[Bioc-devel] R-devel for Windows: Rtools3.5 vs Rtools4.0
Hervé Pagès
hp@ge@ @end|ng |rom |redhutch@org
Tue Apr 21 06:54:43 CEST 2020
Yes, all builds of R 4.0 and above are now using Rtools40 on Windows. See:
https://cran.r-project.org/bin/windows/Rtools/
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: Hervé Pagès <hpages using fredhutch.org>
>> Sent: Tuesday, 21 April 2020 12:01 PM
>> To: Gordon K Smyth <smyth using wehi.edu.au>; Martin Morgan
>> <mtmorgan.bioc using gmail.com>; 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
>>
>> 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=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=hj173hPUpLOLp7dFQ_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
>> 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 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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>>> You must not disclose, forward, print or use it without the permission of the
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>>> Bioc-devel using r-project.org mailing list
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>> 3A__stat.ethz.ch_mailman_listinfo_bioc-
>> 2Ddevel&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY
>> _wJYbW0WYiZvSXAJJKaaPhzWA&m=DRSQA4QbwiZ7f47ejuutRgsCIctSAMUxFFSy
>> 3MRDadA&s=oP2Hrv49vSbxH33yx3wzKQcFGnzAt4vp9_A--YtrpOE&e=
>>>
>>
>> --
>> Hervé Pagès
>>
>> 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 using fredhutch.org
>> Phone: (206) 667-5791
>> Fax: (206) 667-1319
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>
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