CummeRbund installation failing

[cnyh]

Hello. I am quite new to this game, but I have analyzed my RNA-Seq data using TopHat/Bowtie and cufflinks/cuffdiff. I would now like to visualize the results from cuffdiff using cummeRbund. I have the latest installation of R (2.15.2), but when I try to install cummeRbund by following the instructions on the Bioconductor website, I keep getting an error. I'm not sure what the problem is, unfortunately See copy/pasted text below.

Can anyone help? Thank you!






> source("http://bioconductor.org/biocLite.R")
> biocLite("cummeRbund")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
Installing package(s) 'cummeRbund'
also installing the dependencies ‘XML’, ‘RCurl’, ‘biomaRt’, ‘GenomicFeatures’, ‘biovizBase’, ‘rtracklayer’, ‘Gviz’

trying URL 'http://mirrors.dotsrc.org/cran/src/contrib/XML_3.95-0.1.tar.gz'
Content type 'application/x-gzip' length 1724282 bytes (1.6 Mb)
opened URL
==================================================
downloaded 1.6 Mb

trying URL 'http://mirrors.dotsrc.org/cran/src/contrib/RCurl_1.95-3.tar.gz'
Content type 'application/x-gzip' length 868491 bytes (848 Kb)
opened URL
==================================================
downloaded 848 Kb

trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/biomaRt_2.14.0.tar.gz'
Content type 'application/x-gzip' length 276758 bytes (270 Kb)
opened URL
==================================================
downloaded 270 Kb

trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/GenomicFeatures_1.10.1.tar.gz'
Content type 'application/x-gzip' length 742663 bytes (725 Kb)
opened URL
==================================================
downloaded 725 Kb

trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/biovizBase_1.6.2.tar.gz'
Content type 'application/x-gzip' length 1026756 bytes (1002 Kb)
opened URL
==================================================
downloaded 1002 Kb

trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/rtracklayer_1.18.2.tar.gz'
Content type 'application/x-gzip' length 1308890 bytes (1.2 Mb)
opened URL
==================================================
downloaded 1.2 Mb

trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/Gviz_1.2.1.tar.gz'
Content type 'application/x-gzip' length 1392463 bytes (1.3 Mb)
opened URL
==================================================
downloaded 1.3 Mb

trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/cummeRbund_2.0.0.tar.gz'
Content type 'application/x-gzip' length 2327551 bytes (2.2 Mb)
opened URL
==================================================
downloaded 2.2 Mb

* installing *source* package ‘XML’ ...
** package ‘XML’ successfully unpacked and MD5 sums checked
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
No ability to remove finalizers on externalptr objects in this verison of R
checking for sed... /bin/sed
checking for pkg-config... /usr/bin/pkg-config
checking for xml2-config... no
Cannot find xml2-config
ERROR: configuration failed for package ‘XML’
* removing ‘/usr/local/lib/R/site-library/XML’
* installing *source* package ‘RCurl’ ...
** package ‘RCurl’ successfully unpacked and MD5 sums checked
checking for curl-config... no
Cannot find curl-config
ERROR: configuration failed for package ‘RCurl’
* removing ‘/usr/local/lib/R/site-library/RCurl’
ERROR: dependencies ‘XML’, ‘RCurl’ are not available for package ‘biomaRt’
* removing ‘/usr/local/lib/R/site-library/biomaRt’
ERROR: dependencies ‘XML’, ‘RCurl’ are not available for package ‘rtracklayer’
* removing ‘/usr/local/lib/R/site-library/rtracklayer’
ERROR: dependencies ‘rtracklayer’, ‘biomaRt’, ‘RCurl’ are not available for package ‘GenomicFeatures’
* removing ‘/usr/local/lib/R/site-library/GenomicFeatures’
ERROR: dependency ‘GenomicFeatures’ is not available for package ‘biovizBase’
* removing ‘/usr/local/lib/R/site-library/biovizBase’
ERROR: dependencies ‘rtracklayer’, ‘biomaRt’, ‘GenomicFeatures’, ‘biovizBase’ are not available for package ‘Gviz’
* removing ‘/usr/local/lib/R/site-library/Gviz’
ERROR: dependencies ‘rtracklayer’, ‘Gviz’ are not available for package ‘cummeRbund’
* removing ‘/usr/local/lib/R/site-library/cummeRbund’

The downloaded source packages are in
‘/tmp/Rtmpa83rLN/downloaded_packages’
Warning messages:
1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘XML’ had non-zero exit status
2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘RCurl’ had non-zero exit status
3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘biomaRt’ had non-zero exit status
4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘rtracklayer’ had non-zero exit status
5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘GenomicFeatures’ had non-zero exit status
6: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘biovizBase’ had non-zero exit status
7: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘Gviz’ had non-zero exit status
8: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘cummeRbund’ had non-zero exit status
> library(cummeRbund)
Error in library(cummeRbund) : there is no package called ‘cummeRbund’

[GenoMax]

See the system requirements for XML package (http://cran.r-project.org/web/packages/XML/index.html). Your system is likely missing the "libxml2" library.

Same is probably true for "libcurl" library. Needed for Rcurl package: http://cran.r-project.org/web/packages/RCurl/index.html

What kind of unix system is this?

[cnyh]

Thank you for your quick response! I'm using an Ubuntu 12.04 LTS system.

I don't know how to install these, unfortunately. I tried install.packages("...",dependencies=TRUE) where "..." was replaced with "XML", "libxml2", "libcurl" and "Rcurl", but I kept getting the same kind of "non-zero exit status" error message for some of them, and "package ... is not available (for R version 2.15.2) for others"...

[GenoMax]

Your server is missing the libraries on system side (unrelated to R install).

Do you have administrator rights on this machine? If not you may need to ask your sysadmins to install the libraries.

If you do have access to administrator rights then you should able to install the libraries using the "apt-get" method below.

sudo apt-get install libxml2 libcurl

Once these libraries are installed go back into R and try your original cummerBund install.

[cnyh]

I do have admin rights, yes. I copied your command, and it seems libxml2 got installed, but libcurl was not found. Do I need to download it first?

sudo apt-get install libxml2 libcurl
[sudo] password for cnyh:
Reading package lists... Done
Building dependency tree
Reading state information... Done
E: Unable to locate package libcurl

[cnyh]

Update: to install libcurl I tried using the tips on this page: http://ubuntuforums.org/showthread.php?t=1774516

I then tried to install cummeRbund, but I seem to be getting the same errors as before

[GenoMax]

Can you post the errors (or are they *exactly* the same as before)?

[cnyh]

After the download, this is what comes up:

* installing *source* package ‘XML’ ...
** package ‘XML’ successfully unpacked and MD5 sums checked
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
No ability to remove finalizers on externalptr objects in this verison of R
checking for sed... /bin/sed
checking for pkg-config... /usr/bin/pkg-config
checking for xml2-config... no
Cannot find xml2-config
ERROR: configuration failed for package ‘XML’
* removing ‘/usr/local/lib/R/site-library/XML’
ERROR: dependency ‘XML’ is not available for package ‘biomaRt’
* removing ‘/usr/local/lib/R/site-library/biomaRt’
ERROR: dependency ‘XML’ is not available for package ‘rtracklayer’
* removing ‘/usr/local/lib/R/site-library/rtracklayer’
ERROR: dependencies ‘rtracklayer’, ‘biomaRt’ are not available for package ‘GenomicFeatures’
* removing ‘/usr/local/lib/R/site-library/GenomicFeatures’
ERROR: dependency ‘GenomicFeatures’ is not available for package ‘biovizBase’
* removing ‘/usr/local/lib/R/site-library/biovizBase’
ERROR: dependencies ‘rtracklayer’, ‘biomaRt’, ‘GenomicFeatures’, ‘biovizBase’ are not available fo
r package ‘Gviz’
* removing ‘/usr/local/lib/R/site-library/Gviz’
ERROR: dependencies ‘rtracklayer’, ‘Gviz’ are not available for package ‘cummeRbund’
* removing ‘/usr/local/lib/R/site-library/cummeRbund’

The downloaded source packages are in
‘/tmp/RtmpFKAUMp/downloaded_packages’
Warning messages:
1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘XML’ had non-zero exit status
2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘biomaRt’ had non-zero exit status
3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘rtracklayer’ had non-zero exit status
4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘GenomicFeatures’ had non-zero exit status
5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘biovizBase’ had non-zero exit status
6: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘Gviz’ had non-zero exit status
7: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘cummeRbund’ had non-zero exit status

From first glance it looks much the same, but I'm not sure.

[GenoMax]

It appears that you will also need to install the development version of the libxml.

sudo apt-get install libxml2-dev

Then check

which xml2-config

in a terminal window to make sure it is in your path.

[cnyh]

Ok, done. I get this output:

$ which xml2-config
/usr/bin/xml2-config

Is it relevant information that I am using screen, and switching between different windows in the screen?

[GenoMax]

That is good. Try the R install now and post any new errors (hopefully none now).

[cnyh]

It worked! Tested it with "cuff <- readCufflinks()", and it went through without any error messages!

You're brilliant, thank you ever so much!

[GenoMax]

Excellent.

[dishasharma35]

hey.. you solution helpd me too.. but i am stuck in this step after R installtion for CummeRbund.. the error is :
nstalling package(s) into ‘/home/osdd/R/x86_64-pc-linux-gnu-library/2.13’
(as ‘lib’ is unspecified)
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
package ‘cummeRbund’ is not available (for R version 2.13.1)


I followed above solution but still geting the problem

[cnyh]

My solution to this problem was to upgrade R to version 2.15.2. Also, are you installing using the following commands?

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