Re: [Bioc-devel] The new version of the package 'cbaf' is not downloadable for BioC 3.11

2020-05-13 Thread Lluís Revilla
Hi, The maintainer is already aware of this error. I reported it several months ago https://github.com/colearendt/xlsx/issues/132 and is reported multiple times (issues 154, 156, 159) There is a fix on the github version of the package but the maintainter hasn't updated the CRAN version yet.

[Bioc-devel] BgeeCall package present twice

2020-05-13 Thread Julien Wollbrett
Hello, For Bioconductor 3.11 I asked if it was possible to move BgeeCall from workflow section to software section. The package is now present in the software section. Thank you. When I go to this page : https://bioconductor.org/help/search/index.html?q=bgeecall/

Re: [Bioc-devel] Debugging not updated for coexnet package

2020-05-13 Thread Juan David Henao Sanchez
Hi. Thanks for your help solving this issue. Could you please let me know how I can fix the bug in the specific BioC version (3.11). How could I push my current updated code into this specific version? Thanks in advance. I am looking forward to hearing from you soon. Kind regards, Juan El

Re: [Bioc-devel] Debugging not updated for coexnet package

2020-05-13 Thread Shepherd, Lori
There is lots of documentation on how to achieve this. Most specifically for pushing changes to the RELEASE_3_11 branch following the documentation http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/ Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive

[Bioc-devel] Do not push with merge conflicts to Bioconductor git repo.

2020-05-13 Thread Nitesh Turaga
Dear Developers, Every time there is a release for Bioconductor we (the core team), face an issue where developers end up pushing code with the "merge conflicts". One of the reasons why we get the issue "Bad description" file in the build report is because of a merge which has gone bad and

Re: [Bioc-devel] BgeeCall package present twice

2020-05-13 Thread Shepherd, Lori
Yes looking at the links further it is a legacy version. The one that resolves to a workflow page if you look closely is when 3.11 was in development phase https://bioconductor.org/packages/release/workflows/html/BgeeCall.html While the software page is the current release. I'm not exactly

Re: [Bioc-devel] How to use initializing functions correctly ?

2020-05-13 Thread Charles Plessy
Le Tue, May 12, 2020 at 10:18:24AM -0700, Hervé Pagès a écrit : > > Note that the GPos() constructor is NOT the generator function returned by > the setClass() statement that defines the GPos class. It's a constructor > function defined in the GenomicRanges package and it implements a >