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Question: Rsubread installation issues
1
gravatar for lshepard
2.7 years ago by
lshepard10
United States
lshepard10 wrote:

I have been trying to install the Rsubread package with no success for some reason (http://bioconductor.org/packages/release/bioc/html/Rsubread.html).

This is the output of the first option I tried:

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.0 (BiocInstaller 1.16.1), ?biocLite for help
> biocLite("Rsubread")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.1), R version 3.1.2.
Installing package(s) 'Rsubread'

   package ‘Rsubread’ is available as a source package but not as a binary

Warning messages:
1: package ‘Rsubread’ is not available (for R version 3.1.2) 
2: installed directory not writable, cannot update packages 'boot', 'class', 'cluster',
  'codetools', 'foreign', 'KernSmooth', 'lattice', 'MASS', 'Matrix', 'mgcv', 'nlme', 'nnet',
  'rpart', 'spatial', 'survival' 

First I thought that Rsubread would not work with the most current version of R so I installed two previous versions (3.0 and even back to 2.1) and the same happened to them. 

Then I tried installing by downloading the source package and the following messages show:

* installing *source* package 'Rsubread' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************

** libs

*** arch - i386
Warning: running command 'make -f "Makevars" -f "C:/PROGRA~1/R/R-31~1.2/etc/i386/Makeconf" -f "C:/PROGRA~1/R/R-31~1.2/share/make/winshlib.mk" SHLIB="Rsubread.dll" OBJECTS="HelperFunctions.o R_wrapper.o SNPCalling.o aligner.o atgcContent.o build-sam-index.o core-indel.o core-interface-aligner.o core-interface-subjunc.o core-junction.o core.o detectionCall.o detectionCallAnnotation.o exon-algorithms.o exon-align-indel.o exon-align.o fullscan.o fusion-align.o gene-algorithms.o gene-value-index.o hashtable.o index-builder.o input-files.o interval_merge.o mergeVCF.o processExons.o propmapped.o qualityScores.o readSummary.o removeDupReads.o sam2bed.o sambam-file.o sorted-hashtable.o sublog.o"' had status 127
ERROR: compilation failed for package 'Rsubread'
* removing 'C:/Users/lshepard/Documents/R/win-library/3.1/Rsubread'
Warning in install.packages :
  running command '"C:/PROGRA~1/R/R-31~1.2/bin/x64/R" CMD INSTALL -l "C:\Users\lshepard\Documents\R\win-library\3.1" "C:/Users/lshepard/Downloads/Rsubread_1.16.1.tar.gz"' had status 1
Warning in install.packages :
  installation of package ‘C:/Users/lshepard/Downloads/Rsubread_1.16.1.tar.gz’ had non-zero exit status

Any ideas on how to proceed?  

Here is some general info in case it helps:
> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252  
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                         
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.16.1
ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by lshepard10
1
gravatar for Martin Morgan
2.7 years ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k wrote:

Unfortunately, Rsubread is not available on Windows (there's no Windows version of the package listed at the bottom of the landing page). This is because the package requires system libraries that are not easily available. Unfortunately, the solution is to buy another computer (or rent one or emulate one)!

ADD COMMENTlink written 2.7 years ago by Martin Morgan ♦♦ 20k

Or, option 4: install Linux as the primary OS on the CPU that currently runs windows :-)

ADD REPLYlink written 2.7 years ago by Steve Lianoglou12k
0
gravatar for lshepard
2.7 years ago by
lshepard10
United States
lshepard10 wrote:

Hi Martin, this is exactly what I was suspecting and just wanted a confirmation! I am currently in the hunt for friends who have Macs. Again, thank you! :)

ADD COMMENTlink written 2.7 years ago by lshepard10
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