[BioC] Compilation or syntax error in IRanges sort_util.c package
Michael Dondrup
mdondrup at cebitec.uni-bielefeld.de
Wed Apr 1 15:36:36 CEST 2009
Dear Michael and BioC,
thank you for the response and can further report attempts to install the Biostrings package using
cc: Sun C 5.9 SunOS_i386 Patch 124868-08 2008/11/25 on Solaris.
The IRanges packages can now be installed, but the installation of Biostrings fails with many
messages such as (just the relevant portion, Sorry for the lengthy details).
azteca:~/compile/Biostrings/src> 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 -I"/homes/mdondrup/bin/R-2.8.1/lib/R/library/IRanges/include" -KPIC -g -c
IRanges_stubs.c -o IRanges_stubs.o
"/homes/mdondrup/bin/R-2.8.1/lib/R/library/IRanges/include/_IRanges_stubs.c", line 20: void function
cannot return value
"/homes/mdondrup/bin/R-2.8.1/lib/R/library/IRanges/include/_IRanges_stubs.c", line 20: warning:
syntax error: empty declaration
...
Therefore, the problem is still in IRanges in inst/_IRanges_stubs.c which is not compiled during
installation, but with the subsequent package.
I've got the impression that this file is auto-generated, therefore I haven't made more changes yet.
There are in fact two issues.
1. cc does not accept anything after a return in void functions, as with the last probelm
2. cc does not seem to like typecasts with named parameters in type casts such as:
from the preprocessed code:
fun = ( void ( * ) ( const int * x , int x_nelt , int * order ) ) R_GetCCallable ( "IRanges" , "_"
"get_int_array_order" ) ;
instead it can be like
fun = ( void ( * ) ( const int * , int , int * ) R_GetCCallable ( "IRanges" , "_"
"get_int_array_order" ) ;
This code is generated by the DEFINE_CCALLABLE_STUB in _IRanges_stubs.c
To make this more portable I tried to define two makros instead as:
#define DEFINE_CCALLABLE_STUB(retT, stubname, Types, Targs, args) \
retT stubname Targs \
{ \
static retT (*fun)Targs = NULL; \
if (fun == NULL) \
fun = (retT (*)Types) R_GetCCallable("IRanges", "_" #stubname); \
return fun args; \
}
#define DEFINE_CCALLABLE_VOID_STUB(retT, stubname, Types, Targs, args) \
retT stubname Targs \
{ \
static retT (*fun)Targs = NULL; \
if (fun == NULL) \
fun = (retT (*)Types) R_GetCCallable("IRanges", "_" #stubname); \
fun args; \
return; \
}
These could create fuction bodies for void functions and others. Second, these macros have the
additonal 'Types' argument and the function stub definition is then like:
/*
* Stubs for callables defined in sort_utils.c
*/
DEFINE_CCALLABLE_VOID_STUB(void, sort_int_array,
(int *, int),
(int *x, int x_nelt),
( x, x_nelt)
);
....
DEFINE_CCALLABLE_STUB(IntAE, new_IntAE,
(int , int , int),
(int buflength, int nelt, int val),
( buflength, nelt, val)
);
Processor output then looks like:
void sort_int_array ( int * x , int x_nelt ) {
static void ( * fun ) ( int * x , int x_nelt ) = 0 ;
if ( fun == 0 )
fun = ( void ( * ) ( int * , int ) ) R_GetCCallable ( "IRanges" , "_" "sort_int_array" ) ;
return ;
} ;
which does not cause an error. Could this be changed in the code generation, otherwise I can change
the declarations with a perl script.
Best
Michael
Michael Lawrence wrote:
>
>
> On Tue, Mar 31, 2009 at 2:21 AM, Michael Dondrup
> <mdondrup at cebitec.uni-bielefeld.de
> <mailto:mdondrup at cebitec.uni-bielefeld.de>> wrote:
>
> 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)
> [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
>
>
> Probably because qsort returns void, so it's compatible. Obviously,
> return is pointless in the case of 'void' though.
>
>
> 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?
>
>
> Fixed in svn.
>
> Thanks for the report,
> Michael
>
>
>
>
> 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)
> >
>
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>
>
--
--
Dr. Michael Dondrup
CeBiTec - http://www.cebitec.uni-bielefeld.de/~mdondrup
Bielefeld University, D-33594 Bielefeld, Germany
office: V6-147 voice: +49 521 106-4827 fax: -6419
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