Rsubread installation issues

Question

[lshepard]

I have been trying to install the Rsubread package with no success for some reason.

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

[Devon Ryan]

FYI, I suspect you'll get faster help with this problem on the bioconductor support site, given how few people here use R on windows.

Answer 1

[Martin Morgan]

See https://support.bioconductor.org/p/65429/