Error when checking for deprecated package usage

[catavallejos]

Hi all,

I am currently getting an error when running BiocCheck. The issue arises in the call to BiocCheck:::getAllDeprecatedPkgs(), particularly via get_deprecated_status("release"). Here is the error I got:

> BiocCheck:::get_deprecated_status("release")
Error in `[.data.frame`(pkg_status, , "PackageStatus") : 
  undefined columns selected

Any clues?

Many thanks in advance for your help.

Best Cata

[LiNk-NY]

Hi Cata, @catavallejos

What version of BiocCheck are you using? Do you have the latest? If not, try with the latest version and post the sessionInfo here.

Best, Marcel

[catavallejos]

Hi Marcel,

I am using 1.36.0, which is the latest version in Bioc Release.

Best Cata

[catavallejos]

Hi @LiNk-NY

I installed the latest version from Github and I get the same error:

> BiocCheck()
─ BiocCheckVersion: 1.37.2
─ BiocVersion: 3.17
─ Package: BASiCS
─ PackageVersion: 2.13.4
─ sourceDir: /Users/catavallejos/Documents/GitHub/BASiCS
─ installDir: /var/folders/87/27s64xsn2qq4tc1qgkfzq8qm0000gq/T//Rtmp0OZn3E/file950ff25a663
─ BiocCheckDir: /Users/catavallejos/Documents/GitHub/BASiCS.BiocCheck
─ platform: unix
─ isTarBall: FALSE

* Installing package...
* Checking for deprecated package usage...
Error in `[.data.frame`(pkg_status, , "PackageStatus") : 
  undefined columns selected

[LiNk-NY]

It looks like there is a CloudFront issue with the file that is accessed. I've applied a more robust way of querying the file. Version 1.36.1 of BiocCheck should be available on Bioconductor release within 48 hours.

[catavallejos]

Thanks for resolving this so quickly @LiNk-NY !

[LiNk-NY]

FWIW You can install the future release version of the package with

BiocManager::install("Bioconductor/BiocCheck", ref = "RELEASE_3_17")