False positive warning during BiocCheck - Bioconductor software dependencies

[boyiguo1]

Hi,

Thanks for creating and maintaining the package!

I recently experienced false positive warnings that relates to the check on Bioconductor sofware dependencies during Bioconductor Single Package Building.

In short, I tried "Imports" or "Depends" on Bioconductor packages, where the check kept prompt warning messages.

• Checking for Bioconductor software dependencies...
  • WARNING: No Bioconductor dependencies detected; consider a CRAN submission.

See more details via https://github.com/Bioconductor/Contributions/issues/3264#issuecomment-1885564697

I don't see other issues mentioned this problem, and hence report here.

Thanks!

Best, Boyi

[LiNk-NY]

Hi @boyiguo1 I can't seem to reproduce this locally:

> BiocCheck:::checkDESCRIPTIONFile("~/bioc/tpSVG/")
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
    Bioconductor dependencies found in Imports & Depends (62%).
* Checking for pinned package versions in DESCRIPTION...

This suggests that there may be something different in the SPB... I would have to investigate more.

[boyiguo1]

Thank you very much!

[LiNk-NY]

@boyiguo1 No problem! Can you bump your package version and push to git.bioconductor.org for another build?

[boyiguo1]

I just did. The warning message is still there with BiocCheckVersion: 1.39.16. Here is the build report (https://bioconductor.org/spb_reports/tpSVG_buildreport_20240112075527.html).

In addition, I saw there's a new error message

• Checking package installation calls in R code... Error in .getDirFiles(rowdf["filename"]) : 'fpaths' input must be a character vector Calls: BiocCheck ... findSymbolsInParsedCode -> apply -> FUN -> sprintf -> .getDirFiles Execution halted

I'm not 100% sure if it is caused by updates in v1.39.16. I didn't had the error last build run where there's no significant change except I put a package from "Depends" to "Imports" (https://github.com/boyiguo1/tpSVG/commit/89ee5a39a31fbebce2c309cbf8c86204ea873c1a).

Thank you so much!

[LiNk-NY]

Thanks Boyi @boyiguo1 Please disregard the false positive warning on the SPB. I have updated the package to resolve the error. Thanks!

[LiNk-NY]

I found the issue. It looks like there is a difference when the check is run on the tarball. It should be patched in version 1.39.18.