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Old 02-20-2013, 06:58 AM   #1
cnyh
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Default 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’
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Old 02-20-2013, 08:51 AM   #2
GenoMax
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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 08:59 AM.
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Old 02-20-2013, 09:27 AM   #3
cnyh
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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 09:32 AM.
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Old 02-20-2013, 09:39 AM   #4
GenoMax
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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.
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Old 02-20-2013, 11:26 AM   #5
cnyh
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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
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Old 02-20-2013, 11:47 AM   #6
cnyh
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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
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Old 02-20-2013, 12:09 PM   #7
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Can you post the errors (or are they *exactly* the same as before)?
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Old 02-20-2013, 12:19 PM   #8
cnyh
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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.
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Old 02-20-2013, 12:28 PM   #9
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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.
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Old 02-20-2013, 12:39 PM   #10
cnyh
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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?
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Old 02-20-2013, 12:41 PM   #11
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That is good. Try the R install now and post any new errors (hopefully none now).
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Old 02-20-2013, 12:47 PM   #12
cnyh
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It worked! Tested it with "cuff <- readCufflinks()", and it went through without any error messages!

You're brilliant, thank you ever so much!
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Old 02-20-2013, 12:55 PM   #13
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Excellent.
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Old 02-22-2013, 01:18 AM   #14
dishasharma35
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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
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Old 02-22-2013, 03:46 AM   #15
cnyh
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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")
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Old 02-22-2013, 09:59 AM   #16
dishasharma35
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yeaa i have been trying to upgrade but I am not able to. After all the commands it remains R 2.13.0.
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Old 02-22-2013, 10:13 AM   #17
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Quote:
Originally Posted by dishasharma35 View Post
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?
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Old 02-22-2013, 12:18 PM   #18
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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...
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Old 02-22-2013, 09:04 PM   #19
dishasharma35
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yes... I did install by using the command for administrator rights. I guess main problem is the up-gradation for R
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Old 02-25-2013, 12:47 PM   #20
myRNA_Seq
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Default 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 12:52 PM.
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