I want to write an R function using R's C interface that takes a 2-column matrix of increasing, non-overlapping integer intervals and returns a list with those intervals plus some added intervals, such that there are no gaps. For example, it should take the matrix rbind(c(5L, 6L), c(7L, 10L), c(20L, 30L)) and return list(c(5L, 6L), c(7L, 10L), c(11L, 19L), c(20L, 30L)). Because the output is of variable length, I use a pairlist (because it is growable) and then I call Rf_PairToVectorList() at the end to make it into a regular list. I'm getting a strange garbage collection error. My PROTECTed pairlist prlst gets garbage collected away and causes a memory leak error when I try to access it. Here's my code. #include <Rinternals.h> SEXP C_int_mat_nth_row_nrnc(int *int_mat_int, int nr, int nc, int n) { SEXP out = PROTECT(Rf_allocVector(INTSXP, nc)); int *out_int = INTEGER(out); if (n <= 0 | n > nr) { for (int i = 0; i != nc; ++i) { out_int[i] = NA_INTEGER; } } else { for (int i = 0; i != nr; ++i) { out_int[i] = int_mat_int[n - 1 + i * nr]; } } UNPROTECT(1); return out;} SEXP C_make_len2_int_vec(int first, int second) { SEXP out = PROTECT(Rf_allocVector(INTSXP, 2)); int *out_int = INTEGER(out); out_int[0] = first; out_int[1] = second; UNPROTECT(1); return out;} SEXP C_fullocate(SEXP int_mat) { int nr = Rf_nrows(int_mat), *int_mat_int = INTEGER(int_mat); int last, row_num; // row_num will be 1-indexed SEXP prlst0cdr = PROTECT(C_int_mat_nth_row_nrnc(int_mat_int, nr, 2, 1)); SEXP prlst = PROTECT(Rf_list1(prlst0cdr)); SEXP prlst_tail = prlst; last = INTEGER(prlst0cdr)[1]; row_num = 2; while (row_num <= nr) { Rprintf("row_num: %i\n", row_num); SEXP row = PROTECT(C_int_mat_nth_row_nrnc(int_mat_int, nr, 2, row_num)); Rf_PrintValue(prlst); // This is where the error occurs int *row_int = INTEGER(row); if (row_int[0] == last + 1) { Rprintf("here1"); SEXP next = PROTECT(Rf_list1(row)); prlst_tail = SETCDR(prlst_tail, next); last = row_int[1]; UNPROTECT(1); ++row_num; } else { Rprintf("here2"); SEXP next_car = PROTECT(C_make_len2_int_vec(last + 1, row_int[0] - 1)); SEXP next = PROTECT(Rf_list1(next_car)); prlst_tail = SETCDR(prlst_tail, next); last = row_int[0] - 1; UNPROTECT(2); } UNPROTECT(1); } SEXP out = PROTECT(Rf_PairToVectorList(prlst)); UNPROTECT(3); return out;} As you can see, I have some diagnostic print statements in there. The offending line is line 40, which I have marked with a comment of // This is where the error occurs. I have a minimal reproducible package at https://github.com/rorynolan/testpkg and I have run R CMD CHECK with valgrind using GitHub actions, the results of which are at https://github.com/rorynolan/testpkg/runs/1076595757?check_suite_focus=true. That's where I found out which line is causing the error. This function works as expected sometimes, and then sometimes this issue appears. This lends weight to the suspicion that it's a garbage collection issue. I really want to know what my mistake is. I'm not that interested in alternative implementations; I want to understand the mistake that I'm making so that I can avoid making it in future. I have asked the question on stackoverflow to little avail, but the discussion there may prove helpful. https://stackoverflow.com/questions/63759604/garbage-collection-of-seemingly-protected-pairlist. Thanks, Rory [[alternative HTML version deleted]]
peter dalgaard
2020-Sep-12 07:22 UTC
[Rd] Garbage collection of seemingly PROTECTed pairlist
Hm, I'm getting rusty on my C skills, but you repeatedly use a pattern like> while (row_num <= nr) { > Rprintf("row_num: %i\n", row_num); > SEXP row = PROTECT(C_int_mat_nth_row_nrnc(int_mat_int, nr, 2, row_num));I wonder if there is a subtle difference between assignments and initialized declarations. I.e. would it help to write it as> while (row_num <= nr) {SEXP row; Rprintf("row_num: %i\n", row_num); row = PROTECT(C_int_mat_nth_row_nrnc(int_mat_int, nr, 2, row_num)); ? -pd> On 12 Sep 2020, at 00:35 , Rory Nolan <rorynoolan at gmail.com> wrote: > > I want to write an R function using R's C interface that takes a 2-column > matrix of increasing, non-overlapping integer intervals and returns a list > with those intervals plus some added intervals, such that there are no > gaps. For example, it should take the matrix rbind(c(5L, 6L), c(7L, 10L), > c(20L, 30L)) and return list(c(5L, 6L), c(7L, 10L), c(11L, 19L), c(20L, > 30L)). Because the output is of variable length, I use a pairlist (because > it is growable) and then I call Rf_PairToVectorList() at the end to make it > into a regular list. > > I'm getting a strange garbage collection error. My PROTECTed pairlist prlst > gets garbage collected away and causes a memory leak error when I try to > access it. > > Here's my code. > > #include <Rinternals.h> > > > SEXP C_int_mat_nth_row_nrnc(int *int_mat_int, int nr, int nc, int n) { > SEXP out = PROTECT(Rf_allocVector(INTSXP, nc)); > int *out_int = INTEGER(out); > if (n <= 0 | n > nr) { > for (int i = 0; i != nc; ++i) { > out_int[i] = NA_INTEGER; > } > } else { > for (int i = 0; i != nr; ++i) { > out_int[i] = int_mat_int[n - 1 + i * nr]; > } > } > UNPROTECT(1); > return out;} > > SEXP C_make_len2_int_vec(int first, int second) { > SEXP out = PROTECT(Rf_allocVector(INTSXP, 2)); > int *out_int = INTEGER(out); > out_int[0] = first; > out_int[1] = second; > UNPROTECT(1); > return out;} > > SEXP C_fullocate(SEXP int_mat) { > int nr = Rf_nrows(int_mat), *int_mat_int = INTEGER(int_mat); > int last, row_num; // row_num will be 1-indexed > SEXP prlst0cdr = PROTECT(C_int_mat_nth_row_nrnc(int_mat_int, nr, 2, 1)); > SEXP prlst = PROTECT(Rf_list1(prlst0cdr)); > SEXP prlst_tail = prlst; > last = INTEGER(prlst0cdr)[1]; > row_num = 2; > while (row_num <= nr) { > Rprintf("row_num: %i\n", row_num); > SEXP row = PROTECT(C_int_mat_nth_row_nrnc(int_mat_int, nr, 2, row_num)); > Rf_PrintValue(prlst); // This is where the error occurs > int *row_int = INTEGER(row); > if (row_int[0] == last + 1) { > Rprintf("here1"); > SEXP next = PROTECT(Rf_list1(row)); > prlst_tail = SETCDR(prlst_tail, next); > last = row_int[1]; > UNPROTECT(1); > ++row_num; > } else { > Rprintf("here2"); > SEXP next_car = PROTECT(C_make_len2_int_vec(last + 1, row_int[0] - 1)); > SEXP next = PROTECT(Rf_list1(next_car)); > prlst_tail = SETCDR(prlst_tail, next); > last = row_int[0] - 1; > UNPROTECT(2); > } > UNPROTECT(1); > } > SEXP out = PROTECT(Rf_PairToVectorList(prlst)); > UNPROTECT(3); > return out;} > > As you can see, I have some diagnostic print statements in there. The > offending line is line 40, which I have marked with a comment of // This is > where the error occurs. I have a minimal reproducible package at > https://github.com/rorynolan/testpkg and I have run R CMD CHECK with > valgrind using GitHub actions, the results of which are at > https://github.com/rorynolan/testpkg/runs/1076595757?check_suite_focus=true. > That's where I found out which line is causing the error. This function > works as expected sometimes, and then sometimes this issue appears. This > lends weight to the suspicion that it's a garbage collection issue. > > I really want to know what my mistake is. I'm not that interested in > alternative implementations; I want to understand the mistake that I'm > making so that I can avoid making it in future. > > I have asked the question on stackoverflow to little avail, but the > discussion there may prove helpful. > https://stackoverflow.com/questions/63759604/garbage-collection-of-seemingly-protected-pairlist. > > > > Thanks, > > Rory > > [[alternative HTML version deleted]] > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel-- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Office: A 4.23 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
Martin Morgan
2020-Sep-12 10:44 UTC
[Rd] Garbage collection of seemingly PROTECTed pairlist
I put your code into a file tmp.R and eliminated the need for a package by compiling this to a shared object R CMD SHLIB tmp.c I'm then able to use a simple script 'tmp.R' dyn.load("/tmp/tmp.so") fullocate <- function(int_mat) .Call("C_fullocate", int_mat) int_mat <- rbind(c(5L, 6L), c(7L, 10L), c(20L, 30L)) while(TRUE) res <- fullocate(int_mat) to generate a segfault. Looking at your code, it seemed like I could get towards a simpler reproducible example by eliminating most of the 'while' loop and then functions and code branches that are not used #include <Rinternals.h> SEXP C_int_mat_nth_row_nrnc(int *int_mat_int, int nr, int nc, int n) { SEXP out = PROTECT(Rf_allocVector(INTSXP, nc)); int *out_int = INTEGER(out); for (int i = 0; i != nr; ++i) { out_int[i] = int_mat_int[n - 1 + i * nr]; } UNPROTECT(1); return out;} SEXP C_fullocate(SEXP int_mat) { int nr = Rf_nrows(int_mat), *int_mat_int = INTEGER(int_mat); int row_num = 2; // row_num will be 1-indexed SEXP prlst0cdr = PROTECT(C_int_mat_nth_row_nrnc(int_mat_int, nr, 2, 1)); SEXP prlst = PROTECT(Rf_list1(prlst0cdr)); SEXP row = PROTECT(C_int_mat_nth_row_nrnc(int_mat_int, nr, 2, row_num)); Rf_PrintValue(prlst); // This is where the error occurs UNPROTECT(3); return R_NilValue; } my script still gives an error, but not a segfault, and the values printed sometimes differ between calls ... [[1]] [1] 5 6 . [[1]] NULL ... Error in FUN(X[[i]], ...) : cannot coerce type 'NULL' to vector of type 'character' Calls: message -> .makeMessage -> lapply Execution halted The differing values in particular, and the limited PROTECTion in the call and small allocations (hence limited need / opportunity for garbage collection), suggest that you're corrupting memory, rather than having a problem with garbage collection. Indeed, SEXP prlst0cdr = PROTECT(C_int_mat_nth_row_nrnc(int_mat_int, nr, 2, 1)); allocates a vector of length 2 at SEXP out = PROTECT(Rf_allocVector(INTSXP, nc)); but writes three elements (the 0th, 1st, and 2nd) at for (int i = 0; i != nr; ++i) { out_int[i] = int_mat_int[n - 1 + i * nr]; } Martin Morgan ?On 9/11/20, 9:30 PM, "R-devel on behalf of Rory Nolan" <r-devel-bounces at r-project.org on behalf of rorynoolan at gmail.com> wrote: I want to write an R function using R's C interface that takes a 2-column matrix of increasing, non-overlapping integer intervals and returns a list with those intervals plus some added intervals, such that there are no gaps. For example, it should take the matrix rbind(c(5L, 6L), c(7L, 10L), c(20L, 30L)) and return list(c(5L, 6L), c(7L, 10L), c(11L, 19L), c(20L, 30L)). Because the output is of variable length, I use a pairlist (because it is growable) and then I call Rf_PairToVectorList() at the end to make it into a regular list. I'm getting a strange garbage collection error. My PROTECTed pairlist prlst gets garbage collected away and causes a memory leak error when I try to access it. Here's my code. #include <Rinternals.h> SEXP C_int_mat_nth_row_nrnc(int *int_mat_int, int nr, int nc, int n) { SEXP out = PROTECT(Rf_allocVector(INTSXP, nc)); int *out_int = INTEGER(out); if (n <= 0 | n > nr) { for (int i = 0; i != nc; ++i) { out_int[i] = NA_INTEGER; } } else { for (int i = 0; i != nr; ++i) { out_int[i] = int_mat_int[n - 1 + i * nr]; } } UNPROTECT(1); return out;} SEXP C_make_len2_int_vec(int first, int second) { SEXP out = PROTECT(Rf_allocVector(INTSXP, 2)); int *out_int = INTEGER(out); out_int[0] = first; out_int[1] = second; UNPROTECT(1); return out;} SEXP C_fullocate(SEXP int_mat) { int nr = Rf_nrows(int_mat), *int_mat_int = INTEGER(int_mat); int last, row_num; // row_num will be 1-indexed SEXP prlst0cdr = PROTECT(C_int_mat_nth_row_nrnc(int_mat_int, nr, 2, 1)); SEXP prlst = PROTECT(Rf_list1(prlst0cdr)); SEXP prlst_tail = prlst; last = INTEGER(prlst0cdr)[1]; row_num = 2; while (row_num <= nr) { Rprintf("row_num: %i\n", row_num); SEXP row = PROTECT(C_int_mat_nth_row_nrnc(int_mat_int, nr, 2, row_num)); Rf_PrintValue(prlst); // This is where the error occurs int *row_int = INTEGER(row); if (row_int[0] == last + 1) { Rprintf("here1"); SEXP next = PROTECT(Rf_list1(row)); prlst_tail = SETCDR(prlst_tail, next); last = row_int[1]; UNPROTECT(1); ++row_num; } else { Rprintf("here2"); SEXP next_car = PROTECT(C_make_len2_int_vec(last + 1, row_int[0] - 1)); SEXP next = PROTECT(Rf_list1(next_car)); prlst_tail = SETCDR(prlst_tail, next); last = row_int[0] - 1; UNPROTECT(2); } UNPROTECT(1); } SEXP out = PROTECT(Rf_PairToVectorList(prlst)); UNPROTECT(3); return out;} As you can see, I have some diagnostic print statements in there. The offending line is line 40, which I have marked with a comment of // This is where the error occurs. I have a minimal reproducible package at https://github.com/rorynolan/testpkg and I have run R CMD CHECK with valgrind using GitHub actions, the results of which are at https://github.com/rorynolan/testpkg/runs/1076595757?check_suite_focus=true. That's where I found out which line is causing the error. This function works as expected sometimes, and then sometimes this issue appears. This lends weight to the suspicion that it's a garbage collection issue. I really want to know what my mistake is. I'm not that interested in alternative implementations; I want to understand the mistake that I'm making so that I can avoid making it in future. I have asked the question on stackoverflow to little avail, but the discussion there may prove helpful. https://stackoverflow.com/questions/63759604/garbage-collection-of-seemingly-protected-pairlist. Thanks, Rory [[alternative HTML version deleted]] ______________________________________________ R-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Hi, In line 5, you are allocating a vector of length nc. Then, in line 12, you are using nr as a limit, so if nr goes beyond nc, which is happening in line 39, you are in trouble. I?aki On Sat, 12 Sep 2020 at 03:30, Rory Nolan <rorynoolan at gmail.com> wrote:> I want to write an R function using R's C interface that takes a 2-column > matrix of increasing, non-overlapping integer intervals and returns a list > with those intervals plus some added intervals, such that there are no > gaps. For example, it should take the matrix rbind(c(5L, 6L), c(7L, 10L), > c(20L, 30L)) and return list(c(5L, 6L), c(7L, 10L), c(11L, 19L), c(20L, > 30L)). Because the output is of variable length, I use a pairlist (because > it is growable) and then I call Rf_PairToVectorList() at the end to make it > into a regular list. > > I'm getting a strange garbage collection error. My PROTECTed pairlist prlst > gets garbage collected away and causes a memory leak error when I try to > access it. > > Here's my code. > > #include <Rinternals.h> > > > SEXP C_int_mat_nth_row_nrnc(int *int_mat_int, int nr, int nc, int n) { > SEXP out = PROTECT(Rf_allocVector(INTSXP, nc)); > int *out_int = INTEGER(out); > if (n <= 0 | n > nr) { > for (int i = 0; i != nc; ++i) { > out_int[i] = NA_INTEGER; > } > } else { > for (int i = 0; i != nr; ++i) { > out_int[i] = int_mat_int[n - 1 + i * nr]; > } > } > UNPROTECT(1); > return out;} > > SEXP C_make_len2_int_vec(int first, int second) { > SEXP out = PROTECT(Rf_allocVector(INTSXP, 2)); > int *out_int = INTEGER(out); > out_int[0] = first; > out_int[1] = second; > UNPROTECT(1); > return out;} > > SEXP C_fullocate(SEXP int_mat) { > int nr = Rf_nrows(int_mat), *int_mat_int = INTEGER(int_mat); > int last, row_num; // row_num will be 1-indexed > SEXP prlst0cdr = PROTECT(C_int_mat_nth_row_nrnc(int_mat_int, nr, 2, 1)); > SEXP prlst = PROTECT(Rf_list1(prlst0cdr)); > SEXP prlst_tail = prlst; > last = INTEGER(prlst0cdr)[1]; > row_num = 2; > while (row_num <= nr) { > Rprintf("row_num: %i\n", row_num); > SEXP row = PROTECT(C_int_mat_nth_row_nrnc(int_mat_int, nr, 2, > row_num)); > Rf_PrintValue(prlst); // This is where the error occurs > int *row_int = INTEGER(row); > if (row_int[0] == last + 1) { > Rprintf("here1"); > SEXP next = PROTECT(Rf_list1(row)); > prlst_tail = SETCDR(prlst_tail, next); > last = row_int[1]; > UNPROTECT(1); > ++row_num; > } else { > Rprintf("here2"); > SEXP next_car = PROTECT(C_make_len2_int_vec(last + 1, row_int[0] - > 1)); > SEXP next = PROTECT(Rf_list1(next_car)); > prlst_tail = SETCDR(prlst_tail, next); > last = row_int[0] - 1; > UNPROTECT(2); > } > UNPROTECT(1); > } > SEXP out = PROTECT(Rf_PairToVectorList(prlst)); > UNPROTECT(3); > return out;} > > As you can see, I have some diagnostic print statements in there. The > offending line is line 40, which I have marked with a comment of // This is > where the error occurs. I have a minimal reproducible package at > https://github.com/rorynolan/testpkg and I have run R CMD CHECK with > valgrind using GitHub actions, the results of which are at > https://github.com/rorynolan/testpkg/runs/1076595757?check_suite_focus=true > . > That's where I found out which line is causing the error. This function > works as expected sometimes, and then sometimes this issue appears. This > lends weight to the suspicion that it's a garbage collection issue. > > I really want to know what my mistake is. I'm not that interested in > alternative implementations; I want to understand the mistake that I'm > making so that I can avoid making it in future. > > I have asked the question on stackoverflow to little avail, but the > discussion there may prove helpful. > > https://stackoverflow.com/questions/63759604/garbage-collection-of-seemingly-protected-pairlist > . > > > > Thanks, > > Rory > > [[alternative HTML version deleted]] > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel >-- I?aki ?car [[alternative HTML version deleted]]
I?aki is right. This solves it. Kudos to Martin Morgan too for paring down my reprex; I wasn?t aware of the method with R CMD SHLIB that he kindly described. Thanks also to Peter Dalgaard for having a crack at it. Very grateful to you all.> On 12 Sep 2020, at 04:16, I?aki Ucar <iucar at fedoraproject.org> wrote: > > Hi, > > In line 5, you are allocating a vector of length nc. Then, in line 12, you are using nr as a limit, so if nr goes beyond nc, which is happening in line 39, you are in trouble. > > I?aki > > On Sat, 12 Sep 2020 at 03:30, Rory Nolan <rorynoolan at gmail.com <mailto:rorynoolan at gmail.com>> wrote: > I want to write an R function using R's C interface that takes a 2-column > matrix of increasing, non-overlapping integer intervals and returns a list > with those intervals plus some added intervals, such that there are no > gaps. For example, it should take the matrix rbind(c(5L, 6L), c(7L, 10L), > c(20L, 30L)) and return list(c(5L, 6L), c(7L, 10L), c(11L, 19L), c(20L, > 30L)). Because the output is of variable length, I use a pairlist (because > it is growable) and then I call Rf_PairToVectorList() at the end to make it > into a regular list. > > I'm getting a strange garbage collection error. My PROTECTed pairlist prlst > gets garbage collected away and causes a memory leak error when I try to > access it. > > Here's my code. > > #include <Rinternals.h> > > > SEXP C_int_mat_nth_row_nrnc(int *int_mat_int, int nr, int nc, int n) { > SEXP out = PROTECT(Rf_allocVector(INTSXP, nc)); > int *out_int = INTEGER(out); > if (n <= 0 | n > nr) { > for (int i = 0; i != nc; ++i) { > out_int[i] = NA_INTEGER; > } > } else { > for (int i = 0; i != nr; ++i) { > out_int[i] = int_mat_int[n - 1 + i * nr]; > } > } > UNPROTECT(1); > return out;} > > SEXP C_make_len2_int_vec(int first, int second) { > SEXP out = PROTECT(Rf_allocVector(INTSXP, 2)); > int *out_int = INTEGER(out); > out_int[0] = first; > out_int[1] = second; > UNPROTECT(1); > return out;} > > SEXP C_fullocate(SEXP int_mat) { > int nr = Rf_nrows(int_mat), *int_mat_int = INTEGER(int_mat); > int last, row_num; // row_num will be 1-indexed > SEXP prlst0cdr = PROTECT(C_int_mat_nth_row_nrnc(int_mat_int, nr, 2, 1)); > SEXP prlst = PROTECT(Rf_list1(prlst0cdr)); > SEXP prlst_tail = prlst; > last = INTEGER(prlst0cdr)[1]; > row_num = 2; > while (row_num <= nr) { > Rprintf("row_num: %i\n", row_num); > SEXP row = PROTECT(C_int_mat_nth_row_nrnc(int_mat_int, nr, 2, row_num)); > Rf_PrintValue(prlst); // This is where the error occurs > int *row_int = INTEGER(row); > if (row_int[0] == last + 1) { > Rprintf("here1"); > SEXP next = PROTECT(Rf_list1(row)); > prlst_tail = SETCDR(prlst_tail, next); > last = row_int[1]; > UNPROTECT(1); > ++row_num; > } else { > Rprintf("here2"); > SEXP next_car = PROTECT(C_make_len2_int_vec(last + 1, row_int[0] - 1)); > SEXP next = PROTECT(Rf_list1(next_car)); > prlst_tail = SETCDR(prlst_tail, next); > last = row_int[0] - 1; > UNPROTECT(2); > } > UNPROTECT(1); > } > SEXP out = PROTECT(Rf_PairToVectorList(prlst)); > UNPROTECT(3); > return out;} > > As you can see, I have some diagnostic print statements in there. The > offending line is line 40, which I have marked with a comment of // This is > where the error occurs. I have a minimal reproducible package at > https://github.com/rorynolan/testpkg <https://github.com/rorynolan/testpkg> and I have run R CMD CHECK with > valgrind using GitHub actions, the results of which are at > https://github.com/rorynolan/testpkg/runs/1076595757?check_suite_focus=true <https://github.com/rorynolan/testpkg/runs/1076595757?check_suite_focus=true>. > That's where I found out which line is causing the error. This function > works as expected sometimes, and then sometimes this issue appears. This > lends weight to the suspicion that it's a garbage collection issue. > > I really want to know what my mistake is. I'm not that interested in > alternative implementations; I want to understand the mistake that I'm > making so that I can avoid making it in future. > > I have asked the question on stackoverflow to little avail, but the > discussion there may prove helpful. > https://stackoverflow.com/questions/63759604/garbage-collection-of-seemingly-protected-pairlist <https://stackoverflow.com/questions/63759604/garbage-collection-of-seemingly-protected-pairlist>. > > > > Thanks, > > Rory > > [[alternative HTML version deleted]] > > ______________________________________________ > R-devel at r-project.org <mailto:R-devel at r-project.org> mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel <https://stat.ethz.ch/mailman/listinfo/r-devel> > > > -- > I?aki ?car[[alternative HTML version deleted]]
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