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

Mon, Apr 20, 2020 7:38 PM

Hi Herve,

Ah, I see now.

I was getting confused by the CRAN page that points to R-4.1.0 for Windows and says it "will eventually become the next major release of R". I see now that we should be using R-4.0.0 RC instead, which is the patched link.

Can I confirm whether we should be using Rtools3.5 or Rtools4.0 with R-4.0.0 RC for Windows? The release note for R-4.0.0 RC says that it was ported by Guido Masarotto, Brian Ripley and Duncan Murdoch, which to me means it must be using the older toolchain. I had associated that toolchain in my mind with Rtool3.5, 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: Herv? Pag?s <hpages at fredhutch.org>
Sent: Tuesday, 21 April 2020 12:01 PM
To: Gordon K Smyth <smyth at wehi.edu.au>; Martin Morgan
<mtmorgan.bioc at gmail.com>; bioc-devel at r-project.org
Cc: Yunshun Chen <yuchen at wehi.edu.au>
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 CRAN here:

   https://cran.r-project.org/bin/windows/base/rpatched.html

Note that the upcoming devel version of Bioconductor (BioC 3.12) will
still be based on R 4.0. We'll only start using R 4.1 for BioC 3.13.

Cheers,
H.

On 4/20/20 17:42, Gordon K Smyth wrote:

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://urldefense.proofpoint.com/v2/url?u=https-

3A__mirror.aarnet.edu.au_pub_CRAN_bin_windows_contrib_4.1_BiocManager
-
5F1.30.10.zip&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWd
GbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=DRSQA4QbwiZ7f47ejuutRgsCIctSAM
UxFFSy3MRDadA&s=5nTgU8SemnUqthnJ85luoxh9XILEd0cG9DwDvaYJG9o&e= '

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://urldefense.proofpoint.com/v2/url?u=https-
3A__bioconductor.org_packages_3.11_bioc_bin_windows_contrib_4.1&d=DwI
GaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZv
SXAJJKaaPhzWA&m=DRSQA4QbwiZ7f47ejuutRgsCIctSAMUxFFSy3MRDadA&s=N
1ntYHJbzM64QzE10mXfuIkCRE5EOa74pPWKyz9jXBs&e= :

   cannot open URL 'https://urldefense.proofpoint.com/v2/url?u=https-

3A__bioconductor.org_packages_3.11_bioc_bin_windows_contrib_4.1_PACKA
GES&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJ
YbW0WYiZvSXAJJKaaPhzWA&m=DRSQA4QbwiZ7f47ejuutRgsCIctSAMUxFFSy3M
RDadA&s=86-euOILGSDTX4uN2pbWAfyQ-7uTcpiAXMB8w1YQGeg&e= '

Warning: unable to access index for repository

https://urldefense.proofpoint.com/v2/url?u=https-
3A__bioconductor.org_packages_3.11_data_annotation_bin_windows_contrib
_4.1&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJ
YbW0WYiZvSXAJJKaaPhzWA&m=DRSQA4QbwiZ7f47ejuutRgsCIctSAMUxFFSy3M
RDadA&s=0XEOcyZGmPoY-0_TdNiRPRUwS4MWta2X2LPZTYeqzuQ&e= :

   cannot open URL 'https://urldefense.proofpoint.com/v2/url?u=https-

3A__bioconductor.org_packages_3.11_data_annotation_bin_windows_contrib
_4.1_PACKAGES&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvime
WdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=DRSQA4QbwiZ7f47ejuutRgsCIctSA
MUxFFSy3MRDadA&s=Rsz3EC5iYpvb0gWD5S72old9UDv0C0q08i7vgyfhl-Q&e= '

Warning: unable to access index for repository

https://urldefense.proofpoint.com/v2/url?u=https-
3A__bioconductor.org_packages_3.11_data_experiment_bin_windows_contrib
_4.1&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJ
YbW0WYiZvSXAJJKaaPhzWA&m=DRSQA4QbwiZ7f47ejuutRgsCIctSAMUxFFSy3M
RDadA&s=L0PeotXMcsvCuc8RpvvheLWQKI8Wt8OeQchDK_sFgyk&e= :

   cannot open URL 'https://urldefense.proofpoint.com/v2/url?u=https-

3A__bioconductor.org_packages_3.11_data_experiment_bin_windows_contrib
_4.1_PACKAGES&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvime
WdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=DRSQA4QbwiZ7f47ejuutRgsCIctSA
MUxFFSy3MRDadA&s=XOuwgeMamR0EZ1eSO50h2HGufpMZuQB4WUZxuqRszK
w&e= '

Warning: unable to access index for repository

https://urldefense.proofpoint.com/v2/url?u=https-
3A__bioconductor.org_packages_3.11_workflows_bin_windows_contrib_4.1&d
=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0
WYiZvSXAJJKaaPhzWA&m=DRSQA4QbwiZ7f47ejuutRgsCIctSAMUxFFSy3MRDadA
&s=CKBM9wFJThnPfMW3F6AE_RRkqTJxa2eVZ-DSKbzDwWE&e= :

   cannot open URL 'https://urldefense.proofpoint.com/v2/url?u=https-

3A__bioconductor.org_packages_3.11_workflows_bin_windows_contrib_4.1_P
ACKAGES&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbW
Y_wJYbW0WYiZvSXAJJKaaPhzWA&m=DRSQA4QbwiZ7f47ejuutRgsCIctSAMUxFFS
y3MRDadA&s=AaHQ9IYjokUEVz3aqK4RQwERaY4wCpusHTE1mwqiCkc&e= '

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://urldefense.proofpoint.com/v2/url?u=https-

3A__mirror.aarnet.edu.au_pub_CRAN_bin_windows_contrib_4.1_locfit-5F1.5-
2D9.4.zip&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbW
Y_wJYbW0WYiZvSXAJJKaaPhzWA&m=DRSQA4QbwiZ7f47ejuutRgsCIctSAMUxFFS
y3MRDadA&s=sE30CsMU7wFJBEPs_eWWTe_oZA4lBJTUXxT_7JY1jAE&e= '

Content type 'application/zip' length 670513 bytes (654 KB)
downloaded 654 KB

trying URL 'https://urldefense.proofpoint.com/v2/url?u=https-

3A__mirror.aarnet.edu.au_pub_CRAN_bin_windows_contrib_4.1_Rcpp-
5F1.0.4.6.zip&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdG
bWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=DRSQA4QbwiZ7f47ejuutRgsCIctSAMUx
FFSy3MRDadA&s=IV-WYy4dPkxhf5wtp0GuGtGXYYgptdaKaZ0mCmoLDFY&e= '

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://urldefense.proofpoint.com/v2/url?u=https-

3A__bioconductor.org_packages_3.11_bioc_src_contrib_BiocVersion-
5F3.11.1.tar.gz&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeW
dGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=DRSQA4QbwiZ7f47ejuutRgsCIctSAM
UxFFSy3MRDadA&s=Eh_l16sA9zBwdc9KcuEq8ziBm6a7YqR7KMJ3i0q0gDw&e= '

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://urldefense.proofpoint.com/v2/url?u=https-

3A__bioconductor.org_packages_3.11_bioc_bin_windows_contrib_4.0_edgeR-
5F3.29.1.zip&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdG
bWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=DRSQA4QbwiZ7f47ejuutRgsCIctSAMUx
FFSy3MRDadA&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\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 at gmail.com>
Sent: Monday, 20 April 2020 7:44 PM
To: Gordon K Smyth <smyth at wehi.edu.au>; bioc-devel at r-project.org
Cc: Yunshun Chen <yuchen at 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 at r-project.org on behalf of smyth at 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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[Bioc-devel] R-devel for Windows: Rtools3.5 vs Rtools4.0

Thread (10 messages)