[Bioc-devel] Error when building in command line but not in RStudio

[Hervé Pagès]

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 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 
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 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 
> <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 using r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel 
> <https://stat.ethz.ch/mailman/listinfo/bioc-devel>
>> 
> 
> -- 
> Hervé Pagès
> 
> Bioconductor Core Team
> hpages.on.github using gmail.com
> 
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel 
> <https://stat.ethz.ch/mailman/listinfo/bioc-devel>

-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.github using gmail.com