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

Henrik Bengtsson henr|k@bengt@@on @end|ng |rom gm@||@com
Thu Oct 31 19:20:04 CET 2019

(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?



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