[BioC] Problem installing affyio on Solaris 9 with R-2.6.2

Ben Bolstad bmb at bmbolstad.com
Mon Mar 31 16:28:56 CEST 2008

This issue has been fixed in the development series (at 1.17.11). The
main problem being that stdint.h not being available on Solaris 9.
However, luckily there is another header file that provides the
equivalent information (inttypes.h).

I could patch the appropriate fix back to the release branch, though I
am reluctant to do so given it affects a limited number of users and the
next BioC release will be coming shortly.



On Mon, 2008-03-31 at 07:15 -0700, 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' 
> ---------------------------------
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