[Bioc-devel] R-devel for Windows: Rtools3.5 vs Rtools4.0
Gordon K Smyth
@myth @end|ng |rom weh|@edu@@u
Tue Apr 21 04:38:16 CEST 2020
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://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 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
> > _______________________________________________
> >
> > The information in this email is confidential and intended solely 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
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> > _______________________________________________
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> >
>
> --
> 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
_______________________________________________
The information in this email is confidential and intended solely 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.
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