Thank you so much for your work on an incredibly useful package. As a Bioconductor package maintainer, biocthis really helps me carry out checks on my package.
I have been having an issue when I use a bioc-check workflow on my package with the devel versions of R and Bioconductor created with use_bioc_github_action(biocdocker = "devel"). Everything works fine on macOS and Linux, but the Windows workflow fails when installing the dependencies for my package. Because this is devel, I get the message that the following packages are only available in source form and may need compilation:
Everything seems to download fine, and even some packages compile and install properly, including: zlibbioc, S4Vectors, BiocParallel, Rhtslib, XVector, S4Arrays, Biostrings, GenomicRanges, DelayedArray, Rsamtools, GenomicAlignments, InteractionSet, and AnnotationHub. However, once the workflow gets to rtracklayer, compilation fails:
This then prevents other packages with a dependency on rtracklayer to fail, and the workflow exits and cannot go on to check my package.
I am not sure if this is an rtracklayer issue or a compiler issue, but any guidance on how to try to get these dependency installs working in this workflow would be very much appreciated.
Hi!
Thank you so much for your work on an incredibly useful package. As a Bioconductor package maintainer,
biocthisreally helps me carry out checks on my package.I have been having an issue when I use a bioc-check workflow on my package with the
develversions of R and Bioconductor created withuse_bioc_github_action(biocdocker = "devel"). Everything works fine on macOS and Linux, but the Windows workflow fails when installing the dependencies for my package. Because this is devel, I get the message that the following packages are only available in source form and may need compilation:Everything seems to download fine, and even some packages compile and install properly, including:
zlibbioc,S4Vectors,BiocParallel,Rhtslib,XVector,S4Arrays,Biostrings,GenomicRanges,DelayedArray,Rsamtools,GenomicAlignments,InteractionSet, andAnnotationHub. However, once the workflow gets tortracklayer, compilation fails:This then prevents other packages with a dependency on
rtracklayerto fail, and the workflow exits and cannot go on to check my package.I am not sure if this is an
rtracklayerissue or a compiler issue, but any guidance on how to try to get these dependency installs working in this workflow would be very much appreciated.Here I have attached the full logs from the Windows action run as well as the Linux and macOS for reference. 0_ubuntu-latest (devel).txt 1_macOS-latest (devel).txt 2_windows-latest (devel).txt Please let me know if there is any other helpful information I can provide to work through this.
Thank you so much!
Best, Nicole