Something's fishy with my R devel/Bioc 3.1 installation and I fail to see what is wrong.
I want to install Homo.sapiens: > library("BiocInstaller") ## Bioconductor version 3.1 (BiocInstaller 1.17.1), ?biocLite for help > biocLite("Homo.sapiens") ## BioC_mirror: http://bioconductor.org ## Using Bioconductor version 3.1 (BiocInstaller 1.17.1), R version 3.2.0. ## Installing package(s) 'Homo.sapiens' ## trying URL 'http://bioconductor.org/packages/3.1/data/annotation/src/contrib/Homo.sapiens_1.1.2.tar.gz' ## Content type 'application/x-gzip' length 1511 bytes ## opened URL ## ================================================== ## downloaded 1511 bytes ## ## * installing *source* package ‘Homo.sapiens’ ... ## ** R ## ** data ## ** preparing package for lazy loading ## Error : .onLoad failed in loadNamespace() for 'GO.db', details: ## call: ls(envir, all.names = TRUE) ## error: 2 arguments passed to .Internal(ls) which requires 3 ## Error : package ‘GO.db’ could not be loaded ## ERROR: lazy loading failed for package ‘Homo.sapiens’ ## * removing ‘/home/lg390/R/x86_64-unknown-linux-gnu-library/3.2/Homo.sapiens’ ## * restoring previous ‘/home/lg390/R/x86_64-unknown-linux-gnu-library/3.2/Homo.sapiens’ ## ## The downloaded source packages are in ## ‘/tmp/RtmpXYXfis/downloaded_packages’ ## Warning message: ## In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : ## installation of package ‘Homo.sapiens’ had non-zero exit status GO.db is up-to-date, but let's (successfully) biocLite and load it: > biocLite("GO.db") ## BioC_mirror: http://bioconductor.org ## Using Bioconductor version 3.1 (BiocInstaller 1.17.1), R version 3.2.0. ## Installing package(s) 'GO.db' ## trying URL 'http://bioconductor.org/packages/3.1/data/annotation/src/contrib/GO.db_3.0.0.tar.gz' ## Content type 'application/x-gzip' length 28747892 bytes (27.4 MB) ## opened URL ## ================================================== ## downloaded 27.4 MB ## ## * installing *source* package ‘GO.db’ ... ## ** R ## ** inst ## ** preparing package for lazy loading ## ** help ## *** installing help indices ## ** building package indices ## ** testing if installed package can be loaded ## * DONE (GO.db) ## ## The downloaded source packages are in ## ‘/tmp/Rtmprr15y4/downloaded_packages’ > suppressPackageStartupMessages(library("GO.db")) Repeating unsuccessful attempt to install Homo.sapiens fails again: > bioclite("homo.sapiens") ## bioc_mirror: http://bioconductor.org ## using bioconductor version 3.1 (biocinstaller 1.17.1), r version 3.2.0. ## installing package(s) 'homo.sapiens' ## trying url 'http://bioconductor.org/packages/3.1/data/annotation/src/contrib/homo.sapiens_1.1.2.tar.gz' ## content type 'application/x-gzip' length 1511 bytes ## opened url ## ================================================== ## downloaded 1511 bytes ## ## * installing *source* package ‘homo.sapiens’ ... ## ** r ## ** data ## ** preparing package for lazy loading ## error : .onload failed in loadnamespace() for 'go.db', details: ## call: ls(envir, all.names = true) ## error: 2 arguments passed to .internal(ls) which requires 3 ## error : package ‘go.db’ could not be loaded ## error: lazy loading failed for package ‘homo.sapiens’ ## * removing ‘/home/lg390/r/x86_64-unknown-linux-gnu-library/3.2/homo.sapiens’ ## * restoring previous ‘/home/lg390/r/x86_64-unknown-linux-gnu-library/3.2/homo.sapiens’ ## ## the downloaded source packages are in ## ‘/tmp/rtmprr15y4/downloaded_packages’ ## warning message: ## in install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : ## installation of package ‘homo.sapiens’ had non-zero exit status I have the exact same error with ReportingTools/PFAM.db, Mus.musculus/GO.db and probably others. Session info with other relevant package versions below. I experienced the same error with a slightly older R-devel (2014-10-29 r66897). Any hints? Best wishes, Laurent > library("RSQLite") > library("AnnotationDbi") > 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] parallel stats4 stats graphics grDevices utils datasets ## [8] methods base ## ## other attached packages: ## [1] GO.db_3.0.0 RSQLite_1.0.0 DBI_0.3.1 ## [4] AnnotationDbi_1.29.1 GenomeInfoDb_1.3.6 IRanges_2.1.4 ## [7] S4Vectors_0.5.2 Biobase_2.27.0 BiocGenerics_0.13.0 ## [10] BiocInstaller_1.17.1 ## ## loaded via a namespace (and not attached): ## [1] compiler_3.2.0 tools_3.2.0 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel