[BioC] Compilation or syntax error in IRanges sort_util.c package

Michael Dondrup mdondrup at cebitec.uni-bielefeld.de
Tue Mar 31 11:21:24 CEST 2009

Dear list,

I'm trying to install Bioconductor on Solaris using the SunWPro-12 compilers.
cc: Sun C 5.9 SunOS_i386 Patch 124868-08 2008/11/25

 > biocLite('IRanges')
Running biocinstall version 2.3.10 with R version 2.8.1
Your version of R requires version 2.3 of Bioconductor.
trying URL 'http://bioconductor.org/packages/2.3/bioc/src/contrib/IRanges_1.0.14.tar.gz'
Content type 'application/x-gzip' length 175687 bytes (171 Kb)
cc -xc99 -I/homes/mdondrup/bin/R-2.8.1//lib/R/include  -I/opt/SUNWspro/include/ 
-I/vol/tcl-8.4.13/include -I/vol/local/include -I/vol/graphics/include -I/vol/gnu/include     -KPIC 
  -g -c solve_user_SEW.c -o solve_user_SEW.o
cc -xc99 -I/homes/mdondrup/bin/R-2.8.1//lib/R/include  -I/opt/SUNWspro/include/ 
-I/vol/tcl-8.4.13/include -I/vol/local/include -I/vol/graphics/include -I/vol/gnu/include     -KPIC 
  -g -c sort_utils.c -o sort_utils.o
"sort_utils.c", line 18: void function cannot return value
cc: acomp failed for sort_utils.c
make: *** [sort_utils.o] Error 2
ERROR: compilation failed for package 'IRanges'
** Removing '/homes/mdondrup/bin/R-2.8.1/lib/R/library/IRanges'

The downloaded packages are in
Updating HTML index of packages in '.Library'
Warning message:
In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  :
   installation of package 'IRanges' had non-zero exit status

Looking into sort_utils.c line 18 shows that this is the error:
A void funtion trying to return something.

void _sort_int_array(int *x, int x_nelt)
	return qsort(x, x_nelt, sizeof(int), cmpintp);

I do not know why this works with gcc by the way but for me just removing the "return"

void _sort_int_array(int *x, int x_nelt)
	qsort(x, x_nelt, sizeof(int), cmpintp);

  makes the package compilable. I hope that no return value is ever needed somewhere ....

Could you devise a patch to make bioconductor installation possible from the repository?


 > version               _
platform       i386-pc-solaris2.10
arch           i386
os             solaris2.10
system         i386, solaris2.10
status         Patched
major          2
minor          8.1
year           2009
month          03
day            18
svn rev        48212
language       R
version.string R version 2.8.1 Patched (2009-03-18 r48212)

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