On Thu, Oct 31, 2019 at 11:52 AM James W. MacDonald <[email protected]> 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 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. /Henrik 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 <[email protected]> > 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 >> >> _______________________________________________ >> [email protected] 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 _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
