Question: DESeq2 package for R 3.3.3
0
gravatar for valentina.losardo
8 months 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   
deseq2 r 3.3.3 • 195 views
ADD COMMENTlink written 8 months ago by valentina.losardo0
Answer: C: DESeq2 package for R 3.3.3
1
gravatar for Martin Morgan
8 months ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k 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 8 months ago by Martin Morgan ♦♦ 23k

Thanks a lot!!

ADD REPLYlink written 8 months ago by valentina.losardo0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 428 users visited in the last hour