Bioconductor test failures when running tests locally

[kevinushey]

I see:

Failure (test-bundlePackagePackrat.R:56:3): works with BioC packages
Biobase$Source (`actual`) not equal to "Bioconductor" (`expected`).

`actual`:   "BioC"        
`expected`: "Bioconductor"

Failure (test-bundlePackagePackrat.R:60:3): works with BioC packages
BiocGenerics$Source (`actual`) not equal to "Bioconductor" (`expected`).

`actual`:   "BioC"        
`expected`: "Bioconductor"

I suspect this is just because the repository is called "BioC" rather than "Bioconductor", but I'm not sure if rsconnect / packrat is supposed to be normalizing the source name for the repository here?

rsconnect/tests/testthat/test-bundlePackagePackrat.R

Lines 48 to 61 in a3ebf70

	withr::local_options(repos = c(
	CRAN = "https://cran.rstudio.com",
	BioC = "https://bioconductor.org/packages/release/bioc"
	))
	deps <- snapshotPackratDependencies(app)
	Biobase <- deps[deps$Package == "Biobase", ]
	expect_equal(Biobase$Source, "Bioconductor")
	expect_equal(Biobase$Repository, "https://bioconductor.org/packages/release/bioc")
	BiocGenerics <- deps[deps$Package == "BiocGenerics", ]
	expect_equal(BiocGenerics$Source, "Bioconductor")
	expect_equal(BiocGenerics$Repository, "https://bioconductor.org/packages/release/bioc")

In case it's relevant, here's the content of my Biobase DESCRIPTION file.

Package: Biobase
Title: Biobase: Base functions for Bioconductor
Description: Functions that are needed by many other packages or which replace R functions.
biocViews: Infrastructure
URL: https://bioconductor.org/packages/Biobase
BugReports: https://github.com/Bioconductor/Biobase/issues
Version: 2.66.0
License: Artistic-2.0
Authors@R: c( person("R.", "Gentleman", role="aut"), person("V.", "Carey", role = "aut"), person("M.", "Morgan", role="aut"), person("S.", "Falcon", role="aut"), person("Haleema", "Khan", role = "ctb", comment = "'esApply' and 'BiobaseDevelopment' vignette translation from Sweave to Rmarkdown / HTML" ), person("Bioconductor Package Maintainer", role = "cre", email = "[email protected]" ))
Suggests: tools, tkWidgets, ALL, RUnit, golubEsets, BiocStyle, knitr, limma
Depends: R (>= 2.10), BiocGenerics (>= 0.27.1), utils
Imports: methods
VignetteBuilder: knitr
LazyLoad: yes
Collate: tools.R strings.R environment.R vignettes.R packages.R AllGenerics.R
    VersionsClass.R VersionedClasses.R methods-VersionsNull.R
    methods-VersionedClass.R DataClasses.R methods-aggregator.R
    methods-container.R methods-MIAxE.R methods-MIAME.R methods-AssayData.R
    methods-AnnotatedDataFrame.R methods-eSet.R methods-ExpressionSet.R
    methods-MultiSet.R methods-SnpSet.R methods-NChannelSet.R anyMissing.R
    rowOp-methods.R updateObjectTo.R methods-ScalarObject.R zzz.R
git_url: https://git.bioconductor.org/packages/Biobase
git_branch: RELEASE_3_20
git_last_commit: 2cd604f
git_last_commit_date: 2024-10-29
Repository: Bioconductor 3.20
Date/Publication: 2024-10-29
NeedsCompilation: yes
Packaged: 2024-10-29 23:41:04 UTC; biocbuild
Author: R. Gentleman [aut], V. Carey [aut], M. Morgan [aut], S. Falcon [aut], Haleema Khan [ctb] ('esApply' and 'BiobaseDevelopment' vignette translation from Sweave to Rmarkdown / HTML), Bioconductor Package Maintainer [cre]
Maintainer: Bioconductor Package Maintainer <[email protected]>
Built: R 4.4.2; aarch64-apple-darwin20; 2025-01-28 23:54:28 UTC; unix
RemoteType: standard
RemotePkgRef: Biobase
RemoteRef: Biobase
RemoteRepos: https://bioconductor.org/packages/3.20/bioc
RemoteReposName: BioCsoft
RemotePkgPlatform: source
RemoteSha: 2.66.0

[aronatkins]

I have Biobase 2.62.0 locally, and see the tests passing. R 4.3.3 and renv 1.0.11.

These tests are disabled in CI because they've not consistently worked as Bioconductor has changed.

[aronatkins]

In Connect, we specifically look for Source == "Bioconductor".

[aronatkins]

The biocViews: Infrastructure should be enough for Packrat to believe the package is from Bioconductor.
The presence of Repository: Bioconductor 3.20 prevents that logic from running.

My version of the Biobase DESCRIPTION file does not have Repository: xxx.

[aronatkins]

@kevinushey Could you try installing rstudio/packrat#729 to see if that lets you run tests?