Re: [Bioc-devel] reacVcf(remoteFile, "hg19", region) fails in VariantAnnotation 1.39.0 (and friends), works with 1.38.0

2021-07-14 Thread Paul Shannon
Thanks, Martin. Your hunch was right, the problem was in our sever. We had some expired ssl certificates on the nginx server which dispatched to Flask. The irregular behavior we saw - where readVcf worked in some settings, and failed in others - is apparently due to different ssl

Re: [Bioc-devel] Updating stable release

2021-07-14 Thread Nitesh Turaga
Hi Margaret, Please follow the documentation on the website, http://bioconductor.org/developers/how-to/git/. http://bioconductor.org/developers/how-to/version-numbering/ Best, Nitesh Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer

Re: [Bioc-devel] Updating stable release

2021-07-14 Thread James W. MacDonald
The release version of your package is 1.8.0, and the devel is on increment ahead (e.g., 1.9.x). You cannot increment the middle version number of your release package because that makes it a devel package, hence the pre-release hook denying your changes. You should change the version to 1.8.1

Re: [Bioc-devel] Updating stable release

2021-07-14 Thread margaret linan
Hi - I successfully updated my devel PoTRA package recently, now I am trying to push these same changes to the stable PoTRA package. I am encountering the following issue (see highlight below). Note - in the github PoTRA repo, I have pulled and merged from head --> RELEASE_3_13. Also the devel

Re: [Bioc-devel] Updating stable release

2021-07-14 Thread Kern, Lori
Did you push your changes to the RELEASE_3_13 branch in addition to the master branch? Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263

[Bioc-devel] Updating stable release

2021-07-14 Thread margaret linan
Hi Bioc, I recently fixed the build errors for my devel version of PoTRA and the build is succeeding. However, the stable release of PoTRA still displays "build error". What can I do to fix this? Thanks, Margaret [[alternative HTML version deleted]]