Hi folks,

I have not used R in a while (about a year or so) and I wanted to analyze some Cuffdiff data I generated in Galaxy (RNAseq Tuxedo pipeline).  I went to use CummeRbund and found the following message:

> install.packages("CummeRbund")
Warning in install.packages :
  package ‘CummeRbund’ is not available (for R version 3.2.3)

When I went to the repository (http://compbio.mit.edu/cummeRbund/) it looks like it has not been updated since mid-2014.  Am I missing something here?  Does everyone use another program now?  Looks like people are still downloading it.

Thanks!

Install cummeRbund as described on its landing page:

http://bioconductor.org/packages/cummeRbund/

Thanks - that worked, but I did throw a new error.  This time I failed to update "mgcv"  I could not install the package using the install packages window in RStudio either - same error.

ld: warning: directory not found for option '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [mgcv.so] Error 1
ERROR: compilation failed for package ‘mgcv’
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/mgcv’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/mgcv’

The downloaded source packages are in
    ‘/private/var/folders/6w/6f4949nd4w9dblfrqcjbtkbm0000gp/T/Rtmp8aenU8/downloaded_packages’
Warning message:
In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘mgcv’ had non-zero exit status

Thanks.  That still didn't work for mgcv but if you say it doesn't matter for using CummeRbund i will just move on.