I see at http://sourceforge.net/forum/forum.php?forum_id=844544 a link to http://www.bcgsc.ca/pipermail/ssrformat/2008-July/000531.html explaining serious flaw in io_lib-1.11.2. I am not certain what the sci-libs/io_lib-1.11.2.1 contains but it appears to me that we need the "io_lib-1.11.3 released - IMPORTANT FIX". Actually, provide current sci-libs/io_lib-1.11.6.
> I am not certain what the sci-libs/io_lib-1.11.2.1 contains ... I see, the files on sourceforge have always extra .1 in its version number, probably always the initial release. So it appears we really do have the broken version.
Will provide working ebuild for io_lib-1.11.6.1. The config.h file got renamed by upstream to io_lib_config.h. But luckily, "make install" also installs them, so the former troubles discussed in bug #145562 are obsolete.
Created attachment 182838 [details] io_lib-1.11.6.1.ebuild
sci-biology/staden should be able to compile against this newer version as the os.h header files refers to the io_lib_config.h file.
On linux kernel above 2.6.27 there was pipe2() introduced in glibc-2.9. Hence there is a nameclash with io_lib. See https://sourceforge.net/tracker/index.php?func=detail&aid=2629155&group_id=100316&atid=627058 for more details and a patch for io_lib. I just dared to rename the function as it seems to be used only by io_lib itself and not by external apps, like the staden package.
CC-ing due http://sources.redhat.com/ml/glibc-bugs/2008-12/msg00108.html ;-)
the issue there is not relevant to what you mention. pipe2() is now part of the C API so no random 3rd party library can use it.
(In reply to comment #7) > the issue there is not relevant to what you mention. pipe2() is now part of > the C API so no random 3rd party library can use it. > Yes, but io_lib had this function earlier. Anyway, I agree we have to patch io_lib and upstream as well.
Upstream renamed the function. I did not easily find cvs-browse access to io_lib I do not have the patch but except the new name was probably exactly same: > Comment By: James Bonfield (jkbonfield) Date: 2009-04-20 12:37 Message: Now fixed in CVS. I used pipe_into instead of iolibpipe2 as it's a more descriptive name, but essentially it's the same obvious fix as your patch. Thanks. James
done thanks fr reporting
