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).
regards,
Kenneth
Cheers,
Loris
Lars Viklund <[email protected]> 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: [email protected] <[email protected]> on behalf
of Loris Bennett <[email protected]>
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 [email protected]
