DESeq2 package for R 3.3.3
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@valentinalosardo-16555
Last seen 5.7 years ago

 

Hello, I'm a very naive user of R and I'm trying to install packages that I need for RNA sequencing analysis. I would like to use the DESeq2 package and I'm trying to install it on my Mac computer. This is the output that I get. Any suggestion to fix the problem?Thanks!

> install.packages("DESeq2")
Warning in install.packages :
  package ‘DESeq2’ is not available (for R version 3.3.3)
> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
A new version of Bioconductor is available after installing the most recent version of R; see
  http://bioconductor.org/install
> ?biocLite
> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
A new version of Bioconductor is available after installing the most recent version of R; see
  http://bioconductor.org/install
> biocLite("DESeq2")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.3 (2017-03-06).
Installing package(s) ‘DESeq2’
also installing the dependency ‘RcppArmadillo’

  There is a binary version available but the source version is later:
                   binary      source needs_compilation
RcppArmadillo 0.8.300.1.0 0.8.600.0.0              TRUE

Do you want to install from sources the package which needs compilation?
y/n: y

after this it runs for a bit and at the end this is the message

ld: warning: directory not found for option '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [mgcv.so] Error 1
ERROR: compilation failed for package ‘mgcv’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/mgcv’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/mgcv’

The downloaded source packages are in
    ‘/private/var/folders/p3/p1yv73h132gd9w3wfkzq8gfr0000gn/T/RtmpnKaYT6/downloaded_packages’
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘RcppArmadillo’ had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘cluster’ had non-zero exit status
3: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘Matrix’ had non-zero exit status
4: In install.packages(update[instlib == l, "Package"], l, repos = repos,  :
  installation of package ‘mgcv’ had non-zero exit status

> sessionInfo("DESeq2")
R version 3.3.3 (2017-03-06)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X Yosemite 10.10.5

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
character(0)

other attached packages:
[1] DESeq2_1.14.1

loaded via a namespace (and not attached):
[1] BiocInstaller_1.24.0 graphics_3.3.3       tools_3.3.3          utils_3.3.3         
[5] grDevices_3.3.3      stats_3.3.3          datasets_3.3.3       methods_3.3.3       
[9] base_3.3.3   
deseq2 R 3.3.3 • 1.2k views
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@martin-morgan-1513
Last seen 6 weeks ago
United States

Select 'n' instead of 'y' for source installation. But in the long run you would do better to update to current R, version 3.5.1.

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Thanks a lot!!

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