[Bioc-devel] R-devel for Windows: Rtools3.5 vs Rtools4.0

[Gordon K Smyth]

Hi Martin,

I may have jumped to the wrong conclusion as to the cause of the problem. The problem we are observing is that BiocManager::install does not currently work with R Devel for Windows 2020-04-18 (which the installer is calling R 4.1.0) while it still works fine with R Devel for Windows 2020-02-15 (which the installer is calling R 4.0.0). In the former case, the installer is trying to find a 4.1 repository that doesn't seem to exist.

Note that I have not renamed R-devel to R 4.1.0 myself. The r-devel-win.exe installer automatically labels the R shortcut as "R 4.1.0".

I am assuming that Bioconductor packages that need compilation have to be build using the same toolchain as used for R itself. Since I can install Bioc packages with R 4.0.0, I assume that I am getting packages built with Rtools3.5. If there is an Rtools4.0 version of Bioc-devel, where is it?

I can git clone the source code for Bioc packages and compile them successfully for R 4.1.0 using Rtools4.0, but that's more tedious that using install().

It is getting very close to the Bioc 3.11 Release, so we would like to make sure that everything works ok with the latest version of R.

Regards
Gordon

------------- R Session with R 4.1.0 for Windows  (fails) --------------

R Under development (unstable) (2020-04-18 r78255) -- "Unsuffered Consequences"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> install.packages("BiocManager")
--- Please select a CRAN mirror for use in this session ---
trying URL 'https://mirror.aarnet.edu.au/pub/CRAN/bin/windows/contrib/4.1/BiocManager_1.30.10.zip'
Content type 'application/zip' length 99799 bytes (97 KB)
downloaded 97 KB

package ‘BiocManager’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\smyth\AppData\Local\Temp\RtmpaqaFCD\downloaded_packages
> library(BiocManager)
Bioconductor version 3.11 (BiocManager 1.30.10), ?BiocManager::install for help
> install("edgeR")
Bioconductor version 3.11 (BiocManager 1.30.10), R Under development (unstable) (2020-04-18 r78255)
Installing package(s) 'BiocVersion', 'edgeR'
also installing the dependencies ‘limma’, ‘locfit’, ‘Rcpp’

Warning: unable to access index for repository https://bioconductor.org/packages/3.11/bioc/bin/windows/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.11/bioc/bin/windows/contrib/4.1/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.11/data/annotation/bin/windows/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.11/data/annotation/bin/windows/contrib/4.1/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.11/data/experiment/bin/windows/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.11/data/experiment/bin/windows/contrib/4.1/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.11/workflows/bin/windows/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.11/workflows/bin/windows/contrib/4.1/PACKAGES'
Packages which are only available in source form, and may need compilation of
  C/C++/Fortran: ‘limma’ ‘edgeR’
  These will not be installed
trying URL 'https://mirror.aarnet.edu.au/pub/CRAN/bin/windows/contrib/4.1/locfit_1.5-9.4.zip'
Content type 'application/zip' length 670513 bytes (654 KB)
downloaded 654 KB

trying URL 'https://mirror.aarnet.edu.au/pub/CRAN/bin/windows/contrib/4.1/Rcpp_1.0.4.6.zip'
Content type 'application/zip' length 3168097 bytes (3.0 MB)
downloaded 3.0 MB

package ‘locfit’ successfully unpacked and MD5 sums checked
package ‘Rcpp’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\smyth\AppData\Local\Temp\RtmpaqaFCD\downloaded_packages
installing the source package ‘BiocVersion’

trying URL 'https://bioconductor.org/packages/3.11/bioc/src/contrib/BiocVersion_3.11.1.tar.gz'
Content type 'application/x-gzip' length 980 bytes
downloaded 980 bytes

* installing *source* package 'BiocVersion' ...
** using staged installation
** help
*** installing help indices
  converting help for package 'BiocVersion'
    finding HTML links ... done
    BiocVersion-pkg                         html
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BiocVersion)
Making 'packages.html' ... done

The downloaded source packages are in
        ‘C:\Users\smyth\AppData\Local\Temp\RtmpaqaFCD\downloaded_packages’

------------- End of R Session with R 4.0.0 for Windows  --------------

------------- R Session with R 4.0.0 for Windows  (successful) --------------

R Under development (unstable) (2020-02-15 r77808) -- "Unsuffered Consequences"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' 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")

+ > library("BiocManager")
Bioconductor version 3.11 (BiocManager 1.30.10), ?BiocManager::install for help
> install("edgeR")
Bioconductor version 3.11 (BiocManager 1.30.10), R Under development (unstable) (2020-02-15 r77808)
Installing package(s) 'edgeR'
trying URL 'https://bioconductor.org/packages/3.11/bioc/bin/windows/contrib/4.0/edgeR_3.29.1.zip'
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\AppData\Local\Temp\Rtmpy8bFkk\downloaded_packages
Old packages: 'backports', 'BiocFileCache', 'BiocNeighbors', 'BiocStyle', 'broom', 'dbplyr',
  'foreign', 'GenomeInfoDb', 'GenomeInfoDbData', 'gtools', 'isoband', 'MSnbase', 'nlme', 'purrr',
  'Rcpp', 'RcppArmadillo', 'RCurl', 'Rhdf5lib', 'Rsubread', 'scran', 'survival', 'tibble',
  'tinytex', 'withr'
Update all/some/none? [a/s/n]: n
>

------------- R Session with R 4.0.0 for Windows  --------------


> -----Original Message-----
> From: Martin Morgan <mtmorgan.bioc using gmail.com>
> Sent: Monday, 20 April 2020 7:44 PM
> To: Gordon K Smyth <smyth using wehi.edu.au>; bioc-devel using r-project.org
> Cc: Yunshun Chen <yuchen using wehi.edu.au>
> Subject: Re: [Bioc-devel] R-devel for Windows: Rtools3.5 vs Rtools4.0
>
> 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 on behalf of Gordon K Smyth" <bioc-devel-
> bounces using r-project.org on behalf of smyth using wehi.edu.au> wrote:
>
>     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 used the older
> rtool35 toolchain.
>
>     It appears that the Bioconductor developmental repository is using rtools35,
> which means that BiocManager::install is incompatible with the R-Devel build for
> Windows now on CRAN but works with R-Devel from a month or two ago.
>
>     When Bioconductor 3.11 is released, will it be the rtools40 toolchain or
> rtools35?
>
>     Thanks
>     Gordon
>
>     ------------------------------------------
>     Professor Gordon K Smyth
>     Joint Head, Bioinformatics Division
>     Walter and Eliza Hall Institute of Medical Research
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