DEar sirs Im performing an diferencial expression analysis of data. Im working with 3,4,2 version of R. When I try yo install DESeq 2, appear the following commands
ERROR: configuration failed for package ‘XML’
* removing ‘/home/jesus/R/x86_64-pc-linux-gnu-library/3.4/XML’
ERROR: dependency ‘RCurl’ is not available for package ‘GenomeInfoDb’
* removing ‘/home/jesus/R/x86_64-pc-linux-gnu-library/3.4/GenomeInfoDb’
ERROR: dependencies ‘XML’, ‘RCurl’ are not available for package ‘annotate’
* removing ‘/home/jesus/R/x86_64-pc-linux-gnu-library/3.4/annotate’
ERROR: dependency ‘GenomeInfoDb’ is not available for package ‘GenomicRanges’
* removing ‘/home/jesus/R/x86_64-pc-linux-gnu-library/3.4/GenomicRanges’
ERROR: dependency ‘annotate’ is not available for package ‘genefilter’
* removing ‘/home/jesus/R/x86_64-pc-linux-gnu-library/3.4/genefilter’
ERROR: dependency ‘annotate’ is not available for package ‘geneplotter’
* removing ‘/home/jesus/R/x86_64-pc-linux-gnu-library/3.4/geneplotter’
ERROR: dependencies ‘GenomicRanges’, ‘GenomeInfoDb’ are not available for package ‘SummarizedExperiment’
* removing ‘/home/jesus/R/x86_64-pc-linux-gnu-library/3.4/SummarizedExperiment’
ERROR: dependencies ‘GenomicRanges’, ‘SummarizedExperiment’, ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq2’
* removing ‘/home/jesus/R/x86_64-pc-linux-gnu-library/3.4/DESeq2’
The downloaded source packages are in
‘/tmp/RtmprVlTAg/downloaded_packages’
installation path not writeable, unable to update packages: txtplot, codetools, Matrix
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 ‘XML’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘GenomeInfoDb’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘annotate’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘GenomicRanges’ had non-zero exit status
6: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘genefilter’ had non-zero exit status
7: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘geneplotter’ had non-zero exit status
8: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘SummarizedExperiment’ had non-zero exit status
9: In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘DESeq2’ had non-zero exit status
But when I try to install them very few are disponible and others inform thar are not available for 3,4,2 version and Im unable to continue.
What do we do???
thank you
jesus b