Question: Rsubread installation problem
0
gravatar for agustin.gonvi
7 months 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 • 240 views
ADD COMMENTlink modified 7 months ago by Gordon Smyth39k • written 7 months ago by agustin.gonvi10
Answer: Rsubread installation problem
2
gravatar for Gordon Smyth
7 months ago by
Gordon Smyth39k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth39k 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.

Edit 29 August 2019

Starting from version 1.99.0, Rsubread is now available for Windows as well as the other platforms. For the moment, this is only for the developmental version of Bioconductor.

ADD COMMENTlink modified 3 months ago • written 7 months ago by Gordon Smyth39k
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: 195 users visited in the last hour