Re: [R] Problem installing aroma.affymetrix on Solaris 9 with R-2.6.2

From: Prof Brian Ripley <>
Date: Sat, 29 Mar 2008 20:23:37 +0000 (GMT)

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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> and provide commented, minimal, self-contained, reproducible code.

Brian D. Ripley,        
Professor of Applied Statistics,
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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Received on Sat 29 Mar 2008 - 20:27:07 GMT

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