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

Hi Herve,

Are you saying that 'R CMD config CC' returns
/mingw64/bin/x86_64-w64-mingw32-gcc-8.3.0 with the latest
Windows build of R 4.1.0?

No, it doesn't. I was just trying to interpret the note "This build of
R-Devel uses the gcc gcc 8.3.0 toolchain from rtools40." that is attached
to R-4.1.0 for Windows on the CRAN download page. There's no similar note
attached to R-4.0.0 RC, but I may have jumped to the wrong conclusion.

Gordon

-----Original Message-----
From: Herv? Pag?s <hpages at fredhutch.org>
Sent: Tuesday, 21 April 2020 6:51 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

On 4/20/20 23:28, Gordon K Smyth wrote:

Thanks, that does help. So it seems that R-4.0.0 will use

   rtools40/mingw64/bin/gcc.exe

and I'm guessing that R-4.1.0 uses

   rtools40/mingw64/bin/x86_64-w64-mingw32-gcc-8.3.0.exe

I didn't try R 4.1.0 yet so don't know what it uses but I'm surprised it
uses something different than R 4.0.0. Are you saying that 'R CMD config
CC' returns /mingw64/bin/x86_64-w64-mingw32-gcc-8.3.0 with the latest
Windows build of R 4.1.0?

Anyway I still have 6 months to worry about what R 4.1.0 does ;-)

Cheers,
H.

Both files in are in the same directory, so R-4.0.0 and R-4.1.0 should

both work

with same Windows setup (which is afterall what the Rtools webpage says).

Thanks
Gordon

-----Original Message-----
From: Herv? Pag?s <hpages at fredhutch.org>
Sent: Tuesday, 21 April 2020 2:55 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

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=DwIGaQ&c=eRAMFD45gAfqt84VtBcfh
Q&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=Lbl2W3r-
f_jIrRVzr8IFYC0x_V3F3tjiBkHuXyGBhWA&s=Os0nDoCIS80pkl11embl1PwAXrLmd
7lV67FCUN2db-o&e=

AFAIK there has been no official announcement about this on the

various

R-* mailing lists but this is suggested by the output of 'R CMD config
CC' which has changed from C:/Rtools/mingw_64/bin/gcc to
/mingw64/bin/gcc with the most recent Windows builds of R 4.0.0.

/mingw64/bin/gcc and /mingw32/bin/gcc are the paths to the 64-bit and
32-bit compilers **in the Msys environment** that is shipped with
Rtools40. These paths are relative to the location of Rtools40, which

by

default is C:\Rtools40.

Hope this helps,
H.


On 4/20/20 19:38, Gordon K Smyth wrote:

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://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-

2Dproject.org_bin_windows_base_rpatched.html&d=DwIGaQ&c=eRAMFD45gAf

qt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=hj

173hPUpLOLp7dFQ_16azQNCbeFfRPfQqgksa9-
15s&s=H7efBWjbnmjHS7SQKjsjRlOG_7OvsT_Aq6rNUqJTK8c&e=

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

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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

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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

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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

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     cannot open URL '

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3A__bioconductor.org_packages_3.11_data_experiment_bin_windows_contrib

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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

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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

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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

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Content type 'application/x-gzip' length 980 bytes
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* 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

for the

addressee.

You must not disclose, forward, print or use it without the

permission of

the

sender.

The Walter and Eliza Hall Institute acknowledges the Wurundjeri

people

of

the

Kulin

Nation as the traditional owners of the land where our campuses are

located

and

the continuing connection to country and community.

3A__stat.ethz.ch_mailman_listinfo_bioc-

2Ddevel&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY

_wJYbW0WYiZvSXAJJKaaPhzWA&m=DRSQA4QbwiZ7f47ejuutRgsCIctSAMUxFFSy

3MRDadA&s=oP2Hrv49vSbxH33yx3wzKQcFGnzAt4vp9_A--YtrpOE&e=

--
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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Phone:  (206) 667-5791
Fax:    (206) 667-1319

for the

addressee.

You must not disclose, forward, print or use it without the

permission of the

sender.

The Walter and Eliza Hall Institute acknowledges the Wurundjeri

people of

the

Kulin

Nation as the traditional owners of the land where our campuses are

located

and

the continuing connection to country and community.

--
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

the

addressee.

You must not disclose, forward, print or use it without the permission

of the

sender.

The Walter and Eliza Hall Institute acknowledges the Wurundjeri people

of the

Kulin

Nation as the traditional owners of the land where our campuses are

located

and

the continuing connection to country and community.

--
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319