HI,
I don't have a good explanation why it was timing out on kunpeng2 but I
think it will pass from now on!
Here is what I did:
1) I tried to build benchdamic on kunpeng2:
$ R CMD build --keep-empty-dirs --no-resave-data benchdamic
* checking for file ‘benchdamic/DESCRIPTION’ ... OK
* preparing ‘benchdamic’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...
and it hung here for several minutes...
2) I checked the single vignette in the package and I noticed that it
uses/depends on data package HMP16SData
3) in a new terminal session I started R and installed the data package:
BiocManager::install("HMP16SData")
Bioconductor version 3.18 (BiocManager 1.30.21), R 4.3.1 (2023-06-16)
Installing package(s) 'HMP16SData'
trying URL '
https://bioconductor.org/packages/3.18/data/experiment/src/contrib/HMP16SData_1.21.0.tar.gz
'
Content type 'application/x-gzip' length 17066704 bytes (16.3 MB)
==================================================
downloaded 16.3 MB
* installing *source* package ‘HMP16SData’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation
path
* DONE (HMP16SData)
Since it didn't stop early with a message like "The package is already
installed with the last version" it seems this data package was not
installed until now. Should this data package be listed as
dependency/suggest in the DESCRIPTION file ?1
4) and now the build in the first terminal session finished successfully:
...
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘benchdamic_1.7.3.tar.gz’
Since the data package is installed I think from now on
the benchdamic package will not timeout on kunpeng2 until the next update
of the R installation/version when all installed packages in site-library
will be lost and they will have to be downloaded again (automatically or
manually, as I did for HMP16SData)
Regards,
Martin
On Sun, Jul 16, 2023 at 1:19 PM Matteo Calgaro <mcalgar...@gmail.com> wrote:
> Dear all,
> my package benchdamic has been giving TIMEOUT in the build results on
> merida1
> <http://bioconductor.org/checkResults/release/bioc-LATEST/benchdamic/>
> (release macOS) and kunpeng2
> <https://bioconductor.org/checkResults/devel/bioc-LATEST/benchdamic/>
> (devel Linux).
>
> The devel and release versions of benchdamic are equal due to some updates
> I had to do in both versions to avoid errors. Interestingly, the package
> builds well in the macOS platform in devel (Iconway) while it gives TIMEOUT
> in release. I held off reporting the issue until I had implemented the new
> features, even though the TIMEOUT state has been present since the last
> Bioconductor release.
> The build report only seems to indicate that it times out while building
> vignettes. How should I solve this?
>
> Thanks a lot in advance.
> Best regards.
> Matteo Calgaro
>
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>
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