Is probatch still being maintained? Error on build

[jossmi]

I tried to install it on a new computer with the commands provided in GitHub, and got the following error:
Error: Failed to install 'proBatch' from GitHub:
! System command 'Rcmd.exe' failed
In addition: Warning message:
In file.copy(savedcopy, lib, recursive = TRUE) :
problem copying C:\R\R-4.3.1\library\00LOCK\fs\libs\x64\fs.dll to C:\R\R-4.3.1\library\fs\libs\x64\fs.dll: Permission denied

I also noticed that it is no longer part of Bioconductor. I REALLY like probatch and it has been integrated into our bioinformatics workflow. It would be awful it it stopped functioning.

[lzy604]

I got this error:
E creating vignettes (31.3s)
--- re-building ‘proBatch.Rmd’ using rmarkdown

Quitting from lines 933-934 [citation] (proBatch.Rmd)
Error: processing vignette 'proBatch.Rmd' failed with diagnostics:
A bibentry of bibtype 'Article' has to specify the fields: journal, year
--- failed re-building ‘proBatch.Rmd’

SUMMARY: processing the following file failed:
‘proBatch.Rmd’

Error: Vignette re-building failed.
Execution halted

[lyons89]

I'm getting the same error as @lzy604. I also noticed it's no longer part of Bioconductor. If i can't find an alternative I might have to install the 3.16 version of Bioconductor to the older version to work.

[tobiasko]

Hi @symbioticMe, is proBatch still actively maintained and functional? I am looking for a batch correction tool that can deal with 100-1000s of samples, but the fact that proBatch dropped out of bioc and hasn't seen any code updates during the last years worries me a bit. Could you please clarify?

[ozolotareva]

Hi @tobiasko and all, the bug that was preventing the vignette from building has now been fixed, thanks to @Freddsle.
Yes, proBatch will be maintained, and we do plan to bring it back to Bioconductor in the next release. In the meantime, the latest version can be installed directly from GitHub.

[symbioticMe]

Hi @tobiasko

is proBatch still actively maintained and functional?

We are currently trying to pass the ownership of the package to @ozolotareva and @Freddsle . Stay tuned!