I am running R version 3.4.1 (2017-06-30) -- "Single Candle"
Trying to install the GO.db package, but here is what happens.
source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help
> biocLite("GO.db")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.1 (2017-06-30).
Installing package(s) ‘GO.db’
Warning: unable to access index for repository https://cran.cnr.berkeley.edu/src/contrib:
cannot open URL 'https://cran.cnr.berkeley.edu/src/contrib/PACKAGES'
Warning: unable to access index for repository https://cran.cnr.berkeley.edu/bin/macosx/el-capitan/contrib/3.4:
cannot open URL 'https://cran.cnr.berkeley.edu/bin/macosx/el-capitan/contrib/3.4/PACKAGES'
installing the source package ‘GO.db’
trying URL 'https://bioconductor.org/packages/3.5/data/annotation/src/contrib/GO.db_3.4.1.tar.gz'
Content type 'application/x-gzip' length 32989255 bytes (31.5 MB)
==================================================
downloaded 31.5 MB
* installing *source* package ‘GO.db’ ...
** R
** inst
** preparing package for lazy loading
Error: package or namespace load failed for ‘AnnotationDbi’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘DBI’
Error : package ‘AnnotationDbi’ could not be loaded
ERROR: lazy loading failed for package ‘GO.db’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/GO.db’
The downloaded source packages are in
‘/private/var/folders/rp/r7df464x5cg21sh1hyv2sd7h0000gn/T/RtmpRFaW1F/downloaded_packages’
Warning: unable to access index for repository https://cran.cnr.berkeley.edu/src/contrib:
cannot open URL 'https://cran.cnr.berkeley.edu/src/contrib/PACKAGES'
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘GO.db’ had non-zero exit status
>
sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocInstaller_1.26.0
loaded via a namespace (and not attached):
[1] compiler_3.4.1 tools_3.4.1
>
