Entering edit mode
Michael Dondrup
▴
20
@michael-dondrup-3376
Last seen 10.3 years ago
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/IRan
ges_1.0.14.tar.gz'
Content type 'application/x-gzip' length 175687 bytes (171 Kb)
[snip]
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
/tmp/1101064.1.interactive.q/RtmpML0kk8/downloaded_packages
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?
Thanks
Michael
> 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)
>
