[Bioc-devel] BiocManager::install() downgrade installed packages
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
> 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.
Unfortunately, this doesn't seem to make a difference. By searching
the GitHub code base it doesn't look like this option is used
My current workaround it to not use BiocManager and roll my own
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
>> 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?
>> Bioc-devel using r-project.org mailing list
> James W. MacDonald, M.S.
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
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