CummeRbund installation failing

cnyh · 02-20-2013, 05:58 AM

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 · 02-20-2013, 07:51 AM

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 · 02-20-2013, 08:27 AM

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 · 02-20-2013, 08:39 AM

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.

Code:

sudo apt-get install libxml2 libcurl

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

cnyh · 02-20-2013, 10:26 AM

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 · 02-20-2013, 10:47 AM

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 · 02-20-2013, 11:09 AM

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

cnyh · 02-20-2013, 11:19 AM

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 · 02-20-2013, 11:28 AM

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

Code:

sudo apt-get install libxml2-dev

Then check

Code:

which xml2-config

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

cnyh · 02-20-2013, 11:39 AM

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 · 02-20-2013, 11:41 AM

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

cnyh · 02-20-2013, 11:47 AM

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

You're brilliant, thank you ever so much!

GenoMax · 02-20-2013, 11:55 AM

Excellent.

dishasharma35 · 02-22-2013, 12:18 AM

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 · 02-22-2013, 02:46 AM

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

Quote:

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

dishasharma35 · 02-22-2013, 08:59 AM

yeaa i have been trying to upgrade but I am not able to. After all the commands it remains R 2.13.0.

GenoMax · 02-22-2013, 09:13 AM

Quote:

Originally Posted by dishasharma35

yeaa i have been trying to upgrade but I am not able to. After all the commands it remains R 2.13.0.

Do you have administrator rights on this machine?

cnyh · 02-22-2013, 11:18 AM

I had the same problem actually. "Sudo apt-get install r-base" seemed to install an older version (in my case it was 2.14.0 I believe). A friend of mine set it up so that the following text was added to the bottom of /etc/apt/sources.list:

Quote:

## R BACKPORTS
deb http://cran.uib.no/bin/linux/ubuntu precise/

You can replace the "cran.uib.no" part with the appropriate CRAN mirror (http://cran.r-project.org/mirrors.html).

After doing this, running the same command as above installed the latest version of R, and thus also allowing an installation of cummeRbund.

Perhaps GenoMax can confirm whether this is a correct way to go about it...

dishasharma35 · 02-22-2013, 08:04 PM

yes... I did install by using the command for administrator rights. I guess main problem is the up-gradation for R

myRNA_Seq · 02-25-2013, 11:47 AM

I am new to Linux (Ubuntu) and R. I have similar problem when I try to install cummeRbund. I have tried the way that cnyh used. Following are hte detailed message:

> source("http://bioconductor.org/bioocLite.R")
Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help
> 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 ‘RCurl’, ‘biomaRt’, ‘GenomicFeatures’, ‘biovizBase’, ‘rtracklayer’, ‘Gviz’

trying URL 'http://cran.fhcrc.org/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 ‘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 ‘/home/liuzi/R/x86_64-pc-linux-gnu-library/2.15/RCurl’
ERROR: dependency ‘RCurl’ is not available for package ‘biomaRt’
* removing ‘/home/liuzi/R/x86_64-pc-linux-gnu-library/2.15/biomaRt’
ERROR: dependency ‘RCurl’ is not available for package ‘rtracklayer’
* removing ‘/home/liuzi/R/x86_64-pc-linux-gnu-library/2.15/rtracklayer’
ERROR: dependencies ‘rtracklayer’, ‘biomaRt’, ‘RCurl’ are not available for package ‘GenomicFeatures’
* removing ‘/home/liuzi/R/x86_64-pc-linux-gnu-library/2.15/GenomicFeatures’
ERROR: dependency ‘GenomicFeatures’ is not available for package ‘biovizBase’
* removing ‘/home/liuzi/R/x86_64-pc-linux-gnu-library/2.15/biovizBase’
ERROR: dependencies ‘rtracklayer’, ‘biomaRt’, ‘GenomicFeatures’, ‘biovizBase’ are not available for package ‘Gviz’
* removing ‘/home/liuzi/R/x86_64-pc-linux-gnu-library/2.15/Gviz’
ERROR: dependencies ‘rtracklayer’, ‘Gviz’ are not available for package ‘cummeRbund’
* removing ‘/home/liuzi/R/x86_64-pc-linux-gnu-library/2.15/cummeRbund’

The downloaded source packages are in
‘/tmp/RtmpSX1mhe/downloaded_packages’
Warning messages:
1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘RCurl’ 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
8: installed directory not writable, cannot update packages 'boot', 'class',
'cluster', 'foreign', 'lattice', 'MASS', 'Matrix', 'mgcv', 'nlme', 'nnet',
'rpart', 'spatial', 'survival'
> library(cummeRbund)
Error in library(cummeRbund) : there is no package called ‘cummeRbund

BTW, my R version is 2.15.1 (2012-06-22) -

Is anybody can tell me what libs that I need and how to install them?

Thanks,

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
cummeRbund installation	m_elena_bioinfo	Bioinformatics	3	08-02-2012 01:42 AM
Experiment deletion failing	BenjaminL	Ion Torrent	0	07-29-2012 10:10 PM
BWA and Samtools installation failing	JamesT	Bioinformatics	3	07-02-2012 03:24 AM
Tophat problem: failing reads alignment	Annibal	RNA Sequencing	6	05-18-2012 12:34 PM
TopHat 1.1 failing on colorspace SE reads	krobison	Bioinformatics	22	09-22-2011 11:25 AM

02-20-2013, 05:58 AM	#1
cnyh Member Location: Norway Join Date: Feb 2013 Posts: 39	CummeRbund installation failing 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’

02-20-2013, 07:51 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,143	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? Last edited by GenoMax; 02-20-2013 at 07:59 AM.

02-20-2013, 08:27 AM	#3
cnyh Member Location: Norway Join Date: Feb 2013 Posts: 39	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"... Last edited by cnyh; 02-20-2013 at 08:32 AM.

02-20-2013, 08:39 AM	#4
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,143	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. Code: sudo apt-get install libxml2 libcurl Once these libraries are installed go back into R and try your original cummerBund install.

02-20-2013, 10:26 AM	#5
cnyh Member Location: Norway Join Date: Feb 2013 Posts: 39	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

02-20-2013, 10:47 AM	#6
cnyh Member Location: Norway Join Date: Feb 2013 Posts: 39	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

02-20-2013, 11:09 AM	#7
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,143	Can you post the errors (or are they exactly the same as before)?

02-20-2013, 11:19 AM	#8
cnyh Member Location: Norway Join Date: Feb 2013 Posts: 39	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.

02-20-2013, 11:28 AM	#9
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,143	It appears that you will also need to install the development version of the libxml. Code: sudo apt-get install libxml2-dev Then check Code: which xml2-config in a terminal window to make sure it is in your path.

02-20-2013, 11:39 AM	#10
cnyh Member Location: Norway Join Date: Feb 2013 Posts: 39	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?

02-20-2013, 11:41 AM	#11
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,143	That is good. Try the R install now and post any new errors (hopefully none now).

02-20-2013, 11:47 AM	#12
cnyh Member Location: Norway Join Date: Feb 2013 Posts: 39	It worked! Tested it with "cuff <- readCufflinks()", and it went through without any error messages! You're brilliant, thank you ever so much!

02-20-2013, 11:55 AM	#13
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,143	Excellent.

02-22-2013, 12:18 AM	#14
dishasharma35 Junior Member Location: new delhi, india Join Date: Dec 2012 Posts: 4	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

02-22-2013, 08:59 AM	#16
dishasharma35 Junior Member Location: new delhi, india Join Date: Dec 2012 Posts: 4	yeaa i have been trying to upgrade but I am not able to. After all the commands it remains R 2.13.0.

02-22-2013, 08:04 PM	#19
dishasharma35 Junior Member Location: new delhi, india Join Date: Dec 2012 Posts: 4	yes... I did install by using the command for administrator rights. I guess main problem is the up-gradation for R

02-25-2013, 11:47 AM	#20
myRNA_Seq Member Location: Canda Join Date: Feb 2013 Posts: 18	Error in library(cummeRbund) : there is no package called ‘cummeRbund I am new to Linux (Ubuntu) and R. I have similar problem when I try to install cummeRbund. I have tried the way that cnyh used. Following are hte detailed message: > source("http://bioconductor.org/bioocLite.R") Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help > 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 ‘RCurl’, ‘biomaRt’, ‘GenomicFeatures’, ‘biovizBase’, ‘rtracklayer’, ‘Gviz’ trying URL 'http://cran.fhcrc.org/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 ‘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 ‘/home/liuzi/R/x86_64-pc-linux-gnu-library/2.15/RCurl’ ERROR: dependency ‘RCurl’ is not available for package ‘biomaRt’ * removing ‘/home/liuzi/R/x86_64-pc-linux-gnu-library/2.15/biomaRt’ ERROR: dependency ‘RCurl’ is not available for package ‘rtracklayer’ * removing ‘/home/liuzi/R/x86_64-pc-linux-gnu-library/2.15/rtracklayer’ ERROR: dependencies ‘rtracklayer’, ‘biomaRt’, ‘RCurl’ are not available for package ‘GenomicFeatures’ * removing ‘/home/liuzi/R/x86_64-pc-linux-gnu-library/2.15/GenomicFeatures’ ERROR: dependency ‘GenomicFeatures’ is not available for package ‘biovizBase’ * removing ‘/home/liuzi/R/x86_64-pc-linux-gnu-library/2.15/biovizBase’ ERROR: dependencies ‘rtracklayer’, ‘biomaRt’, ‘GenomicFeatures’, ‘biovizBase’ are not available for package ‘Gviz’ * removing ‘/home/liuzi/R/x86_64-pc-linux-gnu-library/2.15/Gviz’ ERROR: dependencies ‘rtracklayer’, ‘Gviz’ are not available for package ‘cummeRbund’ * removing ‘/home/liuzi/R/x86_64-pc-linux-gnu-library/2.15/cummeRbund’ The downloaded source packages are in ‘/tmp/RtmpSX1mhe/downloaded_packages’ Warning messages: 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ‘RCurl’ 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 8: installed directory not writable, cannot update packages 'boot', 'class', 'cluster', 'foreign', 'lattice', 'MASS', 'Matrix', 'mgcv', 'nlme', 'nnet', 'rpart', 'spatial', 'survival' > library(cummeRbund) Error in library(cummeRbund) : there is no package called ‘cummeRbund BTW, my R version is 2.15.1 (2012-06-22) - Is anybody can tell me what libs that I need and how to install them? Thanks, Last edited by myRNA_Seq; 02-25-2013 at 11:52 AM.