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 _______________________________________________ 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
