Sorry, that was a mistake. You are right Antonio, I wanted to say the "-g" flag.
Xavi. -----Mensaje original----- De: Antonio, Fabio Di Narzo [mailto:[EMAIL PROTECTED] Enviado el: dimecres, 7 / març / 2007 13:00 Para: Sole Acha, Xavi CC: r-devel@stat.math.ethz.ch Asunto: Re: [Rd] Garbage collector crashes after calling a C function 2007/3/7, Sole Acha, Xavi <[EMAIL PROTECTED]>: > Dear listers, > > > > a few days ago I asked a question about a problem I had with a C function > programmed by myself to be called from R. Thanks to your help, I have been > able to look a bit further into it, so now I can be a bit more specific when > telling what happens. > > > > The fact is that, when my C function finishes its execution (after calling it > via the ".C" interface), R seems ok but then crashes when the garbage > collector executes, giving a segmentation fault. > > > > As some of you suggested, I have executed my function with valgrind, and I > get no memory errors, but some memory leaks (which I am not able to locate > although compiling my program with the -c flag), In gcc, maybe you mean the '-g' flag > and I also get the memory error from RunGenCollect: (which I suppose is > causes the segmentation fault). You can see a small piece of the valgrind > output below > > > > Using gctorture to make the garbage collector crash inside the execution of > my program didn't work (my program finished). The question is: what are the > typical programming errors that can make R garbage collector crash? Could it > be because of these memory leaks? If so, how could I trace them? I have tried > it, but running my program with gdb is not an easy task to do, as it performs > a huge number of iterations. > > > > Thank you very much in advance for your help. I would appreciate any hint > that could help me solve this tricky problem. > > > > Best regards, > > > > Xavier Solé. > > > > ----------- > > ### This is one of the memory leaks > > ==9370== 162 (160 direct, 2 indirect) bytes in 1 blocks are definitely lost > in loss record 11 of 42 > > ==9370== at 0x4A19D35: malloc (vg_replace_malloc.c:149) > > ==9370== by 0x84490E0: ??? > > ==9370== by 0x844D346: ??? > > ==9370== by 0x4BBE1A2: do_dotCode (in /usr/lib64/R/lib/libR.so) > > ==9370== by 0x4BE9035: Rf_eval (in /usr/lib64/R/lib/libR.so) > > ==9370== by 0x4BEBA3F: do_set (in /usr/lib64/R/lib/libR.so) > > ==9370== by 0x4BE8E5E: Rf_eval (in /usr/lib64/R/lib/libR.so) > > ==9370== by 0x4BEAF0D: do_begin (in /usr/lib64/R/lib/libR.so) > > ==9370== by 0x4BE8E5E: Rf_eval (in /usr/lib64/R/lib/libR.so) > > ==9370== by 0x4BE9711: Rf_applyClosure (in /usr/lib64/R/lib/libR.so) > > ==9370== by 0x4BE9107: Rf_eval (in /usr/lib64/R/lib/libR.so) > > ==9370== by 0x4BEBA3F: do_set (in /usr/lib64/R/lib/libR.so) > > > > ### This is the RunGenCollect memory error > > ==9370== Invalid write of size 8 > > ==9370== at 0x4C1F73A: RunGenCollect (in /usr/lib64/R/lib/libR.so) > > ==9370== by 0x4C23E55: R_gc_internal (in /usr/lib64/R/lib/libR.so) > > ==9370== by 0x4C22DC3: Rf_cons (in /usr/lib64/R/lib/libR.so) > > ==9370== by 0x4C23AE1: Rf_allocList (in /usr/lib64/R/lib/libR.so) > > ==9370== by 0x4B6926B: installAttrib (in /usr/lib64/R/lib/libR.so) > > ==9370== by 0x4B69961: Rf_classgets (in /usr/lib64/R/lib/libR.so) > > ==9370== by 0x4B68DC1: Rf_setAttrib (in /usr/lib64/R/lib/libR.so) > > ==9370== by 0x4B69A40: do_classgets (in /usr/lib64/R/lib/libR.so) > > ==9370== by 0x4BE908E: Rf_eval (in /usr/lib64/R/lib/libR.so) > > ==9370== by 0x4BEB6FD: applydefine (in /usr/lib64/R/lib/libR.so) > > ==9370== by 0x4BEBAE3: do_set (in /usr/lib64/R/lib/libR.so) > > ==9370== by 0x4BE8E5E: Rf_eval (in /usr/lib64/R/lib/libR.so) > > ==9370== Address 0x10 is not stack'd, malloc'd or (recently) free'd > > > > > [[alternative HTML version deleted]] > > > ______________________________________________ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > > -- Antonio, Fabio Di Narzo Ph.D. student at Department of Statistical Sciences University of Bologna, Italy ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
