[BioC] DESeq2 dependency hell
Mark Christie [guest]
guest at bioconductor.org
Wed Aug 14 17:57:11 CEST 2013
Hi all,
I have entered dependency hell when trying to install DESEq2. I am using Rstudio that is running on linux Mint, with R version 3.0.1.
When I run biocLite(c("DESeq2"), dependencies = TRUE), I get the following warnings at the end of what almost seems like a successful install (See below). I don't think this problem is specific to DESeq2, but does anybody have an idea as to what is going on here.
Warning messages:
1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... :
installation of package âRCurlâ had non-zero exit status
2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... :
installation of package âXMLâ had non-zero exit status
3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... :
installation of package âbiomaRtâ had non-zero exit status
4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... :
installation of package âannotateâ had non-zero exit status
5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... :
installation of package âgeneplotterâ had non-zero exit status
6: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... :
installation of package âDEXSeqâ had non-zero exit status
7: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... :
installation of package âgenefilterâ had non-zero exit status
8: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... :
installation of package âDESeqâ had non-zero exit status
9: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... :
installation of package âDESeq2â had non-zero exit status
10: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ... :
installation of package âpasillaâ had non-zero exit status
11: installed directory not writable, cannot update packages 'MASS', 'spatial'
Many Thanks!
Mark Christie
-- output of sessionInfo():
R version 3.0.1 (2013-05-16)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocInstaller_1.10.3
loaded via a namespace (and not attached):
[1] tools_3.0.1
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