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
During the COVID-19 pandemic, scientists observed that while some individuals experienced severe illness when infected with SARS-CoV-2, others were barely affected. These disparities left researchers and clinicians wondering what causes the wide variations in response to viral infections and what role genetics plays.
Jean-Laurent Casanova, M.D., Ph.D., Professor at Rockefeller University, is a leading expert in this crossover between genetics and infectious...-
Channel: Articles
09-09-2024, 10:59 AM -
-
by seqadmin
The first FDA-approved CRISPR-based therapy marked the transition of therapeutic gene editing from a dream to reality1. CRISPR technologies have streamlined gene editing, and CRISPR screens have become an important approach for identifying genes involved in disease processes2. This technique introduces targeted mutations across numerous genes, enabling large-scale identification of gene functions, interactions, and pathways3. Identifying the full range...-
Channel: Articles
08-27-2024, 04:44 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Today, 06:25 AM
|
0 responses
13 views
0 likes
|
Last Post
by seqadmin
Today, 06:25 AM
|
||
Started by seqadmin, Yesterday, 01:02 PM
|
0 responses
12 views
0 likes
|
Last Post
by seqadmin
Yesterday, 01:02 PM
|
||
Started by seqadmin, 09-18-2024, 06:39 AM
|
0 responses
14 views
0 likes
|
Last Post
by seqadmin
09-18-2024, 06:39 AM
|
||
Started by seqadmin, 09-11-2024, 02:44 PM
|
0 responses
14 views
0 likes
|
Last Post
by seqadmin
09-11-2024, 02:44 PM
|
Comment