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Question: DESeq2 package for R 3.3.3
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gravatar for valentina.losardo
28 days ago by
valentina.losardo0 wrote:

 

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   
ADD COMMENTlink written 28 days ago by valentina.losardo0
1
gravatar for Martin Morgan
28 days ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:

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.

ADD COMMENTlink written 28 days ago by Martin Morgan ♦♦ 22k

Thanks a lot!!

ADD REPLYlink written 28 days ago by valentina.losardo0
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