Installing issues with 'gage', 'pathview' and more

Question

[Kaustubh]

Hi all,

I have been trying to install some Bioconductor packages and having several problems with it. Here is the first one. When I tried to install DESeq, I get the following error,

Warning: namespace 'DESeq' is not available and has been replaced
by .GlobalEnv when processing object 'cds

I also tried to install gage and ended up with this,

Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
  there is no package called 'DBI'
Error: package or namespace load failed for 'gage'

and finally for pathview,

Error: package 'org.Hs.eg.db' required by 'pathview' could not be found.

When I try to install org.HS.eg.db,

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.2 (BiocInstaller 1.20.1), ?biocLite for help
> biocLite("org.Hs.eg.db")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.1), R 3.2.3 (2015-12-10).
Installing package(s) 'org.Hs.eg.db'
Warning: unable to access index for repository http://cran.opensourceresources.org/src/contrib:
  cannot open URL 'http://cran.opensourceresources.org/src/contrib/PACKAGES'
Warning: unable to access index for repository http://cran.opensourceresources.org/bin/macosx/mavericks/contrib/3.2:
  cannot open URL 'http://cran.opensourceresources.org/bin/macosx/mavericks/contrib/3.2/PACKAGES'
installing the source package 'org.Hs.eg.db'

trying URL 'https://bioconductor.org/packages/3.2/data/annotation/src/contrib/org.Hs.eg.db_3.2.3.tar.gz'
Content type 'application/x-gzip' length 68856557 bytes (65.7 MB)
==================================================
downloaded 65.7 MB

* installing *source* package 'org.Hs.eg.db' ...
** R
** inst
** preparing package for lazy loading
Error 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 'org.Hs.eg.db'
* removing '/Library/Frameworks/R.framework/Versions/3.2/Resources/library/org.Hs.eg.db'

The downloaded source packages are in
    '/private/var/folders/2h/wbrhr_l17mq9ml2nmnhv8stw0000gn/T/RtmpzHRpkM/downloaded_packages'
Warning: unable to access index for repository http://cran.opensourceresources.org/src/contrib:
  cannot open URL 'http://cran.opensourceresources.org/src/contrib/PACKAGES'
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package 'org.Hs.eg.db' had non-zero exit status

Can anyone please help me with this? Sorry to post multiple issues in one go, but I wonder if they are somehow related.

Thanks!

Kaustubh

Answer 1

[h.mon]

The mirror http://cran.opensourceresources.org/src/contrib/PACKAGES doesn't seem to exist anymore, you should choose a different one. I do not remember if AnnotationDBI automatically installs DBI, but if it doesn't you have to install it with install.packages("DBI").

[Kaustubh]

Hi h.mon,

Thanks!