I ran your example under valgrind on Linux (Ubuntu 20.04) 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
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