Re: [Rd] Setting the path to Rtools for package compilation on Windows

2018-02-14 Thread Jeroen Ooms 
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.

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Re: [Rd] Setting the path to Rtools for package compilation on Windows

2018-02-13 Thread Jeroen Ooms 
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.

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Re: [Rd] Setting the path to Rtools for package compilation on Windows

2018-02-13 Thread Tomas Kalibera 
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

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Re: [Rd] Setting the path to Rtools for package compilation on Windows

2018-02-12 Thread Søren Højsgaard 
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
> 
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