[Bioc-devel] R-devel for Windows: Rtools3.5 vs Rtools4.0
Hervé Pagès
hp@ge@ @end|ng |rom |redhutch@org
Tue Apr 21 04:00:32 CEST 2020
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=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=DRSQA4QbwiZ7f47ejuutRgsCIctSAMUxFFSy3MRDadA&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=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=DRSQA4QbwiZ7f47ejuutRgsCIctSAMUxFFSy3MRDadA&s=N1ntYHJbzM64QzE10mXfuIkCRE5EOa74pPWKyz9jXBs&e= :
> cannot open URL 'https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_packages_3.11_bioc_bin_windows_contrib_4.1_PACKAGES&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=DRSQA4QbwiZ7f47ejuutRgsCIctSAMUxFFSy3MRDadA&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_wJYbW0WYiZvSXAJJKaaPhzWA&m=DRSQA4QbwiZ7f47ejuutRgsCIctSAMUxFFSy3MRDadA&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=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=DRSQA4QbwiZ7f47ejuutRgsCIctSAMUxFFSy3MRDadA&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_wJYbW0WYiZvSXAJJKaaPhzWA&m=DRSQA4QbwiZ7f47ejuutRgsCIctSAMUxFFSy3MRDadA&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=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=DRSQA4QbwiZ7f47ejuutRgsCIctSAMUxFFSy3MRDadA&s=XOuwgeMamR0EZ1eSO50h2HGufpMZuQB4WUZxuqRszKw&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_wJYbW0WYiZvSXAJJKaaPhzWA&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_PACKAGES&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=DRSQA4QbwiZ7f47ejuutRgsCIctSAMUxFFSy3MRDadA&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=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=DRSQA4QbwiZ7f47ejuutRgsCIctSAMUxFFSy3MRDadA&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=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=DRSQA4QbwiZ7f47ejuutRgsCIctSAMUxFFSy3MRDadA&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=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=DRSQA4QbwiZ7f47ejuutRgsCIctSAMUxFFSy3MRDadA&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=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=DRSQA4QbwiZ7f47ejuutRgsCIctSAMUxFFSy3MRDadA&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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