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 <sm...@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 <hpa...@fredhutch.org> > > Sent: Tuesday, 21 April 2020 6:51 PM > > To: Gordon K Smyth <sm...@wehi.edu.au>; Martin Morgan > > <mtmorgan.b...@gmail.com>; bioc-devel@r-project.org > > Cc: Yunshun Chen <yuc...@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 <hpa...@fredhutch.org> > > >> Sent: Tuesday, 21 April 2020 2:55 PM > > >> To: Gordon K Smyth <sm...@wehi.edu.au>; Martin Morgan > > >> <mtmorgan.b...@gmail.com>; bioc-devel@r-project.org > > >> Cc: Yunshun Chen <yuc...@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 <hpa...@fredhutch.org> > > >>>> Sent: Tuesday, 21 April 2020 12:01 PM > > >>>> To: Gordon K Smyth <sm...@wehi.edu.au>; Martin Morgan > > >>>> <mtmorgan.b...@gmail.com>; bioc-devel@r-project.org > > >>>> Cc: Yunshun Chen <yuc...@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.b...@gmail.com> > > >>>>>> Sent: Monday, 20 April 2020 7:44 PM > > >>>>>> To: Gordon K Smyth <sm...@wehi.edu.au>; bioc-devel@r-project.org > > >>>>>> Cc: Yunshun Chen <yuc...@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- > > >>>>>> boun...@r-project.org on behalf of sm...@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@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: hpa...@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: hpa...@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: hpa...@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@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel