New Version of CummeRbund?
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lreiter • 0
@lreiter-9579
Last seen 5.7 years ago

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!

cummerbund rstudio • 2.0k views
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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 7 months ago
United States

Install cummeRbund as described on its landing page:

 

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

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lreiter • 0
@lreiter-9579
Last seen 5.7 years ago

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
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That has nothing to do with cummeRbund which was successfully installed. You chose to update mgcv from source but do not have the appropriate command line tools installed to do that. 

You can ignore this error. if you really want the updated mgcv you can install the binary version:

biocLite("mgcv", type="binary")

Or install Xcode and the command line tools required to build R packages from source.

 

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In addition to installing the Xcode command line tools, it looks like the OP will also need to install gfortran since it seems that mgcv requires that, too.

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lreiter • 0
@lreiter-9579
Last seen 5.7 years ago

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

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