Created
August 29, 2016 12:08
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(partial) EasyBuild log for failed build of /tmp/eb-NkMbkS/files_pr3317/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb (PR #3317)
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| renderproto/0.11-intel-2015b | |
| renderproto/0.11-intel-2016a | |
| requests/ | |
| requests/2.6.2-intel-2015a-Python-2.7.9 | |
| rgeos/ | |
| rgeos/0.3-17-intel-2016a-R-3.2.3 | |
| rhdf5/ | |
| rhdf5/2.14.0-intel-2015b-R-3.2.1 | |
| rhdf5/2.16.0-intel-2016a-R-3.2.3 | |
| ROOT/ | |
| ROOT/v5.34.34-intel-2015b-Python-2.7.10 | |
| ROOT/v5.34.34-intel-2016a-Python-2.7.11 | |
| ROOT/v5.34.36-intel-2016a-Python-2.7.11 | |
| Rust/ | |
| Rust/1.8.0-foss-2016a | |
| Sailfish/ | |
| Sailfish/0.7.4-intel-2015b-Python-2.7.10 | |
| Sailfish/0.8.0-intel-2015b-Python-2.7.10 | |
| Salmon/ | |
| Salmon/0.4.2-intel-2015b-Python-2.7.10 | |
| Salmon/0.5.1-intel-2015b-Python-2.7.10 | |
| SAMtools/ | |
| SAMtools/0.1.20-intel-2015b | |
| SAMtools/1.2-intel-2015b-HTSlib-1.2.1 | |
| SAMtools/1.3-foss-2016a | |
| SAMtools/1.3-intel-2016a | |
| SAMtools/1.3.1-intel-2016b | |
| ScaLAPACK/ | |
| ScaLAPACK/2.0.2-gompi-2015a-OpenBLAS-0.2.13-LAPACK-3.5.0 | |
| ScaLAPACK/2.0.2-gompi-2015b-OpenBLAS-0.2.14-LAPACK-3.5.0 | |
| ScaLAPACK/2.0.2-gompi-2016a-OpenBLAS-0.2.15-LAPACK-3.6.0 | |
| ScaLAPACK/2.0.2-gompi-2016b-OpenBLAS-0.2.18-LAPACK-3.6.1 | |
| SCDE/ | |
| SCDE/20151209-intel-2015b-R-3.2.1 | |
| ScientificPython/ | |
| ScientificPython/2.9.4-intel-2015b-Python-2.7.11 | |
| ScientificPython/2.9.4-intel-2016a-Python-2.7.11 | |
| scikit-image/ | |
| scikit-image/0.11.3-intel-2015b-Python-2.7.10 | |
| scikit-image/0.11.3-intel-2015b-Python-3.5.0 | |
| scikit-learn/ | |
| scikit-learn/0.16.1-intel-2015b-Python-2.7.10 | |
| scikit-learn/0.16.1-intel-2015b-Python-3.5.0 | |
| scikit-learn/0.17.1-intel-2016a-Python-2.7.11-freetype-2.6.3 | |
| scikit-learn/0.17.1-intel-2016a-Python-2.7.11 | |
| scikit-learn/0.17.1-intel-2016a-Python-3.5.1 | |
| scipy/ | |
| scipy/0.15.1-intel-2015a-Python-2.7.9 | |
| scipy/0.16.1-intel-2015b-Python-2.7.10 | |
| SCOOP/ | |
| SCOOP/0.6.2-intel-2015b-Python-2.7.10 | |
| SCOOP/0.7.1.1-intel-2016a-Python-3.5.1 | |
| SCOTCH/ | |
| SCOTCH/6.0.4-gimkl-2.11.5 | |
| SCOTCH/6.0.4-intel-2015a | |
| SCOTCH/6.0.4-intel-2015b | |
| SCOTCH/6.0.4-intel-2016a | |
| scp/ | |
| scp/0.10.2-intel-2015b-Python-2.7.10 | |
| scripts/ | |
| scripts/4.0.0 | |
| Seaborn/ | |
| Seaborn/0.6.0-intel-2015b-Python-2.7.10 | |
| setuptools/ | |
| setuptools/1.4.2 | |
| SIP/ | |
| SIP/4.18-intel-2016a-Python-2.7.11 | |
| SLEPc/ | |
| SLEPc/3.6.2-intel-2015b-Python-2.7.11 | |
| slepc4py/ | |
| slepc4py/3.6.0-intel-2015b-Python-2.7.11 | |
| sleuth/ | |
| sleuth/0.28.0-intel-2015b-R-3.2.1 | |
| SNAPE-pooled/ | |
| SNAPE-pooled/r32-foss-2016a | |
| snappy/ | |
| snappy/1.1.2-GCC-4.9.2 | |
| snappy/1.1.3-GCC-4.9.3 | |
| snappy/1.1.3-GCC-4.9.3-2.25 | |
| SNPhylo/ | |
| SNPhylo/20140701-foss-2016a | |
| SNPhylo/20140701-intel-2016a | |
| SOAPdenovo2/ | |
| SOAPdenovo2/r240-intel-2015a | |
| SOAPdenovo2/r240-intel-2015b | |
| Spark/ | |
| Spark/1.3.0 | |
| Spark/1.4.1 | |
| Spark/1.5.0 | |
| Spark/1.6.0 | |
| Spark/1.6.1 | |
| spglib/ | |
| spglib/1.7.4-intel-2015b | |
| Sphinx/ | |
| Sphinx/1.3.3-intel-2015b-Python-2.7.11 | |
| SQLite/ | |
| SQLite/3.8.8.1-intel-2015a | |
| SQLite/3.8.10.2-foss-2015b | |
| SQLite/3.8.10.2-GCC-4.9.3-2.25 | |
| SQLite/3.8.10.2-gimkl-2.11.5 | |
| SQLite/3.8.10.2-intel-2015a | |
| SQLite/3.8.10.2-intel-2015b | |
| SQLite/3.9.2-foss-2016a | |
| SQLite/3.9.2-GCC-4.9.3-2.25 | |
| SQLite/3.9.2-gimkl-2.11.5 | |
| SQLite/3.9.2-intel-2015b | |
| SQLite/3.9.2-intel-2016a | |
| SQLite/3.13.0-intel-2016b | |
| SRA-Toolkit/ | |
| SRA-Toolkit/2.5.4-1-centos_linux64 | |
| STAMP/ | |
| STAMP/1.2-intel-2016a | |
| statsmodels/ | |
| statsmodels/0.6.1-intel-2016a-Python-3.5.1 | |
| STREAM/ | |
| STREAM/5.10-intel-2015a | |
| SuiteSparse/ | |
| SuiteSparse/4.4.6-intel-2015b-ParMETIS-4.0.3 | |
| SuiteSparse/4.5.3-intel-2016a-ParMETIS-4.0.3 | |
| SWIG/ | |
| SWIG/3.0.7-intel-2015b-Python-2.7.10 | |
| SWIG/3.0.8-intel-2015b-Python-2.7.11 | |
| SWIG/3.0.8-intel-2016a-Python-2.7.11 | |
| SWIG/3.0.10-intel-2016b-Python-2.7.12 | |
| sympy/ | |
| sympy/0.7.6-intel-2015a-Python-2.7.10 | |
| sympy/0.7.6.1-intel-2015b-Python-2.7.10 | |
| sympy/0.7.6.1-intel-2015b-Python-2.7.11 | |
| sympy/1.0-intel-2016a-Python-2.7.11 | |
| Szip/ | |
| Szip/2.1-foss-2016a | |
| Szip/2.1-intel-2015a | |
| Szip/2.1-intel-2015b | |
| Szip/2.1-intel-2016a | |
| Szip/2.1-intel-2016b | |
| TAMkin/ | |
| TAMkin/1.0.8-intel-2015b-Python-2.7.10 | |
| TAMkin/1.0.9-intel-2016a-Python-2.7.11 | |
| tbb/ | |
| tbb/4.3.6.211 | |
| Tcl/ | |
| Tcl/8.6.3-intel-2015a | |
| Tcl/8.6.4-foss-2015b | |
| Tcl/8.6.4-foss-2016a | |
| Tcl/8.6.4-GCC-4.9.3-2.25 | |
| Tcl/8.6.4-gimkl-2.11.5 | |
| Tcl/8.6.4-intel-2015a | |
| Tcl/8.6.4-intel-2015b | |
| Tcl/8.6.4-intel-2016a | |
| Tcl/8.6.5-intel-2016b | |
| tcsh/ | |
| tcsh/6.18.01-intel-2015a | |
| tcsh/6.19.00-intel-2016a | |
| testpath/ | |
| testpath/0.3-intel-2016a-Python-2.7.11 | |
| TiCCutils/ | |
| TiCCutils/0.7-intel-2015b | |
| TiMBL/ | |
| TiMBL/6.4.6-intel-2015b | |
| Tk/ | |
| Tk/8.6.4-foss-2015b-no-X11 | |
| Tk/8.6.4-foss-2016a-no-X11 | |
| Tk/8.6.4-GCC-4.9.3-2.25-no-X11 | |
| Tk/8.6.4-gimkl-2.11.5-no-X11 | |
| Tk/8.6.4-intel-2015a-no-X11 | |
| Tk/8.6.4-intel-2015b-no-X11 | |
| Tk/8.6.4-intel-2016a-no-X11 | |
| Tk/8.6.5-intel-2016b | |
| TopHat/ | |
| TopHat/2.1.0-intel-2015b | |
| traits/ | |
| traits/4.5.0-intel-2015b-Python-2.7.10 | |
| Trilinos/ | |
| Trilinos/12.4.2-intel-2015b-Python-2.7.11 | |
| Trinity/ | |
| Trinity/v2.0.2-intel-2015a | |
| Trinity/2.1.1-intel-2015b | |
| TVB/ | |
| TVB/1.4.1-intel-2016a-Python-2.7.11 | |
| TVB/1.5-intel-2016a-Python-2.7.11 | |
| tvb-data/ | |
| tvb-data/1.5-intel-2016a-Python-2.7.11 | |
| tvb-data/20150915-intel-2016a-Python-2.7.11 | |
| TVB-deps/ | |
| TVB-deps/20160618-intel-2016a-Python-2.7.11 | |
| tvb-framework/ | |
| tvb-framework/1.5-intel-2016a-Python-2.7.11 | |
| tvb-framework/20150921-intel-2016a-Python-2.7.11 | |
| tvb-library/ | |
| tvb-library/1.5-intel-2016a-Python-2.7.11 | |
| tvb-library/20150922-intel-2016a-Python-2.7.11 | |
| UDUNITS/ | |
| UDUNITS/2.2.19-intel-2015b | |
| UFL/ | |
| UFL/1.6.0-intel-2015b-Python-2.7.11 | |
| util-linux/ | |
| util-linux/2.26.1-intel-2015a | |
| util-linux/2.26.2-intel-2015a | |
| util-linux/2.27.1-intel-2015b | |
| util-linux/2.27.1-intel-2016a | |
| util-linux/2.28-intel-2016a | |
| VarScan/ | |
| VarScan/2.4.1-Java-1.7.0_80 | |
| VASP/ | |
| VASP/5.3.3-intel-2015a-mt-dftd3-O2 | |
| VASP/5.3.3-intel-2015a-mt-dftd3 | |
| VASP/5.3.3-intel-2015a-vtst-3.0c-20130327-mt-gamma | |
| VASP/5.3.5-intel-2015a-vtst-3.1-20140328-mt-vaspsol2.01-BEEF | |
| VASP/5.3.5-intel-2015b-vtst-3.1-20140328-mt-vaspsol2.01 | |
| VASP/5.3.5-intel-2015b-vtst-169-mt | |
| VASP/5.3.5-intel-2016a-vtst-3.1-20140328-mt | |
| VASP/5.3.5-intel-2016a-vtst-169-mt | |
| VASP/5.4.1-intel-2015b-mt-vaspsol-20150914-NBO-projection-1.1.2 | |
| VASP/5.4.1-intel-2015b-mt-vaspsol-20150914-O2 | |
| VASP/5.4.1-intel-2015b-mt-vaspsol-20150914 | |
| VASP/5.4.1-intel-2016a-mt-vaspsol-20150914-NBO-projection-1.1.2 | |
| VASP/5.4.1.05Feb16-intel-2016b-mt-vaspsol-20150914-patched-03082016 | |
| VASP/5.4.1.05Feb16-intel-2016b-mt-vaspsol-20150914-O2-patched-03082016 | |
| VCFtools/ | |
| VCFtools/0.1.14-foss-2016a-Perl-5.22.1 | |
| VCFtools/0.1.14-intel-2016a-Perl-5.22.1 | |
| Velvet/ | |
| Velvet/1.2.10-intel-2015b-mt-kmer_31-Perl-5.20.3 | |
| Velvet/1.2.10-intel-2015b-mt-kmer_31 | |
| Velvet/1.2.10-intel-2015b-mt-kmer_100-Perl-5.20.3 | |
| Velvet/1.2.10-intel-2015b-mt-kmer_100 | |
| vincent/ | |
| vincent/0.4.4-intel-2015a-Python-2.7.10 | |
| vincent/0.4.4-intel-2015b-Python-2.7.10 | |
| vsc-base/ | |
| vsc-base/1.9.1 | |
| vsc-base/2.1.2 | |
| vsc-base/2.2.5 | |
| vsc-base/2.4.2-intel-2015b-Python-2.7.10 | |
| vsc-base/2.4.2 | |
| vsc-base/2.4.17-intel-2015b-Python-2.7.11 | |
| vsc-base/2.4.17-intel-2016a-Python-2.7.11 | |
| vsc-base/2.5.1-intel-2016a-Python-2.7.11 | |
| vsc-base/2.5.1-intel-2016b-Python-2.7.12 | |
| vsc-base/2.5.1 | |
| vsc-install/ | |
| vsc-install/0.9.18-intel-2015b-Python-2.7.11 | |
| vsc-install/0.9.18-intel-2016a-Python-2.7.11 | |
| vsc-install/0.10.6-intel-2016a-Python-2.7.11 | |
| vsc-install/0.10.11-intel-2016a-Python-2.7.11 | |
| vsc-install/0.10.11-intel-2016b-Python-2.7.12 | |
| vsc-mympirun/ | |
| vsc-mympirun/3.4.2-intel-2015b-Python-2.7.10-vsc-base-2.4.2 | |
| vsc-mympirun/3.4.2-intel-2015b-Python-2.7.11-vsc-base-2.4.17 | |
| vsc-mympirun/3.4.2-intel-2016a-Python-2.7.11-vsc-base-2.4.17 | |
| vsc-mympirun/3.4.2-intel-2016a-Python-2.7.11-vsc-base-2.5.1 | |
| vsc-mympirun/3.4.2-vsc-base-2.2.5 | |
| vsc-mympirun/3.4.2 | |
| vsc-mympirun/3.4.3-intel-2016b-Python-2.7.12 | |
| vsc-mympirun/3.4.3 | |
| vsc-mympirun-scoop/ | |
| vsc-mympirun-scoop/3.3.0-intel-2015b-Python-2.7.10 | |
| vsc-processcontrol/ | |
| vsc-processcontrol/1.0-vsc-base-2.1.2 | |
| VSC-tools/ | |
| VSC-tools/1.7.1 | |
| VTK/ | |
| VTK/6.3.0-intel-2015b-Python-2.7.11 | |
| VTK/6.3.0-intel-2016a-Python-2.7.11 | |
| VTune/ | |
| VTune/2016_update3 | |
| WEKA/ | |
| WEKA/3.7.0-Java-1.7.0_80 | |
| WIEN2k/ | |
| WIEN2k/14.1-intel-2014b | |
| WIEN2k/14.2-intel-2015a | |
| worker/ | |
| worker/1.6.4-intel-2016a | |
| worker/1.6.5-intel-2016a | |
| WRF/ | |
| WRF/3.6.1-intel-2015a-dmpar | |
| x264/ | |
| x264/20150930-intel-2015b | |
| x264/20160114-intel-2016a | |
| x264/20160430-intel-2016a | |
| x264/20160614-intel-2016b | |
| xbitmaps/ | |
| xbitmaps/1.1.1-intel-2015a | |
| xbitmaps/1.1.1-intel-2016a | |
| xcb-proto/ | |
| xcb-proto/1.10-intel-2015a-Python-2.7.9 | |
| xcb-proto/1.11-intel-2015a-Python-2.7.9 | |
| xcb-proto/1.11-intel-2015b-Python-2.7.10 | |
| xcb-proto/1.11-intel-2015b-Python-2.7.11 | |
| xcb-proto/1.11 | |
| xcb-util/ | |
| xcb-util/0.4.0-intel-2015b-Python-2.7.11 | |
| xcb-util/0.4.0-intel-2015b | |
| xcb-util/0.4.0-intel-2016a | |
| xcb-util-image/ | |
| xcb-util-image/0.4.0-intel-2015b-Python-2.7.11 | |
| xcb-util-image/0.4.0-intel-2015b | |
| xcb-util-image/0.4.0-intel-2016a | |
| xcb-util-keysyms/ | |
| xcb-util-keysyms/0.4.0-intel-2015b-Python-2.7.11 | |
| xcb-util-keysyms/0.4.0-intel-2015b | |
| xcb-util-keysyms/0.4.0-intel-2016a | |
| xcb-util-renderutil/ | |
| xcb-util-renderutil/0.3.9-intel-2015b-Python-2.7.11 | |
| xcb-util-renderutil/0.3.9-intel-2015b | |
| xcb-util-renderutil/0.3.9-intel-2016a | |
| xcb-util-wm/ | |
| xcb-util-wm/0.4.1-intel-2015b-Python-2.7.11 | |
| xcb-util-wm/0.4.1-intel-2015b | |
| xcb-util-wm/0.4.1-intel-2016a | |
| xextproto/ | |
| xextproto/7.2.1-intel-2015a | |
| xextproto/7.3.0-gimkl-2.11.5 | |
| xextproto/7.3.0-intel-2015a | |
| xextproto/7.3.0-intel-2015b | |
| xextproto/7.3.0-intel-2016a | |
| xineramaproto/ | |
| xineramaproto/1.2.1-intel-2015b | |
| xineramaproto/1.2.1-intel-2016a | |
| XKeyboardConfig/ | |
| XKeyboardConfig/2.16-intel-2015b-Python-2.7.11 | |
| XKeyboardConfig/2.16-intel-2015b | |
| XKeyboardConfig/2.17-intel-2016a | |
| XML-Parser/ | |
| XML-Parser/2.41-intel-2015b-Perl-5.20.3 | |
| XML-Parser/2.41-intel-2016a-Perl-5.20.3 | |
| XML-Parser/2.44-intel-2016a-Perl-5.22.1 | |
| xorg-macros/ | |
| xorg-macros/1.17-intel-2015a | |
| xorg-macros/1.19.0-gimkl-2.11.5 | |
| xorg-macros/1.19.0-intel-2015b | |
| xorg-macros/1.19.0-intel-2016a | |
| xprop/ | |
| xprop/1.2.2-intel-2016a | |
| xproto/ | |
| xproto/7.0.26-intel-2015a | |
| xproto/7.0.27-intel-2015a | |
| xproto/7.0.28-gimkl-2.11.5 | |
| xproto/7.0.28-intel-2015b | |
| xproto/7.0.28-intel-2016a | |
| xtrans/ | |
| xtrans/1.2-intel-2015a | |
| xtrans/1.3.4-intel-2015a | |
| xtrans/1.3.5-gimkl-2.11.5 | |
| xtrans/1.3.5-intel-2015a | |
| xtrans/1.3.5-intel-2015b | |
| xtrans/1.3.5-intel-2016a | |
| XZ/ | |
| XZ/5.2.2-foss-2016a-gettext-0.19.7 | |
| XZ/5.2.2-intel-2016a-gettext-0.19.7 | |
| XZ/5.2.2-intel-2016a | |
| XZ/5.2.2-intel-2016b | |
| Yade/ | |
| Yade/1.20.0-intel-2016a-Python-2.7.11 | |
| yaff/ | |
| yaff/1.0.develop.2.14-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial | |
| Yasm/ | |
| Yasm/1.3.0-intel-2015b | |
| Yasm/1.3.0-intel-2016a | |
| Yasm/1.3.0-intel-2016b | |
| ZeroMQ/ | |
| ZeroMQ/3.2.5-intel-2015a | |
| ZeroMQ/4.1.3-intel-2015a | |
| ZeroMQ/4.1.4-intel-2015b | |
| ZeroMQ/4.1.4-intel-2016a | |
| zlib/ | |
| zlib/1.2.8-foss-2015b | |
| zlib/1.2.8-foss-2016a | |
| zlib/1.2.8-GCC-4.9.3-binutils-2.25 | |
| zlib/1.2.8-GCC-4.9.3 | |
| zlib/1.2.8-GCC-4.9.3-2.25 | |
| zlib/1.2.8-GCCcore-4.9.3 | |
| zlib/1.2.8-GCCcore-5.4.0 | |
| zlib/1.2.8-gimkl-2.11.5 | |
| zlib/1.2.8-GNU-4.9.3-2.25 | |
| zlib/1.2.8-intel-2015a | |
| zlib/1.2.8-intel-2015b | |
| zlib/1.2.8-intel-2016a | |
| zlib/1.2.8-intel-2016b | |
| zlib/1.2.8 | |
| zlibbioc/ | |
| zlibbioc/1.16.0-intel-2015b-R-3.2.1 | |
| zlibbioc/1.18.0-intel-2016a-R-3.2.3 | |
| /etc/modulefiles/vsc: | |
| cluster/ | |
| cluster/.banette | |
| cluster/.defaultcluster | |
| cluster/delcatty | |
| cluster/golett | |
| cluster/.metapod | |
| cluster/phanpy | |
| cluster/raichu | |
| cluster/.shuppet | |
| cluster/swalot | |
| software/legacy/ | |
| software/legacy/gastly_SL5 | |
| software/legacy/gengar | |
| software/legacy/haunter_SL5 | |
| == 2016-08-29 14:08:45,945 modules.py:967 DEBUG Output found in stdout, seems like '/usr/share/lmod/6.5.2/libexec/lmod python --terse --show_hidden avail ' ran fine | |
| == 2016-08-29 14:08:45,946 modules.py:679 DEBUG Correcting paths in $LD_LIBRARY_PATH from [''] to [] | |
| == 2016-08-29 14:08:45,946 modules.py:679 DEBUG Correcting paths in $LD_PRELOAD from [''] to [] | |
| == 2016-08-29 14:08:45,963 modules.py:423 DEBUG 'module available ' gave 2323 answers: ['ABAQUS/6.12.1-linux-x86_64', 'ABAQUS/6.14.1-linux-x86_64', 'ABINIT/7.10.5-intel-2016.02-GCC-4.9', 'ABINIT/7.10.5-intel-2016.02-GCC-4.9_libxc', 'ABINIT/7.6.2-foss-2015a', 'ABINIT/8.0.8-intel-2016a', 'ABySS/1.9.0-foss-2016a', 'ADF/2014.02', 'ADF/2014.11.r48287-intel-2016a', 'ADF/2016.101', 'AFNI/20160329-intel-2016a-Python-2.7.11', 'ALADIN/36t1_op2bf1-intel-2015b', 'ALPS/2.2.b4-intel-2016a-Python-2.7.11', 'ANSYS_CFD/16.2', 'ANSYS_CFD/17.0', 'ANTLR/2.7.7-foss-2016a-Python-2.7.11', 'ANTLR/2.7.7-intel-2015a-Python-2.7.10', 'ANTLR/2.7.7-intel-2015b-Python-2.7.10', 'ASE/3.11.0-intel-2016b-Python-2.7.12', 'ASE/3.9.1.4567-intel-2015b-Python-2.7.10', 'ASE/3.9.1.4567-intel-2016a-Python-2.7.11', 'ATK/2.16.0-intel-2015b', 'ATK/2.18.0-intel-2016a', 'ATK/2.20.0-intel-2016a', 'ATLAS/3.10.1-gompi-1.5.12-LAPACK-3.4.2', 'Amber/14-intel-2016a-AmberTools-15-patchlevel-13-13', 'Aspera-Connect/3.6.1', 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| == 2016-08-29 14:08:45,963 modules.py:427 DEBUG Cached result for 'module avail' with key '('MODULEPATH=/user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/CO7/haswell-ib/modules/all:/apps/gent/CO7/haswell-ib/modules/all:/etc/modulefiles/vsc', 'lmod', '--show_hidden')': ['ABAQUS/6.12.1-linux-x86_64', 'ABAQUS/6.14.1-linux-x86_64', 'ABINIT/7.10.5-intel-2016.02-GCC-4.9', 'ABINIT/7.10.5-intel-2016.02-GCC-4.9_libxc', 'ABINIT/7.6.2-foss-2015a', 'ABINIT/8.0.8-intel-2016a', 'ABySS/1.9.0-foss-2016a', 'ADF/2014.02', 'ADF/2014.11.r48287-intel-2016a', 'ADF/2016.101', 'AFNI/20160329-intel-2016a-Python-2.7.11', 'ALADIN/36t1_op2bf1-intel-2015b', 'ALPS/2.2.b4-intel-2016a-Python-2.7.11', 'ANSYS_CFD/16.2', 'ANSYS_CFD/17.0', 'ANTLR/2.7.7-foss-2016a-Python-2.7.11', 'ANTLR/2.7.7-intel-2015a-Python-2.7.10', 'ANTLR/2.7.7-intel-2015b-Python-2.7.10', 'ASE/3.11.0-intel-2016b-Python-2.7.12', 'ASE/3.9.1.4567-intel-2015b-Python-2.7.10', 'ASE/3.9.1.4567-intel-2016a-Python-2.7.11', 'ATK/2.16.0-intel-2015b', 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'scipy/0.16.1-intel-2015a-Python-2.7.10', 'scipy/0.16.1-intel-2015b-Python-2.7.10', 'scipy/0.17.0-intel-2016a-Python-2.7.11', 'scp/0.10.2-intel-2015b-Python-2.7.10', 'scripts/4.0.0', 'setuptools/1.4.2', 'shift/4.0-intel-2016a', 'slepc4py/3.6.0-intel-2015b-Python-2.7.11', 'sleuth/0.28.0-intel-2015b-R-3.2.1', 'snappy/1.1.2-GCC-4.9.2', 'snappy/1.1.3-GCC-4.9.3', 'snappy/1.1.3-GCC-4.9.3-2.25', 'software/legacy/gastly_SL5', 'software/legacy/gengar', 'software/legacy/haunter_SL5', 'sparsehash/2.0.2-foss-2016a', 'spglib/1.7.4-intel-2015b', 'spglib/1.9.4.2-intel-2016b-Python-2.7.12', 'statsmodels/0.6.1-intel-2016a-Python-3.5.1', 'sympy/0.7.6-intel-2015a-Python-2.7.10', 'sympy/0.7.6.1-intel-2015b-Python-2.7.10', 'sympy/0.7.6.1-intel-2015b-Python-2.7.11', 'sympy/1.0-foss-2016a-Python-2.7.11', 'sympy/1.0-intel-2016a-Python-2.7.11', 'tabix/0.2.6-foss-2016a', 'tbb/4.3.6.211', 'tcsh/6.18.01-intel-2015a', 'tcsh/6.19.00-intel-2016a', 'testpath/0.2-intel-2015a-Python-2.7.10', 'testpath/0.3-foss-2016a-Python-2.7.11', 'testpath/0.3-foss-2016a-Python-3.5.1', 'testpath/0.3-intel-2016a-Python-2.7.11', 'testpath/0.3-intel-2016b-Python-2.7.12', 'texinfo/4.13a', 'traits/4.5.0-intel-2015b-Python-2.7.10', 'tvb-data/1.5-intel-2016a-Python-2.7.11', 'tvb-data/20150915-intel-2016a-Python-2.7.11', 'tvb-framework/1.5-intel-2016a-Python-2.7.11', 'tvb-framework/20150921-intel-2016a-Python-2.7.11', 'tvb-library/1.5-intel-2016a-Python-2.7.11', 'tvb-library/20150922-intel-2016a-Python-2.7.11', 'util-linux/2.26.1-intel-2015a', 'util-linux/2.26.2-intel-2015a', 'util-linux/2.27.1-foss-2016a', 'util-linux/2.27.1-intel-2015b', 'util-linux/2.27.1-intel-2016a', 'util-linux/2.28-foss-2016a', 'util-linux/2.28-intel-2016a', 'util-linux/2.28.1-intel-2016b', 'vincent/0.4.4-intel-2015a-Python-2.7.10', 'vincent/0.4.4-intel-2015b-Python-2.7.10', 'vsc-base/1.9.1', 'vsc-base/2.1.2', 'vsc-base/2.2.5', 'vsc-base/2.4.17', 'vsc-base/2.4.17-intel-2015b-Python-2.7.11', 'vsc-base/2.4.17-intel-2016a-Python-2.7.11', 'vsc-base/2.4.2', 'vsc-base/2.4.2-intel-2015b-Python-2.7.10', 'vsc-base/2.5.1', 'vsc-base/2.5.1-intel-2016a-Python-2.7.11', 'vsc-base/2.5.1-intel-2016b-Python-2.7.12', 'vsc-install/0.10.11-intel-2016a-Python-2.7.11', 'vsc-install/0.10.11-intel-2016b-Python-2.7.12', 'vsc-install/0.10.6', 'vsc-install/0.10.6-intel-2016a-Python-2.7.11', 'vsc-install/0.9.18-intel-2015b-Python-2.7.11', 'vsc-install/0.9.18-intel-2016a-Python-2.7.11', 'vsc-mympirun-scoop/3.3.0-intel-2015b-Python-2.7.10', 'vsc-mympirun/3.4.2', 'vsc-mympirun/3.4.2-intel-2015b-Python-2.7.10-vsc-base-2.4.2', 'vsc-mympirun/3.4.2-intel-2015b-Python-2.7.11-vsc-base-2.4.17', 'vsc-mympirun/3.4.2-intel-2016a-Python-2.7.11-vsc-base-2.4.17', 'vsc-mympirun/3.4.2-intel-2016a-Python-2.7.11-vsc-base-2.5.1', 'vsc-mympirun/3.4.2-vsc-base-2.2.5', 'vsc-mympirun/3.4.3', 'vsc-mympirun/3.4.3-intel-2016a-Python-2.7.11', 'vsc-mympirun/3.4.3-intel-2016b-Python-2.7.12', 'vsc-processcontrol/1.0-vsc-base-2.1.2', 'wcwidth/0.1.7-foss-2016a-Python-2.7.11', 'wcwidth/0.1.7-foss-2016a-Python-3.5.1', 'wcwidth/0.1.7-intel-2016a-Python-2.7.11', 'wcwidth/0.1.7-intel-2016b-Python-2.7.12', 'wget/1.17.1-foss-2016a', 'wheel/0.29.0-foss-2016a-Python-2.7.11', 'wheel/0.29.0-foss-2016a-Python-3.5.1', 'wkhtmltopdf/0.12.3-Linux-x86_64', 'worker/1.6.4-intel-2016a', 'worker/1.6.5-intel-2016a', 'wxPython/3.0.2.0-intel-2016a-Python-2.7.11', 'x264/20150930-intel-2015b', 'x264/20160114-intel-2016a', 'x264/20160430-foss-2016a', 'x264/20160430-intel-2016a', 'x264/20160614-intel-2016b', 'xbitmaps/1.1.1-foss-2016a', 'xbitmaps/1.1.1-intel-2015a', 'xbitmaps/1.1.1-intel-2016a', 'xcb-proto/1.10-intel-2015a-Python-2.7.9', 'xcb-proto/1.11', 'xcb-proto/1.11-intel-2015a-Python-2.7.9', 'xcb-proto/1.11-intel-2015b-Python-2.7.10', 'xcb-proto/1.11-intel-2015b-Python-2.7.11', 'xcb-util-image/0.4.0-foss-2016a', 'xcb-util-image/0.4.0-intel-2015b', 'xcb-util-image/0.4.0-intel-2015b-Python-2.7.11', 'xcb-util-image/0.4.0-intel-2016a', 'xcb-util-keysyms/0.4.0-foss-2016a', 'xcb-util-keysyms/0.4.0-intel-2015b', 'xcb-util-keysyms/0.4.0-intel-2015b-Python-2.7.11', 'xcb-util-keysyms/0.4.0-intel-2016a', 'xcb-util-renderutil/0.3.9-foss-2016a', 'xcb-util-renderutil/0.3.9-intel-2015b', 'xcb-util-renderutil/0.3.9-intel-2015b-Python-2.7.11', 'xcb-util-renderutil/0.3.9-intel-2016a', 'xcb-util-wm/0.4.1-foss-2016a', 'xcb-util-wm/0.4.1-intel-2015b', 'xcb-util-wm/0.4.1-intel-2015b-Python-2.7.11', 'xcb-util-wm/0.4.1-intel-2016a', 'xcb-util/0.4.0-foss-2016a', 'xcb-util/0.4.0-intel-2015b', 'xcb-util/0.4.0-intel-2015b-Python-2.7.11', 'xcb-util/0.4.0-intel-2016a', 'xextproto/7.2.1-intel-2015a', 'xextproto/7.3.0-foss-2016a', 'xextproto/7.3.0-gimkl-2.11.5', 'xextproto/7.3.0-intel-2015a', 'xextproto/7.3.0-intel-2015b', 'xextproto/7.3.0-intel-2016a', 'xf86vidmodeproto/2.3.1-foss-2016a', 'xf86vidmodeproto/2.3.1-intel-2016a', 'xineramaproto/1.2.1-foss-2016a', 'xineramaproto/1.2.1-intel-2015b', 'xineramaproto/1.2.1-intel-2016a', 'xonsh/0.3.2-intel-2016a', 'xorg-macros/1.17-intel-2015a', 'xorg-macros/1.19.0-foss-2016a', 'xorg-macros/1.19.0-gimkl-2.11.5', 'xorg-macros/1.19.0-intel-2015b', 'xorg-macros/1.19.0-intel-2016a', 'xprop/1.2.2-foss-2016a', 'xprop/1.2.2-intel-2016a', 'xproto/7.0.26-intel-2015a', 'xproto/7.0.27-intel-2015a', 'xproto/7.0.28-foss-2016a', 'xproto/7.0.28-gimkl-2.11.5', 'xproto/7.0.28-intel-2015b', 'xproto/7.0.28-intel-2016a', 'xproto/7.0.29-intel-2016a', 'xtrans/1.2-intel-2015a', 'xtrans/1.3.4-intel-2015a', 'xtrans/1.3.5-foss-2016a', 'xtrans/1.3.5-gimkl-2.11.5', 'xtrans/1.3.5-intel-2015a', 'xtrans/1.3.5-intel-2015b', 'xtrans/1.3.5-intel-2016a', 'yaff/1.0.develop.2.14-intel-2015b-Python-2.7.10-HDF5-1.8.15-patch1-serial', 'zlib/1.2.8', 'zlib/1.2.8-GCC-4.9.2', 'zlib/1.2.8-GCC-4.9.2-binutils-2.25', 'zlib/1.2.8-GCC-4.9.3', 'zlib/1.2.8-GCC-4.9.3-2.25', 'zlib/1.2.8-GCC-4.9.3-binutils-2.25', 'zlib/1.2.8-GCCcore-4.9.3', 'zlib/1.2.8-GCCcore-4.9.4', 'zlib/1.2.8-GCCcore-5.3.0', 'zlib/1.2.8-GCCcore-5.4.0', 'zlib/1.2.8-GCCcore-6.2.0', 'zlib/1.2.8-GNU-4.9.3-2.25', 'zlib/1.2.8-foss-2015a', 'zlib/1.2.8-foss-2015b', 'zlib/1.2.8-foss-2016.06', 'zlib/1.2.8-foss-2016a', 'zlib/1.2.8-foss-2016b', 'zlib/1.2.8-gimkl-2.11.5', 'zlib/1.2.8-goolf-1.7.20', 'zlib/1.2.8-intel-2015a', 'zlib/1.2.8-intel-2015b', 'zlib/1.2.8-intel-2016.03-GCC-5.4', 'zlib/1.2.8-intel-2016a', 'zlib/1.2.8-intel-2016b', 'zlibbioc/1.16.0-intel-2015b-R-3.2.1', 'zlibbioc/1.18.0-intel-2016a-R-3.2.3'] | |
| == 2016-08-29 14:08:45,967 toolchain.py:382 DEBUG add_dependencies: MODULEPATH: /user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/CO7/haswell-ib/modules/all:/apps/gent/CO7/haswell-ib/modules/all:/etc/modulefiles/vsc | |
| == 2016-08-29 14:08:45,967 toolchain.py:385 DEBUG add_dependencies: added toolchain dependency {'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} | |
| == 2016-08-29 14:08:45,967 toolchain.py:382 DEBUG add_dependencies: MODULEPATH: /user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/CO7/haswell-ib/modules/all:/apps/gent/CO7/haswell-ib/modules/all:/etc/modulefiles/vsc | |
| == 2016-08-29 14:08:45,967 toolchain.py:385 DEBUG add_dependencies: added toolchain dependency {'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} | |
| == 2016-08-29 14:08:45,967 toolchain.py:382 DEBUG add_dependencies: MODULEPATH: /user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/CO7/haswell-ib/modules/all:/apps/gent/CO7/haswell-ib/modules/all:/etc/modulefiles/vsc | |
| == 2016-08-29 14:08:45,967 toolchain.py:385 DEBUG add_dependencies: added toolchain dependency {'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} | |
| == 2016-08-29 14:08:45,967 toolchain.py:382 DEBUG add_dependencies: MODULEPATH: /user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/CO7/haswell-ib/modules/all:/apps/gent/CO7/haswell-ib/modules/all:/etc/modulefiles/vsc | |
| == 2016-08-29 14:08:45,968 toolchain.py:385 DEBUG add_dependencies: added toolchain dependency {'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} | |
| == 2016-08-29 14:08:45,968 toolchain.py:382 DEBUG add_dependencies: MODULEPATH: /user/scratch/gent/vsc400/vsc40023/easybuild_REGTEST/CO7/haswell-ib/modules/all:/apps/gent/CO7/haswell-ib/modules/all:/etc/modulefiles/vsc | |
| == 2016-08-29 14:08:45,968 toolchain.py:385 DEBUG add_dependencies: added toolchain dependency {'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} | |
| == 2016-08-29 14:08:45,968 easyconfig.py:601 DEBUG Dependencies BEFORE filtering: [{'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}] | |
| == 2016-08-29 14:08:45,968 easyblock.py:2139 INFO Running method make_builddir part of step ready | |
| == 2016-08-29 14:08:45,969 easyblock.py:755 DEBUG Creating the build directory /tmp/vsc40023/easybuild_build/PSORTb/3.0.4/foss-2016a-Perl-5.22.1 (cleanup: True) | |
| == 2016-08-29 14:08:45,969 filetools.py:916 INFO Creating directory /tmp/vsc40023/easybuild_build/PSORTb/3.0.4/foss-2016a-Perl-5.22.1 (parents: True, set_gid: False, sticky: False) | |
| == 2016-08-29 14:08:45,969 easyblock.py:2139 INFO Running method env_reset_changes part of step ready | |
| == 2016-08-29 14:08:45,969 easyblock.py:2139 INFO Running method handle_iterate_opts part of step ready | |
| == 2016-08-29 14:08:45,969 easyblock.py:2128 DEBUG Not skipping source step (skippable: True, skip: None, skipsteps: [], module_only: False, force: True | |
| == 2016-08-29 14:08:45,969 build_log.py:227 INFO unpacking... | |
| == 2016-08-29 14:08:45,970 easyblock.py:2136 INFO Starting source step | |
| == 2016-08-29 14:08:45,970 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': [None, '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': [24, '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', 'PSORTb-%(version)s_CC.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')]} | |
| == 2016-08-29 14:08:45,972 templates.py:175 DEBUG version found in easyconfig is 3.0.4 | |
| == 2016-08-29 14:08:45,972 templates.py:212 DEBUG name: github_account, config: None | |
| == 2016-08-29 14:08:45,972 templates.py:212 DEBUG name: name, config: PSORTb | |
| == 2016-08-29 14:08:45,972 templates.py:212 DEBUG name: version, config: 3.0.4 | |
| == 2016-08-29 14:08:45,972 templates.py:212 DEBUG name: versionsuffix, config: -Perl-%(perlver)s | |
| == 2016-08-29 14:08:45,972 templates.py:212 DEBUG name: versionprefix, config: | |
| == 2016-08-29 14:08:45,973 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': [None, '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': [24, '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', 'PSORTb-%(version)s_CC.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')]} | |
| == 2016-08-29 14:08:45,974 templates.py:175 DEBUG version found in easyconfig is 3.0.4 | |
| == 2016-08-29 14:08:45,975 templates.py:212 DEBUG name: github_account, config: None | |
| == 2016-08-29 14:08:45,975 templates.py:212 DEBUG name: name, config: PSORTb | |
| == 2016-08-29 14:08:45,975 templates.py:212 DEBUG name: version, config: 3.0.4 | |
| == 2016-08-29 14:08:45,975 templates.py:212 DEBUG name: versionsuffix, config: -Perl-%(perlver)s | |
| == 2016-08-29 14:08:45,975 templates.py:212 DEBUG name: versionprefix, config: | |
| == 2016-08-29 14:08:45,975 easyblock.py:2139 INFO Running method checksum_step part of step source | |
| == 2016-08-29 14:08:45,975 easyblock.py:1490 INFO Checksum verification for /user/data/gent/vsc400/vsc40023/EasyBuild/sources/p/PSORTb/bio-tools-psort-all.3.0.4.tar.gz using None passed. | |
| == 2016-08-29 14:08:45,975 easyblock.py:1490 INFO Checksum verification for /tmp/eb-NkMbkS/files_pr3317/p/PSORTb/PSORTb-3.0.4-libpsortb.patch using None passed. | |
| == 2016-08-29 14:08:45,976 easyblock.py:1490 INFO Checksum verification for /tmp/eb-NkMbkS/files_pr3317/p/PSORTb/PSORTb-3.0.4_CC.patch using None passed. | |
| == 2016-08-29 14:08:45,976 easyblock.py:2139 INFO Running method extract_step part of step source | |
| == 2016-08-29 14:08:45,976 easyblock.py:1497 INFO Unpacking source bio-tools-psort-all.3.0.4.tar.gz | |
| == 2016-08-29 14:08:45,976 filetools.py:944 DEBUG Not creating existing path /tmp/vsc40023/easybuild_build/PSORTb/3.0.4/foss-2016a-Perl-5.22.1 | |
| == 2016-08-29 14:08:45,976 filetools.py:189 DEBUG Unpacking /user/data/gent/vsc400/vsc40023/EasyBuild/sources/p/PSORTb/bio-tools-psort-all.3.0.4.tar.gz in directory /tmp/vsc40023/easybuild_build/PSORTb/3.0.4/foss-2016a-Perl-5.22.1. | |
| == 2016-08-29 14:08:45,976 run.py:99 DEBUG run_cmd: running cmd tar xzf /user/data/gent/vsc400/vsc40023/EasyBuild/sources/p/PSORTb/bio-tools-psort-all.3.0.4.tar.gz (in /tmp/vsc40023/easybuild_build/PSORTb/3.0.4/foss-2016a-Perl-5.22.1) | |
| == 2016-08-29 14:08:46,940 run.py:395 DEBUG cmd "tar xzf /user/data/gent/vsc400/vsc40023/EasyBuild/sources/p/PSORTb/bio-tools-psort-all.3.0.4.tar.gz" exited with exitcode 0 and output: | |
| == 2016-08-29 14:08:46,940 run.py:439 DEBUG Using default regular expression: (?<![(,-]|\w)(?:error|segmentation fault|failed)(?![(,-]|\.?\w) | |
| == 2016-08-29 14:08:46,940 filetools.py:544 DEBUG Last dir list ['t', 'LICENSE', 'lib', 'INSTALL', 'psort', 'bio-tools-psort-svmloc', 'algorithm-hmm', 'MANIFEST', 'Changes', 'USAGE', 'bio-tools-psort-modhmm', 'README', 'Makefile.PL'] | |
| == 2016-08-29 14:08:46,941 filetools.py:545 DEBUG Possible new dir /tmp/vsc40023/easybuild_build/PSORTb/3.0.4/foss-2016a-Perl-5.22.1/bio-tools-psort-all found | |
| == 2016-08-29 14:08:46,941 easyblock.py:2128 DEBUG Not skipping patch step (skippable: True, skip: None, skipsteps: [], module_only: False, force: True | |
| == 2016-08-29 14:08:46,941 build_log.py:227 INFO patching... | |
| == 2016-08-29 14:08:46,941 easyblock.py:2136 INFO Starting patch step | |
| == 2016-08-29 14:08:46,942 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': [None, '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': [24, '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', 'PSORTb-%(version)s_CC.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')]} | |
| == 2016-08-29 14:08:46,943 templates.py:175 DEBUG version found in easyconfig is 3.0.4 | |
| == 2016-08-29 14:08:46,943 templates.py:212 DEBUG name: github_account, config: None | |
| == 2016-08-29 14:08:46,944 templates.py:212 DEBUG name: name, config: PSORTb | |
| == 2016-08-29 14:08:46,944 templates.py:212 DEBUG name: version, config: 3.0.4 | |
| == 2016-08-29 14:08:46,944 templates.py:212 DEBUG name: versionsuffix, config: -Perl-%(perlver)s | |
| == 2016-08-29 14:08:46,944 templates.py:212 DEBUG name: versionprefix, config: | |
| == 2016-08-29 14:08:46,945 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': [None, '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': [24, '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', 'PSORTb-%(version)s_CC.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')]} | |
| == 2016-08-29 14:08:46,946 templates.py:175 DEBUG version found in easyconfig is 3.0.4 | |
| == 2016-08-29 14:08:46,946 templates.py:212 DEBUG name: github_account, config: None | |
| == 2016-08-29 14:08:46,946 templates.py:212 DEBUG name: name, config: PSORTb | |
| == 2016-08-29 14:08:46,946 templates.py:212 DEBUG name: version, config: 3.0.4 | |
| == 2016-08-29 14:08:46,946 templates.py:212 DEBUG name: versionsuffix, config: -Perl-%(perlver)s | |
| == 2016-08-29 14:08:46,947 templates.py:212 DEBUG name: versionprefix, config: | |
| == 2016-08-29 14:08:46,947 easyblock.py:2139 INFO Running method patch_step part of step patch | |
| == 2016-08-29 14:08:46,947 easyblock.py:1509 INFO Applying patch PSORTb-3.0.4-libpsortb.patch | |
| == 2016-08-29 14:08:46,947 easyblock.py:1521 DEBUG Source index: 0; patch level: None; source path suffix: ; copy patch: <module 'copy' from '/usr/lib64/python2.7/copy.pyo'> | |
| == 2016-08-29 14:08:46,947 easyblock.py:1526 DEBUG Determine begin path for patch PSORTb-3.0.4-libpsortb.patch: /tmp/vsc40023/easybuild_build/PSORTb/3.0.4/foss-2016a-Perl-5.22.1/bio-tools-psort-all | |
| == 2016-08-29 14:08:46,947 easyblock.py:1535 DEBUG Applying patch {'path': '/tmp/eb-NkMbkS/files_pr3317/p/PSORTb/PSORTb-3.0.4-libpsortb.patch', 'md5': '3043eb81c0ab9f6921eec0f85a1b5f63', 'name': 'PSORTb-3.0.4-libpsortb.patch', 'checksum': None} in path /tmp/vsc40023/easybuild_build/PSORTb/3.0.4/foss-2016a-Perl-5.22.1/bio-tools-psort-all | |
| == 2016-08-29 14:08:46,949 filetools.py:721 DEBUG Guessed patch level 1 for patch /tmp/eb-NkMbkS/files_pr3317/p/PSORTb/PSORTb-3.0.4-libpsortb.patch | |
| == 2016-08-29 14:08:46,949 run.py:99 DEBUG run_cmd: running cmd patch -b -p1 -i /tmp/eb-NkMbkS/files_pr3317/p/PSORTb/PSORTb-3.0.4-libpsortb.patch (in /tmp/vsc40023/easybuild_build/PSORTb/3.0.4/foss-2016a-Perl-5.22.1/bio-tools-psort-all) | |
| == 2016-08-29 14:08:46,955 run.py:395 DEBUG cmd "patch -b -p1 -i /tmp/eb-NkMbkS/files_pr3317/p/PSORTb/PSORTb-3.0.4-libpsortb.patch" exited with exitcode 0 and output: | |
| patching file lib/Bio/Tools/PSort/Install.pm | |
| patching file Makefile.PL | |
| Hunk #1 succeeded at 104 (offset 7 lines). | |
| patching file psort/bin/check-sig | |
| patching file psort/bin/psort | |
| patching file psort/bin/psort.tmpt | |
| patching file psort/conf/analysis/signal/archaea/check-sig | |
| patching file psort/conf/analysis/signal/gramneg/check-sig | |
| patching file psort/conf/analysis/signal/grampos/check-sig | |
| patching file psort/server/rpc/classify.xpl | |
| patching file psort/server/startup.pl | |
| patching file psort/server/www/results.pl | |
| patching file t/sclblast.pl | |
| == 2016-08-29 14:08:46,955 run.py:439 DEBUG Using default regular expression: (?<![(,-]|\w)(?:error|segmentation fault|failed)(?![(,-]|\.?\w) | |
| == 2016-08-29 14:08:46,955 easyblock.py:1509 INFO Applying patch PSORTb-3.0.4_CC.patch | |
| == 2016-08-29 14:08:46,956 easyblock.py:1521 DEBUG Source index: 0; patch level: None; source path suffix: ; copy patch: <module 'copy' from '/usr/lib64/python2.7/copy.pyo'> | |
| == 2016-08-29 14:08:46,956 easyblock.py:1531 DEBUG Using specified begin path for patch PSORTb-3.0.4_CC.patch: /tmp/vsc40023/easybuild_build/PSORTb/3.0.4/foss-2016a-Perl-5.22.1/bio-tools-psort-all | |
| == 2016-08-29 14:08:46,956 easyblock.py:1535 DEBUG Applying patch {'path': '/tmp/eb-NkMbkS/files_pr3317/p/PSORTb/PSORTb-3.0.4_CC.patch', 'md5': '6489557ae5f318887ef975312503ab60', 'name': 'PSORTb-3.0.4_CC.patch', 'checksum': None} in path /tmp/vsc40023/easybuild_build/PSORTb/3.0.4/foss-2016a-Perl-5.22.1/bio-tools-psort-all | |
| == 2016-08-29 14:08:46,956 filetools.py:659 DEBUG No match found for bio-tools-psort-all/bio-tools-psort-modhmm/Makefile, trying next patched file... | |
| == 2016-08-29 14:08:47,130 build_log.py:152 ERROR Can't determine patch level for patch /tmp/eb-NkMbkS/files_pr3317/p/PSORTb/PSORTb-3.0.4_CC.patch from directory /tmp/vsc40023/easybuild_build/PSORTb/3.0.4/foss-2016a-Perl-5.22.1/bio-tools-psort-all (at easybuild/tools/filetools.py:719 in apply_patch) | |
| == 2016-08-29 14:08:47,130 easyblock.py:2368 WARNING build failed (first 300 chars): Can't determine patch level for patch /tmp/eb-NkMbkS/files_pr3317/p/PSORTb/PSORTb-3.0.4_CC.patch from directory /tmp/vsc40023/easybuild_build/PSORTb/3.0.4/foss-2016a-Perl-5.22.1/bio-tools-psort-all | |
| == 2016-08-29 14:08:47,130 easyblock.py:269 INFO Closing log for application name PSORTb version 3.0.4 |
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