[Bioc-devel] benchdamic TIMEOUT in merida1 and kunpeng2

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

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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