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Problem installing aroma.affymetrix on Solaris 9 with R-2.6.2
2 messages · Jun Zhang, Brian Ripley
This is the wrong list for questions about Bioconductor packages: please do study the posting guide (and no HTML mail, please). stdint.h is part of C99. My guess is that your unspecified compiler + obsolete OS is not C99 compliant. Since Solaris 8 has inttypes.h (which is supposed by POSIX to include stdint.h), it is a reasonable guess that you could might be able to replace stdint.h by inttypes.h (especially as R has been compiled on your OS and R uses inttypes.h as a fallback). When you find a solution, you should report it to the maintainer of the affyio package (see the posting guide).
On Sat, 29 Mar 2008, Jun Zhang wrote:
Hi List, I'm trying to install aroma.affymetrix, which depend on many packages, affyio is one of them. The task is done on 32-bit Linux without problem. The same task was done on Solaris 9 with R-2.5.1 without problem. Following is the error message when installation affyio. I did try to put a file stdint.h I got from the web in the path, but got more error messages. Jun root at biostatsun1 R# R CMD INSTALL affyio_1.6.1.tar.gz * Installing to library '/apps/R-2.6.2/lib/R/library' * Installing *source* package 'affyio' ... creating cache ./config.cache checking how to run the C preprocessor... grep: can't open conftest.out cc -E checking for main in -lz... no updating cache ./config.cache creating ./config.status creating src/Makevars ** libs gcc -std=gnu99 -I/apps/R-2.6.2/lib/R/include -I/apps/R-2.6.2/lib/R/include -I/apps/mpich-1.2.7p1/include -fPIC -g -O2 -c fread_functions.c -o fread_functions.o gcc -std=gnu99 -I/apps/R-2.6.2/lib/R/include -I/apps/R-2.6.2/lib/R/include -I/apps/mpich-1.2.7p1/include -fPIC -g -O2 -c read_abatch.c -o read_abatch.o gcc -std=gnu99 -I/apps/R-2.6.2/lib/R/include -I/apps/R-2.6.2/lib/R/include -I/apps/mpich-1.2.7p1/include -fPIC -g -O2 -c read_bpmap.c -o read_bpmap.o gcc -std=gnu99 -I/apps/R-2.6.2/lib/R/include -I/apps/R-2.6.2/lib/R/include -I/apps/mpich-1.2.7p1/include -fPIC -g -O2 -c read_cdf_xda.c -o read_cdf_xda.o read_cdf_xda.c: In function `isPM': read_cdf_xda.c:614: warning: implicit declaration of function `toupper' gcc -std=gnu99 -I/apps/R-2.6.2/lib/R/include -I/apps/R-2.6.2/lib/R/include -I/apps/mpich-1.2.7p1/include -fPIC -g -O2 -c read_cdffile2.c -o read_cdffile2.o gcc -std=gnu99 -I/apps/R-2.6.2/lib/R/include -I/apps/R-2.6.2/lib/R/include -I/apps/mpich-1.2.7p1/include -fPIC -g -O2 -c read_celfile_generic.c -o read_celfile_generic.o read_celfile_generic.c:31:20: stdint.h: No such file or directory *** Error code 1 make: Fatal error: Command failed for target `read_celfile_generic.o' chmod: WARNING: can't access /apps/R-2.6.2/lib/R/library/affyio/libs/* ERROR: compilation failed for package 'affyio' ** Removing '/apps/R-2.6.2/lib/R/library/affyio' --------------------------------- [[alternative HTML version deleted]]
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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