Question: Rsubread installation problem
0
gravatar for agustin.gonvi
5 weeks ago by
Cleveland, OH
agustin.gonvi10 wrote:

Hi, I updated today to R version 3.6.0 (2019-04-26) -- "Planting of a Tree" and I am having trouble installing Rsubread. The message in console is bellow. Any suggestion to solve this? Thanks

>if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
 BiocManager::install("Rsubread")
Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26)
Installing package(s) 'Rsubread'
Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘Rsubread’
  These will not be installed
installation path not writeable, unable to update packages: cluster, nlme
Update old packages: 'BiocParallel'
Update all/some/none? [a/s/n]: 
a
  There is a binary version available but the source version is later:
              binary source needs_compilation
BiocParallel 1.17.18 1.18.0              TRUE
Binaries will be installed
trying URL 'https://bioconductor.org/packages/3.9/bioc/bin/windows/contrib/3.6/BiocParallel_1.17.18.zip'
Content type 'application/zip' length 1633203 bytes (1.6 MB)
downloaded 1.6 MB
package ‘BiocParallel’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
    C:\Users\xxx\AppData\Local\Temp\RtmpqkY4Ed\downloaded_packages
>
rsubread biocparallel • 114 views
ADD COMMENTlink modified 5 weeks ago by Gordon Smyth37k • written 5 weeks ago by agustin.gonvi10
Answer: Rsubread installation problem
2
gravatar for Gordon Smyth
5 weeks ago by
Gordon Smyth37k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth37k wrote:

You appear to be running Windows but Rsubread is only available for Unix or Mac, not Windows. This is a frequently asked question:

I agree that the message from BiocManager could be more helpful, in fact the remarks about compiling the source code are quite misleading.

There is no way around it. Rsubread would need quite a bit of extra code, especially with respect to multi-threading, before it could be made available for Windows.

ADD COMMENTlink modified 4 weeks ago • written 5 weeks ago by Gordon Smyth37k
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