Configure errors say to report here... (PR#11470)
Simon, I apologize for wasting your time. When a configure script sets three lines of text apart to say, "Report this to r-bugs at R-project.org" on three different occasions, I figured it was polite to do so...but I do thank you for your help, which with Dr. Ripley's was sufficient to get me compiled and speedy. Thanks again! --Adam
On Fri, 16 May 2008, Simon Urbanek wrote:
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, 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.
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 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"
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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