Re: [Bioc-devel] Package DOI broken

2021-02-12 Thread Martin Morgan
This seems to be a problem with many newer packages; I'll look into this. It had been reported (and fixed) previously, but apparently some additional gremlins have entered the system... Martin On 2/12/21, 1:23 PM, "Bioc-devel on behalf of Laurent Gatto" wrote: I just realised that the

[Bioc-devel] Package DOI broken

2021-02-12 Thread Laurent Gatto
I just realised that the scp package (http://bioconductor.org/packages/release/bioc/html/scp.html) DOI (https://doi.org/doi:10.18129/B9.bioc.scp) is broken. Any idea why? Thanks in advance. Laurent ___ Bioc-devel@r-project.org mailing list https

Re: [Bioc-devel] What is the Timeout limit on R CMD check?

2021-02-12 Thread Kern, Lori
The page you have listed is for long tests. If long tests are implemented through the documented process, those checks have 40 minutes to run and are currently only run once per week. The daily builders do not give such a large time limit to packages. We build and check all packages so there i

[Bioc-devel] What is the Timeout limit on R CMD check?

2021-02-12 Thread migdal migdal
Dear all, I am currently in the process of submitting my package to Bioconductor and I got a bit stuck trying to go through the R CMD CHECK. The problem I am facing at the moment is TIMEOUT: R CMD check exceeded 14 mins (here is full report if needed http://bioconductor.org/spb_reports/midasHLA_

[Bioc-devel] How to know the version of a package installed on the package builder ?

2021-02-12 Thread Ilyess RACHEDI
Dear community, Is there a way to know what version of a package is used by the Bioconductor package builder on malbec2 Linux ? The biomRt package was updated recently, but I still get the same kind of error as if it was the previous version. Best, Ilyess [[alternative HTML version de

Re: [Bioc-devel] Problem with my setters on Windows during the build and the check

2021-02-12 Thread Kern, Lori
Please ignore this for now. The reviewer is also aware to ignore. We think this is related to how we are building/checking the packages and are investigating a solution. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformati

[Bioc-devel] Problem with my setters on Windows during the build and the check

2021-02-12 Thread Ilyess RACHEDI
Dear community, When my package is building, I have this error that I have only on Windows and only for my setters. For example for my setter setExperimentName, I have : for R CMD check : Rd warning: cannot open file 'C:/Users/pkgbuild/packagebuilder/workers/jobs/1830/d043cea2e7e43217f0b1e