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{devel}[foss/2017b,intel/2017b] GConf v3.2.6 #6985

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{devel}[foss/2017b,intel/2017b] GConf v3.2.6 #6985

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vanzod
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@vanzod vanzod commented Oct 9, 2018

(created using eb --new-pr)

@vanzod
adding easyconfigs: DBus-1.12.2-GCCcore-6.4.0.eb, dbus-glib-0.108-GCC…
a462437 
…core-6.4.0.eb, GConf-3.2.6-foss-2017b.eb, GConf-3.2.6-intel-2017b.eb
@vanzod vanzod added the update label Oct 9, 2018
@vanzod vanzod added this to the 3.7.1 milestone Oct 9, 2018
@vanzod vanzod changed the title {devel}[GCCcore/6.4.0] DBus v1.12.2, dbus-glib v0.108, GConf v3.2.6 {devel}[foss/2017b,intel/2017b] GConf v3.2.6 Oct 9, 2018
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vanzod commented Oct 9, 2018

Test report by @vanzod
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in this PR)
cermis - Linux debian 9.5, Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, Python 2.7.13
See https://gist.github.com/4ab9a16997dc6473b5c2f47f06f3c5bf for a full test report.

@vanzod vanzod mentioned this pull request Oct 10, 2018
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@boegel boegel modified the milestones: 3.7.1, next release Oct 10, 2018
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boegel commented Oct 10, 2018

Test report by @boegel
FAILED
Build succeeded for 2 out of 4 (4 easyconfigs in this PR)
node2021.delcatty.os - Linux centos linux 7.5.1804, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.7.5
See https://gist.github.com/daafd876f2870e33f229462ddbf9c58c for a full test report.

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Travis test report: 7/7 runs failed - see https://travis-ci.org/easybuilders/easybuild-easyconfigs/builds/443272939

Only showing partial log for 1st failed test suite run 11369.1;
full log at https://travis-ci.org/easybuilders/easybuild-easyconfigs/jobs/443272940

...
FAIL: Check whether any conflicts occur in software dependency graphs.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/travis/build/easybuilders/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 155, in test_conflicts
    "No conflicts detected")
AssertionError: No conflicts detected

======================================================================
FAIL: test_dep_versions_per_toolchain_generation (test.easyconfigs.easyconfigs.EasyConfigTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/travis/build/easybuilders/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 299, in test_dep_versions_per_toolchain_generation
    self.assertFalse(multi_dep_vars, error_msg)
AssertionError: No multi-variant deps found for '^.*-(?P<tc_gen>201[89][ab]).*\.eb$' easyconfigs:

found 2 variants of 'expat' dependency in easyconfigs using '2018a' toolchain generation
* version: 2.2.4; versionsuffix:  as dep for set(['RSEM-1.3.1-intel-2018a.eb', 'parallel-20180422-intel-2018a.eb', 'FastQ_Screen-0.12.0-intel-2018a-Perl-5.26.1.eb', 'Roary-3.12.0-intel-2018a-Perl-5.26.1.eb', 'Kraken-1.0-intel-2018a-Perl-5.26.1.eb', 'GIMIC-2018.04.20-intel-2018a-Python-2.7.14.eb', 'Graphviz-2.40.1-intel-2018a.eb', 'GDGraph-1.54-intel-2018a-Perl-5.26.1.eb', 'Bio-DB-HTS-2.11-intel-2018a-Perl-5.26.1.eb', 'bcgTree-1.0.10-intel-2018a-Perl-5.26.1.eb', 'Trinity-2.6.6-intel-2018a.eb', 'prokka-1.13-intel-2018a-BioPerl-1.7.2.eb', 'VEP-93.4-intel-2018a-Perl-5.26.1.eb', 'DBD-mysql-4.046-intel-2018a-Perl-5.26.1.eb', 'graphviz-0.8.2-intel-2018a-Python-3.6.4.eb', 'BioPerl-1.7.2-intel-2018a-Perl-5.26.1.eb', 'InterProScan-5.28-67.0-intel-2018a.eb', 'OrthoFinder-2.2.7-intel-2018a-Python-2.7.14.eb'])
* version: 2.2.5; versionsuffix:  as dep for set(['GDB-8.1-foss-2018a-Python-2.7.14.eb', 'Seurat-2.3.4-intel-2018a-R-3.4.4.eb', 'InterProScan-5.28-67.0-intel-2018a.eb', 'R-bundle-Bioconductor-3.6-intel-2018a-R-3.4.4.eb', 'matplotlib-2.1.2-intel-2018a-Python-2.7.14.eb', 'RELION-2.1-foss-2018a.eb', 'VCFtools-0.1.15-foss-2018a-Perl-5.26.1.eb', 'HiCExplorer-2.1.1-foss-2018a-Python-3.6.4.eb', 'graphviz-0.8.2-intel-2018a-Python-3.6.4.eb', 'Qt-4.8.7-intel-2018a.eb', 'Subversion-1.9.7-iomkl-2018a.eb', 'GDAL-2.2.3-foss-2018a-Python-3.6.4.eb', 'SDL2-2.0.8-intel-2018a.eb', 'STIR-3.0-intel-2018a.eb', 'FFmpeg-4.0-intel-2018a.eb', 'NCO-4.7.6-intel-2018a.eb', 'VMD-1.9.3-intel-2018a-Python-2.7.14.eb', 'poretools-0.6.0-intel-2018a-Python-2.7.14.eb', 'FFmpeg-3.4.2-intel-2018a.eb', 'FLTK-1.3.4-fosscuda-2018a.eb', 'imbalanced-learn-0.3.3-foss-2018a-Python-3.6.4.eb', 'R-keras-2.1.6-foss-2018a-R-3.4.4.eb', 'ITK-4.13.0-foss-2018a-Python-3.6.4.eb', 'GL2PS-1.4.0-intel-2018a.eb', 'FreeFem++-3.61-1-intel-2018a-downloaded-deps.eb', 'Scoary-1.6.16-intel-2018a-Python-2.7.14.eb', 'libGLU-9.0.0-foss-2018a.eb', 'OpenCV-3.4.1-foss-2018a-Python-2.7.14.eb', 'KAT-2.4.2-foss-2018a-Python-3.6.4.eb', 'Octave-4.2.2-foss-2018a.eb', 'scikit-image-0.13.1-foss-2018a-Python-3.6.4.eb', 'Qt5-5.10.1-foss-2018a.eb', 'IPython-6.4.0-foss-2018a-Python-3.6.4.eb', 'APR-util-1.6.1-iomkl-2018a.eb', 'UDUNITS-2.2.26-foss-2018a.eb', 'mympingpong-0.8.0-intel-2018a-Python-2.7.14.eb', 'freeglut-3.0.0-foss-2018a.eb', 'DOLFIN-2018.1.0.post1-foss-2018a-Python-3.6.4.eb', 'FFmpeg-4.0.1-intel-2018a.eb', 'R-3.5.0-iomkl-2018a-X11-20180131.eb', 'ImageMagick-7.0.7-26-foss-2018a.eb', 'GDAL-2.2.3-iomkl-2018a-Python-3.6.4.eb', 'phonopy-1.13.0.64-intel-2018a-Python-2.7.14.eb', 'gnuplot-5.2.2-foss-2018a.eb', 'SpiecEasi-1.0.0-intel-2018a-R-3.4.4.eb', 'libGLU-9.0.0-iomkl-2018a.eb', 'Serf-1.3.9-iomkl-2018a.eb', 'Seaborn-0.8.1-intel-2018a-Python-2.7.14.eb', 'GTK+-2.24.32-foss-2018a.eb', 'Tkinter-3.6.4-intel-2018a-Python-3.6.4.eb', 'Pango-1.41.1-intel-2018a.eb', 'Tk-8.6.8-foss-2018a.eb', 'FreeFem++-3.60-intel-2018a-downloaded-deps.eb', 'phono3py-1.12.7.55-foss-2018a-Python-2.7.14.eb', 'Kraken2-2.0.6-beta-foss-2018a-Perl-5.26.1.eb', 'Tk-8.6.8-iomkl-2018a.eb', 'gnuplot-5.2.2-intel-2018a.eb', 'ncview-2.1.7-intel-2018a.eb', 'UDUNITS-2.2.26-intel-2018a.eb', 'FastQ_Screen-0.12.0-intel-2018a-Perl-5.26.1.eb', 'elastix-4.9.0-foss-2018a.eb', 'meshio-2.0.2-intel-2018a-Python-2.7.14.eb', 'Tkinter-2.7.14-foss-2018a-Python-2.7.14.eb', 'PyQt-4.12.1-foss-2018a-Python-2.7.14.eb', 'OpenFOAM-5.0-20180108-foss-2018a.eb', 'meshio-2.0.2-intel-2018a-Python-3.6.4.eb', 'Graphviz-2.40.1-intel-2018a.eb', 'Molden-5.8-foss-2018a.eb', 'wxWidgets-3.0.3-foss-2018a.eb', 'HarfBuzz-1.7.5-intel-2018a.eb', 'VTK-8.1.0-foss-2018a-Python-3.6.4.eb', 'libGLU-9.0.0-intel-2018a.eb', 'VTK-8.1.0-foss-2018a-Python-2.7.14.eb', 'GMT-4.5.17-foss-2018a.eb', 'libQGLViewer-2.7.1-intel-2018a.eb', 'scikit-learn-0.19.1-foss-2018a-Python-3.6.4.eb', 'basemap-1.0.7-intel-2018a-Python-3.6.4.eb', 'VTK-8.1.0-intel-2018a-Python-2.7.14.eb', 'ncdf4-1.16-intel-2018a-R-3.4.4.eb', 'R-3.4.4-foss-2018a-X11-20180131.eb', 'FTGL-2.1.3-rc5-foss-2018a.eb', 'FLTK-1.3.4-intel-2018a.eb', 'opencv_contrib-3.4.1-foss-2018a-Python-3.6.4.eb', 'GDB-8.1.1-intel-2018a-Python-2.7.14.eb', 'GDAL-2.2.3-intel-2018a-Python-2.7.14.eb', 'RELION-2.1-foss-2018a-CUDA-9.1.85.eb', 'QUAST-4.6.3-foss-2018a-Python-3.6.4.eb', 'RELION-3.0_beta.2018.08.02-fosscuda-2018a.eb', 'SimpleITK-1.1.0-foss-2018a-Python-3.6.4.eb', 'VTK-8.1.0-intel-2018a-Python-3.6.4.eb', 'GraphicsMagick-1.3.28-foss-2018a.eb', 'Perl-5.26.1-foss-2018a.eb', 'Proteinortho-5.16b-foss-2018a-Python-3.6.4-Perl-5.26.1.eb', 'freeglut-3.0.0-intel-2018a.eb', 'ParaView-5.4.1-intel-2018a-mpi.eb', 'FFmpeg-3.4.2-foss-2018a.eb', 'HTSeq-0.10.0-foss-2018a-Python-2.7.14.eb', 'matplotlib-2.1.2-intel-2018a-Python-3.6.4.eb', 'OpenFOAM-5.0-20180108-intel-2018a.eb', 'RSEM-1.3.1-intel-2018a.eb', 'FLTK-1.3.4-foss-2018a.eb', 'WISExome-20180517-intel-2018a-Python-2.7.14.eb', 'motif-2.3.8-intel-2018a.eb', 'cisTEM-1.0.0-beta-foss-2018a.eb', 'IPython-5.7.0-foss-2018a-Python-2.7.14.eb', 'ToFu-1.3.17-foss-2018a-Python-3.6.4.eb', 'Roary-3.12.0-intel-2018a-Perl-5.26.1.eb', 'OpenCV-3.4.1-intel-2018a-Python-3.6.4.eb', 'Octave-4.2.1-foss-2018a.eb', 'Grace-5.1.25-foss-2018a-5build1.eb', 'Qt5-5.10.1-intel-2018a.eb', 'VTK-8.1.1-intel-2018a-Python-2.7.14.eb', 'GDGraph-1.54-intel-2018a-Perl-5.26.1.eb', 'NeuroKit-0.2.7-intel-2018a-Python-3.6.4.eb', 'ToFu-1.3.17-foss-2018a-Python-2.7.14.eb', 'KmerGenie-1.7048-intel-2018a.eb', 'GDAL-2.2.3-intel-2018a-Python-3.6.4.eb', 'ParaView-5.4.1-foss-2018a-mpi.eb', 'fullrmc-3.2.0-intel-2018a-Python-2.7.14.eb', 'Tkinter-3.6.4-foss-2018a-Python-3.6.4.eb', 'CGAL-4.11.1-foss-2018a-Python-3.6.4.eb', 'Pango-1.41.1-foss-2018a.eb', 'libgd-2.2.5-intel-2018a.eb', 'NCL-6.5.0-intel-2018a.eb', 'PyOpenGL-3.1.1a1-foss-2018a-Python-2.7.14.eb', 'ASE-3.16.2-iomkl-2018a-Python-3.6.4.eb', 'MAJIQ-1.1.1-intel-2018a-Python-3.6.4.eb', 'IPython-5.7.0-intel-2018a-Python-2.7.14.eb', 'R-3.4.4-iomkl-2018a-X11-20180131.eb', 'MathGL-2.4.1-foss-2018a.eb', 'FFmpeg-4.0-foss-2018a.eb', 'phonopy-1.12.6.66-intel-2018a-Python-2.7.14.eb', 'HTSeq-0.9.1-intel-2018a-Python-2.7.14.eb', 'GMT-5.4.3-foss-2018a.eb', 'CGAL-4.11.1-intel-2018a-Python-2.7.14.eb', 'POV-Ray-3.7.0.7-intel-2018a.eb', 'git-2.16.1-foss-2018a.eb', 'matplotlib-2.1.2-foss-2018a-Python-3.6.4.eb', 'NCL-6.4.0-intel-2018a.eb', 'Mesa-17.3.6-iomkl-2018a.eb', 'EMAN2-2.21a-foss-2018a-Python-2.7.14-Boost-1.63.0.eb', 'HarfBuzz-1.7.5-foss-2018a.eb', 'RELION-3.0_beta.2018.08.02-intel-2018a.eb', 'OpenCV-3.4.1-foss-2018a-Python-3.6.4.eb', 'R-3.4.4-intel-2018a-X11-20180131.eb', 'IPython-6.3.1-intel-2018a-Python-3.6.4.eb', 'plotly-4.8.0-intel-2018a-R-3.4.4.eb', 'RELION-2.1-fosscuda-2018a.eb', 'Mesa-17.3.6-intel-2018a.eb', 'GDAL-2.2.3-foss-2018a-Python-2.7.14.eb', 'phonopy-1.12.6.66-foss-2018a-Python-2.7.14.eb', 'ITK-4.13.0-foss-2018a-Python-2.7.14.eb', 'spectral.methods-0.7.2.133-intel-2018a-R-3.4.4.eb', 'GL2PS-1.4.0-foss-2018a.eb', 'matplotlib-2.1.2-iomkl-2018a-Python-3.6.4.eb', 'Trilinos-12.12.1-foss-2018a-Python-3.6.4.eb', 'Tkinter-3.6.4-iomkl-2018a-Python-3.6.4.eb', 'libGLU-9.0.0-fosscuda-2018a.eb', 'phono3py-1.12.7.55-intel-2018a-Python-2.7.14.eb', 'Mesa-17.3.6-fosscuda-2018a.eb', 'Tkinter-2.7.14-intel-2018a-Python-2.7.14.eb', 'scikit-learn-0.19.1-intel-2018a-Python-3.6.4.eb', 'motif-2.3.8-foss-2018a.eb', 'R-bundle-Bioconductor-3.7-iomkl-2018a-R-3.5.0.eb', 'GTK+-2.24.32-intel-2018a.eb', 'matplotlib-2.1.2-foss-2018a-Python-2.7.14.eb', 'CGAL-4.11.1-foss-2018a-Python-2.7.14.eb', 'Mesa-17.3.6-foss-2018a.eb', 'Qt-4.8.7-foss-2018a.eb'])


----------------------------------------------------------------------
Ran 9811 tests in 675.741s

FAILED (failures=2)
ERROR: Not all tests were successful.

(bleep, bloop, I'm just a bot, please talk to my owner @boegel if you notice you me acting stupid)

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Travis test report: 7/7 runs failed - see https://travis-ci.org/easybuilders/easybuild-easyconfigs/builds/443367951

Only showing partial log for 1st failed test suite run 11371.1;
full log at https://travis-ci.org/easybuilders/easybuild-easyconfigs/jobs/443367952

...
FAIL: Check whether any conflicts occur in software dependency graphs.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/travis/build/easybuilders/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 155, in test_conflicts
    "No conflicts detected")
AssertionError: No conflicts detected

======================================================================
FAIL: test_dep_versions_per_toolchain_generation (test.easyconfigs.easyconfigs.EasyConfigTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/travis/build/easybuilders/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 299, in test_dep_versions_per_toolchain_generation
    self.assertFalse(multi_dep_vars, error_msg)
AssertionError: No multi-variant deps found for '^.*-(?P<tc_gen>201[89][ab]).*\.eb$' easyconfigs:

found 2 variants of 'expat' dependency in easyconfigs using '2018a' toolchain generation
* version: 2.2.4; versionsuffix:  as dep for set(['scikit-image-0.13.1-foss-2018a-Python-3.6.4.eb', 'Seurat-2.3.4-intel-2018a-R-3.4.4.eb', 'InterProScan-5.28-67.0-intel-2018a.eb', 'R-bundle-Bioconductor-3.6-intel-2018a-R-3.4.4.eb', 'matplotlib-2.1.2-intel-2018a-Python-2.7.14.eb', 'RELION-2.1-foss-2018a.eb', 'HiCExplorer-2.1.1-foss-2018a-Python-3.6.4.eb', 'graphviz-0.8.2-intel-2018a-Python-3.6.4.eb', 'Qt-4.8.7-intel-2018a.eb', 'gnuplot-5.2.2-intel-2018a.eb', 'OpenFOAM-5.0-20180108-foss-2018a.eb', 'SDL2-2.0.8-intel-2018a.eb', 'STIR-3.0-intel-2018a.eb', 'FFmpeg-4.0-intel-2018a.eb', 'VMD-1.9.3-intel-2018a-Python-2.7.14.eb', 'poretools-0.6.0-intel-2018a-Python-2.7.14.eb', 'FFmpeg-3.4.2-intel-2018a.eb', 'FLTK-1.3.4-fosscuda-2018a.eb', 'Bio-DB-HTS-2.11-intel-2018a-Perl-5.26.1.eb', 'imbalanced-learn-0.3.3-foss-2018a-Python-3.6.4.eb', 'ITK-4.13.0-foss-2018a-Python-3.6.4.eb', 'GL2PS-1.4.0-intel-2018a.eb', 'FreeFem++-3.61-1-intel-2018a-downloaded-deps.eb', 'Scoary-1.6.16-intel-2018a-Python-2.7.14.eb', 'parallel-20180422-intel-2018a.eb', 'IPython-6.3.1-intel-2018a-Python-3.6.4.eb', 'OpenCV-3.4.1-foss-2018a-Python-2.7.14.eb', 'KAT-2.4.2-foss-2018a-Python-3.6.4.eb', 'Qt5-5.10.1-foss-2018a.eb', 'BioPerl-1.7.2-intel-2018a-Perl-5.26.1.eb', 'IPython-6.4.0-foss-2018a-Python-3.6.4.eb', 'Octave-4.2.2-foss-2018a.eb', 'mympingpong-0.8.0-intel-2018a-Python-2.7.14.eb', 'freeglut-3.0.0-foss-2018a.eb', 'DOLFIN-2018.1.0.post1-foss-2018a-Python-3.6.4.eb', 'FFmpeg-4.0.1-intel-2018a.eb', 'phono3py-1.12.7.55-foss-2018a-Python-2.7.14.eb', 'ImageMagick-7.0.7-26-foss-2018a.eb', 'phonopy-1.13.0.64-intel-2018a-Python-2.7.14.eb', 'SpiecEasi-1.0.0-intel-2018a-R-3.4.4.eb', 'libGLU-9.0.0-iomkl-2018a.eb', 'freeglut-3.0.0-intel-2018a.eb', 'Seaborn-0.8.1-intel-2018a-Python-2.7.14.eb', 'GTK+-2.24.32-foss-2018a.eb', 'Tkinter-3.6.4-intel-2018a-Python-3.6.4.eb', 'Pango-1.41.1-intel-2018a.eb', 'Tk-8.6.8-foss-2018a.eb', 'FreeFem++-3.60-intel-2018a-downloaded-deps.eb', 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----------------------------------------------------------------------
Ran 9811 tests in 724.008s

FAILED (failures=2)
ERROR: Not all tests were successful.

(bleep, bloop, I'm just a bot, please talk to my owner @boegel if you notice you me acting stupid)

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vanzod commented Oct 18, 2018

The source of all the issues with expat is because both foss-2017b and foss-2018a use GCCcore-6.4.0 but different versions of expat. So if I fix the version clashes for 2017b I create new ones for easyconfigs in 2018a...

boegel
boegel requested changes Oct 19, 2018
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easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.108-GCCcore-6.4.0.eb
dependencies = [
('GLib', '2.53.5'),
('DBus', '1.12.2'),
('expat', '2.2.4'),
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@vanzod Since we're stuck between a rock & a hard place here with expat, can we make it a build dependency here somehow, for example by linking it statically?

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I'll look into this option

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@vanzod Any updates on this?

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@boegel I tried but all attempts of building it statically failed. How do you want to proceed?

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@vanzod Well, we shouldn't be introducing conflicts, not sure how to proceed...

@easybuilders easybuilders deleted a comment from boegelbot Oct 19, 2018
@easybuilders easybuilders deleted a comment from boegelbot Oct 19, 2018
@boegel boegel modified the milestones: 3.8.0, 3.8.1 Dec 14, 2018
@boegel boegel modified the milestones: 3.8.1, 3.x Jan 19, 2019
@vanzod vanzod mentioned this pull request Mar 8, 2019
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@boegel boegel mentioned this pull request Mar 14, 2019
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vanzod commented Mar 29, 2019

The conflict cannot be easily solved. Closing

@vanzod vanzod closed this Mar 29, 2019
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