Re: [Bioc-devel] JAVA_HOME cannot be determined on Windows on Bioconductor platform report

I found ``` Error in `toSBGN(system.file("extdata", "biopax3-short-metabolic-pathway.owl", package = "paxtoolsr"), outFile)`: java.lang.UnsatisfiedLinkError: C:\Program Files\Java\jre1.8.0_311\bin\awt.dll: Can't find dependent libraries [ FAIL 1 | WARN 1 | SKIP 3 | PASS 58 ] ``` on a pretty

Re: [Bioc-devel] Updating the vignette in the published package

The changes to the vignette did not include a valid version bump. Could you please trying bumping the version of your description. Regardless of if this is needed to update the website, it would be needed to propagate and have the correct version available from within R using the vignette()

[Bioc-devel] Updating the vignette in the published package

Dear Bioconductor community members, I am wondering how to update the vignette after the package is available from the Bioconductor website? As I have noticed, the available vignette for my package (*https://bioconductor.org/packages/HPiP/ *) includes two

Re: [Bioc-devel] JAVA_HOME cannot be determined on Windows on Bioconductor platform report

Thanks for the responses. But they are not addressing my problem. I have GitHub Actions checking the package on Windows/macOS/Linux using Java OpenJDK 14 with tests/examples running fine on both R release and devel. https://github.com/BioPAX/paxtoolsr/actions/runs/1372348962 At this point, I'm

[Bioc-devel] methylclock error in vignette (windows build)

Hello, In an example of the methylclock package vignette we use a GEO dataset (GSE58045). The data is downloaded during the vignette generation and now in the windows build we get the error : File stored at: D:\biocbuild\bbs-3.14-bioc\tmpdir\RtmpqS7RSx/GPL8490.soft.gz Warning in readBin(inn,

Re: [Bioc-devel] Package name

For CRAN packages it's easy. Packages on CRAN are eternal. They may be archived, but they are never removed, so in a sense they're always "currently on CRAN". Archived packages may still be installed, but only with some efforts of the user. Some packages go in an out of "archived" status depending

Re: [Bioc-devel] Deprecation genphen

Thank you for letting us know. We will begin the deprecation process. The package will be deprecated in 3.15 and removed in 3.16. Cheers, Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets

Re: [Bioc-devel] Package name

This is probably a niche concern, but I’d find it a pity if a good package name (*) became unavailable forever, esp. if it refers to a real-world concept not owned by the authors of the original package. Perhaps we could allow re-using a name after a grace period (say 1 or 2 years)? To be extra