Kenneth Hoste <[email protected]> writes: > On 15/05/2019 10:31, Loris Bennett wrote: >> 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? > > In this case, you should probably re-download the nlme source tarball (or let > EB > re-download it for you). > > The checksum for the upstream source tarball indeed changed, so we fixed the > checksum (see > https://github.com/easybuilders/easybuild-easyconfigs/pull/8052). > > There were no actual code changes though (see PR description), so a > re-download > should be safe to do. > > We went through a similar issue for 'boot' recently (see > https://github.com/easybuilders/easybuild-easyconfigs/pull/8054), after which > they restored the original source tarball, so we had to revert that (see > https://github.com/easybuilders/easybuild-easyconfigs/pull/8271).
Yes, I have just bumped into the 'boot' problem. So I guess I have to get the GitHub integration set up so that I can make use of the PRs, right? Has anyone reached out to the R people to point out that switching a package but keeping the version the same is a poke in the eye for anyone who gives a fig about reproducibility, not just for easybuilders? Cheers, Loris [snip (63 lines)] -- Dr. Loris Bennett (Mr.) ZEDAT, Freie Universität Berlin Email [email protected]
