note
> attached to R-4.0.0 RC, but I may have jumped to the wrong conclusion.
>
> Gordon
>
> > -Original Message-
> > From: Hervé Pagès
> > Sent: Tuesday, 21 April 2020 6:51 PM
> > To: Gordon K Smyth ; Martin Morgan
> > ; bioc-devel@r-project.org
>
To: Gordon K Smyth ; Martin Morgan
> ; bioc-devel@r-project.org
> Cc: Yunshun Chen
> Subject: Re: [Bioc-devel] R-devel for Windows: Rtools3.5 vs Rtools4.0
>
> On 4/20/20 23:28, Gordon K Smyth wrote:
> > Thanks, that does help. So it seems that R-4.0.0 will use
> >
r-project.org
Cc: Yunshun Chen
Subject: Re: [Bioc-devel] R-devel for Windows: Rtools3.5 vs Rtools4.0
Yes, all builds of R 4.0 and above are now using Rtools40 on Windows. See:
https://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-2Dproject.org_bin_windows_Rtools_&d
.5, but perhaps without any proper justification. Maybe Rtools4.0
> supports both the 4.0.0 and 4.1.0 pipelines.
> >
> > Thanks
> > Gordon
> >
> >> -----Original Message-----
> >> From: Hervé Pagès
> >> Sent: Tuesday, 21 April 2020 12:01 PM
>
M
To: Gordon K Smyth ; Martin Morgan
; bioc-devel@r-project.org
Cc: Yunshun Chen
Subject: Re: [Bioc-devel] R-devel for Windows: Rtools3.5 vs Rtools4.0
Hi Gordon,
The Bioconductor version to be released (BioC 3.11) uses R 4.0, not R
4.1. The latest Windows built of R 4.0 is available on CR
art()' for an HTML browser interface to help.
> > Type 'q()' to quit R.
> >
> >> install("edgeR")
> > Error in install("edgeR") : could not find function "install"
> >> library(BiocManager")
> >
> > + > l
gsCIctSAMUxFFSy3MRDadA&s=k3mNrMHBrm7lJNPmek3Hxf9nhnh5wbosiLl_G07B2dg&e=
'
Content type 'application/zip' length 3181389 bytes (3.0 MB)
downloaded 3.0 MB
package ‘edgeR’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\smyth\Ap
mpy8bFkk\downloaded_packages
Old packages: 'backports', 'BiocFileCache', 'BiocNeighbors', 'BiocStyle',
'broom', 'dbplyr',
'foreign', 'GenomeInfoDb', 'GenomeInfoDbData', 'gtools', 'isoband'
The Bioconductor 3.11 builds transitioned in the last week to using the new
tool chain, following CRAN's lead.
As a sanity check (ours!) what makes you say
> It appears that the Bioconductor developmental repository is using
> rtools35
?
Martin Morgan
On 4/19/20, 10:41 PM, "Bioc-devel o
Dear Biocore team,
How is Bioconductor handling the transition to the new R for Windows toolchain?
The R-Devel build for Windows currently available from CRAN uses Jerome Oom's
new gcc 8.3.0 toolchain from rtools40, whereas R-Devel builds for Windows
downloaded from CRAN a couple of months ago
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