb v3.0.4 is the most precise bacterial localization prediction tool available.', 'A short description of the software', (0, 'mandatory')], 'modextrapaths': [{}, 'Extra paths to be prepended in module file', (8, 'modules')], 'exts_list': [[], 'List with extensions added to the base installation', (7, 'extensions')], 'docurls': [None, 'List of urls with documentation of the software (not necessarily on homepage)', (0, 'mandatory')], 'stop': [None, 'Keyword to halt the build process after a certain step.', (3, 'build')], 'sanity_check_commands': [[], "format: [(name, options)] e.g. [('gzip','-h')]. Using a non-tuple is equivalent to (name, '-h')", (3, 'build')], 'exts_classmap': [{}, 'Map of extension name to class for handling build and installation.', (7, 'extensions')], 'moduleforceunload': [False, 'Force unload of all modules when loading the extension', (8, 'modules')], 'dependencies': [[{'external_module_metadata': {}, 'full_mod_name': 'Perl/5.22.1-foss-2016a', 'toolchain': {'version': '2016a', 'name': 'foss'}, 'name': 'Perl', 'dummy': False, 'short_mod_name': 'Perl/5.22.1-foss-2016a', 'external_module': False, 'versionsuffix': '', 'version': '5.22.1', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}, {'external_module_metadata': {}, 'full_mod_name': 'libpsortb/1.0-foss-2016a', 'toolchain': {'version': '2016a', 'name': 'foss'}, 'name': 'libpsortb', 'dummy': False, 'short_mod_name': 'libpsortb/1.0-foss-2016a', 'external_module': False, 'versionsuffix': '', 'version': '1.0', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}, {'external_module_metadata': {}, 'full_mod_name': 'BioPerl/1.6.924-foss-2016a-Perl-5.22.1', 'toolchain': {'version': '2016a', 'name': 'foss'}, 'name': 'BioPerl', 'dummy': False, 'short_mod_name': 'BioPerl/1.6.924-foss-2016a-Perl-5.22.1', 'external_module': False, 'versionsuffix': '-Perl-5.22.1', 'version': '1.6.924', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}, {'external_module_metadata': {}, 'full_mod_name': 'BLAST/2.2.26-Linux_x86_64', 'toolchain': {'version': 'dummy', 'name': 'dummy'}, 'name': 'BLAST', 'dummy': True, 'short_mod_name': 'BLAST/2.2.26-Linux_x86_64', 'external_module': False, 'versionsuffix': '-Linux_x86_64', 'version': '2.2.26', 'toolchain_inherited': False, 'hidden': False, 'build_only': False}, {'external_module_metadata': {}, 'full_mod_name': 'pftoolsV3/20160324-foss-2016a', 'toolchain': {'version': '2016a', 'name': 'foss'}, 'name': 'pftoolsV3', 'dummy': False, 'short_mod_name': 'pftoolsV3/20160324-foss-2016a', 'external_module': False, 'versionsuffix': '', 'version': '20160324', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}], 'List of dependencies', (5, 'dependencies')], 'moduleclass': ['bio', 'Module class to be used for this software', (8, 'modules')], 'key': [None, 'Key for installing software', (6, 'license')], 'include_modpath_extensions': [True, 'Include $MODULEPATH extensions specified by module naming scheme.', (8, 'modules')], 'modtclfooter': ['', 'Footer to include in generated module file (Tcl syntax)', (8, 'modules')], 'modloadmsg': [{}, 'Message that should be printed when generated module is loaded', (8, 'modules')], 'parallel': [16, 'Degree of parallelism for e.g. make (default: based on the number of cores, active cpuset and restrictions in ulimit)', (3, 'build')], 'buildininstalldir': [False, 'Boolean to build (True) or not build (False) in the installation directory', (4, 'file-management')], 'patches': [['PSORTb-%(version)s-libpsortb.patch'], 'List of patches to apply', (3, 'build')], 'sanity_check_paths': [{'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Algorithm/HMM.pm', 'lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Bio/Tools/PSort.pm'], 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Algorithm/HMM', 'lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Bio/Tools/PSort']}, "List of files and directories to check (format: {'files':<list>, 'dirs':<list>})", (3, 'build')], 'runtest': ['test', 'Run unit tests.', (1, 'easyblock-specific')], 'onlytcmod': [False, 'Boolean/string to indicate if the toolchain should only load the environment with module (True) or also set all other variables (False) like compiler CC etc (if string: comma separated list of variables that will be ignored).', (2, 'toolchain')], 'github_account': [None, 'GitHub account name to be used to resolve template values in source URLs', (3, 'build')], 'unwanted_env_vars': [{}, "List of environment variables that shouldn't be set during build", (3, 'build')], 'name': ['PSORTb', 'Name of software', (0, 'mandatory')], 'recursive_module_unload': [False, 'Recursive unload of all dependencies when unloading module', (8, 'modules')], 'toolchain': [{'version': '2016a', 'name': 'foss'}, 'Name and version of toolchain', (0, 'mandatory')], 'preconfigopts': ['export PSORTROOT=%(installdir)s && ', 'Extra options pre-passed to configure.', (3, 'build')], 'maxparallel': [None, 'Max degree of parallelism', (3, 'build')], 'license_server_port': [None, 'Port for license server', (6, 'license')], 'exts_defaultclass': [None, 'List of module for and name of the default extension class', (7, 'extensions')], 'toolchainopts': [None, 'Extra options for compilers', (2, 'toolchain')], 'source_urls': [['http://www.psort.org/download/'], 'List of URLs for source files', (3, 'build')], 'easyblock': ['PerlModule', 'EasyBlock to use for building; if set to None, an easyblock is selected based on the software name', (3, 'build')], 'whatis': [None, 'List of brief (one line) package description entries', (8, 'modules')], 'software_license': [None, 'Software license', (0, 'mandatory')], 'options': [{'modulename': 'Bio::Tools::PSort'}, 'Dictionary with extension options.', (1, 'easyblock-specific')], 'configopts': ['', 'Extra options passed to configure (default already has --prefix)', (3, 'build')], 'software_license_urls': [None, 'List of software license locations', (0, 'mandatory')]} | |
| == 2016-08-26 16:16:14,486 templates.py:175 DEBUG version found in easyconfig is 3.0.4 | |
| == 2016-08-26 16:16:14,486 templates.py:212 DEBUG name: github_account, config: None | |
| == 2016-08-26 16:16:14,486 templates.py:212 DEBUG name: name, config: PSORTb | |
| == 2016-08-26 16:16:14,486 templates.py:212 DEBUG name: version, config: 3.0.4 | |
| == 2016-08-26 16:16:14,487 templates.py:212 DEBUG name: versionsuffix, config: -Perl-%(perlver)s | |
| == 2016-08-26 16:16:14,487 templates.py:212 DEBUG name: versionprefix, config: | |
| == 2016-08-26 16:16:14,488 templates.py:151 DEBUG config: {'preinstallopts': ['', 'Extra prefix options for installation.', (3, 'build')], 'postinstallcmds': [['cp -r psort/* %(installdir)s/.'], 'Commands to run after the install step.', (3, 'build')], 'moduleloadnoconflict': [False, "Don't check for conflicts, unload other versions instead ", (8, 'modules')], 'skip': [False, 'Skip existing software', (3, 'build')], 'cleanupoldbuild': [True, 'Boolean to remove (True) or backup (False) the previous build directory with identical name or not.', (4, 'file-management')], 'installopts': ['', 'Extra options for installation', (3, 'build')], 'sources': [['bio-tools-psort-all.%(version)s.tar.gz'], 'List of source files', (3, 'build')], 'versionsuffix': ['-Perl-%(perlver)s', 'Additional suffix for software version (placed after toolchain name)', (3, 'build')], 'license_server': [None, 'License server for software', (6, 'license')], 'modaltsoftname': [None, 'Module name to use (rather than using software name', (8, 'modules')], 'keeppreviousinstall': [False, 'Boolean to keep the previous installation with identical name. Experts only!', (4, 'file-management')], 'hiddendependencies': [[], 'List of dependencies available as hidden modules', (5, 'dependencies')], 'checksums': [[], 'Checksums for sources and patches', (3, 'build')], 'keepsymlinks': [False, 'Boolean to determine whether symlinks are to be kept during copying or if the content of the files pointed to should be copied', (4, 'file-management')], 'cleanupoldinstall': [True, 'Boolean to remove (True) or backup (False) the previous install directory with identical name or not.', (4, 'file-management')], 'builddependencies': [[], 'List of build dependencies', (5, 'dependencies')], 'dontcreateinstalldir': [False, 'Boolean to create (False) or not create (True) the install directory', (4, 'file-management')], 'modextravars': [{}, 'Extra environment variables to be added to module file', (8, 'modules')], 'unpack_options': ['', 'Extra options for unpacking source', (3, 'build')], 'group': [None, 'Name of the user group for which the software should be available', (6, 'license')], 'versionprefix': ['', 'Additional prefix for software version (placed before version and toolchain name)', (3, 'build')], 'parsed': [True, 'This is a parsed easyconfig', 'HIDDEN'], 'prebuildopts': ['', 'Extra options pre-passed to build command.', (3, 'build')], 'easybuild_version': [None, 'EasyBuild-version this spec-file was written for', (3, 'build')], 'skipsteps': [[], 'Skip these steps', (3, 'build')], 'start_dir': ['/tmp/vsc40023/easybuild_build/PSORTb/3.0.4/foss-2016a-Perl-5.22.1/bio-tools-psort-all/', 'Path to start the make in. If the path is absolute, use that path. If not, this is added to the guessed path.', (4, 'file-management')], 'version': ['3.0.4', 'Version of software', (0, 'mandatory')], 'exts_filter': [None, 'Extension filter details: template for cmd and input to cmd (templates for name, version and src).', (7, 'extensions')], 'modaliases': [{}, 'Aliases to be defined in module file', (8, 'modules')], 'allow_system_deps': [[], 'Allow listed system dependencies (format: (<name>, <version>))', (5, 'dependencies')], 'osdependencies': [[], 'OS dependencies that should be present on the system', (5, 'dependencies')], 'hidden': [False, "Install module file as 'hidden' by prefixing its version with '.'", (3, 'build')], 'modluafooter': ['', 'Footer to include in generated module file (Lua syntax)', (8, 'modules')], 'homepage': ['http://psort.org/psortb/index.html', 'The homepage of the software', (0, 'mandatory')], 'buildstats': [None, 'A list of dicts with build statistics', (9, 'other')], 'license_file': [None, 'License file for software', (6, 'license')], 'tests': [[], 'List of test-scripts to run after install. A test script should return a non-zero exit status to fail', (3, 'build')], 'buildopts': ['', 'Extra options passed to make step (default already has -j X)', (3, 'build')], 'description': ['PSORTb v3.0.4 is the most precise bacterial localization prediction tool available.', 'A short description of the software', (0, 'mandatory')], 'modextrapaths': [{}, 'Extra paths to be prepended in module file', (8, 'modules')], 'exts_list': [[], 'List with extensions added to the base installation', (7, 'extensions')], 'docurls': [None, 'List of urls with documentation of the software (not necessarily on homepage)', (0, 'mandatory')], 'stop': [None, 'Keyword to halt the build process after a certain step.', (3, 'build')], 'sanity_check_commands': [[], "format: [(name, options)] e.g. [('gzip','-h')]. Using a non-tuple is equivalent to (name, '-h')", (3, 'build')], 'exts_classmap': [{}, 'Map of extension name to class for handling build and installation.', (7, 'extensions')], 'moduleforceunload': [False, 'Force unload of all modules when loading the extension', (8, 'modules')], 'dependencies': [[{'external_module_metadata': {}, 'full_mod_name': 'Perl/5.22.1-foss-2016a', 'toolchain': {'version': '2016a', 'name': 'foss'}, 'name': 'Perl', 'dummy': False, 'short_mod_name': 'Perl/5.22.1-foss-2016a', 'external_module': False, 'versionsuffix': '', 'version': '5.22.1', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}, {'external_module_metadata': {}, 'full_mod_name': 'libpsortb/1.0-foss-2016a', 'toolchain': {'version': '2016a', 'name': 'foss'}, 'name': 'libpsortb', 'dummy': False, 'short_mod_name': 'libpsortb/1.0-foss-2016a', 'external_module': False, 'versionsuffix': '', 'version': '1.0', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}, {'external_module_metadata': {}, 'full_mod_name': 'BioPerl/1.6.924-foss-2016a-Perl-5.22.1', 'toolchain': {'version': '2016a', 'name': 'foss'}, 'name': 'BioPerl', 'dummy': False, 'short_mod_name': 'BioPerl/1.6.924-foss-2016a-Perl-5.22.1', 'external_module': False, 'versionsuffix': '-Perl-5.22.1', 'version': '1.6.924', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}, {'external_module_metadata': {}, 'full_mod_name': 'BLAST/2.2.26-Linux_x86_64', 'toolchain': {'version': 'dummy', 'name': 'dummy'}, 'name': 'BLAST', 'dummy': True, 'short_mod_name': 'BLAST/2.2.26-Linux_x86_64', 'external_module': False, 'versionsuffix': '-Linux_x86_64', 'version': '2.2.26', 'toolchain_inherited': False, 'hidden': False, 'build_only': False}, {'external_module_metadata': {}, 'full_mod_name': 'pftoolsV3/20160324-foss-2016a', 'toolchain': {'version': '2016a', 'name': 'foss'}, 'name': 'pftoolsV3', 'dummy': False, 'short_mod_name': 'pftoolsV3/20160324-foss-2016a', 'external_module': False, 'versionsuffix': '', 'version': '20160324', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}], 'List of dependencies', (5, 'dependencies')], 'moduleclass': ['bio', 'Module class to be used for this software', (8, 'modules')], 'key': [None, 'Key for installing software', (6, 'license')], 'include_modpath_extensions': [True, 'Include $MODULEPATH extensions specified by module naming scheme.', (8, 'modules')], 'modtclfooter': ['', 'Footer to include in generated module file (Tcl syntax)', (8, 'modules')], 'modloadmsg': [{}, 'Message that should be printed when generated module is loaded', (8, 'modules')], 'parallel': [16, 'Degree of parallelism for e.g. make (default: based on the number of cores, active cpuset and restrictions in ulimit)', (3, 'build')], 'buildininstalldir': [False, 'Boolean to build (True) or not build (False) in the installation directory', (4, 'file-management')], 'patches': [['PSORTb-%(version)s-libpsortb.patch'], 'List of patches to apply', (3, 'build')], 'sanity_check_paths': [{'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Algorithm/HMM.pm', 'lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Bio/Tools/PSort.pm'], 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Algorithm/HMM', 'lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Bio/Tools/PSort']}, "List of files and directories to check (format: {'files':<list>, 'dirs':<list>})", (3, 'build')], 'runtest': ['test', 'Run unit tests.', (1, 'easyblock-specific')], 'onlytcmod': [False, 'Boolean/string to indicate if the toolchain should only load the environment with module (True) or also set all other variables (False) like compiler CC etc (if string: comma separated list of variables that will be ignored).', (2, 'toolchain')], 'github_account': [None, 'GitHub account name to be used to resolve template values in source URLs', (3, 'build')], 'unwanted_env_vars': [{}, "List of environment variables that shouldn't be set during build", (3, 'build')], 'name': ['PSORTb', 'Name of software', (0, 'mandatory')], 'recursive_module_unload': [False, 'Recursive unload of all dependencies when unloading module', (8, 'modules')], 'toolchain': [{'version': '2016a', 'name': 'foss'}, 'Name and version of toolchain', (0, 'mandatory')], 'preconfigopts': ['export PSORTROOT=%(installdir)s && ', 'Extra options pre-passed to configure.', (3, 'build')], 'maxparallel': [None, 'Max degree of parallelism', (3, 'build')], 'license_server_port': [None, 'Port for license server', (6, 'license')], 'exts_defaultclass': [None, 'List of module for and name of the default extension class', (7, 'extensions')], 'toolchainopts': [None, 'Extra options for compilers', (2, 'toolchain')], 'source_urls': [['http://www.psort.org/download/'], 'List of URLs for source files', (3, 'build')], 'easyblock': ['PerlModule', 'EasyBlock to use for building; if set to None, an easyblock is selected based on the software name', (3, 'build')], 'whatis': [None, 'List of brief (one line) package description entries', (8, 'modules')], 'software_license': [None, 'Software license', (0, 'mandatory')], 'options': [{'modulename': 'Bio::Tools::PSort'}, 'Dictionary with extension options.', (1, 'easyblock-specific')], 'configopts': ['', 'Extra options passed to configure (default already has --prefix)', (3, 'build')], 'software_license_urls': [None, 'List of software license locations', (0, 'mandatory')]} | |
| == 2016-08-26 16:16:14,489 templates.py:175 DEBUG version found in easyconfig is 3.0.4 | |
| == 2016-08-26 16:16:14,489 templates.py:212 DEBUG name: github_account, config: None | |
| == 2016-08-26 16:16:14,490 templates.py:212 DEBUG name: name, config: PSORTb | |
| == 2016-08-26 16:16:14,490 templates.py:212 DEBUG name: version, config: 3.0.4 | |
| == 2016-08-26 16:16:14,490 templates.py:212 DEBUG name: versionsuffix, config: -Perl-%(perlver)s | |
| == 2016-08-26 16:16:14,490 templates.py:212 DEBUG name: versionprefix, config: | |
| == 2016-08-26 16:16:14,491 easyblock.py:2139 INFO Running method stage_install_step part of step install | |
| == 2016-08-26 16:16:14,491 easyblock.py:2139 INFO Running method make_installdir part of step install | |
| == 2016-08-26 16:16:14,491 easyblock.py:793 DEBUG Creating the installation directory /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/PSORTb/3.0.4-foss-2016a-Perl-5.22.1 (cleanup: True) | |
| == 2016-08-26 16:16:14,492 easyblock.py:804 INFO Found old directory /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/PSORTb/3.0.4-foss-2016a-Perl-5.22.1 | |
| == 2016-08-26 16:16:14,493 filetools.py:1017 INFO Path /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/PSORTb/3.0.4-foss-2016a-Perl-5.22.1 successfully removed. | |
| == 2016-08-26 16:16:14,493 easyblock.py:811 INFO Removed old directory /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/PSORTb/3.0.4-foss-2016a-Perl-5.22.1 | |
| == 2016-08-26 16:16:14,493 filetools.py:916 INFO Creating directory /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/PSORTb/3.0.4-foss-2016a-Perl-5.22.1 (parents: True, set_gid: False, sticky: False) | |
| == 2016-08-26 16:16:14,494 easyblock.py:2139 INFO Running method install_step part of step install | |
| == 2016-08-26 16:16:14,494 run.py:99 DEBUG run_cmd: running cmd export PSORTROOT=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/PSORTb/3.0.4-foss-2016a-Perl-5.22.1 && perl Makefile.PL PREFIX=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/PSORTb/3.0.4-foss-2016a-Perl-5.22.1 (in /tmp/vsc40023/easybuild_build/PSORTb/3.0.4/foss-2016a-Perl-5.22.1/bio-tools-psort-all) | |
| == 2016-08-26 16:16:16,682 run.py:395 DEBUG cmd "export PSORTROOT=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/PSORTb/3.0.4-foss-2016a-Perl-5.22.1 && perl Makefile.PL PREFIX=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/PSORTb/3.0.4-foss-2016a-Perl-5.22.1 " exited with exitcode 0 and output: | |
| External Module XML::RPC, XML Based RPC client, is not installed on this computer. | |
| The XML::RPC in PSortb needs it for making calls to remote PSortb servers, if you don't plan to do this, ignore this warning | |
| We think we've found blastall, please enter the path if this isn't correct [/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/BLAST/2.2.26-Linux_x86_64/bin/] /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/BLAST/2.2.26-Linux_x86_64/bin/ | |
| We think we've found pfscan, please enter the path if this isn't correct [/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/pftoolsV3/20160324-foss-2016a/bin/] /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/pftoolsV3/20160324-foss-2016a/bin/ | |
| Where do you plan to install the psort configuration files? [/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/PSORTb/3.0.4-foss-2016a-Perl-5.22.1] /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/PSORTb/3.0.4-foss-2016a-Perl-5.22.1 | |
| Checking if your kit is complete... | |
| Looks good | |
| Warning (mostly harmless): No library found for -lhmmer | |
| hmmer was not found in the dynamic linker path, is there somewhere else we should check? [/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/libpsortb/1.0-foss-2016a/lib64] /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/libpsortb/1.0-foss-2016a/lib64 | |
| We found hmmer in /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/libpsortb/1.0-foss-2016a/lib64, that's the good news. | |
| The bad news is hmmer is likely not in your dynamic linker path, you must do one of two things: | |
| - have your system administrator add /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/libpsortb/1.0-foss-2016a/lib64 to '/etc/ld.so.conf' (RECOMMENDED!) | |
| - add /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/libpsortb/1.0-foss-2016a/lib64 to the 'LD_LIBRARY_PATH' environment variable before each execution | |
| Please consult your system administrator or email us for further assistance. | |
| Do you want to continue anyways? [Y/n] [Y] Y | |
| Warning (mostly harmless): No library found for -lsquid | |
| squid was not found in the dynamic linker path, is there somewhere else we should check? [/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/libpsortb/1.0-foss-2016a/lib64] /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/libpsortb/1.0-foss-2016a/lib64 | |
| We found squid in /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/libpsortb/1.0-foss-2016a/lib64, that's the good news. | |
| The bad news is squid is likely not in your dynamic linker path, you must do one of two things: | |
| - have your system administrator add /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/libpsortb/1.0-foss-2016a/lib64 to '/etc/ld.so.conf' (RECOMMENDED!) | |
| - add /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/libpsortb/1.0-foss-2016a/lib64 to the 'LD_LIBRARY_PATH' environment variable before each execution | |
| Please consult your system administrator or email us for further assistance. | |
| Do you want to continue anyways? [Y/n] [Y] Y | |
| Checking if your kit is complete... | |
| Looks good | |
| Generating a Unix-style Makefile | |
| Writing Makefile for Algorithm::HMM | |
| Writing MYMETA.yml and MYMETA.json | |
| Warning (mostly harmless): No library found for -lsvmloc | |
| svmloc was not found in the dynamic linker path, is there somewhere else we should check? [/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/libpsortb/1.0-foss-2016a/lib64] /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/libpsortb/1.0-foss-2016a/lib64 | |
| We found svmloc in /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/libpsortb/1.0-foss-2016a/lib64, that's the good news. | |
| The bad news is svmloc is likely not in your dynamic linker path, you must do one of two things: | |
| - have your system administrator add /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/libpsortb/1.0-foss-2016a/lib64 to '/etc/ld.so.conf' (RECOMMENDED!) | |
| - add /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/libpsortb/1.0-foss-2016a/lib64 to the 'LD_LIBRARY_PATH' environment variable before each execution | |
| Please consult your system administrator or email us for further assistance. | |
| Do you want to continue anyways? [Y/n] [Y] Y | |
| Checking if your kit is complete... | |
| Looks good | |
| Generating a Unix-style Makefile | |
| Writing Makefile for Bio::Tools::PSort::SVMLoc | |
| Writing MYMETA.yml and MYMETA.json | |
| Warning (mostly harmless): No library found for -lmodhmm | |
| modhmm was not found in the dynamic linker path, is there somewhere else we should check? [/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/libpsortb/1.0-foss-2016a/lib64] /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/libpsortb/1.0-foss-2016a/lib64 | |
| We found modhmm in /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/libpsortb/1.0-foss-2016a/lib64, that's the good news. | |
| The bad news is modhmm is likely not in your dynamic linker path, you must do one of two things: | |
| - have your system administrator add /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/libpsortb/1.0-foss-2016a/lib64 to '/etc/ld.so.conf' (RECOMMENDED!) | |
| - add /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/libpsortb/1.0-foss-2016a/lib64 to the 'LD_LIBRARY_PATH' environment variable before each execution | |
| Please consult your system administrator or email us for further assistance. | |
| Do you want to continue anyways? [Y/n] [Y] Y | |
| Generating a Unix-style Makefile | |
| Writing Makefile for Bio::Tools::PSort::ModHMM | |
| Writing MYMETA.yml and MYMETA.json | |
| Generating a Unix-style Makefile | |
| Writing Makefile for Bio::Tools::PSort | |
| Writing MYMETA.yml and MYMETA.json | |
| Warning, /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/PSORTb/3.0.4-foss-2016a-Perl-5.22.1 exists, are you reinstalling or upgrading Psortb? | |
| That's ok, we're just pointing it out. | |
| Updating psort/bin/psort with path hints | |
| Making sclblast databases | |
| Ready for make, next steps you must run: | |
| $ make | |
| $ make test | |
| $ make install | |
| RECOMMENDED: | |
| cp -r psort /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/PSORTb/3.0.4-foss-2016a-Perl-5.22.1 | |
| PSortb will then be available at /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/PSORTb/3.0.4-foss-2016a-Perl-5.22.1/bin/psort or in your path depending on your configuration | |
| == 2016-08-26 16:16:16,683 run.py:439 DEBUG Using default regular expression: (?<![(,-]|\w)(?:error|segmentation fault|failed)(?![(,-]|\.?\w) | |
| == 2016-08-26 16:16:16,684 run.py:99 DEBUG run_cmd: running cmd make -j 16 (in /tmp/vsc40023/easybuild_build/PSORTb/3.0.4/foss-2016a-Perl-5.22.1/bio-tools-psort-all) | |
| == 2016-08-26 16:16:20,591 run.py:395 DEBUG cmd " make -j 16 " exited with exitcode 2 and output: | |
| make[1]: Entering directory `/tmp/vsc40023/easybuild_build/PSORTb/3.0.4/foss-2016a-Perl-5.22.1/bio-tools-psort-all/algorithm-hmm' | |
| "/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/Perl/5.22.1-foss-2016a/bin/perl" "/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/Perl/5.22.1-foss-2016a/lib/perl5/5.22.1/ExtUtils/xsubpp" -C++ -typemap "/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/Perl/5.22.1-foss-2016a/lib/perl5/5.22.1/ExtUtils/typemap" -typemap "typemap" HMM.xs > HMM.xsc && mv HMM.xsc HMM.c | |
| cp lib/Bio/Tools/PSort/Profile.pm blib/lib/Bio/Tools/PSort/Profile.pm | |
| cp lib/Bio/Tools/PSort/Report/Formatter/long.pm blib/lib/Bio/Tools/PSort/Report/Formatter/long.pm | |
| cp lib/Bio/Tools/PSort/Module/OutputI.pm blib/lib/Bio/Tools/PSort/Module/OutputI.pm | |
| cp lib/Bio/Tools/PSort/Module/ModHMM.pm blib/lib/Bio/Tools/PSort/Module/ModHMM.pm | |
| cp lib/Bio/Tools/PSort/Module/Null.pm blib/lib/Bio/Tools/PSort/Module/Null.pm | |
| cp lib/Bio/Tools/PSort/Module/AnalysisI.pm blib/lib/Bio/Tools/PSort/Module/AnalysisI.pm | |
| cp lib/Bio/Tools/Motif.pm blib/lib/Bio/Tools/Motif.pm | |
| cp lib/Bio/Tools/PSort/Profile/Match.pm blib/lib/Bio/Tools/PSort/Profile/Match.pm | |
| cp lib/Bio/Tools/PSort/Module/HMMTOP.pm blib/lib/Bio/Tools/PSort/Module/HMMTOP.pm | |
| cp lib/Bio/Tools/PSort/Module/SCLBlast.pm blib/lib/Bio/Tools/PSort/Module/SCLBlast.pm | |
| cp lib/Bio/Tools/PSort/Report/Result.pm blib/lib/Bio/Tools/PSort/Report/Result.pm | |
| cp lib/Bio/Tools/PSort/Module/Rules.pm blib/lib/Bio/Tools/PSort/Module/Rules.pm | |
| cp lib/Bio/Tools/PSort/Report.pm blib/lib/Bio/Tools/PSort/Report.pm | |
| cp lib/Bio/Tools/Motif/Match.pm blib/lib/Bio/Tools/Motif/Match.pm | |
| cp lib/Bio/Tools/PSort/Report/Formatter.pm blib/lib/Bio/Tools/PSort/Report/Formatter.pm | |
| cp lib/Bio/Tools/PSort/ModuleI.pm blib/lib/Bio/Tools/PSort/ModuleI.pm | |
| cp lib/Bio/Tools/PSort/Constants.pm blib/lib/Bio/Tools/PSort/Constants.pm | |
| cp lib/Bio/Tools/PSort/Module/InputI.pm blib/lib/Bio/Tools/PSort/Module/InputI.pm | |
| cp lib/Bio/Tools/PSort/Module/Bayesian.pm blib/lib/Bio/Tools/PSort/Module/Bayesian.pm | |
| cp lib/Bio/Tools/PSort/Install.pm.orig blib/lib/Bio/Tools/PSort/Install.pm.orig | |
| cp lib/Bio/Tools/PSort/Install.pm blib/lib/Bio/Tools/PSort/Install.pm | |
| cp lib/Bio/Tools/PSort/Report/Formatter/html.pm blib/lib/Bio/Tools/PSort/Report/Formatter/html.pm | |
| cp lib/Bio/Tools/PSort/Module/Motif.pm blib/lib/Bio/Tools/PSort/Module/Motif.pm | |
| cp lib/Bio/Tools/PSort/Module/SVMLocApache.pm blib/lib/Bio/Tools/PSort/Module/SVMLocApache.pm | |
| cp lib/Bio/Tools/PSort/Module/Signal.pm blib/lib/Bio/Tools/PSort/Module/Signal.pm | |
| cp lib/Bio/Tools/PSort/Module/OMPMotif.pm blib/lib/Bio/Tools/PSort/Module/OMPMotif.pm | |
| cp lib/Bio/Tools/PSort/Report/Formatter/normal.pm blib/lib/Bio/Tools/PSort/Report/Formatter/normal.pm | |
| cp lib/Bio/Tools/PSort/Module/SVMLoc.pm blib/lib/Bio/Tools/PSort/Module/SVMLoc.pm | |
| cp lib/Bio/Tools/PSort/Pathway.pm blib/lib/Bio/Tools/PSort/Pathway.pm | |
| cp lib/Bio/Tools/PSort/Report/Formatter/terse.pm blib/lib/Bio/Tools/PSort/Report/Formatter/terse.pm | |
| cp lib/Bio/Tools/PSort.pm blib/lib/Bio/Tools/PSort.pm | |
| cp lib/Bio/Tools/PSort/Module/Profile.pm blib/lib/Bio/Tools/PSort/Module/Profile.pm | |
| cp lib/Bio/Tools/Motif/Pattern.pm blib/lib/Bio/Tools/Motif/Pattern.pm | |
| g++ -c -Isrc/include -D_REENTRANT -D_GNU_SOURCE -fPIC -O2 -march=native -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2 -O2 -DVERSION=\"0.02\" -DXS_VERSION=\"0.02\" -fPIC "-I/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/Perl/5.22.1-foss-2016a/lib/perl5/5.22.1/x86_64-linux-thread-multi/CORE" hmm-binding.cpp | |
| Running Mkbootstrap for Algorithm::HMM () | |
| cp lib/Algorithm/HMM/Hit/Global.pm ../blib/lib/Algorithm/HMM/Hit/Global.pm | |
| cp lib/Algorithm/HMM/Report.pm ../blib/lib/Algorithm/HMM/Report.pm | |
| cp lib/Algorithm/HMM/Hit/Domain.pm ../blib/lib/Algorithm/HMM/Hit/Domain.pm | |
| cp lib/Algorithm/HMM/Hit.pm ../blib/lib/Algorithm/HMM/Hit.pm | |
| cp lib/Algorithm/HMM.pm ../blib/lib/Algorithm/HMM.pm | |
| AutoSplitting ../blib/lib/Algorithm/HMM.pm (../blib/lib/auto/Algorithm/HMM) | |
| chmod 644 "HMM.bs" | |
| cp lib/Bio/Tools/Run/SCLBlast.pm blib/lib/Bio/Tools/Run/SCLBlast.pm | |
| cp lib/Bio/Tools/Signal/Report.pm blib/lib/Bio/Tools/Signal/Report.pm | |
| cp lib/Bio/Tools/Run/SCLBlastLocal.pm blib/lib/Bio/Tools/Run/SCLBlastLocal.pm | |
| cp lib/Bio/Tools/Run/SCLBlast/Hit.pm blib/lib/Bio/Tools/Run/SCLBlast/Hit.pm | |
| cp lib/Bio/Tools/Run/HMMTOP.pm blib/lib/Bio/Tools/Run/HMMTOP.pm | |
| cp lib/Bio/Tools/Run/SCLBlast/Report.pm blib/lib/Bio/Tools/Run/SCLBlast/Report.pm | |
| cp lib/Bio/Tools/Signal.pm blib/lib/Bio/Tools/Signal.pm | |
| cp lib/Bio/Tools/SVMLoc.pm blib/lib/Bio/Tools/SVMLoc.pm | |
| cp lib/Bio/Tools/Run/HMMTOP/Report.pm blib/lib/Bio/Tools/Run/HMMTOP/Report.pm | |
| cp lib/Bio/Tools/Run/HMMTOP/Helix.pm blib/lib/Bio/Tools/Run/HMMTOP/Helix.pm | |
| cp lib/Bio/Tools/PSort/XMLRPC/Client.pm blib/lib/Bio/Tools/PSort/XMLRPC/Client.pm | |
| Please specify prototyping behavior for HMM.xs (see perlxs manual) | |
| g++ -c -Isrc/include -D_REENTRANT -D_GNU_SOURCE -fPIC -O2 -march=native -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2 -O2 -DVERSION=\"0.02\" -DXS_VERSION=\"0.02\" -fPIC "-I/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/Perl/5.22.1-foss-2016a/lib/perl5/5.22.1/x86_64-linux-thread-multi/CORE" HMM.c | |
| hmm-binding.cpp: In member function ‘int HMM::load(char*)’: | |
| hmm-binding.cpp:74:46: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] | |
| if((hmmfp = HMMFileOpen(filename, "HMMERDB")) == NULL) return -1; | |
| ^ | |
| hmm-binding.cpp: In member function ‘HMMReport* HMM::search(char*)’: | |
| hmm-binding.cpp:137:15: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] | |
| FALSE); | |
| ^ | |
| rm -f ../blib/arch/auto/Algorithm/HMM/HMM.so | |
| LD_RUN_PATH="/usr/lib:/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/libpsortb/1.0-foss-2016a/lib64" g++ -shared -O2 -L/usr/local/lib -fstack-protector-strong HMM.o hmm-binding.o -o ../blib/arch/auto/Algorithm/HMM/HMM.so \ | |
| -lm -lpthread -lstdc++ -L/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/libpsortb/1.0-foss-2016a/lib64 -lhmmer -lsquid \ | |
| chmod 755 ../blib/arch/auto/Algorithm/HMM/HMM.so | |
| "/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/Perl/5.22.1-foss-2016a/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- HMM.bs ../blib/arch/auto/Algorithm/HMM/HMM.bs 644 | |
| Manifying 5 pod documents | |
| make[1]: Leaving directory `/tmp/vsc40023/easybuild_build/PSORTb/3.0.4/foss-2016a-Perl-5.22.1/bio-tools-psort-all/algorithm-hmm' | |
| make[1]: Entering directory `/tmp/vsc40023/easybuild_build/PSORTb/3.0.4/foss-2016a-Perl-5.22.1/bio-tools-psort-all/bio-tools-psort-svmloc' | |
| "/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/Perl/5.22.1-foss-2016a/bin/perl" "/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/Perl/5.22.1-foss-2016a/lib/perl5/5.22.1/ExtUtils/xsubpp" -C++ -typemap "/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/Perl/5.22.1-foss-2016a/lib/perl5/5.22.1/ExtUtils/typemap" -typemap "typemap" SVMLoc.xs > SVMLoc.xsc && mv SVMLoc.xsc SVMLoc.c | |
| Running Mkbootstrap for Bio::Tools::PSort::SVMLoc () | |
| cp lib/Bio/Tools/PSort/SVMLoc/DataSet.pm ../blib/lib/Bio/Tools/PSort/SVMLoc/DataSet.pm | |
| cp lib/Bio/Tools/PSort/SVMLoc.pm ../blib/lib/Bio/Tools/PSort/SVMLoc.pm | |
| AutoSplitting ../blib/lib/Bio/Tools/PSort/SVMLoc.pm (../blib/lib/auto/Bio/Tools/PSort/SVMLoc) | |
| chmod 644 "SVMLoc.bs" | |
| Please specify prototyping behavior for SVMLoc.xs (see perlxs manual) | |
| g++ -c -D_REENTRANT -D_GNU_SOURCE -fPIC -O2 -march=native -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2 -O2 -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\" -fPIC "-I/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/Perl/5.22.1-foss-2016a/lib/perl5/5.22.1/x86_64-linux-thread-multi/CORE" SVMLoc.c | |
| rm -f ../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.so | |
| LD_RUN_PATH="/usr/lib:/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/libpsortb/1.0-foss-2016a/lib64" g++ -shared -O2 -L/usr/local/lib -fstack-protector-strong SVMLoc.o -o ../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.so \ | |
| -lm -lstdc++ -L/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/libpsortb/1.0-foss-2016a/lib64 -lsvmloc \ | |
| chmod 755 ../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.so | |
| "/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/Perl/5.22.1-foss-2016a/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- SVMLoc.bs ../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.bs 644 | |
| Manifying 2 pod documents | |
| make[1]: Leaving directory `/tmp/vsc40023/easybuild_build/PSORTb/3.0.4/foss-2016a-Perl-5.22.1/bio-tools-psort-all/bio-tools-psort-svmloc' | |
| make[1]: Entering directory `/tmp/vsc40023/easybuild_build/PSORTb/3.0.4/foss-2016a-Perl-5.22.1/bio-tools-psort-all/bio-tools-psort-modhmm' | |
| "/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/Perl/5.22.1-foss-2016a/bin/perl" "/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/Perl/5.22.1-foss-2016a/lib/perl5/5.22.1/ExtUtils/xsubpp" -typemap "/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/Perl/5.22.1-foss-2016a/lib/perl5/5.22.1/ExtUtils/typemap" -typemap "typemap" modhmm.xs > modhmm.xsc && mv modhmm.xsc modhmm.c | |
| cc -c -D_REENTRANT -D_GNU_SOURCE -fPIC -O2 -march=native -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2 -O2 -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\" -fPIC "-I/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/Perl/5.22.1-foss-2016a/lib/perl5/5.22.1/x86_64-linux-thread-multi/CORE" binding.c | |
| cc1: error: unrecognized command line option "-fstack-protector-strong" | |
| make[1]: *** [binding.o] Error 1 | |
| make[1]: *** Waiting for unfinished jobs.... | |
| cp lib/Bio/Tools/PSort/ModHMM.pm ../blib/lib/Bio/Tools/PSort/ModHMM.pm | |
| AutoSplitting ../blib/lib/Bio/Tools/PSort/ModHMM.pm (../blib/lib/auto/Bio/Tools/PSort/ModHMM) | |
| make[1]: Leaving directory `/tmp/vsc40023/easybuild_build/PSORTb/3.0.4/foss-2016a-Perl-5.22.1/bio-tools-psort-all/bio-tools-psort-modhmm' | |
| make: *** [subdirs] Error 2 | |
| == 2016-08-26 16:16:21,074 build_log.py:152 ERROR cmd " make -j 16 " exited with exitcode 2 and output: | |
| make[1]: Entering directory `/tmp/vsc40023/easybuild_build/PSORTb/3.0.4/foss-2016a-Perl-5.22.1/bio-tools-psort-all/algorithm-hmm' | |
| "/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/Perl/5.22.1-foss-2016a/bin/perl" "/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/Perl/5.22.1-foss-2016a/lib/perl5/5.22.1/ExtUtils/xsubpp" -C++ -typemap "/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/Perl/5.22.1-foss-2016a/lib/perl5/5.22.1/ExtUtils/typemap" -typemap "typemap" HMM.xs > HMM.xsc && mv HMM.xsc HMM.c | |
| cp lib/Bio/Tools/PSort/Profile.pm blib/lib/Bio/Tools/PSort/Profile.pm | |
| cp lib/Bio/Tools/PSort/Report/Formatter/long.pm blib/lib/Bio/Tools/PSort/Report/Formatter/long.pm | |
| cp lib/Bio/Tools/PSort/Module/OutputI.pm blib/lib/Bio/Tools/PSort/Module/OutputI.pm | |
| cp lib/Bio/Tools/PSort/Module/ModHMM.pm blib/lib/Bio/Tools/PSort/Module/ModHMM.pm | |
| cp lib/Bio/Tools/PSort/Module/Null.pm blib/lib/Bio/Tools/PSort/Module/Null.pm | |
| cp lib/Bio/Tools/PSort/Module/AnalysisI.pm blib/lib/Bio/Tools/PSort/Module/AnalysisI.pm | |
| cp lib/Bio/Tools/Motif.pm blib/lib/Bio/Tools/Motif.pm | |
| cp lib/Bio/Tools/PSort/Profile/Match.pm blib/lib/Bio/Tools/PSort/Profile/Match.pm | |
| cp lib/Bio/Tools/PSort/Module/HMMTOP.pm blib/lib/Bio/Tools/PSort/Module/HMMTOP.pm | |
| cp lib/Bio/Tools/PSort/Module/SCLBlast.pm blib/lib/Bio/Tools/PSort/Module/SCLBlast.pm | |
| cp lib/Bio/Tools/PSort/Report/Result.pm blib/lib/Bio/Tools/PSort/Report/Result.pm | |
| cp lib/Bio/Tools/PSort/Module/Rules.pm blib/lib/Bio/Tools/PSort/Module/Rules.pm | |
| cp lib/Bio/Tools/PSort/Report.pm blib/lib/Bio/Tools/PSort/Report.pm | |
| cp lib/Bio/Tools/Motif/Match.pm blib/lib/Bio/Tools/Motif/Match.pm | |
| cp lib/Bio/Tools/PSort/Report/Formatter.pm blib/lib/Bio/Tools/PSort/Report/Formatter.pm | |
| cp lib/Bio/Tools/PSort/ModuleI.pm blib/lib/Bio/Tools/PSort/ModuleI.pm | |
| cp lib/Bio/Tools/PSort/Constants.pm blib/lib/Bio/Tools/PSort/Constants.pm | |
| cp lib/Bio/Tools/PSort/Module/InputI.pm blib/lib/Bio/Tools/PSort/Module/InputI.pm | |
| cp lib/Bio/Tools/PSort/Module/Bayesian.pm blib/lib/Bio/Tools/PSort/Module/Bayesian.pm | |
| cp lib/Bio/Tools/PSort/Install.pm.orig blib/lib/Bio/Tools/PSort/Install.pm.orig | |
| cp lib/Bio/Tools/PSort/Install.pm blib/lib/Bio/Tools/PSort/Install.pm | |
| cp lib/Bio/Tools/PSort/Report/Formatter/html.pm blib/lib/Bio/Tools/PSort/Report/Formatter/html.pm | |
| cp lib/Bio/Tools/PSort/Module/Motif.pm blib/lib/Bio/Tools/PSort/Module/Motif.pm | |
| cp lib/Bio/Tools/PSort/Module/SVMLocApache.pm blib/lib/Bio/Tools/PSort/Module/SVMLocApache.pm | |
| cp lib/Bio/Tools/PSort/Module/Signal.pm blib/lib/Bio/Tools/PSort/Module/Signal.pm | |
| cp lib/Bio/Tools/PSort/Module/OMPMotif.pm blib/lib/Bio/Tools/PSort/Module/OMPMotif.pm | |
| cp lib/Bio/Tools/PSort/Report/Formatter/normal.pm blib/lib/Bio/Tools/PSort/Report/Formatter/normal.pm | |
| cp lib/Bio/Tools/PSort/Module/SVMLoc.pm blib/lib/Bio/Tools/PSort/Module/SVMLoc.pm | |
| cp lib/Bio/Tools/PSort/Pathway.pm blib/lib/Bio/Tools/PSort/Pathway.pm | |
| cp lib/Bio/Tools/PSort/Report/Formatter/terse.pm blib/lib/Bio/Tools/PSort/Report/Formatter/terse.pm | |
| cp lib/Bio/Tools/PSort.pm blib/lib/Bio/Tools/PSort.pm | |
| cp lib/Bio/Tools/PSort/Module/Profile.pm blib/lib/Bio/Tools/PSort/Module/Profile.pm | |
| cp lib/Bio/Tools/Motif/Pattern.pm blib/lib/Bio/Tools/Motif/Pattern.pm | |
| g++ -c -Isrc/include -D_REENTRANT -D_GNU_SOURCE -fPIC -O2 -march=native -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2 -O2 -DVERSION=\"0.02\" -DXS_VERSION=\"0.02\" -fPIC "-I/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/Perl/5.22.1-foss-2016a/lib/perl5/5.22.1/x86_64-linux-thread-multi/CORE" hmm-binding.cpp | |
| Running Mkbootstrap for Algorithm::HMM () | |
| cp lib/Algorithm/HMM/Hit/Global.pm ../blib/lib/Algorithm/HMM/Hit/Global.pm | |
| cp lib/Algorithm/HMM/Report.pm ../blib/lib/Algorithm/HMM/Report.pm | |
| cp lib/Algorithm/HMM/Hit/Domain.pm ../blib/lib/Algorithm/HMM/Hit/Domain.pm | |
| cp lib/Algorithm/HMM/Hit.pm ../blib/lib/Algorithm/HMM/Hit.pm | |
| cp lib/Algorithm/HMM.pm ../blib/lib/Algorithm/HMM.pm | |
| AutoSplitting ../blib/lib/Algorithm/HMM.pm (../blib/lib/auto/Algorithm/HMM) | |
| chmod 644 "HMM.bs" | |
| cp lib/Bio/Tools/Run/SCLBlast.pm blib/lib/Bio/Tools/Run/SCLBlast.pm | |
| cp lib/Bio/Tools/Signal/Report.pm blib/lib/Bio/Tools/Signal/Report.pm | |
| cp lib/Bio/Tools/Run/SCLBlastLocal.pm blib/lib/Bio/Tools/Run/SCLBlastLocal.pm | |
| cp lib/Bio/Tools/Run/SCLBlast/Hit.pm blib/lib/Bio/Tools/Run/SCLBlast/Hit.pm | |
| cp lib/Bio/Tools/Run/HMMTOP.pm blib/lib/Bio/Tools/Run/HMMTOP.pm | |
| cp lib/Bio/Tools/Run/SCLBlast/Report.pm blib/lib/Bio/Tools/Run/SCLBlast/Report.pm | |
| cp lib/Bio/Tools/Signal.pm blib/lib/Bio/Tools/Signal.pm | |
| cp lib/Bio/Tools/SVMLoc.pm blib/lib/Bio/Tools/SVMLoc.pm | |
| cp lib/Bio/Tools/Run/HMMTOP/Report.pm blib/lib/Bio/Tools/Run/HMMTOP/Report.pm | |
| cp lib/Bio/Tools/Run/HMMTOP/Helix.pm blib/lib/Bio/Tools/Run/HMMTOP/Helix.pm | |
| cp lib/Bio/Tools/PSort/XMLRPC/Client.pm blib/lib/Bio/Tools/PSort/XMLRPC/Client.pm | |
| Please specify prototyping behavior for HMM.xs (see perlxs manual) | |
| g++ -c -Isrc/include -D_REENTRANT -D_GNU_SOURCE -fPIC -O2 -march=native -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2 -O2 -DVERSION=\"0.02\" -DXS_VERSION=\"0.02\" -fPIC "-I/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/Perl/5.22.1-foss-2016a/lib/perl5/5.22.1/x86_64-linux-thread-multi/CORE" HMM.c | |
| hmm-binding.cpp: In member function ‘int HMM::load(char*)’: | |
| hmm-binding.cpp:74:46: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] | |
| if((hmmfp = HMMFileOpen(filename, "HMMERDB")) == NULL) return -1; | |
| ^ | |
| hmm-binding.cpp: In member function ‘HMMReport* HMM::search(char*)’: | |
| hmm-binding.cpp:137:15: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] | |
| FALSE); | |
| ^ | |
| rm -f ../blib/arch/auto/Algorithm/HMM/HMM.so | |
| LD_RUN_PATH="/usr/lib:/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/libpsortb/1.0-foss-2016a/lib64" g++ -shared -O2 -L/usr/local/lib -fstack-protector-strong HMM.o hmm-binding.o -o ../blib/arch/auto/Algorithm/HMM/HMM.so \ | |
| -lm -lpthread -lstdc++ -L/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/libpsortb/1.0-foss-2016a/lib64 -lhmmer -lsquid \ | |
| chmod 755 ../blib/arch/auto/Algorithm/HMM/HMM.so | |
| "/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/Perl/5.22.1-foss-2016a/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- HMM.bs ../blib/arch/auto/Algorithm/HMM/HMM.bs 644 | |
| Manifying 5 pod documents | |
| make[1]: Leaving directory `/tmp/vsc40023/easybuild_build/PSORTb/3.0.4/foss-2016a-Perl-5.22.1/bio-tools-psort-all/algorithm-hmm' | |
| make[1]: Entering directory `/tmp/vsc40023/easybuild_build/PSORTb/3.0.4/foss-2016a-Perl-5.22.1/bio-tools-psort-all/bio-tools-psort-svmloc' | |
| "/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/Perl/5.22.1-foss-2016a/bin/perl" "/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/Perl/5.22.1-foss-2016a/lib/perl5/5.22.1/ExtUtils/xsubpp" -C++ -typemap "/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/Perl/5.22.1-foss-2016a/lib/perl5/5.22.1/ExtUtils/typemap" -typemap "typemap" SVMLoc.xs > SVMLoc.xsc && mv SVMLoc.xsc SVMLoc.c | |
| Running Mkbootstrap for Bio::Tools::PSort::SVMLoc () | |
| cp lib/Bio/Tools/PSort/SVMLoc/DataSet.pm ../blib/lib/Bio/Tools/PSort/SVMLoc/DataSet.pm | |
| cp lib/Bio/Tools/PSort/SVMLoc.pm ../blib/lib/Bio/Tools/PSort/SVMLoc.pm | |
| AutoSplitting ../blib/lib/Bio/Tools/PSort/SVMLoc.pm (../blib/lib/auto/Bio/Tools/PSort/SVMLoc) | |
| chmod 644 "SVMLoc.bs" | |
| Please specify prototyping behavior for SVMLoc.xs (see perlxs manual) | |
| g++ -c -D_REENTRANT -D_GNU_SOURCE -fPIC -O2 -march=native -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2 -O2 -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\" -fPIC "-I/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/Perl/5.22.1-foss-2016a/lib/perl5/5.22.1/x86_64-linux-thread-multi/CORE" SVMLoc.c | |
| rm -f ../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.so | |
| LD_RUN_PATH="/usr/lib:/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/libpsortb/1.0-foss-2016a/lib64" g++ -shared -O2 -L/usr/local/lib -fstack-protector-strong SVMLoc.o -o ../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.so \ | |
| -lm -lstdc++ -L/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/libpsortb/1.0-foss-2016a/lib64 -lsvmloc \ | |
| chmod 755 ../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.so | |
| "/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/Perl/5.22.1-foss-2016a/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- SVMLoc.bs ../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.bs 644 | |
| Manifying 2 pod documents | |
| make[1]: Leaving directory `/tmp/vsc40023/easybuild_build/PSORTb/3.0.4/foss-2016a-Perl-5.22.1/bio-tools-psort-all/bio-tools-psort-svmloc' | |
| make[1]: Entering directory `/tmp/vsc40023/easybuild_build/PSORTb/3.0.4/foss-2016a-Perl-5.22.1/bio-tools-psort-all/bio-tools-psort-modhmm' | |
| "/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/Perl/5.22.1-foss-2016a/bin/perl" "/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/Perl/5.22.1-foss-2016a/lib/perl5/5.22.1/ExtUtils/xsubpp" -typemap "/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/Perl/5.22.1-foss-2016a/lib/perl5/5.22.1/ExtUtils/typemap" -typemap "typemap" modhmm.xs > modhmm.xsc && mv modhmm.xsc modhmm.c | |
| cc -c -D_REENTRANT -D_GNU_SOURCE -fPIC -O2 -march=native -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2 -O2 -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\" -fPIC "-I/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/SL6/sandybridge/software/Perl/5.22.1-foss-2016a/lib/perl5/5.22.1/x86_64-linux-thread-multi/CORE" binding.c | |
| cc1: error: unrecognized command line option "-fstack-protector-strong" | |
| make[1]: *** [binding.o] Error 1 | |
| make[1]: *** Waiting for unfinished jobs.... | |
| cp lib/Bio/Tools/PSort/ModHMM.pm ../blib/lib/Bio/Tools/PSort/ModHMM.pm | |
| AutoSplitting ../blib/lib/Bio/Tools/PSort/ModHMM.pm (../blib/lib/auto/Bio/Tools/PSort/ModHMM) | |
| make[1]: Leaving directory `/tmp/vsc40023/easybuild_build/PSORTb/3.0.4/foss-2016a-Perl-5.22.1/bio-tools-psort-all/bio-tools-psort-modhmm' | |
| make: *** [subdirs] Error 2 | |
| (at easybuild/tools/run.py:400 in parse_cmd_output) | |
| == 2016-08-26 16:16:21,075 easyblock.py:2368 WARNING build failed (first 300 chars): cmd " make -j 16 " exited with exitcode 2 and output: | |
| make[1]: Entering directory `/tmp/vsc40023/easybuild_build/PSORTb/3.0.4/foss-2016a-Perl-5.22.1/bio-tools-psort-all/algorithm-hmm' | |
| "/user/scratchphanpy/gent/gvo000/gvo00002/vsc40023/easybuild_REGTEST/SL6/sandybridge/software/Perl/5.22.1-foss-2016a | |
| == 2016-08-26 16:16:21,075 easyblock.py:269 INFO Closing log for application name PSORTb version 3.0.4 |
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