[Bioc-devel] Error when building in command line but not in RStudio
Let's keep this conversation on the bioc-devel mailing list where it started.
On 3/25/21 5:31 PM, Xinan Yang wrote:
Herve, on March 25, 2021 3:58 PM Herv? Pag?s 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 data-experiment packages: https://bioconductor.org/packages/3.13/seq2pathway.data Like with software package seq2pathway, you also need to update seq2pathway.data by pushing your changes to the git repo at https://git.bioconductor.org/packages/seq2pathway.data The build/check report for BioC 3.13 **data-experiment** packages is published here: https://bioconductor.org/checkResults/3.13/data-experiment-LATEST/ 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. Cheers, H.
Thank you, Holly ------------------------------------------------------------------------ *From:* Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Herv? Pag?s <hpages.on.github at gmail.com> *Sent:* Thursday, March 25, 2021 3:58 PM *To:* AJ Kinstlick <akinstlick at uchicago.edu>; bioc-devel at r-project.org <bioc-devel at 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 <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: https://bioconductor.org/checkResults/3.13/bioc-LATEST/ <https://bioconductor.org/checkResults/3.13/bioc-LATEST/> 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? H.
Thank you, AJ Kinstlick ??????? [[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
-- Herv? Pag?s Bioconductor Core Team hpages.on.github at gmail.com
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel <https://stat.ethz.ch/mailman/listinfo/bioc-devel>
Herv? Pag?s Bioconductor Core Team hpages.on.github at gmail.com