From adik at ilovebacon.org  Fri May 16 23:48:57 2008
From: adik at ilovebacon.org (Adam D. I. Kramer)
Date: Fri, 16 May 2008 14:48:57 -0700 (PDT)
Subject: [Rd] Configure errors say to report here... (PR#11470)
In-Reply-To: <alpine.LFD.1.10.0805161052070.28443@auk.stats.ox.ac.uk>
References: <20080516044025.294D52834170@mail.pubhealth.ku.dk>
	<alpine.LFD.1.10.0805161052070.28443@auk.stats.ox.ac.uk>
Message-ID: <Pine.LNX.4.64.0805161058310.3325@parser.ilovebacon.org>

Dear Dr. Ripley,

 	Thanks for your response. I'm running Xcode Tools 3.0, and the
latest Xquartz X11 (Xquartz 2.2.1, xorg-server 1.3.0-apple20) as has been
maintained by Apple's X11 mailing list (see http://xquartz.macosforge.org/ )

 	...the CFLAGS included were the same ones I was passing gfortran for
the lapack-3.1.1 and ATLAS builds, though at your suggestion I left them off
in favor of those listed at
https://stat.ethz.ch/pipermail/r-sig-mac/2005-February/001641.html for use
on the G5. I moved /sw last in my $PATH to ensure that I'm actually using
Apple's gcc, properly included /usr/local/lib/libptcblas.a, and used
--disable-R-framework instead of --without (oops). After fixing these
foolish errors, R compiles and installs correctly, and runs! Only 5-10%
faster, but hey.

 	Many thanks. Of course, if you are interested in debugging the error
based on the earlier compile (i.e., the one that told me to email this
list), I am happy to help.

--Adam

On Fri, 16 May 2008, Prof Brian Ripley wrote:

> What version are your Xcode tools?  What X11 do you have installed (I see 
> /sw/include in your path, and that is not normally needed)?
>
> Although configure says to report here, it is reporting a bug in your OS, not 
> in R.  There will be more information in your config.log, (and perhaps some 
> of it useful).
>
> Where did all those gcc flags come from?  I don't see them in 'R Installation 
> and Administration'. Perhaps leaving them off might solve the problem.
>
> On Fri, 16 May 2008, adik at ilovebacon.org wrote:
>
>> Hi,
>>
>> 	I'm attempting to compile R 2.7.0 on my G5, which is running OSX
>> 10.5.2. Yes, I know there is a precompiled binary, but my experience has
>> shown that if I hand-compile ATLAS on my machine and then link R against it
>> when compiling, R runs faster, hence me compiling it myself.
>> 
>> Anyway, I have this set of errors:
>> 
>> checking X11/Intrinsic.h usability... no
>> checking X11/Intrinsic.h presence... yes
>> configure: WARNING: X11/Intrinsic.h: present but cannot be compiled
>> configure: WARNING: X11/Intrinsic.h:     check for missing prerequisite 
>> headers?
>> configure: WARNING: X11/Intrinsic.h: see the Autoconf documentation
>> configure: WARNING: X11/Intrinsic.h:     section "Present But Cannot Be 
>> Compiled"
>> configure: WARNING: X11/Intrinsic.h: proceeding with the preprocessor's 
>> result
>> configure: WARNING: X11/Intrinsic.h: in the future, the compiler will take 
>> precedence
>> configure: WARNING:     ## ----------------------------------- ##
>> configure: WARNING:     ## Report this to r-bugs at R-project.org ##
>> configure: WARNING:     ## ----------------------------------- ##
>> ...
>> checking X11/Xmu/Atoms.h usability... no
>> checking X11/Xmu/Atoms.h presence... yes
>> configure: WARNING: X11/Xmu/Atoms.h: present but cannot be compiled
>> configure: WARNING: X11/Xmu/Atoms.h:     check for missing prerequisite 
>> headers?
>> configure: WARNING: X11/Xmu/Atoms.h: see the Autoconf documentation
>> configure: WARNING: X11/Xmu/Atoms.h:     section "Present But Cannot Be 
>> Compiled"
>> configure: WARNING: X11/Xmu/Atoms.h: proceeding with the preprocessor's 
>> result
>> configure: WARNING: X11/Xmu/Atoms.h: in the future, the compiler will take 
>> precedence
>> configure: WARNING:     ## ----------------------------------- ##
>> configure: WARNING:     ## Report this to r-bugs at R-project.org ##
>> configure: WARNING:     ## ----------------------------------- ##
>> ...
>> checking tk.h usability... no
>> checking tk.h presence... yes
>> configure: WARNING: tk.h: present but cannot be compiled
>> configure: WARNING: tk.h:     check for missing prerequisite headers?
>> configure: WARNING: tk.h: see the Autoconf documentation
>> configure: WARNING: tk.h:     section "Present But Cannot Be Compiled"
>> configure: WARNING: tk.h: proceeding with the preprocessor's result
>> configure: WARNING: tk.h: in the future, the compiler will take precedence
>> configure: WARNING:     ## ----------------------------------- ##
>> configure: WARNING:     ## Report this to r-bugs at R-project.org ##
>> configure: WARNING:     ## ----------------------------------- ##
>> 
>> ...the command line item I pass to configure is this:
>> 
>> feta:R-2.7.0> ./configure --prefix=/usr/local --with-x 
>> --without-R-framework --without-aqua 
>> --with-blas="/usr/local/lib/libptf77blas.a /usr/local/lib/libatlas.a" 
>> --with-lapack="/usr/local/lib/liblapack.a /usr/local/lib/libptf77blas.a 
>> /usr/local/lib/libatlas.a" CFLAGS="-maltivec -mabi=altivec -mtune=970 
>> -faltivec -O3" CXXFLAGS="-maltivec -mabi=altivec -mtune=970 -faltivec -O3"
>> 
>> ...the rest of configure completes fine, though when I try to build R, I
>> make eventually ends up failing in this manner:
>> 
>> gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/sw/include
>> -I/usr/
>> local/include -DHAVE_CONFIG_H   -fPIC  -maltivec -mabi=altivec -mtune=970
>> -falti
>> vec -O3 -c cpoly.c -o cpoly.o
>> cpoly.c: In function 'fxshft':
>> cpoly.c:299: error: expected identifier or '(' before 'unsigned'
>> cpoly.c:310: error: 'test' undeclared (first use in this function)
>> cpoly.c:310: error: (Each undeclared identifier is reported only once
>> cpoly.c:310: error: for each function it appears in.)
>> cpoly.c:315: error: expected expression before '__attribute__'
>> cpoly.c:326: error: expected expression before '__attribute__'
>> cpoly.c:327: error: expected expression before '__attribute__'
>> cpoly.c:334: error: expected expression before '__attribute__'
>> cpoly.c:370: error: expected expression before '__attribute__'
>> cpoly.c: In function 'vrshft':
>> cpoly.c:394: error: two or more data types in declaration specifiers
>> cpoly.c:394: error: expected identifier or '(' before ',' token
>> cpoly.c:399: error: 'b' undeclared (first use in this function)
>> cpoly.c:439: error: expected expression before '__attribute__'
>> cpoly.c:440: error: expected expression before '__attribute__'
>> cpoly.c:459: error: expected expression before '__attribute__'
>> cpoly.c:460: error: expected expression before '__attribute__'
>> cpoly.c:461: error: expected expression before '__attribute__'
>> cpoly.c:462: error: expected expression before '__attribute__'
>> cpoly.c: At top level:
>> cpoly.c:476: error: expected ';', ',' or ')' before 'unsigned'
>> cpoly.c:498: error: two or more data types in declaration specifiers
>> cpoly.c:498: error: conflicting types for 'nexth'
>> cpoly.c:81: error: previous declaration of 'nexth' was here
>> cpoly.c: In function 'nexth':
>> cpoly.c:498: error: parameter name omitted
>> cpoly.c:506: error: expected expression before '__attribute__'
>> make[3]: *** [cpoly.o] Error 1
>> make[2]: *** [R] Error 2
>> make[1]: *** [R] Error 1
>> make: *** [R] Error 1
>> 
>> ...the one reference to a problem like this I could find via google 
>> searches
>> is the post at
>> 
>> http://osdir.com/ml/lang.r.mac/2006-10/msg00016.html
>> 
>> regarding R 2.4.0, which I could not find a response to.
>> 
>> Any help is appreciated!
>> 
>> Thanks,
>> Adam Kramer
>> 
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>> 
>
> -- 
> Brian D. Ripley,                  ripley at stats.ox.ac.uk
> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
> University of Oxford,             Tel:  +44 1865 272861 (self)
> 1 South Parks Road,                     +44 1865 272866 (PA)
> Oxford OX1 3TG, UK                Fax:  +44 1865 272595
>



[Rd] Configure errors say to report here... (PR#11470)
Adam D. I. Kramer