[Rcpp-devel] R Session Sometimes Aborts
Bill Dunlap
williamwdunlap at gmail.com
Wed Dec 15 18:49:48 CET 2021
To make this easier to debug, I added a check that the values in the x
given to C_make_glcm are within bounds:
for(int i=0; i < nr; ++i){
for(int j=0; j < nc; ++j){
int focal_val = x(i,j);
if (focal_val >= n_levels || focal_val < 0) { // sanity check
Rf_error("programmer error: out-of-bounds focal_val=%d: i=%d,
j=%d, n_levels=%d", focal_val, i, j, n_levels);
}
Now you don't need valgrind to see the problem; just set a breakpoint at
Rf_error. The debugger shows that the 'x' in given to
.Call(_GLCMTextures_C_glcm_textures_helper2,x,...) in this case is a
21-long integer vector with values 1:21. C_glcm_textures_helper2 seems to
use this as a C++ subscript -- should it be 0:20? (I did not try to
analyze the code very closely.)
-Bill
On Wed, Dec 15, 2021 at 9:26 AM Alex Ilich <alexilich93 at gmail.com> wrote:
> Thanks, I thought I was onto something there but I guess that wasn't the
> issue (that only came up because when I made edits to my function to just
> return the actual values as a check, I was converting them in an unsafe way
> from int to double). I'm still confused on how the valgrind check Bill was
> running was finding that focal_val was evaluating to 16 leading to an out
> of bounds error in some cases when the data is constrained to 0-15
> (n_levels-1). Additionally if I set out[i] = max(curr_window); and make out
> an IntegerVector (so that the NA's aren't converted), the maximum value of
> the resulting surface is 15. focal_val is directly drawn from curr_window
> so I don't see how it could be 16. If anyone has any thoughts or ideas on
> this it would be greatly appreciated.
>
> Thanks,
> Alex
>
> C++ functions:
> https://github.com/ailich/GLCMTextures/blob/terra/src/glcm_cpp_functions.cpp
> R function that calls C++ functions:
> https://github.com/ailich/GLCMTextures/blob/terra/R/glcm_textures2.R
>
>
>
>
> On Wed, Dec 15, 2021 at 11:49 AM Dirk Eddelbuettel <edd at debian.org> wrote:
>
>>
>> On 15 December 2021 at 11:22, Alex Ilich wrote:
>> | 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
>>
>> That is a misunderstanding. That would be a *major* bug. Brining Rob in
>> just
>> in case.
>>
>> Rcpp faithfully and reliably maps back and forth between
>>
>> std::vector<int32_t> and Rcpp::IntegerVector
>> std::vector<double> and Rcpp::NumericVector
>>
>> as well as other numerics and of course std::string etc
>>
>> What you may be confusing is that writing something such as
>>
>> > Rcpp::cppFunction("int mysum(IntegerVector x) { return sum(x); }")
>> > mysum(c(1.0, 2.0, 3.0))
>> [1] 6
>> > Rcpp::cppFunction("double myothersum(NumericVector x) { return
>> sum(x); }")
>> > myothersum(1:3) # the : creates an _int_ sequence
>> [1] 6
>> > myothersum(c(1L,2L,3L))
>> [1] 6
>> >
>>
>> cast up/down from/to int and double _when access from R_ which is a _very_
>> different story.
>>
>>
>> | 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?
>>
>> It's a bug in your code as you don't cast right. And you also 'call it
>> incorrectly' just as per my example above. NA is a _double_ as is 1. We
>> then
>> help you by making the _now int_ value a matching NA _as an int_.
>>
>> And here is a *very* important bit: Int NAs are an R-only thing. The
>> assignment you make is a C/C++ one *which does not know this* and you
>> loose
>> NAness.
>>
>> No more, no less. Just a usage bug on your end.
>>
>> | 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
>>
>> Simpler fixed version:
>>
>>
>> > Rcpp::cppFunction("double alex(IntegerVector x) { NumericVector
>> y(x); return y[0];}")
>> > alex(c(NA, 1))
>> [1] NA
>> > alex(c(NA_integer_, 1L)) # "correct" call with actual int
>> arguments
>> [1] NA
>> >
>>
>> This ensure we build a proper R-context aware vector of doubles and then
>> return its first element. You can use the same logic in your code, we
>> also
>> do this (I think) when using std::vector<> of these base types as they
>> are so
>> common.
>>
>> Dirk
>>
>> | On Mon, Dec 13, 2021 at 3:43 PM Alex Ilich <alexilich93 at 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 <williamwdunlap at 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 <
>> williamwdunlap at 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 <edd at 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 <
>> ailich at 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 at 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 at lists.r-forge.r-project.org
>> | >>>> |
>> | >>>>
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
>> | >>>> --
>> | >>>> https://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
>> | >>>>
>> | >>> _______________________________________________
>> | >> Rcpp-devel mailing list
>> | >> Rcpp-devel at lists.r-forge.r-project.org
>> | >>
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
>> | >
>> | >
>>
>> --
>> https://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
>>
>
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