Thanks for digging into this for me. If focal_val is 16, then this is an
out of bounds error as the matrix is 16x16 and the maximum index can be 15.
What I'm confused about is that focal_val comes from the data which has
been transformed to be restricted to integers in the range of 0-15 (0 -
n_levels-1). This is explicitly checked for in the glcm_textures2 function
with the line " if((terra::global(r, fun = max) > (n_levels-1)) |
(terra::global(r, fun = min) < 0)){stop("Error: raster must have values
between 0 and n_levels-1")}". Additionally, if I start with numbers in 0-15
and don't do any transformation (quantization="none"), I still run into
this issue (see code below).Thanks, Alex library(terra) library(raster) library(GLCMTextures) r1b<- terra::rast(volcano) set.seed(5) values(r1b)<- sample(0:15, size = ncell(r1b), replace = TRUE) # Replace values with random integers from 0-15 r2b<- glcm_textures2(r1b, w=c(3,7), n_levels = 16, quantization = "none", shift=c(0,1)) #Often leads to Rsession Aborted On Mon, Dec 13, 2021 at 3:12 PM Bill Dunlap <williamwdun...@gmail.com> wrote: > 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 >>> >> _______________________________________________ > 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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