yeaa i have been trying to upgrade but I am not able to. After all the commands it remains R 2.13.0.
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
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/
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...
Comment
-
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, 12:52 PM.
Comment
-
> library(cummeRbund) Error in library(cummeRbund) : there is no package called ‘cumm
I also tried the following as GenoMax suggested to cnyh:
liuzi@iitm50ws1255:/$ 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
Comment
-
-
Originally posted by myRNA_Seq View PostThank 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’
Code:> source("http://bioconductor.org/biocLite.R") > biocLite("cummeRbund")
Comment
-
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=$PATH:~/cufflinks-2.0.2.Linux_x86_64/cuffcompare
When I tried to run cuffcompare, it gave me a warning:
Warning: Your version of Cufflinks is not up-to-date. It is recommended that you upgrade to Cufflinks v2.0.2 to benefit from the most recent features and bug fixes (http://cufflinks.cbcb.umd.edu).
and without *.tmap file generated.
So far I have checked, there isn't a copy of cufflinks in other PATHs, such as .: /usr/bin /usr/local/bin etc...
Is there any problem in terms of the path setting?
Thanks a lotLast edited by myRNA_Seq; 02-27-2013, 06:41 AM.
Comment
-
Originally posted by myRNA_Seq View PostI have another problem now.
So far I have checked, there isn't a copy of cufflinks in other PATHs, such as .: /usr/bin /usr/local/bin etc...
Is there any problem in terms of the path setting?
Thanks a lot
Code:$which cufflinks
Comment
-
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
Comment
Latest Articles
Collapse
-
by seqadmin
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...-
Channel: Articles
04-22-2024, 07:01 AM -
-
by seqadmin
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...-
Channel: Articles
04-04-2024, 04:25 PM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 04-25-2024, 11:49 AM
|
0 responses
19 views
0 likes
|
Last Post
by seqadmin
04-25-2024, 11:49 AM
|
||
Started by seqadmin, 04-24-2024, 08:47 AM
|
0 responses
19 views
0 likes
|
Last Post
by seqadmin
04-24-2024, 08:47 AM
|
||
Started by seqadmin, 04-11-2024, 12:08 PM
|
0 responses
62 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
60 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
Comment