[Bioc-devel] R-devel for Windows: Rtools3.5 vs Rtools4.0
Leonardo Collado Torres
|co||@dotor @end|ng |rom gm@||@com
Fri Apr 24 13:54:49 CEST 2020
Hi,
This seems related
https://twitter.com/opencpu/status/1253649367946444802?s=21
Best,
Leo
On Wed, Apr 22, 2020 at 6:54 AM Gordon K Smyth <smyth using wehi.edu.au> wrote:
> 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: Hervé Pagès <hpages using fredhutch.org>
> > Sent: Tuesday, 21 April 2020 6:51 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
> >
> > 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: Hervé Pagès <hpages using fredhutch.org>
> > >> Sent: Tuesday, 21 April 2020 2:55 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
> > >>
> > >> 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: 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=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
> > >>>>
> > >>
> > 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
> > >>>>> the continuing connection to country and community.
> > >>>>> _______________________________________________
> > >>>>> _______________________________________________
> > >>>>> Bioc-devel using r-project.org mailing list
> > >>>>> https://urldefense.proofpoint.com/v2/url?u=https-
> > >>>> 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
> > >>> _______________________________________________
> > >>>
> > >>> 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.
> > >>> _______________________________________________
> > >>>
> > >>
> > >> --
> > >> 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.
> > > _______________________________________________
> > >
> >
> > --
> > 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.
> _______________________________________________
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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