Having Trouble Upgrading Bioconductor

Question

[jobinv]

I recently upgraded my R version to 3.0.0, and just now discovered that I can no longer load my previous installation of cummeRbund, getting the error message

Error: package ‘cummeRbund’ was built before R 3.0.0: please re-install it

I try to reinstall it by using the straightforward command from http://www.bioconductor.org/packages/2.12/bioc/html/cummeRbund.html:

source("http://bioconductor.org/biocLite.R")
    biocLite("cummeRbund")

However, this keeps running through a bunch of commands, then giving the following warning messages:

The downloaded source packages are in
        ‘/tmp/RtmplVNTcn/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning messages:
1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘cummeRbund’ had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  installation of package ‘munsell’ had non-zero exit status
3: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  installation of package ‘biomaRt’ had non-zero exit status
4: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  installation of package ‘rtracklayer’ had non-zero exit status
5: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  installation of package ‘GenomicFeatures’ had non-zero exit status
6: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  installation of package ‘biovizBase’ had non-zero exit status
7: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  installation of package ‘Gviz’ had non-zero exit status
8: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  installation of package ‘cummeRbund’ had non-zero exit status

And the error message still stands:

> library(cummeRbund)
Error: package ‘cummeRbund’ was built before R 3.0.0: please re-install it

What am I doing wrong?

[Martin Morgan]

It sort of looks like a dependency fails to install, and then everything downstream of that fails. I'd look in that 'bunch of commands' for the first package that fails, and work from there. My guess is biomaRt, perhaps because of issues with XML or RCurl (both of which have system dependencies -- libxml2-devel, libcurl-devel, I think).

[Sudeep]

Did you manage to install cummeRbund finally ? Perhaps you could also try installing one of the dependencies of cummeRbund separately and see what error message is thrown

[jobinv]

I did now, a full package reinstall seemed to be the best solution.

Answer 1

[Neilfws]

If the major version of R has changed (from 2 to 3), the "straightforward" biocLite() installation will not work.

First, you need to make sure that the biocLite installer is itself up to date:

source("http://bioconductor.org/biocLite.R")
biocLite()

You can check for package issues using:

biocValid()

And a full package re-install is recommended as explained on the install page:

pkgs <- rownames(installed.packages())
biocLite(pkgs)

[jobinv]

It seems even the first part is failing:

> source("http://bioconductor.org/biocLite.R")
> biocLite()

[Martin Morgan]

Try either updating each failing dependency -- RCurl, munsel, ... -- one at a time, or following the advice to perform a full re-intsall via pkgs <- rownames(installed.packages()); biocLite(pkgs). Probably you originally installed the 'devel' version of R, and you've been caught by a change made just before this version became the 'release'.

[Neilfws]

Well, I did not say that you should "select a" when asked "Update all/some/none". Follow the instructions.

In addition: it is very difficult to provide installation troubleshooting advice, since we cannot know precisely how users may have messed up their own installations :)

[jobinv]

True, you didn't, but you also didn't tell me what to pick when the question came up. I made an honest misunderstanding and selected "a", assuming that upgrading packages is precisely what I want.

Good news is, the full package reinstall that you suggested, did the trick for me. Thanks!

Answer 2

[Leonor Palmeira]

I have R 3.0.1 installed and cummeRbund installs flawlessly (although with a long list of library dependencies) with:

source("http://bioconductor.org/biocLite.R")
biocLite("cummeRbund")

It does ask me if I want to update some other libraries (which I agree to):

Old packages: 'evaluate', 'maps', 'maptools', 'multcomp', 'quantreg', 'SparseM'
Update all/some/none? [a/s/n]: a

I suspect a conflict between your old packages and the ones from your updated R version. For R, from my own experience, I would definitely recommend installing it in a special directory instead of using updating tools, this allows for such conflicts to disappear and leaves you able to run whichever R version you want with the libraries you want for that version.