Question: Having Trouble Upgrading Bioconductor
1
gravatar for jobinv
4.3 years ago by
jobinv1.1k
Bergen, Norway
jobinv1.1k wrote:

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 • 10.0k views
ADD COMMENTlink modified 4.3 years ago by Neilfws47k • written 4.3 years ago by jobinv1.1k
1

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 REPLYlink written 4.3 years ago by Martin Morgan1.5k

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 REPLYlink written 4.3 years ago by Sudeep1.5k

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

ADD REPLYlink written 4.3 years ago by jobinv1.1k
2
gravatar for Neilfws
4.3 years ago by
Neilfws47k
Sydney, Australia
Neilfws47k wrote:

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 COMMENTlink written 4.3 years ago by Neilfws47k

It seems even the first part is failing:

> source("http://bioconductor.org/biocLite.R")
> biocLite()
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.12 (BiocInstaller 1.10.3), R version 3.0.1.
Old packages: 'biomaRt', 'biovizBase', 'cummeRbund', 'GenomicFeatures', 'Gviz',
  'munsell', 'rtracklayer'
Update all/some/none? [a/s/n]: a
trying URL 'http://bioconductor.org/packages/2.12/bioc/src/contrib/biomaRt_2.16.0.tar.gz'
Content type 'application/x-gzip' length 255617 bytes (249 Kb)

[...]

* installing *source* package ‘biomaRt’ ...
** R
** inst
** preparing package for lazy loading
Error : package ‘RCurl’ was built before R 3.0.0: please re-install it
ERROR: lazy loading failed for package ‘biomaRt’
* removing ‘/usr/local/lib/R/site-library/biomaRt’
* restoring previous ‘/usr/local/lib/R/site-library/biomaRt’
* installing *source* package ‘munsell’ ...
** package ‘munsell’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
Error : package ‘colorspace’ was built before R 3.0.0: please re-install it
ERROR: lazy loading failed for package ‘munsell’
* removing ‘/usr/local/lib/R/site-library/munsell’
* restoring previous ‘/usr/local/lib/R/site-library/munsell’
* installing *source* package ‘rtracklayer’ ...
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64  -I"/usr/local/lib/R/site-library/IRanges/include"  -g -fpic  -O3 -pipe  -g  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64  -I"/usr/local/lib/R/site-library/IRanges/include"  -g -fpic  -O3 -pipe  -g  -c R_init_rtracklayer.c -o R_init_rtracklayer.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64  -I"/usr/local/lib/R/site-library/IRanges/include"  -g -fpic  -O3 -pipe  -g  -c bigWig.c -o bigWig.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64  -I"/usr/local/lib/R/site-library/IRanges/include"  -g -fpic  -O3 -pipe  -g  -c chain_io.c -o chain_io.o
chain_io.c: In function ‘read_chain_file’:
chain_io.c:119:14: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64  -I"/usr/local/lib/R/site-library/IRanges/include"  -g -fpic  -O3 -pipe  -g  -c twoBit.c -o twoBit.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64  -I"/usr/local/lib/R/site-library/IRanges/include"  -g -fpic  -O3 -pipe  -g  -c handlers.c -o handlers.o

[...]

gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64  -I"/usr/local/lib/R/site-library/IRanges/include"  -g -fpic  -O3 -pipe  -g  -c ucsc/udc.c -o ucsc/udc.o
ucsc/udc.c: In function ‘udcInfoViaHttp’:
ucsc/udc.c:405:1: warning: implicit declaration of function ‘strptime’ [-Wimplicit-function-declaration]
ucsc/udc.c:405:62: warning: comparison between pointer and integer [enabled by default]
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64  -I"/usr/local/lib/R/site-library/IRanges/include"  -g -fpic  -O3 -pipe  -g  -c ucsc/net.c -o ucsc/net.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64  -I"/usr/local/lib/R/site-library/IRanges/include"  -g -fpic  -O3 -pipe  -g  -c ucsc/bits.c -o ucsc/bits.o

[...]

gcc -std=gnu99 -shared -o rtracklayer.so IRanges_stubs.o R_init_rtracklayer.o bigWig.o chain_io.o twoBit.o handlers.o utils.o ucsc/bPlusTree.o ucsc/bbiRead.o ucsc/bbiWrite.o ucsc/bwgCreate.o ucsc/bwgQuery.o ucsc/cirTree.o ucsc/common.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/errabort.o ucsc/hash.o ucsc/linefile.o ucsc/localmem.o ucsc/sqlNum.o ucsc/zlibFace.o ucsc/dystring.o ucsc/hmmstats.o ucsc/obscure.o ucsc/pipeline.o ucsc/rangeTree.o ucsc/rbTree.o ucsc/memalloc.o ucsc/dlist.o ucsc/udc.o ucsc/net.o ucsc/bits.o ucsc/twoBit.o ucsc/_cheapcgi.o ucsc/internet.o ucsc/https.o ucsc/base64.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o ucsc/_portimpl.o -lz -pthread -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/rtracklayer/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
Error : package ‘RCurl’ was built before R 3.0.0: please re-install it
ERROR: lazy loading failed for package ‘rtracklayer’
* removing ‘/usr/local/lib/R/site-library/rtracklayer’
* restoring previous ‘/usr/local/lib/R/site-library/rtracklayer’
* installing *source* package ‘GenomicFeatures’ ...
** R
** inst
** preparing package for lazy loading
Error : package ‘RCurl’ was built before R 3.0.0: please re-install it
ERROR: lazy loading failed for package ‘GenomicFeatures’
* removing ‘/usr/local/lib/R/site-library/GenomicFeatures’
* restoring previous ‘/usr/local/lib/R/site-library/GenomicFeatures’
* installing *source* package ‘biovizBase’ ...
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3 -pipe  -g  -c R_init_biovizBase.c -o R_init_biovizBase.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -O3 -pipe  -g  -c bin_offsets.c -o bin_offsets.o
gcc -std=gnu99 -shared -o biovizBase.so R_init_biovizBase.o bin_offsets.o -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/biovizBase/libs
** R
** data
** inst
** preparing package for lazy loading
Error : package ‘RColorBrewer’ was built before R 3.0.0: please re-install it
ERROR: lazy loading failed for package ‘biovizBase’
* removing ‘/usr/local/lib/R/site-library/biovizBase’
* restoring previous ‘/usr/local/lib/R/site-library/biovizBase’
* installing *source* package ‘Gviz’ ...
** R
** data
** inst
** preparing package for lazy loading
Error : package ‘biomaRt’ was built before R 3.0.0: please re-install it
ERROR: lazy loading failed for package ‘Gviz’
* removing ‘/usr/local/lib/R/site-library/Gviz’
* restoring previous ‘/usr/local/lib/R/site-library/Gviz’
* installing *source* package ‘cummeRbund’ ...
** R
** data
** inst
** preparing package for lazy loading
Error : package ‘ggplot2’ was built before R 3.0.0: please re-install it
ERROR: lazy loading failed for package ‘cummeRbund’
* removing ‘/usr/local/lib/R/site-library/cummeRbund’
* restoring previous ‘/usr/local/lib/R/site-library/cummeRbund’

The downloaded source packages are in
        ‘/tmp/RtmplVNTcn/downloaded_packages’
Warning messages:
1: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  installation of package ‘biomaRt’ 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 ‘rtracklayer’ had non-zero exit status
4: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  installation of package ‘GenomicFeatures’ had non-zero exit status
5: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  installation of package ‘biovizBase’ had non-zero exit status
6: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  installation of package ‘Gviz’ had non-zero exit status
7: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  installation of package ‘cummeRbund’ had non-zero exit status
ADD REPLYlink written 4.3 years ago by jobinv1.1k
1

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 REPLYlink written 4.3 years ago by Martin Morgan1.5k

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 REPLYlink written 4.3 years ago by Neilfws47k

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 REPLYlink written 4.3 years ago by jobinv1.1k
0
gravatar for Leonor Palmeira
4.3 years ago by
Leonor Palmeira3.6k
Liège, Belgium
Leonor Palmeira3.6k wrote:

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 COMMENTlink modified 4.3 years ago • written 4.3 years ago by Leonor Palmeira3.6k
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