On 15/05/2019 11:34, Loris Bennett wrote:
Kenneth Hoste <kenneth.ho...@ugent.be> 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?
"eb --from-pr" should just work, no setup needed at all I think...
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?
I've brought it up, yes, see for example
https://github.com/easybuilders/easybuild-easyconfigs/pull/6446#issuecomment-396621378
and
https://github.com/easybuilders/easybuild-easyconfigs/pull/7122#issuecomment-436573707
.
Cheers,
Loris
[snip (63 lines)]
