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

Henrik Bengtsson henr|k@bengt@@on @end|ng |rom gm@||@com
Thu Oct 31 20:53:49 CET 2019

On Thu, Oct 31, 2019 at 11:52 AM James W. MacDonald <jmacdon using uw.edu> wrote:
> 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
> 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.

Unfortunately, this doesn't seem to make a difference.  By searching
the GitHub code base it doesn't look like this option is used
anywhere: https://github.com/search?q=org%3ABioconductor+BIOCMANAGER_CRANCHECK_BEHAVIOR&type=Code

My current workaround it to not use BiocManager and roll my own
'repos' settings;

> unname(getOption("repos"))
[1] "https://cloud.r-project.org"
[2] "https://bioconductor.org/packages/3.10/bioc"
[3] "https://bioconductor.org/packages/3.10/data/annotation"
[4] "https://bioconductor.org/packages/3.10/data/experiment"
[5] "https://bioconductor.org/packages/3.10/workflows"

and use good old update.packages().

Alternative wish: It would be handy if there was a
BiocManager::repositories(version = "3.10") for finding these,
especially since some of them come and go depending on Bioc version.


PS. I also tried setting ditto env var because it looked more like an
env var than R option name to me.

> 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
>> _______________________________________________
>> 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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