[R-SIG-Mac] building R under Lion

[Simon Urbanek]

On Aug 29, 2012, at 2:29 AM, peter dalgaard wrote:

> 
> On Aug 29, 2012, at 02:51 , Simon Urbanek wrote:
> 
>> You were on the right path - it's only about renaming vecLib to Accelerate, so you just have to apply the patch below. It is annoying, since -framework vecLib still works just fine so you don't even need to change the configure flags. The patch will in some modified form make it to R eventually.
> 
> Just to clarify: This is due to quite recent XCode changes? In my versions on Lion and Snow Leopard, Accelerate.h just #includes vecLib.h.
> 

It's just yet another Apple nonsense in Mountain Lion - it still just includes vecLib but now vecLib checks whether __ACCELERATE__ is defined and bails out with an error if it's not ... So another work-around is to set CPPFLAGS=-D__ACCELERATE__

Cheers,
Simon


> 
>> 
>> Cheers,
>> Simon
>> 
>> 
>> Index: vecLibg95c.c
>> ===================================================================
>> --- vecLibg95c.c	(revision 59442)
>> +++ vecLibg95c.c	(working copy)
>> @@ -2,7 +2,7 @@
>> #include <config.h>
>> #endif
>> 
>> -#include <vecLib/vecLib.h>
>> +#include <Accelerate/Accelerate.h>
>> 
>> void F77_FUNC_(rcblas_cdotu_sub,)(const int *N, const void *X, const int *incX,
>>                       const void *Y, const int *incY, void *dotu) 
>> 
>> 
>> 
>> 
>> 
>> On Aug 28, 2012, at 5:22 PM, Kasper Daniel Hansen wrote:
>> 
>>> I am running Lion, with the newest version of Xcode, and the 5666
>>> build of gcc+gfortran from Simon's page.  This is on Macbook pro last
>>> generation, with a quad core i7.  I have installed the latest stable
>>> release of Xquartz.
>>> 
>>> I am building R, not as a framework (--disable-framework), but I am
>>> using --with-blas='-framework vecLib' which at least used to be much
>>> better than the built-in BLAS.
>>> 
>>> My entire configure call is
>>> ../${SRCDIR}/configure SHELL='/bin/bash' \
>>> --prefix=/usr/local/R/R-${R_VERSION} --disable-R-framework\
>>> CC="/usr/bin/gcc-4.2 -arch x86_64 -std=gnu99" \
>>> CFLAGS="-g -O2 -std=gnu99 -march=nocona" \
>>> CXX="/usr/bin/g++-4.2 -arch x86_64" \
>>> CXXFLAGS="-g -O2 -march=nocona" \
>>> OBJC="/usr/bin/gcc-4.2 -arch x86_64" \
>>> F77="/usr/bin/gfortran-4.2 -arch x86_64" \
>>> FFLAGS="-g -O2 -march=nocona" \
>>> FC="/usr/bin/gfortran-4.2 -arch x86_64" \
>>> FCFLAGS="-g -O2 -march=nocona" \
>>> --enable-memory-profiling\
>>> --x-includes=/usr/X11/include --x-libraries=/usr/X11/lib\
>>> --with-system-zlib\
>>> --with-blas='-framework vecLib' --with-lapack
>>> 
>>> When I build R-2.15.1-patched, I get
>>> 
>>> making internet.d from ../../../../R-2.15.x-src/src/modules/internet/internet.c
>>> In file included from
>>> ../../../../R-2.15.x-src/src/modules/lapack/vecLibg95c.c:5:
>>> /System/Library/Frameworks/vecLib.framework/Headers/vecLib.h:22:4:
>>> error: #error "<vecLib/vecLib.h> is deprecated.  Please #include
>>> <Accelerate/Accelerate.h> and link to Accelerate.framework."
>>> make[3]: *** [vecLibg95c.d] Error 1
>>> make[2]: *** [make.lapack] Error 2
>>> make[2]: *** Waiting for unfinished jobs....
>>> making nanoftp.d from ../../../../R-2.15.x-src/src/modules/internet/nanoftp.c
>>> 
>>> <SNIP>
>>> 
>>> /usr/bin/gcc-4.2 -arch x86_64 -std=gnu99 -I. -I../../../src/include
>>> -I../../../../R-2.15.x-src/src/include -I/usr/local/include
>>> -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2 -std=gnu99 -march=nocona   -c
>>> ../../../../R-2.15.x-src/src/modules/internet/sockconn.c -o sockconn.o
>>> /usr/bin/gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib
>>> -Wl,-headerpad_max_install_names  -undefined dynamic_lookup
>>> -single_module -multiply_defined suppress -L/usr/local/lib -o
>>> internet.so Rhttpd.o Rsock.o internet.o nanoftp.o nanohttp.o sock.o
>>> sockconn.o   -Wl,-framework -Wl,CoreFoundation
>>> mkdir /Users/khansen/build/R/R-2.15.x-build/modules
>>> make[1]: *** [R] Error 1
>>> make: *** [R] Error 1
>>> 
>>> So it seems that it does not like -framework vecLib.  I tried with
>>> -framework Accelerate, but I get the same error.
>>> 
>>> My guess is that there is some new thing I have to do here, but I
>>> tried reading the admin guide for R-devel and could not see anything
>>> particular (except I do not need -arch x86_64 anymore).
>>> 
>>> Thanks,
>>> Kasper
>>> 
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>> 
>>> 
>> 
>> _______________________________________________
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> 
> -- 
> Peter Dalgaard, Professor,
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> Phone: (+45)38153501
> Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com
> 
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