Adam,
this it not a bug in R, this is merely a user error. Please don't file
self-inflicted problems as bugs (see posting guide). For Mac-related
questions there is R-SIG-Mac. Brian's response was to the point - you
break the compilation with the custom flags you use. See details below.
On May 16, 2008, at 12:40 AM, [EMAIL PROTECTED] 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.
FWIW that is not necessary in general, you can plug in any BLAS by
pointing the libRblas.dylib symlink at it (or an umbrella stub created
for it if it's incomplete).
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
This is likely a mess up of your headers and libraries. It's not
causing the error, but still you're heading for trouble.
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 [EMAIL PROTECTED] ##
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 [EMAIL PROTECTED] ##
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 [EMAIL PROTECTED] ##
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"
Depending on your compiler this may not work, because you're forcing
altivec constructs which introduces new keywords to the C language. R
doesn't use any altivec commands so it will break the compilation (as
you can see below). [This is based on my memory - I cannot reproduce
the problem on my G5, but then I'm using more recent tools and OS, so
your milleage may vary].
BTW: I have no idea what you're trying to achieve with those flags,
they are essentially no-ops, because R doesn't contain any altivec
code (and reals are "double" in R and thus AltiVec is of no use
anyway). If you want to optimize for speed, have a look at posts by
Jan de Leeuw and the old OptimizingR wiki page (also see -fast in gcc
and what it implies, although you need dynamic).
...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 -faltivec -O3 -c cpoly.c -o cpoly.o
You're including /sw (Fink) - this is asking for trouble, because Fink
contains incompatible versions of system libraries and headers (likely
this causes the cpp problems above). Again, this is not the primary
reason for the failure, but I hope you won't ask for help with that
binary ;).
Cheers,
Simon
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.
You found the right thread with the right hint, except you interpreted
it the wrong way - altivec was needed by the Apple's Carbon headers
(which are no longer used), but in R itself it caused the problem you
see in the post (and thus yours).
Any help is appreciated!
Thanks,
Adam Kramer
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