problems with updating deseq2

Question

[grant.hovhannisyan]

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

[Kevin Blighe]

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.