Please cc me when replying to the list. With Version 2.1.1 (2005-06-20) on Power Mac G5 running Mac OS X 10.4.2 (8C46): Some compilations work (e.g., MatchIt, RGraphics, Zelig), and some don't, e.g., mgcv, spatstat, and the following (Matrix, cluster): trying URL 'http://www.ibiblio.org/pub/languages/R/CRAN/src/contrib/ Matrix_0.98-3.tar.gz' Content type 'application/x-tar' length 626712 bytes opened URL ================================================== downloaded 612Kb * Installing *source* package 'Matrix' ... ** libs The downloaded packages are in /private/tmp/RtmpPddsAE/downloaded_packages gcc-3.3 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/ include -I/usr/local/include -I./Metis -fno-common -g -O2 -c HBMM.c -o HBMM.o In file included from HBMM.c:2: iohb.h:6:19: malloc.h: No such file or directory make: *** [HBMM.o] Error 1 ERROR: compilation failed for package 'Matrix' trying URL 'http://www.ibiblio.org/pub/languages/R/CRAN/src/contrib/ cluster_1.10.1.tar.gz' Content type 'application/x-tar' length 190975 bytes opened URL ================================================== downloaded 186Kb * Installing *source* package 'cluster' ... ** libs gcc-3.3 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/ include -I/usr/local/include -fno-common -g -O2 -c clara.c -o clara.o g77 -fno-common -g -O2 -c daisy.f -o daisy.o g77 -fno-common -g -O2 -c dysta.f -o dysta.o g77 -fno-common -g -O2 -c fanny.f -o fanny.o g77 -fno-common -g -O2 -c meet.f -o meet.o g77 -fno-common -g -O2 -c mona.f -o mona.o gcc-3.3 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/ include -I/usr/local/include -fno-common -g -O2 -c pam.c -o pam.o gcc-3.3 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/ include -I/usr/local/include -fno-common -g -O2 -c spannel.c -o spannel.o g77 -fno-common -g -O2 -c twins.f -o twins.o The downloaded packages are in /private/tmp/RtmpPddsAE/downloaded_packages gcc-3.3 -bundle -flat_namespace -undefined suppress -L/usr/local/lib - o cluster.so clara.o daisy.o dysta.o fanny.o meet.o mona.o pam.o spannel.o twins.o -L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2 -lg2c -lSystem -framework R ** Removing '/Library/Frameworks/R.framework/Versions/2.1.1/Resources/ library/cluster' ** Restoring previous '/Library/Frameworks/R.framework/Versions/2.1.1/ Resources/library/cluster' ld: clara.o has external relocation entries in non-writable section (__TEXT,__text) for symbols: restFP saveFP make: *** [cluster.so] Error 1 ERROR: compilation failed for package 'cluster' _____________________________ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400 Charlottesville, VA 22904-4400 Parcels: Room 102 Gilmer Hall McCormick Road Charlottesville, VA 22903 Office: B011 +1-434-982-4729 Lab: B019 +1-434-982-4751 Fax: +1-434-982-4766 WWW: http://www.people.virginia.edu/~mk9y/
Compilation failures: mgcv, spatstat, Matrix, cluster
3 messages · Michael Kubovy, Paul Roebuck, Douglas Bates
On Sat, 13 Aug 2005, Michael Kubovy wrote:
With Version 2.1.1 (2005-06-20) on Power Mac G5 running Mac OS X 10.4.2 (8C46): Some compilations work (e.g., MatchIt, RGraphics, Zelig), and some don't, e.g., mgcv, spatstat, and the following (Matrix, cluster): trying URL 'http://www.ibiblio.org/pub/languages/R/CRAN/src/contrib/ Matrix_0.98-3.tar.gz' Content type 'application/x-tar' length 626712 bytes opened URL ================================================== downloaded 612Kb * Installing *source* package 'Matrix' ... ** libs The downloaded packages are in /private/tmp/RtmpPddsAE/downloaded_packages gcc-3.3 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/ include -I/usr/local/include -I./Metis -fno-common -g -O2 -c HBMM.c -o HBMM.o In file included from HBMM.c:2: iohb.h:6:19: malloc.h: No such file or directory make: *** [HBMM.o] Error 1 ERROR: compilation failed for package 'Matrix'
Didn't check package for actually functioning correctly,
but the following changes will allow compilation on OS X
10.3. In ANSI C, the standard memory allocation routines
are declared in <stdlib.h>; <malloc.h> is obsolete for that
purpose and isn't guaranteed to exist.
Matrix/src/mmio.c:
Add #include <stdlib.h>
Remove #include <malloc.h>
Matrix/src/iohb.h:
Remove #include <malloc.h>
----------------------------------------------------------
SIGSIG -- signature too long (core dumped)
1 day later
On 8/13/05, Paul Roebuck <roebuck at odin.mdacc.tmc.edu> wrote:
On Sat, 13 Aug 2005, Michael Kubovy wrote:
With Version 2.1.1 (2005-06-20) on Power Mac G5 running Mac OS X 10.4.2 (8C46): Some compilations work (e.g., MatchIt, RGraphics, Zelig), and some don't, e.g., mgcv, spatstat, and the following (Matrix, cluster): trying URL 'http://www.ibiblio.org/pub/languages/R/CRAN/src/contrib/ Matrix_0.98-3.tar.gz' Content type 'application/x-tar' length 626712 bytes opened URL ================================================== downloaded 612Kb * Installing *source* package 'Matrix' ... ** libs The downloaded packages are in /private/tmp/RtmpPddsAE/downloaded_packages gcc-3.3 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/ include -I/usr/local/include -I./Metis -fno-common -g -O2 -c HBMM.c -o HBMM.o In file included from HBMM.c:2: iohb.h:6:19: malloc.h: No such file or directory make: *** [HBMM.o] Error 1 ERROR: compilation failed for package 'Matrix'
Didn't check package for actually functioning correctly,
but the following changes will allow compilation on OS X
10.3. In ANSI C, the standard memory allocation routines
are declared in <stdlib.h>; <malloc.h> is obsolete for that
purpose and isn't guaranteed to exist.
Matrix/src/mmio.c:
Add #include <stdlib.h>
Remove #include <malloc.h>
Matrix/src/iohb.h:
Remove #include <malloc.h>
Thanks for the suggestion, Paul. I wasn't quite as sloppy as it may seem. I recently introduced the iohb.[hc] and mmio.[hc] files from NIST into the Matrix package but I didn't check them thoroughly before doing so. I should have. Those are not the only antiquated C constructs in those files. The author of iohb.c also assumes that he can pass a string constant to a function that modifies the contents of that argument and, of course, gcc will produce code that segfaults at that point if you do not use -fwriteable-strings and we don't want to do that.