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SofieVG / FlowSOM

Using self-organizing maps for visualization and interpretation of cytometry data
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Building error on Bioconductor #56

Closed Kayla-Morrell closed 1 year ago

Kayla-Morrell commented 1 year ago

Hello Sofie,

I tried to send the following email to you via the email listed in the DESCRIPTION file but it was undeliverable. Please double check that this email is correct so that we may be able to contact you in the future. It is crucial that the packages within Bioconductor list an active maintainer email that responds to inquires.

The next Bioconductor release 3.16 is scheduled for November 2nd. Commits to the current 3.15 release should be made by October 14th and the last day to commit to the devel branch is October 28th. We like to make an effort to have all Bioconductor packages building and checking without ERROR or TIMEOUT in both release and devel versions.

Currently your package is producing an ERROR on the Windows builder in both the release and devel versions of Bioconductor. Could you please investigate the error as soon as possible?

Release version - https://bioconductor.org/checkResults/3.15/bioc-LATEST/FlowSOM/ Devel version - https://bioconductor.org/checkResults/3.16/bioc-LATEST/FlowSOM/

If you need any assistance please feel free to ask questions at bioc-devel@r-project.org.

Thank you, Kayla

SamGG commented 1 year ago

@Kayla-Morrell That might be the reason why I could not install FlowSOM under Windows in binary mode this afternoon. I don't understand why the same C code is passing checks under Linux but not Windows. This sounds like it is due to external libraries. While being not part of the dev team, I will have a look. @SofieVG I sincerely believe that FlowSOM should stay in BC. Hope to bring some clue.

SofieVG commented 1 year ago

@Kayla-Morrell I have no idea why the email was undeliverable, sofie.vangassen@ugent.be should still work (and has worked before for previous errors). I was aware of an issue in the release branch, which had been resolved in the devel branch (but the fix has indeed not yet been committed to the release branch). I was not aware of the new failure yet, and will investigate and update as soon as possible. @SamGG, any additional insights from you are certainly welcome, we strongly appreciate all the help you provide for our package! I would also hope FlowSOM can stay available in Bioconductor.

SamGG commented 1 year ago

Hi,

Current version from this repo is OK on my fresh install of R421, Bioc 3.15 under Windows10. It is also OK in the 3.16 devel branch of Bioc. There is only a note concerning the C code compilation in the check process, but this note is not present in the install process. Not the same compilation options?

XML package is not used in FlowSOM, so could be safely removed from DESCRIPTION; it will be installed as a requirement of flowWorkspace which is part of Suggests:. In fact the following could be safely removed and the documentation rebuilt to update NAMESPACE. https://github.com/SofieVG/FlowSOM/blob/c70beb09ca2242e0d6e75956d460a5120a749898/R/0_FlowSOM.R#L88 In the vignette there should an 's' after color https://github.com/SofieVG/FlowSOM/blob/c70beb09ca2242e0d6e75956d460a5120a749898/vignettes/FlowSOM.Rnw#L337 Not sure I will test the current version of Bioc 3.15. Let me know.

Best.