I actually think that the issue may be related to conversions between int/IntegerVectors and double/NumericVector/std::vector<double>. I was talking with the terra package author to see if the focalCpp function can take an IntegerVector instead of a NumericVector/ /std::vector<double>, as it seemed initially to be working and he said that Rcpp automatically coerces a std::vector<double> to an Rcpp::IntegerVector. However, when I replace the call to C_make_glcm which was causing the issue to just out(i,0) = xw[0] (i.e. return the first value), the edges that should be NA evaluate to -2147483648 so maybe this automatic conversion doesn't work if there are NAs. I can reproduce this using only Rcpp by having a function that takes an IntegerVector and returns the first value of that vector as a double, in which case NA's are changed to -2147483648 (code below). Is this expected behavior, and are there any ways to guard against this?
Thanks, Alex library(Rcpp) cppFunction('double C_fun2(IntegerVector x){ size_t start = 0; size_t end = x.length()-1; IntegerVector xw = x[Rcpp::Range(start,end)]; //Current window of elevation values double out=xw[0]; return(out); }') C_fun2(c(NA,1)) # -2147483648 On Mon, Dec 13, 2021 at 3:43 PM Alex Ilich <alexilic...@gmail.com> wrote: > 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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