Hi Lars, Thanks for the info. I hadn't realised that the package list for a specific version-toolchain combination could change.
However, if I do '--force --skip' I get the following error: [build@admin ~]$ eb R-3.5.1-foss-2018b.eb --robot --force --skip == temporary log file in case of crash /tmp/eb-yj4XcQ/easybuild-x7nh9l.log == resolving dependencies ... == processing EasyBuild easyconfig /trinity/shared/easybuild/software/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyconfigs-3.9.0-py2.7.egg/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb == building and installing R/3.5.1-foss-2018b... == fetching files... == FAILED: Installation ended unsuccessfully (build directory: /trinity/shared/easybuild/build/R/3.5.1/foss-2018b): build failed (first 300 chars): Checksum verification for extension source nlme_3.1-137.tar.gz failed == Results of the build can be found in the log file(s) /tmp/eb-yj4XcQ/easybuild-R-3.5.1-20190515.102021.kwjjO.log ERROR: Build of /trinity/shared/easybuild/software/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyconfigs-3.9.0-py2.7.egg/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb failed (err: 'build failed (first 300 chars): Checksum verification for extension source nlme_3.1-137.tar.gz failed') I assume this means that the CRAN nlme package has been surreptitiously swapped without the version number being changed. Is '--inject-checksums' the best way dealing with this? Cheers, Loris Lars Viklund <lars.vikl...@umu.se> writes: > R-3.5.1-foss-2018.eb was refreshed adding some extensions, including the > `shinythemes` that Bioconductor is lacking. > I ran into this just last week. > > https://github.com/easybuilders/easybuild-easyconfigs/pull/7420 > > You should be able to address this by an `eb --force --skip` to install the > missing extensions. > > This is apparently something that happens occasionally judging by the list of > pull requests in the easyconfigs repo. > > The PR for Bioconductor/3.7 now mentions that it depends on the refreshed > R/3.5.1 PR. > > // Lars > ________________________________________ > From: easybuild-requ...@lists.ugent.be <easybuild-requ...@lists.ugent.be> on > behalf of Loris Bennett <loris.benn...@fu-berlin.de> > Sent: Tuesday, May 14, 2019 16:58 > To: easybuild > Subject: [easybuild] Installation of R/3.5.1-foss-2018b successful but > incomplete > > Hi, > > I just tried to do > > eb R-bundle-Bioconductor-3.7-foss-2018b-R-3.5.1.eb --robot > > This failed on the last of 134 packages with > > ERROR: dependency ‘shinythemes’ is not available for package ‘GSVA’ > > The package 'shinythemes' is one which should be installed by > > R-3.5.1-foss-2018b.eb > > but as it turns out, of the 668 packages which should be installed, only > 648 in fact are. > > If some of the packages had failed to install, I would have expected the > whole thing to fail and the module file not to be generated, but in fact > it was. > > Am I missing something here? How could I debug the issue? > > Cheers, > > Loris > > -- > Dr. Loris Bennett (Mr.) > ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de -- Dr. Loris Bennett (Mr.) ZEDAT, Freie Universität Berlin Email loris.benn...@fu-berlin.de
