Bioconductor: Package "Is Not Available"

Question

[Shigeta]

I'm having trouble installing bioconductor packages - it just pretends that they dont' exist:

> source("http://bioconductor.org/biocLite.R")
 BioC_mirror = http://bioconductor.org
 Change using chooseBioCmirror().
 Warning messages:
 1: In safeSource() : Redefining ‘biocinstall’
 2: In safeSource() : Redefining ‘biocinstallPkgGroups’
 3: In safeSource() : Redefining ‘biocinstallRepos’
> install.packages("GEOQuery")
 Installing package(s) into ‘C:/Users/ron/Documents/R/win-library/2.13’
 (as ‘lib’ is unspecified)
 Warning in install.packages :
  package ‘GEOQuery’ is not available (for R version 2.13.1)

I have R 2.13 installed - its the current install for Ubuntu 11 and RStudio. the latest bioconductor docs say they are for R2.14.
After building another build in ubuntu which installed fine, I get the same response:

> install.packages("GEOQuery")
Installing package(s) into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
Warning in install.packages :
  package ‘GEOQuery’ is not available (for R version 2.14.1)

Can anyone help here? Going bonkers. Have gotten this to work on my Mac laptop, but that's not a great place to do work that can take days to run...

thanks!

[Shigeta]

I take it nobody else running ubuntu 11 is having this problem with R 2.13?

[Neilfws]

Nope. See my answer.

Answer 1

[Neilfws]

Edit by Kevin Blighe: This is now outdated. The correct procedure to install a Bioconductor package is now

BiocManager::install("GEOquery")

----------------------------

Like the other answers, I originally thought that your problem was spelling, i.e. GEOquery (correct) not GEOQuery (incorrect).

However, now I see that you are using:

install.packages("GEOquery")

When you should be using:

biocLite("GEOquery")

[Shigeta]

bingo - first time bioconductor install issue.

Answer 2

[Laurent]

You might be looking for GEOquery, rather than GEOQuery.

[Michael]

Exactly: http://bioconductor.org/packages/release/bioc/html/GEOquery.html

[Shigeta]

whoo you had me for a second there, but i think it spelled correctly. I get the same results for 'limma' as well. :(

[Shigeta]

PS i tried both spellings to make sure too.

[Neilfws]

No point trying different spellings. Only one is correct :)

Answer 3

[Zev.Kronenberg]

You have two options that I know of.

1) go to bioconductor and download the packages and install them using R CMD (command line) for R 2.13. You will build the packages manually. It's not too hard.

2) install and older version of R that is compatible with the package you are using.

I would recommend the first option.

[Martin Morgan]

The first option will only set you up for frustration -- you'll install packages that do not have appropriate versions for your R version, or that do not have dependencies with correct versions installed. The second option isn't usually the right solution either, because Bioc packages have a long life; the mis-capitalized GEOQuery won't be in those earlier releases either! The recommended installation instructions are at http://bioconductor.org/install/ and packages available with each R version are described on pages linked in the 'Previous Versions' box of http://bioconductor.org/help/

[Zev.Kronenberg]

@Martin_Morgan is of course correct, unless you like painful {R} sessions.

[Shigeta]

good point - its painful to not get anything done though too. :| i'll try this if no other answer shows up in a day or two.