Question: problems with updating deseq2
0
gravatar for grant.hovhannisyan
3 months ago by
grant.hovhannisyan360 wrote:

Hi All,

Previously I was using the old version of DESeq2 and now decided to update to the latest one. I have updated R and Rstudio.

When I do

 source("https://bioconductor.org/biocLite.R")
 biocLite()

I get

Bioconductor version 3.5 (BiocInstaller 1.26.1), ?biocLite for help 
> biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.2 (2017-09-28).
installation path not writeable, unable to update packages: codetools, lattice, spatial

WHen I do

source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")

I get

BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.2 (2017-09-28).
Installing package(s) ‘DESeq2’
also installing the dependencies ‘RCurl’, ‘GenomeInfoDb’, ‘annotate’, ‘GenomicRanges’,     ‘SummarizedExperiment’, ‘genefilter’, ‘geneplotter’

trying URL 'https://cran.rstudio.com/src/contrib/RCurl_1.95-4.8.tar.gz'
Content type 'application/x-gzip' length 916934 bytes (895 KB)
==================================================
downloaded 895 KB

trying URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/GenomeInfoDb_1.12.3.tar.gz'
Content type 'application/x-gzip' length 3332126 bytes (3.2 MB)
==================================================
downloaded 3.2 MB

trying URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/annotate_1.54.0.tar.gz'
Content type 'application/x-gzip' length 1866174 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/GenomicRanges_1.28.6.tar.gz'
Content type 'application/x-gzip' length 1010422 bytes (986 KB)
==================================================
downloaded 986 KB

trying URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/SummarizedExperiment_1.6.5.tar.gz'
Content type 'application/x-gzip' length 980552 bytes (957 KB)
==================================================
downloaded 957 KB

trying URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/genefilter_1.58.1.tar.gz'
Content type 'application/x-gzip' length 1432383 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

trying URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/geneplotter_1.54.0.tar.gz'
Content type 'application/x-gzip' length 1426788 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

trying URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/DESeq2_1.16.1.tar.gz'
Content type 'application/x-gzip' length 2120407 bytes (2.0 MB)
==================================================
downloaded 2.0 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/ghovhannisyan/R/x86_64-pc-linux-gnu-library/3.4/RCurl’
ERROR: dependency ‘RCurl’ is not available for package ‘GenomeInfoDb’
* removing ‘/home/ghovhannisyan/R/x86_64-pc-linux-gnu-library/3.4/GenomeInfoDb’
ERROR: dependency ‘RCurl’ is not available for package ‘annotate’
* removing ‘/home/ghovhannisyan/R/x86_64-pc-linux-gnu-library/3.4/annotate’
ERROR: dependency ‘GenomeInfoDb’ is not available for package ‘GenomicRanges’
* removing ‘/home/ghovhannisyan/R/x86_64-pc-linux-gnu-library/3.4/GenomicRanges’
ERROR: dependency ‘annotate’ is not available for package ‘genefilter’
* removing ‘/home/ghovhannisyan/R/x86_64-pc-linux-gnu-library/3.4/genefilter’
ERROR: dependency ‘annotate’ is not available for package ‘geneplotter’
* removing ‘/home/ghovhannisyan/R/x86_64-pc-linux-gnu-library/3.4/geneplotter’
ERROR: dependencies ‘GenomicRanges’, ‘GenomeInfoDb’ are not available for package     ‘SummarizedExperiment’
* removing ‘/home/ghovhannisyan/R/x86_64-pc-linux-gnu-library/3.4/SummarizedExperiment’
ERROR: dependencies ‘GenomicRanges’, ‘SummarizedExperiment’, ‘genefilter’, ‘geneplotter’ are not   available for package ‘DESeq2’
* removing ‘/home/ghovhannisyan/R/x86_64-pc-linux-gnu-library/3.4/DESeq2’

The downloaded source packages are in
    ‘/tmp/RtmpAM76K8/downloaded_packages’
installation path not writeable, unable to update packages: codetools, lattice, spatial
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘RCurl’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GenomeInfoDb’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘annotate’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GenomicRanges’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) : 
  installation of package ‘genefilter’ had non-zero exit status
6: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘geneplotter’ had non-zero exit status
7: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘SummarizedExperiment’ had non-zero exit status
8: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘DESeq2’ had non-zero exit status

Very annoying, because need to do a lot of analysis in two days... Will appreciate any help

rstudio deseq2 R • 333 views
ADD COMMENTlink modified 3 months ago • written 3 months ago by grant.hovhannisyan360

The first error relates to RCurl. Take a look at this thread in relation to this: https://github.com/sagemath/cloud/issues/114

Also, it looks like you don't have write permissions to write to whatever disk you're using. Are you running R on a UNIX/linux cluster? You should have the option of installing to a local directory.

ADD REPLYlink written 3 months ago by Kevin Blighe12k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1171 users visited in the last hour