Jun Zhang
2008-Mar-29 16:09 UTC
[R] Problem installing aroma.affymetrix on Solaris 9 with R-2.6.2
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@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]]
Prof Brian Ripley
2008-Mar-29 20:23 UTC
[R] Problem installing aroma.affymetrix on Solaris 9 with R-2.6.2
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]] > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >-- 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