Re: [Bioc-devel] R-devel for Windows: Rtools3.5 vs Rtools4.0
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 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 > > Sent: Tuesday, 21 April 2020 6:51 PM > > To: Gordon K Smyth ; Martin Morgan > > ; bioc-devel@r-project.org > > Cc: Yunshun Chen > > 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 > > >> Sent: Tuesday, 21 April 2020 2:55 PM > > >> To: Gordon K Smyth ; Martin Morgan > > >> ; bioc-devel@r-project.org > > >> Cc: Yunshun Chen > > >> 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_=DwIGaQ=eRAMFD45gAfqt84VtBcfh > > Q=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Lbl2W3r- > > f_jIrRVzr8IFYC0x_V3F3tjiBkHuXyGBhWA=Os0nDoCIS80pkl11embl1PwAXrLmd > > 7lV67FCUN2db-o= > > >> > > >> 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 > > >
Re: [Bioc-devel] R-devel for Windows: Rtools3.5 vs Rtools4.0
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 > Sent: Tuesday, 21 April 2020 6:51 PM > To: Gordon K Smyth ; Martin Morgan > ; bioc-devel@r-project.org > Cc: Yunshun Chen > 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 > >> Sent: Tuesday, 21 April 2020 2:55 PM > >> To: Gordon K Smyth ; Martin Morgan > >> ; bioc-devel@r-project.org > >> Cc: Yunshun Chen > >> 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_=DwIGaQ=eRAMFD45gAfqt84VtBcfh > Q=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Lbl2W3r- > f_jIrRVzr8IFYC0x_V3F3tjiBkHuXyGBhWA=Os0nDoCIS80pkl11embl1PwAXrLmd > 7lV67FCUN2db-o= > >> > >> 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 > >>>> Sent: Tuesday, 21 April 2020 12:01 PM > >>>> To: Gordon K Smyth ; Martin Morgan > >>>> ; bioc-devel@r-project.org > >>>> Cc: Yunshun Chen > >>>> 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- > >> > 2Dpro
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 Sent: Tuesday, 21 April 2020 2:55 PM To: Gordon K Smyth ; Martin Morgan ; bioc-devel@r-project.org Cc: Yunshun Chen 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_=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Lbl2W3r-f_jIrRVzr8IFYC0x_V3F3tjiBkHuXyGBhWA=Os0nDoCIS80pkl11embl1PwAXrLmd7lV67FCUN2db-o= 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 Sent: Tuesday, 21 April 2020 12:01 PM To: Gordon K Smyth ; Martin Morgan ; bioc-devel@r-project.org Cc: Yunshun Chen 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=DwIGaQ=eRAMFD45gAf qt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=hj 173hPUpLOLp7dFQ_16azQNCbeFfRPfQqgksa9- 15s=H7efBWjbnmjHS7SQKjsjRlOG_7OvsT_Aq6rNUqJTK8c= 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
Re: [Bioc-devel] R-devel for Windows: Rtools3.5 vs Rtools4.0
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 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 > Sent: Tuesday, 21 April 2020 2:55 PM > To: Gordon K Smyth ; Martin Morgan > ; bioc-devel@r-project.org > Cc: Yunshun Chen > 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://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 > >> Sent: Tuesday, 21 April 2020 12:01 PM > >> To: Gordon K Smyth ; Martin Morgan > >> ; bioc-devel@r-project.org > >> Cc: Yunshun Chen > >> 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=DwIGaQ=eRAMFD45gAf > qt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=hj > 173hPUpLOLp7dFQ_16azQNCbeFfRPfQqgksa9- > 15s=H7efBWjbnmjHS7SQKjsjRlOG_7OvsT_Aq6rNUqJTK8c= > >> > >> 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
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://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
Sent: Tuesday, 21 April 2020 12:01 PM
To: Gordon K Smyth ; Martin Morgan
; bioc-devel@r-project.org
Cc: Yunshun Chen
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=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=hj173hPUpLOLp7dFQ_16azQNCbeFfRPfQqgksa9-15s=H7efBWjbnmjHS7SQKjsjRlOG_7OvsT_Aq6rNUqJTK8c=
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=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWd
GbWY_wJYbW0WYiZvSXAJJKaaPhzWA=DRSQA4QbwiZ7f47ejuutRgsCIctSAM
UxFFSy3MRDadA=5nTgU8SemnUqthnJ85luoxh9XILEd0cG9DwDvaYJG9o= '
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
ins
Re: [Bioc-devel] R-devel for Windows: Rtools3.5 vs Rtools4.0
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
> Sent: Tuesday, 21 April 2020 12:01 PM
> To: Gordon K Smyth ; Martin Morgan
> ; bioc-devel@r-project.org
> Cc: Yunshun Chen
> 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=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWd
> GbWY_wJYbW0WYiZvSXAJJKaaPhzWA=DRSQA4QbwiZ7f47ejuutRgsCIctSAM
> UxFFSy3MRDadA=5nTgU8SemnUqthnJ85luoxh9XILEd0cG9DwDvaYJG9o= '
> > 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) 'BiocVersio
Re: [Bioc-devel] R-devel for Windows: Rtools3.5 vs Rtools4.0
nloaded_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
Sent: Monday, 20 April 2020 7:44 PM
To: Gordon K Smyth ; bioc-devel@r-project.org
Cc: Yunshun Chen
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" 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 inte...{{dropped:26}}
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] R-devel for Windows: Rtools3.5 vs Rtools4.0
al 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://bioconductor.org/packages/3.11/bioc/bin/windows/contrib/4.0/edgeR_3.29.1.zip'
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
> Sent: Monday, 20 April 2020 7:44 PM
> To: Gordon K Smyth ; bioc-devel@r-project.org
> Cc: Yunshun Chen
> 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" 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
___
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You must not disclose, forward, print or use it without the permission of the
sender.
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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"
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 intend...{{dropped:12}}
___
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___
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