I'm trying to install GO.db on Mac OS X with R3.5.0 and Bioconductor 3.7.0:
> library(AnnotationDbi) Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, basename, cbind, colMeans, colnames, colSums, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: IRanges Loading required package: S4Vectors Attaching package: ‘S4Vectors’ The following object is masked from ‘package:base’: expand.grid > biocLite("GO.db") BioC_mirror: https://bioconductor.org Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.0 (2018-04-23). Installing package(s) ‘GO.db’ installing the source package ‘GO.db’ trying URL 'https://bioconductor.org/packages/3.7/data/annotation/src/contrib/GO.db_3.6.0.tar.gz' Content type 'application/x-gzip' length 31763273 bytes (30.3 MB) ================================================== downloaded 30.3 MB * installing *source* package ‘GO.db’ ... ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded Error : package ‘AnnotationDbi’ required by ‘GO.db’ could not be found Error: loading failed Execution halted ERROR: loading failed * removing ‘/Users/jpreuss/Library/R/3.5/library/GO.db’ The downloaded source packages are in ‘/private/var/folders/1v/3by9kjrd6ljd1jz3d04x8dqm7cdgs6/T/RtmpEmgcl1/downloaded_packages’ Warning message: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘GO.db’ had non-zero exit status
I tried specifying
lib.loc and installing via
R CMD INSTALL, but both failed with the same error. Also installing other annotation packages, like
BSgenome.Mmusculus.UCSC.mm10 fail for me. There is no
Any ideas? Many thanks, Jens
R version 3.5.0 (2018-04-23) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Sierra 10.12.6 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib locale:  en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages:  parallel stats4 stats graphics grDevices utils datasets methods base other attached packages:  AnnotationDbi_1.42.1 IRanges_2.14.10 S4Vectors_0.18.2 Biobase_2.40.0 BiocGenerics_0.26.0 BiocInstaller_1.30.0 loaded via a namespace (and not attached):  Rcpp_0.12.17 digest_0.6.15 DBI_1.0.0 RSQLite_2.1.1 blob_1.1.1 tools_3.5.0 bit64_0.9-7 bit_1.1-14 compiler_3.5.0 memoise_1.1.0
Thanks for your reply.
AnnotationDbiinstallation is successful, but
GO.dbfails afterwards with the error message seen above.
Can you investigate where AnnotationDbi is installed, e.g., looking at something like
I don't really know where this will lead, but I would guess that you have two or more .libPaths(), that AnnotationDbi is in a path different from the location (probably the first entry in .libPaths()) where GO.db is being installed.
Another approach might first remove AnnotationDbi (via
remove.packages("AnnotationDbi"), repeated until R says there is no package to remove) and then (in a new session) install it again...
A different tack might be to try to install GO.db without testing that it can be loaded, and one installed in a new session try to load -- exploring the idea that the libPaths() at installation are different from the run-time installation. This could be done at the command line with
or from within R with
Thats great! Thank you for your time and effort.
R CMD INSTALL --no-test-load GO.db_...did the trick! Who knows why the
.libPaths()are different between installation and run time, but it worked now. Thanks again for your help! Highly appreciated!
Glad that worked, can you provide me with the output of
sapply(.libPaths(), function(elt) "AnnotationDbi" %in% dir(elt))? it will help to debug this further.