CummeRbund installation failing

[dishasharma35]

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

[GenoMax]

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]

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:

## 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]

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

[myRNA_Seq]

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,

[myRNA_Seq]

Error in library(cummeRbund) : there is no package called ‘cummeRbund

duplicated posting

[myRNA_Seq]

> library(cummeRbund) Error in library(cummeRbund) : there is no package called ‘cumm

I also tried the following as GenoMax suggested to cnyh:

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

[myRNA_Seq]

I also tried the following
sudo apt-get install libxml2-dev;
and still get the same error message...

[GenoMax]

I also tried the following
sudo apt-get install libxml2-dev;
and still get the same error message...

I think you will need one of the dev packages for curl. Try this one

sudo apt-get install libcurl4-openssl-dev

[myRNA_Seq]

Thank you,GenoMax for your quick reply.

I installed "sudo apt-get install libcurl4-openssl-dev" as you suggested.
I still get the same error below.

> library(cummeRbund)
Error in library(cummeRbund) : there is no package called ‘cummeRbund’

[GenoMax]

Thank you,GenoMax for your quick reply.

I installed "sudo apt-get install libcurl4-openssl-dev" as you suggested.
I still get the same error below.

> library(cummeRbund)
Error in library(cummeRbund) : there is no package called ‘cummeRbund’

Did you try to re-install cummeRbund in R after installing the curl library?

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

[myRNA_Seq]

Thank you so much GenoMax!
Following your instruction, I re-installed cummeRbund in R, now it works very well.

[myRNA_Seq]

I have another problem now.

I downloaded latest version of cufflinks binary and also added them to my path as following:
export PATH=$PATH:~/cufflinks-2.0.2.Linux_x86_64/cufflinks
export PATH=$PATH:~/cufflinks-2.0.2.Linux_x86_64/cuffdiff
export PATH=$PATH:~/cufflinks-2.0.2.Linux_x86_64/cuffcompare

When I tried to run cuffcompare, it gave me a warning:

Warning: Your version of Cufflinks is not up-to-date. It is recommended that you upgrade to Cufflinks v2.0.2 to benefit from the most recent features and bug fixes (http://cufflinks.cbcb.umd.edu).

and without *.tmap file generated.

So far I have checked, there isn't a copy of cufflinks in other PATHs, such as .: /usr/bin /usr/local/bin etc...

Is there any problem in terms of the path setting?

Thanks a lot

[GenoMax]

I have another problem now.


So far I have checked, there isn't a copy of cufflinks in other PATHs, such as .: /usr/bin /usr/local/bin etc...

Is there any problem in terms of the path setting?

Thanks a lot

Can you check the following and verify that you are indeed pointing to the right cufflinks executable?

$which cufflinks

[myRNA_Seq]

It says: /usr/bin/cufflinks.
When I use echo $PATH, it didn't show there, why?

************
I have tried full path. It works without warning anymore, and got all the output files except *.refmap *.tmap file. Do you know why?

I followed the instruction from the paper "Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks" (http://www.nature.com/nprot/journal/....2012.016.html) and use exact files in the examples.

$ find . -name transcripts.gtf > gtf_out_list.txt
$ ~/cufflinks-2.0.2.Linux_x86_64/cuffcompare - i gtf_out_list.txt -r gene.gtf