[Bioc-devel] BiocManager::install() downgrade installed packages

[James W. MacDonald]

The main goal for BiocManager is to help end users ensure that their R/BioC
installation is consistent for the version of R that they are using. So by
definition, any packages that are outside the versions for a given R/BioC
installation should be up or down-graded to make the installation valid.
There are those of us who are l33t enough to mix'n'match packages and debug
errors that may then occur. But it's probably not a good idea to make it
easily hacked by naive users, allowing them to do things that might cause
problems.

Anyway, I believe doing

options("BIOCMANAGER_CRANCHECK_BEHAVIOR" = FALSE)

will stop BiocManager::install from changing any installed CRAN packages.
And it's suitably obscure to limit that to the cool kids who can find it.

On Thu, Oct 31, 2019 at 2:21 PM Henrik Bengtsson <henrik.bengtsson using gmail.com>
wrote:

> (posting this here since I think it's not a support question per se)
>
> Hi, I just started an upgrade from Bioc 3.9 to 3.10 on my local R 3.6.1
> setup:
>
> > BiocManager::install(version = "3.10")
> Upgrade 73 packages to Bioconductor version '3.10'? [y/n]: y
> Bioconductor version 3.10 (BiocManager 1.30.9), R 3.6.1 Patched (2019-09-12
>   r77183)
> Installing package(s) 'BiocVersion'
> ...
> Installing package(s) 'base64enc', 'future', 'future.callr', 'listenv',
>   'matrixStats', 'munsell', 'png', 'profmem', 'R.oo', 'rcmdcheck',
> 'scales',
>   'affxparser', 'affy', 'affyio', 'AffymetrixDataTestFiles', 'annotate',
>   'AnnotationDbi', 'AnnotationForge', 'aroma.light', 'Biobase',
> 'BiocCheck',
>   'BiocGenerics', 'BiocParallel', 'BiocStyle', 'BiocVersion', 'biocViews',
>   'Biostrings', 'BSgenome', 'CGHbase', 'CGHcall', 'cytolib',
> 'DelayedArray',
>   'DNAcopy', 'edgeR', 'flowCore', 'flowViz', 'genefilter', 'GenomeInfoDb',
>   'GenomeInfoDbData', 'GenomicAlignments', 'GenomicRanges', 'GO.db',
> 'graph',
>   'GSEABase', 'IlluminaDataTestFiles', 'illuminaio', 'impute', 'IRanges',
>   'limma', 'marray', 'ncdfFlow', 'oligo', 'oligoClasses', 'org.Hs.eg.db',
>   'pdInfoBuilder', 'preprocessCore', 'QDNAseq', 'QDNAseq.hg19',
> 'QDNAseq.mm10',
>   'RBGL', 'Rgraphviz', 'Rhdf5lib', 'Rhtslib', 'RProtoBufLib', 'Rsamtools',
>   'rtracklayer', 'S4Vectors', 'ShortRead', 'STROMA4',
> 'SummarizedExperiment',
>   'XVector', 'zlibbioc'
> trying URL 'https://cloud.r-project.org/src/contrib/base64enc_0.1-3.tar.gz
> '
> Content type 'application/x-gzip' length 7833 bytes
> ==================================================
> downloaded 7833 bytes
>
> trying URL 'https://cloud.r-project.org/src/contrib/future_1.14.0.tar.gz'
> Content type 'application/x-gzip' length 294967 bytes (288 KB)
> ==================================================
> downloaded 288 KB
> ...
>
> It surprised me that BiocManager::install() will _downgrade_ to CRAN(*)
> package versions, even if you have newer versions installed.  For
> instance, I've got base64enc 0.1.4 from
> http://www.rforge.net/base64enc/, my own development version of future
> 1.14.0-9000, and so on.  Note that the prompt says nothing about
> downgrading. Is this really wanted and is there a way to avoid this?
>
> (*) Will this also downgrade Bioc developers' Bioc packages?
>
> Thanks,
>
> Henrik
>
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> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>


-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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