Re: [Bioc-devel] 'IMMAN' Bioconductor package

2018-09-27 Thread Minoo Ashtiani
Hi to all, Thanks a lot for your all efforts. My package "IMMAN" has ERRORS in Multiple platform build/check report for BioC 3.7 : https://bioconductor.org/checkResults/3.7/bioc-LATEST/IMMAN/tokay2-buildsrc.html But the error is related to the connection lost and is not for the package. How

[Bioc-devel] Bad version number have been corrected for the following packages

2018-09-27 Thread Turaga, Nitesh
Hi Maintainers, The packages mentioned below have malformed version number which is being updated by me to 1.1.0 in this development cycle. This is because the ‘y' should usually be in the range 0-99, in the version format ‘x.y.z’. Please only update the ‘z’ when you make a change. During the

Re: [Bioc-devel] GenomeInfoDB SeqInfo function error

2018-09-27 Thread Hervé Pagès
Hi Dario, On 09/13/2018 09:18 AM, Dario Righelli wrote: Hello everyone, I'm using in DEScan2 package the GenomeInfoDb::Seqinfo function with genome="mm10". And sometimes it appens to retrieve this error message "cannot open the connection to 'https://urldefense.proofpoint.com/v2/url?u=ftp-3

[Bioc-devel] Packages with 'Bad DESCRIPTION' on build report

2018-09-27 Thread Obenchain, Valerie
In the past, packages with a malformed DESCRIPTION file were skipped in the nightly builds and not posted on the build report. This was a little confusing for both the maintainer (what happened to my package?) and maintainers of packages that depended on it. These packages are now reported as "

[Bioc-devel] Invalid Parameter - /figure-html

2018-09-27 Thread Tiago Chedraoui Silva
Hello, The workflow I'm maintaining is giving this message "Invalid Parameter - /figure-html" in the devel and release windows environment. http://bioconductor.org/checkResults/devel/workflows-LATEST/TCGAWorkflow/tokay1-buildsrc.html It seems other users had the same problem before: https://sta

Re: [Bioc-devel] Issue with syncing Github to Bioconductor /devel landing page

2018-09-27 Thread Shepherd, Lori
The build system will not recognize the changes unless there is a valid version bump. Please bump the version to 1.7.3. The landing page will be updated after the build system builds and checks the package cleanly; it therefore can take up to 2 days to be reflected on the landing page depend

Re: [Bioc-devel] NEWS file: bug fix referring to a Github issue

2018-09-27 Thread Shepherd, Lori
It is always recommended to add updates and bug fixes to the news file. When we do the release we post a release announcement that includes updates from the previous release as a summary of updates based on the NEWS file. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute De

[Bioc-devel] NEWS file: bug fix referring to a Github issue

2018-09-27 Thread David Rasp
Hi all, I just fixed a bug in the R-package I maintain from an issue on Github. Should I refer to this issue in the NEWS file as it is recommened in the following tutorial: http://r-pkgs.had.co.nz/release.html I don't know if this recommendation also applies to Bioconductor packages. Thanks in ad