Question: Bioconductor: Package "Is Not Available"
3
gravatar for Shigeta
7.4 years ago by
Shigeta460
Berkeley, CA
Shigeta460 wrote:

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!

R bioconductor • 8.0k views
ADD COMMENTlink written 7.4 years ago by Shigeta460

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

ADD REPLYlink written 7.4 years ago by Shigeta460

Nope. See my answer.

ADD REPLYlink written 7.4 years ago by Neilfws48k
12
gravatar for Neilfws
7.4 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

Edit by Kevin Blighe: This is now outdated.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")

ADD COMMENTlink modified 7 days ago by Kevin Blighe44k • written 7.4 years ago by Neilfws48k

bingo - first time bioconductor install issue.

ADD REPLYlink written 7.4 years ago by Shigeta460
7
gravatar for Laurent
7.4 years ago by
Laurent1.6k
Cambridge, UK
Laurent1.6k wrote:

You might be looking for GEOquery, rather than GEOQuery.

ADD COMMENTlink written 7.4 years ago by Laurent1.6k
1

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

ADD REPLYlink written 7.4 years ago by Michael Dondrup46k
1

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

ADD REPLYlink written 7.4 years ago by Shigeta460
1

PS i tried both spellings to make sure too.

ADD REPLYlink written 7.4 years ago by Shigeta460
1

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

ADD REPLYlink written 7.4 years ago by Neilfws48k
1
gravatar for Zev.Kronenberg
7.4 years ago by
United States
Zev.Kronenberg11k wrote:

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.

ADD COMMENTlink modified 7.4 years ago • written 7.4 years ago by Zev.Kronenberg11k
3

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/

ADD REPLYlink written 7.4 years ago by Martin Morgan1.6k
1

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

ADD REPLYlink written 7.4 years ago by Zev.Kronenberg11k
1

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.

ADD REPLYlink written 7.4 years ago by Shigeta460
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