Having Trouble Upgrading Bioconductor
2
1
Entering edit mode
7.7 years ago
jobinv ★ 1.1k

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?

bioconductor • 13k views
ADD COMMENT
1
Entering edit mode

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).

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
2
Entering edit mode
7.7 years ago
Neilfws 49k

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)
ADD COMMENT
0
Entering edit mode

It seems even the first part is failing:

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

ADD REPLY
1
Entering edit mode

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'.

ADD REPLY
0
Entering edit mode

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 :)

ADD REPLY
0
Entering edit mode

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!

ADD REPLY
0
Entering edit mode
7.7 years ago

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.

ADD COMMENT

Login before adding your answer.

Traffic: 1231 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6