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Make BiocManager work for a version of Bioconductor that doesn't "officially exist" yet

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#46 7 comments 0 reactions 0 assignees View on GitHub

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
35/100
Issue type
Feature
Clarity
Mostly clear
Activity status
Stale
Tech stack
r
Domain
tooling

Research direction

Start with the implementations of BiocManager::version(), BiocManager::repositories(), and BiocManager::install(), then review the BBS/utils/createPropagationDB.R usage mentioned in the report. Done means version and repository queries work when an installed BiocVersion identifies an unreleased version, while installation reports unavailable repositories normally.

Written by the indexing model from the issue text.

Description

So we have a bunch of failures on the BioC 3.10 report today because BiocManager is complaining with:

unknown Bioconductor version '3.10'; see https://bioconductor.org/install`

That's because the build system installed the new BiocVersion (3.10.0) at the beginning of the builds yesterday. Then later during the R CMD build and R CMD check stages of the builds BiocManager detected that BioC 3.10 was being used and didn't like it.

This affected 19 packages on all platforms:

affyILM
BiocCheck
BSgenome
cellscape
CEMiTool
ELBOW
enrichTF
maskBAD
motifbreakR
MutationalPatterns
OmicsLonDA
OPWeight
OrganismDbi
pipeFrame
pkgDepTools
QSutils
quantro
QuasR
Ularcirc

This could be avoided by having BiocManager::version() and BiocManager::repositories() "work" as long as BiocVersion is installed. This would also address other problems we've seen earlier like Marcel's inability to use BioC 3.10 yesterday, or the problem with the BBS/utils/createPropagationDB.R script that broke this afternoon when trying to generate the propagation DB at the end of the BioC 3.10 builds.

Even if the config files at bioconductor.org didn't officially acknowledge its existence until today, BioC 3.10 started to "exist" when we branched yesterday. Furthermore, the 3.10 repos have been available (and populated) for the last 2 weeks and there is no reason why BiocManager couldn't have been used to install stuff from these repos. When the repos are not yet available, BiocManager::install() would emit a warning (it would be the warning coming from install.packages()) and wouldn't be able to install anything, but BiocManager::version() and BiocManager::repositories() would still work.

Is that a reasonable request?

Thanks!

Dominant language
R
Stars
76
Forks
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PR merge metrics
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