R devel - Feb 2018 - 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

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
S?ren


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 at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

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, S?ren H?jsgaard 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
> S?ren
>
>
> 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 at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

On Tue, Feb 13, 2018 at 7:45 AM, Peter Langfelder
<peter.langfelder at gmail.com> 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
<tomas.kalibera at gmail.com> 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.

On Tue, Feb 13, 2018 at 2:20 AM, Jeroen Ooms <jeroenooms at gmail.com>
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