[Bioc-devel] Error when building in command line but not in RStudio
hp@ge@@on@g|thub @end|ng |rom gm@||@com
Fri Mar 26 03:30:11 CET 2021
Let's keep this conversation on the bioc-devel mailing list where it
On 3/25/21 5:31 PM, Xinan Yang wrote:
> on March 25, 2021 3:58 PM Hervé Pagès wrote:
>> With Bioconductor packages you push
>> changes to your package git repo at
> > https://git.bioconductor.org/packages/seq2pathway
> <https://git.bioconductor.org/packages/seq2pathway>and we do the rest.
> Thank you for the help. I have a related question.
> Seq2pathway dependents on a package, called seq2pathway.data, for which
> AJ also upgraded its supporting genomes.
> For this data package, should we build new git for it?
I don't understand the question.
seq2pathway.data is already in Bioconductor in the category of
Like with software package seq2pathway, you also need to update
seq2pathway.data by pushing your changes to the git repo at
The build/check report for BioC 3.13 **data-experiment** packages is
Unlike the builds for software packages, which run daily, the
data-experiment builds run only twice a week (Mondays and Thursdays).
Another difference with software packages is that we only build and
distribute source tarballs for the data-experiment packages. No Windows
or Mac binaries for these packages.
> Thank you,
> *From:* Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Hervé
> Pagès <hpages.on.github using gmail.com>
> *Sent:* Thursday, March 25, 2021 3:58 PM
> *To:* AJ Kinstlick <akinstlick using uchicago.edu>; bioc-devel using r-project.org
> <bioc-devel using r-project.org>
> *Subject:* Re: [Bioc-devel] Error when building in command line but not
> in RStudio
> On 3/25/21 1:50 PM, AJ Kinstlick wrote:
>> Any help on this would be greatly appreciated, but once again I'm not sure
>> it's even necessary if I can just build the package in RStudio and submit
>> it to Bioconductor.
> That's not how Bioconductor works. With Bioconductor packages you push
> changes to your package git repo at
> <https://git.bioconductor.org/packages/seq2pathway> and we do the rest. Of
> course 'R CMD build' needs to work on your package because that's what
> the daily builds are going to do to produce the source tarball.
> The daily build/check report for BioC 3.13 is published here:
> Note that seq2pathway is currently broken on nebbiolo1 (Linux builder).
> Maybe that is the same error that you are seeing when you do 'R CMD
> build seq2pathway' on your own machine?
>> Thank you,
>> AJ Kinstlick
>> [[alternative HTML version deleted]]
>> Bioc-devel using r-project.org mailing list
> Hervé Pagès
> Bioconductor Core Team
> hpages.on.github using gmail.com
> Bioc-devel using r-project.org mailing list
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