In this example vgdb shows that valgrind's first complaint is at (gdb) where 5 #0 0x000000001c1ada01 in C_make_glcm (x=..., n_levels=16, shift=..., na_opt=...) at glcm_cpp_functions.cpp:73 #1 0x000000001c1b2238 in C_glcm_textures_helper2 (x=..., w2=..., n_levels=16, shift=..., na_opt=..., ni=1, nw=21) at glcm_cpp_functions.cpp:218 #2 0x000000001c1a098e in _GLCMTextures_C_glcm_textures_helper2 (xSEXP=0x19023168, w2SEXP=0x92cbde8, n_levelsSEXP=0xa3138d8, shiftSEXP=0x92cc468, na_optSEXP=0xa313398, niSEXP=0xb655560, nwSEXP=0x1aeec7d0) at RcppExports.cpp:94 #3 0x00000000001f6b02 in R_doDotCall ( ofun=0x1c1a0732 <_GLCMTextures_C_glcm_textures_helper2(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)>, nargs=7, cargs=0x1ffeff6830, call=0x15ed3c88) at /mnt/c/R/R-svn/trunk/src/main/dotcode.c:622 #4 0x00000000002637ca in bcEval (body=0x15ed4078, rho=0x19023210, useCache=TRUE) at /mnt/c/R/R-svn/trunk/src/main/eval.c:7695
Line 73 is GLCM(neighbor_val,focal_val) = GLCM(neighbor_val,focal_val)+1; where GLCM is a 16 x 16 IntegerMatrix and focal_val is 16: (gdb) print neighbor_val $1 = 9 (gdb) print focal_val $2 = 16 (gdb) print i $3 = 2 (gdb) print j $4 = 1 -Bill On Mon, Dec 13, 2021 at 11:37 AM Bill Dunlap <williamwdun...@gmail.com> wrote: > Thanks, I hadn't noticed the --use-valgrind option to check. > > I often run R under valgrind with the command line: > $ R --quiet --no-save --debugger=valgrind > --debugger-args="--track-origins=yes --vgdb=full --vgdb-error=0" > then in another window start a debugger process with > $ gdb RHOME/bin/exec/R > ... > (gdb) target remote | vgdb > (gdb) cont > You may need to supply a complete path to vgdb, valgrind's interface to > gdb. > Then gdb will set breakpoints where valgrind reports memory misuse and you > can inspect variables, etc., where an error occurs. > You can check for memory leaks from gdb with > (gdb) monitor leak_check full > > -Bill > > > On Mon, Dec 13, 2021 at 10:29 AM Dirk Eddelbuettel <e...@debian.org> wrote: > >> >> On 13 December 2021 at 09:15, Bill Dunlap wrote: >> | I ran your example under valgrind on Linux (Ubuntu 20.04) >> >> Excellent call, as usual! Thanks for doing that. >> >> R actually makes is so easy to run with valgrind by calling >> >> R CMD check --use-valgrind somePkg_1.2-3.tar.gz >> >> that I started to add it to some CI setups. >> >> Dirk >> >> | and valgrind found some memory misuse: >> | >> | $ R --quiet --no-save --debugger=valgrind >> | --debugger-args="--track-origins=yes" >> | ==1533== Memcheck, a memory error detector >> | ==1533== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. >> | ==1533== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright >> info >> | ==1533== Command: /home/bill/R-devel/R-build/bin/exec/R --quiet >> --no-save >> | ==1533== >> | > library(terra) >> | terra version 1.5.2 >> | > library(raster) >> | Loading required package: sp >> | > library(GLCMTextures) >> | > >> | > r1a<- raster::raster(volcano) >> | > r2a<- glcm_textures(r1a, w=c(3,7), n_levels = 16, quantization = >> "equal >> | prob", shift=c(0,1)) >> | > >> | > r1b<- terra::rast(volcano) >> | > r2b<- glcm_textures2(r1b, w=c(3,7), n_levels = 16, quantization = >> "equal >> | prob", shift=c(0,1)) #Often leads to Rsession Aborted >> | ==1533== Invalid read of size 4 >> | ==1533== at 0x1C1ADA01: C_make_glcm(Rcpp::Matrix<13, >> | Rcpp::PreserveStorage>, int, Rcpp::Vector<13, Rcpp::PreserveStorage>, >> | Rcpp::String) (glcm_cpp_functions.cpp:73) >> | ==1533== by 0x1C1B2237: C_glcm_textures_helper2(Rcpp::Vector<13, >> | Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, int, >> | Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::String, unsigned long, >> | unsigned long) (glcm_cpp_functions.cpp:218) >> | ==1533== by 0x1C1A098D: _GLCMTextures_C_glcm_textures_helper2 >> | (RcppExports.cpp:94) >> | ==1533== by 0x1F6B01: R_doDotCall (dotcode.c:622) >> | ==1533== by 0x2637C9: bcEval (eval.c:7695) >> | ==1533== by 0x240653: Rf_eval (eval.c:748) >> | ==1533== by 0x243223: R_execClosure (eval.c:1918) >> | ==1533== by 0x242EFD: Rf_applyClosure (eval.c:1844) >> | ==1533== by 0x240E06: Rf_eval (eval.c:871) >> | ==1533== by 0x246CD6: do_set (eval.c:2990) >> | ==1533== by 0x240A8C: Rf_eval (eval.c:823) >> | ==1533== by 0x2457DA: do_begin (eval.c:2538) >> | ==1533== Address 0xa59c0c4 is 28 bytes before a block of size 64 in >> arena >> | "client" >> | ==1533== >> | ==1533== Invalid write of size 4 >> | ==1533== at 0x1C1ADA44: C_make_glcm(Rcpp::Matrix<13, >> | Rcpp::PreserveStorage>, int, Rcpp::Vector<13, Rcpp::PreserveStorage>, >> | Rcpp::String) (glcm_cpp_functions.cpp:73) >> | ==1533== by 0x1C1B2237: C_glcm_textures_helper2(Rcpp::Vector<13, >> | Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, int, >> | Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::String, unsigned long, >> | unsigned long) (glcm_cpp_functions.cpp:218) >> | ==1533== by 0x1C1A098D: _GLCMTextures_C_glcm_textures_helper2 >> | (RcppExports.cpp:94) >> | ==1533== by 0x1F6B01: R_doDotCall (dotcode.c:622) >> | ==1533== by 0x2637C9: bcEval (eval.c:7695) >> | ==1533== by 0x240653: Rf_eval (eval.c:748) >> | ==1533== by 0x243223: R_execClosure (eval.c:1918) >> | ==1533== by 0x242EFD: Rf_applyClosure (eval.c:1844) >> | ==1533== by 0x240E06: Rf_eval (eval.c:871) >> | ==1533== by 0x246CD6: do_set (eval.c:2990) >> | ==1533== by 0x240A8C: Rf_eval (eval.c:823) >> | ==1533== by 0x2457DA: do_begin (eval.c:2538) >> | ==1533== Address 0xa59c0c4 is 28 bytes before a block of size 64 in >> arena >> | "client" >> | ==1533== >> | --1533-- VALGRIND INTERNAL ERROR: Valgrind received a signal 11 >> (SIGSEGV) - >> | exiting >> | --1533-- si_code=1; Faulting address: 0x10A59C138; sp: 0x10090e2e20 >> | >> | valgrind: the 'impossible' happened: >> | Killed by fatal signal >> | >> | host stacktrace: >> | ==1533== at 0x580505C4: ??? (in >> | /usr/lib/x86_64-linux-gnu/valgrind/memcheck-amd64-linux) >> | ==1533== by 0x58004EBB: ??? (in >> | /usr/lib/x86_64-linux-gnu/valgrind/memcheck-amd64-linux) >> | ==1533== by 0x58005DA7: ??? (in >> | /usr/lib/x86_64-linux-gnu/valgrind/memcheck-amd64-linux) >> | ==1533== by 0x580A7204: ??? (in >> | /usr/lib/x86_64-linux-gnu/valgrind/memcheck-amd64-linux) >> | ==1533== by 0x580F5FD4: ??? (in >> | /usr/lib/x86_64-linux-gnu/valgrind/memcheck-amd64-linux) >> | >> | sched status: >> | running_tid=1 >> | >> | Thread 1: status = VgTs_Runnable (lwpid 1533) >> | ==1533== at 0x483BE63: operator new(unsigned long) (in >> | /usr/lib/x86_64-linux-gnu/valgrind/vgpreload_memcheck-amd64-linux.so) >> | ==1533== by 0x6E92D3C: void std::__cxx11::basic_string<char, >> | std::char_traits<char>, std::allocator<char> >::_M_construct<char >> | const*>(char const*, char const*, std::forward_iterator_tag) (in >> | /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.28) >> | ==1533== by 0x1C1B2377: C_glcm_textures_helper2(Rcpp::Vector<13, >> | Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, int, >> | Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::String, unsigned long, >> | unsigned long) (glcm_cpp_functions.cpp:221) >> | ==1533== by 0x1C1A098D: _GLCMTextures_C_glcm_textures_helper2 >> | (RcppExports.cpp:94) >> | ==1533== by 0x1F6B01: R_doDotCall (dotcode.c:622) >> | ==1533== by 0x2637C9: bcEval (eval.c:7695) >> | ==1533== by 0x240653: Rf_eval (eval.c:748) >> | ==1533== by 0x243223: R_execClosure (eval.c:1918) >> | ==1533== by 0x242EFD: Rf_applyClosure (eval.c:1844) >> | ==1533== by 0x240E06: Rf_eval (eval.c:871) >> | ==1533== by 0x246CD6: do_set (eval.c:2990) >> | ==1533== by 0x240A8C: Rf_eval (eval.c:823) >> | ==1533== by 0x2457DA: do_begin (eval.c:2538) >> | ==1533== by 0x240A8C: Rf_eval (eval.c:823) >> | ==1533== by 0x244FC9: do_for (eval.c:2420) >> | ==1533== by 0x240A8C: Rf_eval (eval.c:823) >> | ==1533== by 0x2457DA: do_begin (eval.c:2538) >> | ==1533== by 0x240A8C: Rf_eval (eval.c:823) >> | ==1533== by 0x244FC9: do_for (eval.c:2420) >> | ==1533== by 0x240A8C: Rf_eval (eval.c:823) >> | ==1533== by 0x2457DA: do_begin (eval.c:2538) >> | ==1533== by 0x240A8C: Rf_eval (eval.c:823) >> | ==1533== by 0x243223: R_execClosure (eval.c:1918) >> | ==1533== by 0x242EFD: Rf_applyClosure (eval.c:1844) >> | ==1533== by 0x253F32: bcEval (eval.c:7107) >> | ==1533== by 0x240653: Rf_eval (eval.c:748) >> | ==1533== by 0x243223: R_execClosure (eval.c:1918) >> | ==1533== by 0x243D9C: R_execMethod (eval.c:2094) >> | ==1533== by 0x8800187: R_dispatchGeneric >> (methods_list_dispatch.c:1145) >> | ==1533== by 0x2B15F4: do_standardGeneric (objects.c:1285) >> | ==1533== by 0x253DB3: bcEval (eval.c:7096) >> | ==1533== by 0x240653: Rf_eval (eval.c:748) >> | ==1533== by 0x243223: R_execClosure (eval.c:1918) >> | ==1533== by 0x242EFD: Rf_applyClosure (eval.c:1844) >> | ==1533== by 0x253F32: bcEval (eval.c:7107) >> | ==1533== by 0x240653: Rf_eval (eval.c:748) >> | ==1533== by 0x243223: R_execClosure (eval.c:1918) >> | ==1533== by 0x242EFD: Rf_applyClosure (eval.c:1844) >> | ==1533== by 0x240E06: Rf_eval (eval.c:871) >> | ==1533== by 0x246CD6: do_set (eval.c:2990) >> | ==1533== by 0x240A8C: Rf_eval (eval.c:823) >> | ==1533== by 0x28EF5E: Rf_ReplIteration (main.c:264) >> | ==1533== by 0x28F157: R_ReplConsole (main.c:316) >> | ==1533== by 0x290BC0: run_Rmainloop (main.c:1130) >> | ==1533== by 0x290BDA: Rf_mainloop (main.c:1137) >> | ==1533== by 0x16F74B: main (Rmain.c:29) >> | client stack range: [0x1FFEED3000 0x1FFF000FFF] client SP: 0x1FFEFF35F0 >> | valgrind stack range: [0x1008FE3000 0x10090E2FFF] top usage: 12336 of >> | 1048576 >> | >> | >> | Note: see also the FAQ in the source distribution. >> | It contains workarounds to several common problems. >> | In particular, if Valgrind aborted or crashed after >> | identifying problems in your program, there's a good chance >> | that fixing those problems will prevent Valgrind aborting or >> | crashing, especially if it happened in m_mallocfree.c. >> | >> | If that doesn't help, please report this bug to: www.valgrind.org >> | >> | In the bug report, send all the above text, the valgrind >> | version, and what OS and version you are using. Thanks. >> | >> | On Mon, Dec 13, 2021 at 8:15 AM Alexander Ilich <ail...@mail.usf.edu> >> wrote: >> | >> | > Hi, I'm upgrading one of my R packages to rely on the terra package >> | > instead of the raster package for the handling of spatial raster data. >> | > Previously when relying on the raster package I had to convert the >> data to >> | > a matrix and send it to C++ to loop through the cells manually, but >> with >> | > the new features in the terra package I can supply a C++ function that >> | > returns multiple values directly to terra::focalCpp to perform focal >> | > operations >> | > < >> https://desktop.arcgis.com/en/arcmap/10.3/tools/spatial-analyst-toolbox/how-focal-statistics-works.htm >> >. >> | > I get the same values using both the old and new versions of the >> functions, >> | > but the new version often causes the R session to abort, especially at >> | > larger window sizes. For example, a 3x3 or a 3x5 window seems to >> always >> | > run, but a 3x7 window will often cause the R session to abort. >> However, >> | > when it doesn't, I get the correct values. Functions followed by 2 >> are the >> | > terra versions of the function. By commenting out things and >> rebuilding I >> | > was able to determine the line that causes the crash in the terra >> version >> | > is "NumericMatrix curr_GLCM = C_make_glcm(curr_window, n_levels, >> shift, >> | > na_opt); //Tabulate the GLCM"; however, this line is also included in >> the >> | > raster version of the function so I'm not sure why this would happen. >> Any >> | > help would be greatly appreciated. Here is the github repository >> | > <https://github.com/ailich/GLCMTextures/tree/terra>, and I've added >> some >> | > sample code below to illustrate the issue. >> | > >> | > Thanks, >> | > Alex >> | > >> | > install.packages('raster', repos='https://rspatial.r-universe.dev') >> | > #install development version of raster >> | > install.packages('terra', repos='https://rspatial.r-universe.dev') >> | > #install development version of terra >> | > >> | > remotes::install_github("ailich/GLCMTextures", ref = "terra") #Install >> | > branch of my package testing terra versions of functions >> | > >> | > library(terra) >> | > library(raster) >> | > library(GLCMTextures) >> | > >> | > r1a<- raster::raster(volcano) >> | > r2a<- glcm_textures(r1a, w=c(3,7), n_levels = 16, quantization = >> "equal >> | > prob", shift=c(0,1)) >> | > >> | > r1b<- terra::rast(volcano) >> | > r2b<- glcm_textures2(r1b, w=c(3,7), n_levels = 16, quantization = >> "equal >> | > prob", shift=c(0,1)) #Often leads to Rsession Aborted >> | > >> | > all.equal(values(r2a),values(r2b)) #TRUE >> | > >> | > >> | > >> | > #System Information >> | > #OS: Windows 10 >> | > R.version >> | > # platform x86_64-w64-mingw32 >> | > # arch x86_64 >> | > # os mingw32 >> | > # system x86_64, mingw32 >> | > # status >> | > # major 4 >> | > # minor 0.4 >> | > # year 2021 >> | > # month 02 >> | > # day 15 >> | > # svn rev 80002 >> | > # language R >> | > # version.string R version 4.0.4 (2021-02-15) >> | > # nickname Lost Library Book >> | > >> | > packageVersion("terra") >> | > # ‘1.5.2’ >> | > packageVersion("raster") >> | > # ‘3.5.10’ >> | > packageVersion("Rcpp") >> | > # ‘1.0.7’ >> | > packageVersion("RcppArmadillo") >> | > # ‘0.10.7.3.0’ >> | > _______________________________________________ >> | > Rcpp-devel mailing list >> | > Rcpp-devel@lists.r-forge.r-project.org >> | > >> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel >> | _______________________________________________ >> | Rcpp-devel mailing list >> | Rcpp-devel@lists.r-forge.r-project.org >> | https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel >> -- >> https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org >> >
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