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
>

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

• https://support.bioconductor.org/p/42495/
• https://support.bioconductor.org/p/65429/
• https://support.bioconductor.org/p/97666/
• https://support.bioconductor.org/p/115623/

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.