As others have said, this needs tools not CPU cycles: gctorture or valgrind.
Valgrind found (after a few seconds and on the first pass)
==23057== Invalid read of size 4 ==23057== at 0x3CF4E645: ssc_symbolic_permute (Mutils.c:373) ==23057== by 0x3CF5BF75: ssclme_create (ssclme.c:168) ==23057== by 0x80AF5E8: do_dotcall (/users/ripley/R/svn/R-devel/src/main/dotcode.c:640) ==23057== by 0x80CFA84: Rf_eval (/users/ripley/R/svn/R-devel/src/main/eval.c:399) ==23057== Address 0x3C7F3BD0 is 4 bytes before a block of size 524 alloc'd ==23057== at 0x3C01CB56: calloc (in /opt/local/lib/valgrind/vgpreload_memcheck.so) ==23057== by 0x80F9EBE: R_chk_calloc (/users/ripley/R/svn/R-devel/src/main/memory.c:2151) ==23057== by 0x3CF4E515: ssc_symbolic_permute (Mutils.c:352) ==23057== by 0x3CF5BF75: ssclme_create (ssclme.c:168) ==23057== ==23057== Use of uninitialised value of size 8 ==23057== at 0x80C0137: Rf_duplicate (/users/ripley/R/svn/R-devel/src/main/duplicate.c:160) ==23057== by 0x80BFA85: Rf_duplicate (/users/ripley/R/svn/R-devel/src/main/duplicate.c:101) ==23057== by 0x80BFEB3: Rf_duplicate (/users/ripley/R/svn/R-devel/src/main/duplicate.c:154) ==23057== by 0x816ED96: do_subset2_dflt (/users/ripley/R/svn/R-devel/src/main/subset.c:816) ==23057== ==23057== Conditional jump or move depends on uninitialised value(s) ==23057== at 0x3CF62229: ssclme_fitted (ssclme.c:1587) ==23057== by 0x80AF646: do_dotcall (/users/ripley/R/svn/R-devel/src/main/dotcode.c:646) ==23057== by 0x80CFA84: Rf_eval (/users/ripley/R/svn/R-devel/src/main/eval.c:399) ==23057== by 0x80D1D80: do_set (/users/ripley/R/svn/R-devel/src/main/eval.c:1280)
which is pretty definitive evidence of a problem (possibly 2) in the code.
I strongly recommend valgrind (http://valgrind.kde.org/) if you are using x86 Linux. It has found quite a few errors in R and in certain packages recently. The only thing to watch is that optimized BLASes will probably crash it.
You're right. I had (at least) two thinko's in that code. The problems show up in the lme4 package but the errors in the C code are in the Matrix package. I will upload a repaired version of the Matrix package.
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