search for: rf_duplicate

First, thanks to those of you who responded to my previous post about my code that was taking longer and longer to process. After following your suggestions, and I now thinking that the problem was some calls to Rf_duplicate in my C code. So I'm hoping I could get some clarification on what Rf_duplicate actually does. What is the real difference between PROTECT(y=x); and PROTECT (y = duplicate(x)); ? I do use duplicate on the list objects that are passed directly from R, since in the passed, I got some odd re...

...s worth a sample trace below: (gdb) where #0 0x00a22096 in _int_free () from /lib/tls/libc.so.6 #1 0x00a2101b in free () from /lib/tls/libc.so.6 #2 0x080d632a in R_SetPPSize () #3 0x080d7d13 in do_regFinaliz () #4 0x080d9503 in do_gctime () #5 0x080d8fcb in Rf_allocVector () #6 0x080a9f7f in Rf_duplicate () #7 0x080aa18c in Rf_duplicate () #8 0x080b7b28 in R_execMethod () #9 0x080b8a0f in do_function () #10 0x080b8bf9 in do_function () #11 0x080b70b7 in Rf_eval () #12 0x080b87a5 in do_begin () #13 0x080b70b7 in Rf_eval () #14 0x080b80b1 in do_for () #15 0x080b70b7 in Rf_eval () #16 0x080b87a5 in...

...D848: ReleaseLargeFreeVectors (memory.c:760) ==25398== by 0x4F359E9: RunGenCollect (memory.c:1378) ==25398== by 0x4F38938: R_gc_internal (memory.c:2171) ==25398== by 0x4F38046: Rf_allocVector (memory.c:1961) ==25398== by 0x4EDE779: duplicate1 (duplicate.c:221) ==25398== by 0x4EDD698: Rf_duplicate (duplicate.c:115) ==25398== by 0x4E7BB34: cbind (bind.c:1258) ==25398== by 0x4E7B430: do_bind (bind.c:1113) ==25398== by 0x4F42A1B: do_internal (names.c:1116) ==25398== by 0x4EF959B: Rf_eval (eval.c:463) ==25398== by 0x4EF9F91: Rf_applyClosure (eval.c:666) gdb says (gdb) backtrace...

...tation fault. 0x763cc in Rf_allocVector (type=14, length=2) at memory.c:1551 1551 CLASS_GET_FREE_NODE(node_class, s); (gdb) bactrace Undefined command: "bactrace". Try "help". (gdb) backtrace #0 0x763cc in Rf_allocVector (type=14, length=2) at memory.c:1551 #1 0x5561c in Rf_duplicate (s=0xbcd6f0) at duplicate.c:140 #2 0x55518 in Rf_duplicate (s=0x99c508) at duplicate.c:133 #3 0x55518 in Rf_duplicate (s=0xc63468) at duplicate.c:133 #4 0x5b958 in do_set (call=0xb72804, op=0x1c6304, args=0xb727cc, rho=0x499a38) at eval.c:1012 #5 0x5a114 in Rf_eval (e=0xb72804, rho=0x499a38...

If anyone has a few extra CPU cycles to spare, I'd appreciate it if you could verify a problem that I have encountered. Run the code below and tell me if it crashes your R before completion. library(lme4) data(bdf) dump<-sapply( 1:50000, function(i) { fm <- lme(langPOST ~ IQ.ver.cen + avg.IQ.ver.cen, data = bdf, random = ~ IQ.ver.cen | schoolNR); cat("

Generating a model matrix with very large numbers of columns overflows the stack and/or runs very slowly, due to the implementation of TrimRepeats(). This patch modifies it to use Rf_duplicated() to find the duplicates. This makes the running time linear in the number of columns and eliminates the recursive function calls. Thanks -------------- next part -------------- A non-text attachment was scrubbed... Name: stats_model.patch Type: text/x-patch Size: 2182 bytes Desc: not available U...

...new VECSXP B of length M and /duplicate/ the elements of A. Since I do this often, it appears to be wasteful, so can I a) is there a resize function for a VECSXP? if not b) can i just do something like SET_VECTOR_ELT(B,i, VECTOR_ELT(A,i)) instead of wrapping VECTOR_ELT(A,i) inside a call to Rf_duplicate (i will be UNPROTECTING A and B, though I will return B) I suppose I can do (b), since B (since it is being returned) is automatically protected and therefore all its elements will also be protected, correct? Thank you Saptarshi

...t it quite obvious. After installing "inline" the example should just work by copy-pasting. Best and thanks in advance, Oleg code <- character(17) code[1] <- " SEXP res;" code[2] <- " int nprotect = 0, nx, ny, nz, x, y;" code[3] <- " PROTECT(res = Rf_duplicate(a)); nprotect++;" code[4] <- " nx = INTEGER(GET_DIM(a))[0];" code[5] <- " ny = INTEGER(GET_DIM(a))[1];" code[6] <- " nz = INTEGER(GET_DIM(a))[2];" code[7] <- " double sigma2 = REAL(s)[0] * REAL(s)[0], d2 ;" code[8] <- " double cx...

...arabid[,1], ntree=100) > predict(fit, arabid[,-1]) Done! Program received signal SIGSEGV, Segmentation fault. 0x40152a48 in malloc () from /lib/libc.so.6 [If I change the DUP=FALSE in the .C() call to TRUE, I get the following: Program received signal SIGSEGV, Segmentation fault. 0x080b412b in Rf_duplicate (s=0x1) at duplicate.c:75 75 switch (TYPEOF(s)) { ] At this point I'm clueless as to what to do next, and would very much appreciate any help! Best, Andy Andy Liaw, PhD Biometrics Research PO Box 2000, RY33-300 Merck Research Labs Rahway, NJ 07065 mailto:andy_lia...

...und? Thanks for help, Oleg Sklyar Here goes an example, the inline C-code does exactly what I would prefer R were doing, but both R examples do remove the element 'b': x = list(a=c(1L,2L), b=matrix(runif(4),2,2), c=LETTERS[1:3]) library(inline) code=" SEXP res; PROTECT(res = Rf_duplicate(x)); SET_VECTOR_ELT(res,1,R_NilValue); UNPROTECT(1); return res; " setnull = cfunction(signature(x="list"),code) setnull(x) # $a # [1] 1 2 # $b # NULL # $c # [1] "A" "B" "C" y = x x[[2]] = NULL x # $a # [1] 1 2 # $c # [1] "A" "B...

...t;> on Fri, 26 Feb 2016 15:58:20 -0800 writes: > > > Generating a model matrix with very large numbers of > > columns overflows the stack and/or runs very slowly, due > > to the implementation of TrimRepeats(). > > > This patch modifies it to use Rf_duplicated() to find the > > duplicates. This makes the running time linear in the > > number of columns and eliminates the recursive function > > calls. > > Thank you, Karl. > I've committed this (very slightly modified) to R-devel, > > (also after looking f...

...at malloc.c:3023 #2 0x80a6b60 in ReleaseLargeFreeVectors () at memory.c:673 #3 0x80a82b2 in RunGenCollect (size_needed=2000) at memory.c:1079 #4 0x80a9365 in R_gc_internal (size_needed=2000) at memory.c:1669 #5 0x80a9027 in Rf_allocVector (type=14, length=2000) at memory.c:1541 #6 0x808cb58 in Rf_duplicate (s=0x9548498) at duplicate.c:140 #7 0x80660fa in do_makelist (call=0x8a3f7c0, op=0x81a7c00, args=0x8239258, rho=0x824e510) at builtin.c:367 #8 0x809136f in Rf_eval (e=0x8a3f7c0, rho=0x824e510) at eval.c:424 #9 0x8092cf1 in Rf_evalList (el=0x8a3ee30, rho=0x824e510) at eval.c:1171 #10 0x80912...

...xel> PixelPrQueue; SEXP lib_filterInvWS (SEXP x) { SEXP res; int i, j, index; double val; PixelPrQueue pq; int nx = INTEGER ( GET_DIM(x) )[0]; int ny = INTEGER ( GET_DIM(x) )[1]; int nz = INTEGER ( GET_DIM(x) )[2]; int nprotect = 0; PROTECT ( res = Rf_duplicate(x) ); nprotect++; // Pixel px; for (int im = 0; im < nz; im++ ) { double * src = &( REAL(x)[ im * nx * ny ] ); double * tgt = &( REAL(res)[ im * nx * ny ] ); for ( j = 0; j < ny; j++ ) for ( i = 0; i < nx; i++ ) {...

Hi All, I have some questions regarding the R C API. Let's assume I have a function which is defined as follows: R file: myfunc <- function(a, b, ...) .External(Cfun, a, b, ...) C file: SEXP Cfun(SEXP args) { args = CDR(args); SEXP a = CAR(args); args = CDR(args); SEXP b = CAR(args); args = CDR(args); /* continue to do something with remaining arguments in "..."

...oject.org> >>>>> on Fri, 26 Feb 2016 15:58:20 -0800 writes: > Generating a model matrix with very large numbers of > columns overflows the stack and/or runs very slowly, due > to the implementation of TrimRepeats(). > This patch modifies it to use Rf_duplicated() to find the > duplicates. This makes the running time linear in the > number of columns and eliminates the recursive function > calls. Thank you, Karl. I've committed this (very slightly modified) to R-devel, (also after looking for a an example that runs on a non-hug...

....5 -5.5 -8.5 [3,] -3.5 -6.5 -9.5 > # -------------------------------------------------------------------------------------------------------------------------- library( inline ) c.code <- " SEXP res; int nprotect = 0, nx, ny, x, y; double *dptr, *resptr, sum; PROTECT(res = Rf_duplicate(a)); nprotect++; nx = INTEGER(GET_DIM(a))[0]; ny = INTEGER(GET_DIM(a))[1]; dptr = REAL(a); resptr = REAL( res ); sum = 0.0; for (x = 0; x < nx; x++) for (y = 0; y < ny; y++) { resptr[ x + y*nx ] = -dptr[ x + y*nx ]; sum += -dptr[ x + y*nx ]; } UNPROTECT...

...know. alas (gdb) bt #0 0x00007ff956be3857 in ?? () from /usr/lib/R/lib/libR.so #1 0x00007ff956be67d3 in Rf_allocVector () from /usr/lib/R/lib/libR.so #2 0x00007ff956b90338 in ?? () from /usr/lib/R/lib/libR.so #3 0x00007ff956b8fcfa in ?? () from /usr/lib/R/lib/libR.so #4 0x00007ff956b90875 in Rf_duplicate () from /usr/lib/R/lib/libR.so #5 0x00007ff956b48e98 in ?? () from /usr/lib/R/lib/libR.so #6 0x00007ff956bb56da in ?? () from /usr/lib/R/lib/libR.so #7 0x00007ff956bba9a8 in Rf_eval () from /usr/lib/R/lib/libR.so #8 0x00007ff956bbec39 in Rf_applyClosure () from /usr/lib/R/lib/libR.so #9 0x0000...

...bug.report() from R-1.3.1 at the end.) The relevant part of the log is below. Any ideas? gcc -shared -o methods.so do_substitute_direct.o methods_list_dispatch.o method_meta_data.o slot.o -L/usr/local/lib /usr/ucb/ld: Warning: Unresolved: TYPEOF Rf_error Rf_protect Rf_substitute Rf_unprotect Rf_duplicate Rf_VectorToPairList R_NilValue Rf_NewEnvironment R_set_standardGeneric_ptr R_GlobalEnv R_set_quick_method_check Rf_install Rf_allocVector LOGICAL R_PreserveObject Rf_mkChar SET_STRING_ELT Rf_findVar R_UnboundValue VECTOR_ELT R_NamesSymbol Rf_getAttrib Rf_length STRING_ELT R_CHAR R_do_slot Rf_asChar...

Hi Morgan, My solutions might not be the best one(I believe it's not), but it should work for your question. 1. Have you considered Rf_duplicate function? If you want to change the value of `a` and reset it later, you have to have a duplication somewhere for resetting it. Instead of changing the value of `a` directly, why not changing the value of a duplicated `a`? So you do not have to reset it. 2. I think a pairlist behaves like a linked...

# Your mailer is set to "none" (default on Windows), # hence we cannot send the bug report directly from R. # Please copy the bug report (after finishing it) to # your favorite email program and send it to # # r-bugs@r-project.org # ###################################################### # The last line of following code produces a segmentation fault: x <- 1:10 f <- gl(5,2)