[Bioc-devel] genefilter package update?

[Martin Morgan]

Hi Paul --

Sorry for the delay in replying to your message.

The C++ code in genefilter is very straight-forward, and this implies
that your problems compiling it are likely to occur with any package
containing C++ code. A similarly simple package to try might be plier;
EBImage or RBGL would be challenging packages. Does plier have similar
problems?

If plier does have problems then the solution belongs at the R level
and not at the package level. However, R does get regular use on
Solaris boxes, presumably sometimes with the default compilers. So it
might be something more unique to your set up. One possibility is that
you configured and made R with a different compiler than you are using
to compile packages. Is that, or other questionable practice, likely?

If it seems that R does not in fact get configured correctly, then
probably R's configure.ac needs to be updated. This probably requires
more specific information about the OS and compiler versions that are
causing problems. Can you provide that information?

Martin

Paul Gordon <gordonp at ucalgary.ca> writes:

> Hi all,
>
> Not sure exactly who is maintaining genefilter (the info page lists a
> group), so I thought I'd post here.  The genefilter package (version
> 1.16.0)
> compiles fine under Solaris using the default Sun compiler, but if you
> actually try to use it you get a nasty error:
>
>  ld.so.1: R: fatal: relocation error: file
> /export/home/gordonp/R/lib/R/library/genefilter/libs/genefilter.so:
> symbol __1cDstdJbad_allocG__vtbl_: referenced symbol not found
>
> This is because under Solaris libCrun.so needs to explicitly linked
> for the C++ code in genefilter's src directory.  I got around this by
> creating
> a GNU configure script (in keeping with the recommended R package
> approach) that checks if -lCrun is needed.   With configure in the
> top-level
> direxctory of the package, it works fine.  Hopefully this can be
> incorporated into the distribution, as I think it would affect anyone
> not using gcc on
> Solaris.  Not sure if the mailing list strips off small text
> attachments, but the configure.in and src/Makevars.in for autoconf are
> attached.  I can
> send them directly to the relevant party if they e-mail me.
>
> Regards,
>
> Paul
> PKG_CFLAGS = @CFLAGS@  
> PKG_LIBS = @LIBS@
> PKG_CPPFLAGS = @DEFS@
> AC_INIT("DESCRIPTION")
>
> AC_CHECK_LIB(Crun, _fini, [use_libcrun=yes], [use_libcrun=no])
>
> AC_MSG_CHECKING([if we need to explicitly link libCrun])
> if test "x$use_libcrun" = "xyes"
> then
>     LIBS="$LIBS -lCrun"
> fi
> AC_MSG_RESULT($use_libcrun)
>
> AC_CONFIG_FILES([src/Makevars])
> AC_OUTPUT
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-- 
Martin Morgan
Computational Biology Shared Resource Director
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M2 B169
Phone: (208) 667-2793