I am curious as to why biocValid and biocLite do not seem to agree on the update of certain packages:
> library("BiocInstaller") > biocValid() ## ## * sessionInfo() ## ## R Under development (unstable) (2014-11-01 r66923) ## Platform: x86_64-unknown-linux-gnu (64-bit) ## ## locale: ## [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C ## [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 ## [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 ## [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C ## [9] LC_ADDRESS=C LC_TELEPHONE=C ## [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C ## ## attached base packages: ## [1] stats graphics grDevices utils datasets methods base ## ## other attached packages: ## [1] BiocInstaller_1.17.1 ## ## loaded via a namespace (and not attached): ## [1] compiler_3.2.0 tools_3.2.0 ## ## * Out-of-date packages ## Package ## Homo.sapiens "Homo.sapiens" ## Mus.musculus "Mus.musculus" ## qtpaint "qtpaint" ## SNPlocs.Hsapiens.dbSNP.20090506 "SNPlocs.Hsapiens.dbSNP.20090506" ## SNPlocs.Hsapiens.dbSNP.20120608 "SNPlocs.Hsapiens.dbSNP.20120608" ## LibPath ## Homo.sapiens "/home/lg390/R/x86_64-unknown-linux-gnu-library/3.2" ## Mus.musculus "/home/lg390/R/x86_64-unknown-linux-gnu-library/3.2" ## qtpaint "/home/lg390/R/x86_64-unknown-linux-gnu-library/3.2" ## SNPlocs.Hsapiens.dbSNP.20090506 "/home/lg390/R/x86_64-unknown-linux-gnu-library/3.2" ## SNPlocs.Hsapiens.dbSNP.20120608 "/home/lg390/R/x86_64-unknown-linux-gnu-library/3.2" ## Installed Built ReposVer ## Homo.sapiens "1.1.2" "3.1.0" "1.1.2" ## Mus.musculus "1.1.2" "3.1.0" "1.1.2" ## qtpaint "0.9.0" "2.16.0" "0.9.0" ## SNPlocs.Hsapiens.dbSNP.20090506 "0.99.8" "3.0.0" "0.99.8" ## SNPlocs.Hsapiens.dbSNP.20120608 "0.99.9" "3.1.0" "0.99.9" ## Repository ## Homo.sapiens "http://bioconductor.org/packages/3.1/data/annotation/src/contrib" ## Mus.musculus "http://bioconductor.org/packages/3.1/data/annotation/src/contrib" ## qtpaint "http://cran.ma.imperial.ac.uk/src/contrib" ## SNPlocs.Hsapiens.dbSNP.20090506 "http://bioconductor.org/packages/3.1/data/annotation/src/contrib" ## SNPlocs.Hsapiens.dbSNP.20120608 "http://bioconductor.org/packages/3.1/data/annotation/src/contrib" ## ## update with biocLite() ## ## * Packages too new for Bioconductor version '3.1' ## ## Version LibPath ## GenomicRanges "1.19.3" "/home/lg390/R/x86_64-unknown-linux-gnu-library/3.2" ## ## downgrade with biocLite("GenomicRanges") ## ## Error: 5 package(s) out of date; 1 package(s) too new Even though the installed and repo version are the same, I assume that biocValid marks the packages above as out-of-data because they have been built with previous R versions. But, if I run biocLite, no package gets updated. > biocLite() ## BioC_mirror: http://bioconductor.org ## Using Bioconductor version 3.1 (BiocInstaller 1.17.1), R version 3.2.0. Running biocValid(fix=TRUE) will initiate a package download/install. Thank you very much in advance. Laurent _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel