Re: [Rd] Setting the path to Rtools for package compilation on Windows
If there is work going on to improve Rtools 1. one of the most annoying aspects of it is that it does not play nice with builtin Windows commands. In particular, it defines a command called find which works like UNIX find but it masks Windows find if you add the Rtools folders to your PATH making it quite dangerous to do so. 2. Another annoyance is that what to put on the PATH can change from one Rtools version to another and it is not straight forward to discover that automatically. One can extract it from the unins000.dat (and I have done that) but it is not straight forward. 3. Ideally it would be nice if it were as easy to install Rtools as installing an R package. In fact, maybe Rtools could be an R package or maybe it could be part of the R installation process itself. On Wed, Feb 14, 2018 at 7:32 AM, Jeroen Ooms wrote: > On Tue, Feb 13, 2018 at 7:58 PM, Peter Langfelder > wrote: >> On Tue, Feb 13, 2018 at 2:20 AM, Jeroen Ooms wrote: >> >>> Thanks for your question. Your logs show that 'gcc' is not found. As >>> of R 3.3 you need to set the path to the compiler using the BINPREF >>> variable. This is because we ship two separate versions of gcc, one >>> targeting win32 and one targeting win64. I am not sure what your >>> rtools installation looks like, but could you try setting this >>> environment variable: >>> >>> BINPREF="M:/R/Rtools-3.4/mingw_$(WIN)/bin/" >>> >>> I think this will do the job. >> >> Thanks, that indeed did the trick. May I suggest that this hint be >> also included in "REMAINING TASKS" section of the file Rtools.txt that >> is part of the Rtools distribution? The R installation manual does >> mention BINPREF and BINPREF64 but I missed that part... > > Glad it worked. Actually BINPREF64 only exists when building R itself. > For the R user there is no BINPREF64. There is only BINPREF which has > to point to a 32bit gcc when R runs in 32bit, and a 64bit compiler > when R runs in 64bit. But if you compile R packages you need both at > the same time. Hence the "$(WIN)" variable in the BINPREF above. > > Yes the rtools setup is a bit convoluted, and we're currently > discussing ways to improve this. Thanks for your suggestion. > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel -- Statistics & Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Setting the path to Rtools for package compilation on Windows
On Tue, Feb 13, 2018 at 7:58 PM, Peter Langfelder wrote: > On Tue, Feb 13, 2018 at 2:20 AM, Jeroen Ooms wrote: > >> Thanks for your question. Your logs show that 'gcc' is not found. As >> of R 3.3 you need to set the path to the compiler using the BINPREF >> variable. This is because we ship two separate versions of gcc, one >> targeting win32 and one targeting win64. I am not sure what your >> rtools installation looks like, but could you try setting this >> environment variable: >> >> BINPREF="M:/R/Rtools-3.4/mingw_$(WIN)/bin/" >> >> I think this will do the job. > > Thanks, that indeed did the trick. May I suggest that this hint be > also included in "REMAINING TASKS" section of the file Rtools.txt that > is part of the Rtools distribution? The R installation manual does > mention BINPREF and BINPREF64 but I missed that part... Glad it worked. Actually BINPREF64 only exists when building R itself. For the R user there is no BINPREF64. There is only BINPREF which has to point to a 32bit gcc when R runs in 32bit, and a 64bit compiler when R runs in 64bit. But if you compile R packages you need both at the same time. Hence the "$(WIN)" variable in the BINPREF above. Yes the rtools setup is a bit convoluted, and we're currently discussing ways to improve this. Thanks for your suggestion. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Setting the path to Rtools for package compilation on Windows
On Tue, Feb 13, 2018 at 2:20 AM, Jeroen Ooms wrote: > Thanks for your question. Your logs show that 'gcc' is not found. As > of R 3.3 you need to set the path to the compiler using the BINPREF > variable. This is because we ship two separate versions of gcc, one > targeting win32 and one targeting win64. I am not sure what your > rtools installation looks like, but could you try setting this > environment variable: > > BINPREF="M:/R/Rtools-3.4/mingw_$(WIN)/bin/" > > I think this will do the job. Thanks, that indeed did the trick. May I suggest that this hint be also included in "REMAINING TASKS" section of the file Rtools.txt that is part of the Rtools distribution? The R installation manual does mention BINPREF and BINPREF64 but I missed that part... Peter __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Setting the path to Rtools for package compilation on Windows
On Tue, Feb 13, 2018 at 7:45 AM, Peter Langfelder wrote: > Hi all, > > I'm trying to set up the Windows Rtools toolset for building packages > with compiled code. I installed for Windows R-3.4.3 from CRAN and > installed Rtools-3.4 in a custom location M:\R\R-3.4.3 and > M:\R\Rtools-3.4 > > Following the instructions, in shell, I set > Path=M:\R\Rtools-3.4\bin;M:\R\Rtools-3.4\gcc-4.6.3\bin;M:\R\R-3.4.3\bin;... > (the ... are other paths irrelevant for R/Rtools). Thanks for your question. Your logs show that 'gcc' is not found. As of R 3.3 you need to set the path to the compiler using the BINPREF variable. This is because we ship two separate versions of gcc, one targeting win32 and one targeting win64. I am not sure what your rtools installation looks like, but could you try setting this environment variable: BINPREF="M:/R/Rtools-3.4/mingw_$(WIN)/bin/" I think this will do the job. On Tue, Feb 13, 2018 at 10:21 AM, Tomas Kalibera wrote: > Thanks for the report - this has been already reported as bug 17376, it is > caused by scripts that build the Windows binaries and by now has been fixed > in R-patched and R-devel snapshot builds. So as a solution that works now I > would recommend using R-patched. This issue is unrelated, I doubt your advice will solve anything. The only thing that 17376 does is add c:/rtools/bin to the default path. But this dir does not exist for this user, so it is ignored by windows when searching the PATH. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Setting the path to Rtools for package compilation on Windows
Thanks for the report - this has been already reported as bug 17376, it is caused by scripts that build the Windows binaries and by now has been fixed in R-patched and R-devel snapshot builds. So as a solution that works now I would recommend using R-patched. Tomas On 02/13/2018 08:33 AM, Søren Højsgaard wrote: I can confirm the behaviour that you report. Usually I put Rtools in c:\programs\Rtools and modify the path accordingly. Recently (don't recall for how long) I have encountered the same problems as you have and I have resorted to moving Rtools to c:\Rtools I have no idea as how to proceed; perhaps it could be worth trying an older version of Rtools (though that may cause other problems). Regards Søren On Mon, 2018-02-12 at 22:45 -0800, Peter Langfelder wrote: Hi all, I'm trying to set up the Windows Rtools toolset for building packages with compiled code. I installed for Windows R-3.4.3 from CRAN and installed Rtools-3.4 in a custom location M:\R\R-3.4.3 and M:\R\Rtools-3.4 Following the instructions, in shell, I set Path=M:\R\Rtools-3.4\bin;M:\R\Rtools-3.4\gcc-4.6.3\bin;M:\R\R- 3.4.3\bin;... (the ... are other paths irrelevant for R/Rtools). When I run M:\Work\RLibs>R.exe CMD INSTALL --build WGCNA I get the following ouput: In R CMD INSTALL * installing to library 'M:/R/R-3.4.3/library' * installing *source* package 'WGCNA' ... ** libs *** arch - i386 c:/Rtools/mingw_32/bin/g++ -I"M:/R/R-3.4.3/include" -DNDEBUG -O2 -Wall -mtune=generic -c bucketApproxSort.cc -o bucketApproxSort.o c:/Rtools/mingw_32/bin/g++: not found make: *** [bucketApproxSort.o] Error 127 Warning: running command 'make -f "Makevars.win" -f "M:/R/R-3.4.3/etc/i386/Makeconf" -f "M:/R/R-3.4.3/share/make/winshli b.mk" SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)' SHLIB="WGCNA.dll" OBJECTS="bucketApproxSort.o corFun ctions-common.o corFunctions-unified.o networkFunctions.o pivot.o quantileC.o"' had status 2 ERROR: compilation failed for package 'WGCNA' * removing 'M:/R/R-3.4.3/library/WGCNA' * restoring previous 'M:/R/R-3.4.3/library/WGCNA' Apparently the install is looking for Rtools in c:\Rtools. I am a perpetual Windows newbie and would be really thankful for any pointers as to how to proceed. Peter __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Setting the path to Rtools for package compilation on Windows
I can confirm the behaviour that you report. Usually I put Rtools in c:\programs\Rtools and modify the path accordingly. Recently (don't recall for how long) I have encountered the same problems as you have and I have resorted to moving Rtools to c:\Rtools I have no idea as how to proceed; perhaps it could be worth trying an older version of Rtools (though that may cause other problems). Regards Søren On Mon, 2018-02-12 at 22:45 -0800, Peter Langfelder wrote: > Hi all, > > I'm trying to set up the Windows Rtools toolset for building packages > with compiled code. I installed for Windows R-3.4.3 from CRAN and > installed Rtools-3.4 in a custom location M:\R\R-3.4.3 and > M:\R\Rtools-3.4 > > Following the instructions, in shell, I set > Path=M:\R\Rtools-3.4\bin;M:\R\Rtools-3.4\gcc-4.6.3\bin;M:\R\R- > 3.4.3\bin;... > (the ... are other paths irrelevant for R/Rtools). > > When I run > > M:\Work\RLibs>R.exe CMD INSTALL --build WGCNA > > I get the following ouput: > > In R CMD INSTALL > * installing to library 'M:/R/R-3.4.3/library' > * installing *source* package 'WGCNA' ... > ** libs > > *** arch - i386 > c:/Rtools/mingw_32/bin/g++ -I"M:/R/R-3.4.3/include" -DNDEBUG > -O2 -Wall -mtune=generic -c bucketApproxSort.cc > -o bucketApproxSort.o > c:/Rtools/mingw_32/bin/g++: not found > make: *** [bucketApproxSort.o] Error 127 > Warning: running command 'make -f "Makevars.win" -f > "M:/R/R-3.4.3/etc/i386/Makeconf" -f "M:/R/R-3.4.3/share/make/winshli > b.mk" SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)' > SHLIB="WGCNA.dll" OBJECTS="bucketApproxSort.o corFun > ctions-common.o corFunctions-unified.o networkFunctions.o pivot.o > quantileC.o"' had status 2 > ERROR: compilation failed for package 'WGCNA' > * removing 'M:/R/R-3.4.3/library/WGCNA' > * restoring previous 'M:/R/R-3.4.3/library/WGCNA' > > > Apparently the install is looking for Rtools in c:\Rtools. I am a > perpetual Windows newbie and would be really thankful for any > pointers > as to how to proceed. > > Peter > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Setting the path to Rtools for package compilation on Windows
Hi all, I'm trying to set up the Windows Rtools toolset for building packages with compiled code. I installed for Windows R-3.4.3 from CRAN and installed Rtools-3.4 in a custom location M:\R\R-3.4.3 and M:\R\Rtools-3.4 Following the instructions, in shell, I set Path=M:\R\Rtools-3.4\bin;M:\R\Rtools-3.4\gcc-4.6.3\bin;M:\R\R-3.4.3\bin;... (the ... are other paths irrelevant for R/Rtools). When I run M:\Work\RLibs>R.exe CMD INSTALL --build WGCNA I get the following ouput: In R CMD INSTALL * installing to library 'M:/R/R-3.4.3/library' * installing *source* package 'WGCNA' ... ** libs *** arch - i386 c:/Rtools/mingw_32/bin/g++ -I"M:/R/R-3.4.3/include" -DNDEBUG -O2 -Wall -mtune=generic -c bucketApproxSort.cc -o bucketApproxSort.o c:/Rtools/mingw_32/bin/g++: not found make: *** [bucketApproxSort.o] Error 127 Warning: running command 'make -f "Makevars.win" -f "M:/R/R-3.4.3/etc/i386/Makeconf" -f "M:/R/R-3.4.3/share/make/winshli b.mk" SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)' SHLIB="WGCNA.dll" OBJECTS="bucketApproxSort.o corFun ctions-common.o corFunctions-unified.o networkFunctions.o pivot.o quantileC.o"' had status 2 ERROR: compilation failed for package 'WGCNA' * removing 'M:/R/R-3.4.3/library/WGCNA' * restoring previous 'M:/R/R-3.4.3/library/WGCNA' Apparently the install is looking for Rtools in c:\Rtools. I am a perpetual Windows newbie and would be really thankful for any pointers as to how to proceed. Peter __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
