I have been trying to download GO.db, but it keeps failing with the following message:
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
Installing package(s) ‘GO.db’
installing the source package ‘GO.db’
trying URL 'https://bioconductor.org/packages/3.4/data/annotation/src/contrib/GO.db_3.4.0.tar.gz'
Content type 'application/x-gzip' length 31897756 bytes (30.4 MB)
downloaded 30.4 MB
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported. Defaulting to Windows directory.
'\\nfvx341\homeshares3$\HOME.ODO\R\R-3.3.2' is not recognized as an internal or external command,
operable program or batch file.
1: running command '"//nfv/homeshares3$/HOME.ODO/R/R-3.3.2/bin/x64/R" CMD INSTALL -l "\\nfvx341\homeshares3$\HOME\R\R-3.3.2\library" C:\Users\HOME~1.ODO\AppData\Local\Temp\RtmpYtru21/downloaded_packages/GO.db_3.4.0.tar.gz' had status 1
2: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘GO.db’ had non-zero exit status
R version 3.3.2 (2016-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
 LC_COLLATE=English_Ireland.1252 LC_CTYPE=English_Ireland.1252
 LC_MONETARY=English_Ireland.1252 LC_NUMERIC=C
attached base packages:
 parallel stats4 stats graphics grDevices utils datasets
 methods base
other attached packages:
 AnnotationDbi_1.36.2 IRanges_2.8.1 S4Vectors_0.12.1
 Biobase_2.34.0 BiocGenerics_0.20.0 RSQLite_1.1-2
 BiocInstaller_1.24.0 limma_3.30.11
loaded via a namespace (and not attached):
 DBI_0.5-1 tools_3.3.2 memoise_1.0.0 Rcpp_0.12.9 digest_0.6.12
My R and Bioconductor seems to be up-to-date (Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31)), as is my RSQLite (1.1-2) and AnnotationDbi (1.36.2).
I had seen in one group that biocValid(fix=TRUE) worked for them, but this was not the case for me.
Any ideas what I am doing wrong?