Port of the Triangle Two-Dimensional Quality Mesh Generator and Delaunay Triangulator to R
Home Page: https://cran.r-project.org/package=RTriangle
This is the development version of the RTriangle package available from CRAN.
To install and test, type the following within R:
install.packages("devtools")
devtools::install_github("davidcsterratt/RTriangle", subdir="pkg")
Old bug reports are hosted on RForge
When checking the package I get the following NOTE:
Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols
This will be fixed by using tools::package_native_routine_registration_skeleton() to generate the registration code.
The issue that PB is a numeric vector, which is.na() is vectorised over. So if() sees a vector of FALSE which rightly throws a warning in newer versions of R.
Here's a Reprex:
library(tidyverse)
library(magrittr)
structure(list(
P = structure(c(2, 3, 3, 2, 1, 1, 0, 0, 0, 1,
2, 2, 3, 3, 2.25, 2.75, 2.75, 2.25, 0.25, 0.75, 0.75, 0.25, 0.25,
0.75, 0.75, 0.25, 1.1, 1.1, 2, 2, 1, 0, 0, 1, 2, 2, 0, 1, 1,
0, 1.25, 1.25, 1.75, 1.75, 0.25, 0.25, 0.75, 0.75, 1.25, 1.25,
1.75, 1.75), .Dim = c(26L, 2L), .Dimnames = list(NULL, c("x",
"y"))),
PB = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
S = structure(c(1L, 2L, 3L, 4L,
5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L,
19L, 20L, 21L, 22L, 23L, 24L, 25L, 26L, 2L, 3L, 4L, 1L, 6L, 7L,
8L, 9L, 10L, 5L, 12L, 13L, 14L, 11L, 16L, 17L, 18L, 15L, 20L,
21L, 22L, 19L, 24L, 25L, 26L, 23L), .Dim = c(26L, 2L), .Dimnames = list(
NULL, c("segment_start", "segment_end"))),
SB = c(1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0),
H = structure(c(2.5, 0.5, 0.5, 1.5, 0.5, 1.5), .Dim = c(3L,
2L))), .Names = c("P", "PB", "S", "SB", "H")) %>%
do.call(RTriangle::pslg, .) %>%
RTriangle::triangulate()
#> Warning in if (is.na(PB)) {: the condition has length > 1 and only the
#> first element will be usedThe CRAN maintainers have let me know about the following warnings on:
https://cran.r-project.org/web/checks/check_results_RTriangle.html
They need to be fixed, otherwise RTriangle will be removed from CRAN.
Version: 1.6-0.10
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
./triangle.h:287:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
./triangle.h:288:13: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
interface.c:28:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
interface.c:249:14: warning: passing arguments to 'triangulate' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
triangle.c:1372:5: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
triangle.c:1419:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
triangle.c:1434:7: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
triangle.c:1455:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
./triangle.h:288:6: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a subsequent definition [-Wdeprecated-non-prototype]
triangle.c:3284:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
CRAN reports the following errors with the C compiler: 'gcc.exe (GCC) 12.3.0':
Version: 1.6-0.12
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
triangle.c:1428:9: warning: too many arguments for format [-Wformat-extra-args]
triangle.c:3699:23: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
triangle.c:3705:26: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
triangle.c:3712:26: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
triangle.c:3719:26: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
triangle.c:3727:33: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=]
triangle.c:3734:33: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=]
triangle.c:3741:33: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=]
triangle.c:3748:28: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
triangle.c:3753:28: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
triangle.c:3758:28: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
triangle.c:3793:25: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
triangle.c:3799:26: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
triangle.c:3806:26: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
triangle.c:3814:33: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=]
triangle.c:3821:33: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=]
triangle.c:3829:26: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
triangle.c:3836:26: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
triangle.c:3844:41: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=]
triangle.c:3851:41: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/4.4/RTriangle.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
triangle.c: In function 'printtriangle':
triangle.c:3699:23: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
3699 | printf("triangle x%lx with orientation %d:\n", (uintptr_t) t->tri,
| ~~^ ~~~~~~~~~~~~~~~~~~
| | |
| long unsigned int long long unsigned int
| %llx
triangle.c:3705:26: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
3705 | printf(" [0] = x%lx %d\n", (uintptr_t) printtri.tri,
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| | long long unsigned int
| long unsigned int
| %llx
triangle.c:3712:26: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
3712 | printf(" [1] = x%lx %d\n", (uintptr_t) printtri.tri,
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| | long long unsigned int
| long unsigned int
| %llx
triangle.c:3719:26: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
3719 | printf(" [2] = x%lx %d\n", (uintptr_t) printtri.tri,
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| | long long unsigned int
| long unsigned int
| %llx
triangle.c:3727:33: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=]
3727 | printf(" Origin[%d] = x%lx (%.12g, %.12g)\n",
| ~~^
| |
| long unsigned int
| %llx
3728 | (t->orient + 1) % 3 + 3, (uintptr_t) printvertex,
| ~~~~~~~~~~~~~~~~~~~~~~~
| |
| long long unsigned int
triangle.c:3734:33: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=]
3734 | printf(" Dest [%d] = x%lx (%.12g, %.12g)\n",
| ~~^
| |
| long unsigned int
| %llx
3735 | (t->orient + 2) % 3 + 3, (uintptr_t) printvertex,
| ~~~~~~~~~~~~~~~~~~~~~~~
| |
| long long unsigned int
triangle.c:3741:33: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=]
3741 | printf(" Apex [%d] = x%lx (%.12g, %.12g)\n",
| ~~^
| |
| long unsigned int
| %llx
3742 | t->orient + 3, (uintptr_t) printvertex,
| ~~~~~~~~~~~~~~~~~~~~~~~
| |
| long long unsigned int
triangle.c:3748:28: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
3748 | printf(" [6] = x%lx %d\n", (uintptr_t) printsh.ss,
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~
| | |
| | long long unsigned int
| long unsigned int
| %llx
triangle.c:3753:28: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
3753 | printf(" [7] = x%lx %d\n", (uintptr_t) printsh.ss,
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~
| | |
| | long long unsigned int
| long unsigned int
| %llx
triangle.c:3758:28: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
3758 | printf(" [8] = x%lx %d\n", (uintptr_t) printsh.ss,
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~
| | |
| | long long unsigned int
| long unsigned int
| %llx
triangle.c: In function 'printsubseg':
triangle.c:3793:25: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
3793 | printf("subsegment x%lx with orientation %d and mark %d:\n",
| ~~^
| |
| long unsigned int
| %llx
3794 | (uintptr_t) s->ss, s->ssorient, mark(*s));
| ~~~~~~~~~~~~~~~~~
| |
| long long unsigned int
triangle.c:3799:26: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
3799 | printf(" [0] = x%lx %d\n", (uintptr_t) printsh.ss,
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~
| | |
| | long long unsigned int
| long unsigned int
| %llx
triangle.c:3806:26: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
3806 | printf(" [1] = x%lx %d\n", (uintptr_t) printsh.ss,
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~
| | |
| | long long unsigned int
| long unsigned int
| %llx
triangle.c:3814:33: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=]
3814 | printf(" Origin[%d] = x%lx (%.12g, %.12g)\n",
| ~~^
| |
| long unsigned int
| %llx
3815 | 2 + s->ssorient, (uintptr_t) printvertex,
| ~~~~~~~~~~~~~~~~~~~~~~~
| |
| long long unsigned int
triangle.c:3821:33: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=]
3821 | printf(" Dest [%d] = x%lx (%.12g, %.12g)\n",
| ~~^
| |
| long unsigned int
| %llx
3822 | 3 - s->ssorient, (uintptr_t) printvertex,
| ~~~~~~~~~~~~~~~~~~~~~~~
| |
| long long unsigned int
triangle.c:3829:26: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
3829 | printf(" [6] = x%lx %d\n", (uintptr_t) printtri.tri,
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| | long long unsigned int
| long unsigned int
| %llx
triangle.c:3836:26: warning: format '%lx' expects argument of type 'long unsigned int', but argument 2 has type 'long long unsigned int' [-Wformat=]
3836 | printf(" [7] = x%lx %d\n", (uintptr_t) printtri.tri,
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| | long long unsigned int
| long unsigned int
| %llx
triangle.c:3844:41: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=]
3844 | printf(" Segment origin[%d] = x%lx (%.12g, %.12g)\n",
| ~~^
| |
| long unsigned int
| %llx
3845 | 4 + s->ssorient, (uintptr_t) printvertex,
| ~~~~~~~~~~~~~~~~~~~~~~~
| |
| long long unsigned int
triangle.c:3851:41: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'long long unsigned int' [-Wformat=]
3851 | printf(" Segment dest [%d] = x%lx (%.12g, %.12g)\n",
| ~~^
| |
| long unsigned int
| %llx
3852 | 5 - s->ssorient, (uintptr_t) printvertex,
| ~~~~~~~~~~~~~~~~~~~~~~~
| |
| long long unsigned int
This problem emerged because of the Retistruct package failing a test: davidcsterratt/retistruct#14
Wonder if RTriangle also provides information to plot the corresponding voronoi tessellation and if there is a simple way of generating these plots?
R-Triangle shows array overruns consistently with both gcc and clang's sanitizers. From https://www.stats.ox.ac.uk/pub/bdr/memtests/clang-ASAN/RTriangle/tests/testthat.Rout.fail:
R Under development (unstable) (2018-01-24 r74157) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
>
> test_check("RTriangle")
Loading required package: RTriangle
=================================================================
==34355==ERROR: AddressSanitizer: stack-buffer-overflow on address 0x7ffe227a7a20 at pc 0x7fa825894cec bp 0x7ffe227a7920 sp 0x7ffe227a7918
READ of size 8 at 0x7ffe227a7a20 thread T0
#0 0x7fa825894ceb in fast_expansion_sum_zeroelim /data/gannet/ripley/R/packages/tests-clang-SAN/RTriangle/src/triangle.c:5022:16
#1 0x7fa82589709f in counterclockwiseadapt /data/gannet/ripley/R/packages/tests-clang-SAN/RTriangle/src/triangle.c:5237:14
#2 0x7fa825900694 in mergehulls /data/gannet/ripley/R/packages/tests-clang-SAN/RTriangle/src/triangle.c:9573:20
#3 0x7fa8259097b1 in divconqrecurse /data/gannet/ripley/R/packages/tests-clang-SAN/RTriangle/src/triangle.c:9921:5
#4 0x7fa825909714 in divconqrecurse /data/gannet/ripley/R/packages/tests-clang-SAN/RTriangle/src/triangle.c:9914:5
#5 0x7fa825909714 in divconqrecurse /data/gannet/ripley/R/packages/tests-clang-SAN/RTriangle/src/triangle.c:9914:5
#6 0x7fa825909714 in divconqrecurse /data/gannet/ripley/R/packages/tests-clang-SAN/RTriangle/src/triangle.c:9914:5
#7 0x7fa825909691 in divconqrecurse /data/gannet/ripley/R/packages/tests-clang-SAN/RTriangle/src/triangle.c:9913:5
#8 0x7fa825914a71 in divconqdelaunay /data/gannet/ripley/R/packages/tests-clang-SAN/RTriangle/src/triangle.c:10048:3
#9 0x7fa82592d830 in delaunay /data/gannet/ripley/R/packages/tests-clang-SAN/RTriangle/src/triangle.c:11068:17
#10 0x7fa8259755de in triangulate /data/gannet/ripley/R/packages/tests-clang-SAN/RTriangle/src/triangle.c:15766:18
#11 0x7fa825873b5b in R_triangulate /data/gannet/ripley/R/packages/tests-clang-SAN/RTriangle/src/interface.c:249:3
#12 0x7e828a in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c
#13 0x85a2fd in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1252:11
#14 0x9c4a16 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6766:14
#15 0x9af30d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8
#16 0xa22c9b in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c
#17 0x9b04e4 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:747:12
#18 0xa31c3c in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2774:8
#19 0x9aff1d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:699:12
#20 0xa3015d in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2391:10
#21 0x9aff1d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:699:12
#22 0xa3b5ac in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3153:13
#23 0x9c4a16 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6766:14
#24 0x9af30d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8
#25 0xa22c9b in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c
#26 0x9d4198 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6734:12
#27 0x9af30d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8
#28 0xa1ba3a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8
#29 0xa63022 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4966:15
#30 0xa6346b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5008:10
#31 0x9dcaa7 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6503:20
#32 0x9af30d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8
#33 0xa22c9b in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c
#34 0x9d4198 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6734:12
#35 0x9af30d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8
#36 0xa1ba3a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8
#37 0xa63022 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4966:15
#38 0xa6346b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5008:10
#39 0x9dcaa7 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6503:20
#40 0x9af30d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8
#41 0xa1ba3a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8
#42 0xa63022 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4966:15
#43 0xa6346b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5008:10
#44 0x9dcaa7 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6503:20
#45 0x9af30d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8
#46 0xa1ba3a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8
#47 0xa63022 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4966:15
#48 0xa6346b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5008:10
#49 0x9dcaa7 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6503:20
#50 0x9af30d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8
#51 0xa1ba3a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8
#52 0xa63022 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4966:15
#53 0xa6346b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5008:10
#54 0x9dcaa7 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6503:20
#55 0x9af30d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8
#56 0xa1ba3a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8
#57 0xa63022 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4966:15
#58 0xa6346b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5008:10
#59 0x9dcaa7 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6503:20
#60 0x9af30d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8
#61 0xa22c9b in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c
#62 0x9d4198 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6734:12
#63 0x9af30d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8
#64 0xa22c9b in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c
#65 0x9d4198 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6734:12
#66 0x9af30d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8
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Address 0x7ffe227a7a20 is located in stack of thread T0 at offset 64 in frame
#0 0x7fa82589645f in counterclockwiseadapt /data/gannet/ripley/R/packages/tests-clang-SAN/RTriangle/src/triangle.c:5175
This frame has 5 object(s):
[32, 64) 'B' (line 5181) <== Memory access at offset 64 overflows this variable
[96, 160) 'C1' (line 5181)
[192, 288) 'C2' (line 5181)
[320, 448) 'D' (line 5181)
[480, 512) 'u' (line 5184)
HINT: this may be a false positive if your program uses some custom stack unwind mechanism or swapcontext
(longjmp and C++ exceptions *are* supported)
SUMMARY: AddressSanitizer: stack-buffer-overflow /data/gannet/ripley/R/packages/tests-clang-SAN/RTriangle/src/triangle.c:5022:16 in fast_expansion_sum_zeroelim
Shadow bytes around the buggy address:
0x1000444ecef0: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
0x1000444ecf00: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
0x1000444ecf10: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
0x1000444ecf20: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
0x1000444ecf30: 00 00 00 00 00 00 00 00 00 00 00 00 f1 f1 f1 f1
=>0x1000444ecf40: 00 00 00 00[f2]f2 f2 f2 00 00 00 00 00 00 00 00
0x1000444ecf50: f2 f2 f2 f2 00 00 00 00 00 00 00 00 00 00 00 00
0x1000444ecf60: f2 f2 f2 f2 00 00 00 00 00 00 00 00 00 00 00 00
0x1000444ecf70: 00 00 00 00 f2 f2 f2 f2 00 00 00 00 f3 f3 f3 f3
0x1000444ecf80: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
0x1000444ecf90: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
Shadow byte legend (one shadow byte represents 8 application bytes):
Addressable: 00
Partially addressable: 01 02 03 04 05 06 07
Heap left redzone: fa
Freed heap region: fd
Stack left redzone: f1
Stack mid redzone: f2
Stack right redzone: f3
Stack after return: f5
Stack use after scope: f8
Global redzone: f9
Global init order: f6
Poisoned by user: f7
Container overflow: fc
Array cookie: ac
Intra object redzone: bb
ASan internal: fe
Left alloca redzone: ca
Right alloca redzone: cb
==34355==ABORTING
When triangulating certain PSLGs subject to area and angle quality constraints (a and q options), and with the insertion of Steiner points in the boundary suppressed (Y=TRUE), triangulate() can try to generate infinite numbers of internal Steiner points, leading to an out of memory error.
I've had a bug report from Paolo Piras:
With one hole pslg() and triangulate() properly triangulate the shape, with two holes it is not the case. Here below a fully reproducible example
library(RTriangle)
myshape<-matrix(c
(1507,1370,1470,1598,1685,1551,1470,1490,1779,2249,2517,2652,2598,2370,2209,2162,2323,2517,2611,2544,2370,2276,2081,2054,1994,1893,1745,1611,1605,1887,1794,1913,2226,2306,2140,1998,1851,1799,1856,2016,2081,1988,2333,2126,1938,1723,1515,1233,944,669,535,508,703,1025,1253,1381,1575,1703,1891,1944,2092,2179,2186,2112,2105,2280,2481,2374,2099,2206,2307,972,822,672,716,947,1009,1022,1909,1834,1681,1676,1787,1917),ncol
=2)
plot(myshape,asp=1)
text(myshape[,1],myshape[,2],c(1:nrow(myshape)))
links<-matrix(c
(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,36,30,31,32,33,34,35,42,37,38,39,40,41,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,1,30,31,32,33,34,35,36,37,38,39,40,41,42),ncol
=2)
for(i in 1:nrow(links)){
segments(myshape[links[i,1],1],myshape[links[i,1],2],myshape[links
[i,2],1],myshape[links[i,2],2])
}
#### Let's try with one hole structure
p<-pslg(myshape,S=links,H=rbind(apply(myshape[30:36,],2,mean)))
pt<-triangulate(p)
plot(pt,asp=1)#### with one hole it works
#### try with two holes
p<-pslg(myshape,S=links,H=rbind(apply(myshape[30:36,],2,mean),apply(myshape
[37:42,],2,mean)))
pt<-triangulate(p)
plot(pt,asp=1)#### why it does not work with two holes?
anyDuplicated.matrix is quite slow, as it uses apply(), which means pslg is a fair bit slower than the actual triangulate call. There's a substantial speed up in using the .data.frame method rather than .matrix, as in pslg2 below.
I think there are faster ways still to speed this up, and while it's easy enough to construct the pslg manually with my own validations, this might be a useful modification - thanks!
library(RTriangle)
set.seed(98)
xy <- matrix(rnorm(1e6), ncol = 2)
system.time(sl1 <- pslg(xy)) # 10s
system.time(sl2 <- pslg2(xy)) # 3s
system.time(triangulate(sl1)) # 2s
## simple modification for anyDuplicated at 1.
pslg2 <-
function (P, PB = NA, PA = NA, S = NA, SB = NA, H = NA) {
P <- as.matrix(P)
PB <- as.integer(PB)
PA <- as.matrix(PA)
S <- as.matrix(S)
SB <- as.integer(SB)
H <- as.matrix(H)
check.na.nan <- function(x) {
if (!is.null(x)) {
if (any(is.nan(x))) {
stop(paste("NaN in", deparse(substitute(x))))
}
if (any(is.na(x))) {
stop(paste("NA in", deparse(substitute(x))))
}
}
}
check.na.nan(P)
if (ncol(P) != 2) {
stop("Matrix of vertices P should have 2 columns")
}
## 1. modification, anyDuplicated(data.frame) rather than matrix
if (anyDuplicated(as.data.frame(P))) {
stop("Duplicated vertices in P.")
}
if (any(is.na(PA))) {
PA <- matrix(0, nrow(P), 0)
}
if (nrow(PA) != nrow(P)) {
stop("Point attribute matrix PA does not have same number of rows the point matrix P")
}
if (is.na(PB)) {
PB <- 0
}
PB <- rep(PB, length.out = nrow(P))
if (any(is.na(S))) {
S <- matrix(0, 0, 2)
}
else {
if (ncol(S) != 2) {
stop("Matrix of segments S should have 2 columns")
}
}
if (any(is.na(SB))) {
SB <- 0
}
SB <- rep(SB, length.out = nrow(S))
if (any(is.na(H))) {
H <- matrix(0, 0, 2)
}
else {
if (ncol(H) != 2) {
stop("Matrix of holes H should have 2 columns")
}
}
storage.mode(P) <- "double"
storage.mode(PA) <- "double"
storage.mode(PB) <- "integer"
storage.mode(S) <- "integer"
storage.mode(SB) <- "integer"
storage.mode(H) <- "double"
ret <- list(P = P, PA = PA, PB = PB, S = S, SB = SB, H = H)
class(ret) <- "pslg"
return(ret)
}
As described in this PR #13
It is very useful to export the neighbor-relationship with the triangles.
I am trying to use the RTriangle Package in my PIHMgisR tool, that is a GIS-processing for Penn State Integrated Hydrologic Model (PIHM). After I build the triangle, it is necessary to define the neighbor-relationship among triangles for modeling.
I have my own code to build the topological relationship in R and C, but due to the algorithm, it is very time-consuming to build the relationship when the number of triangles become larger than larger. I notice the C version of the code already exports the neighbor-relationship, so it would be nice to update these two files and export the topological relationship explicitly.
CRAN have reported the following warning on various compilers:
Version: 1.6-0.12
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
triangle.c:1428:35: warning: data argument not used by format string [-Wformat-extra-args]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/RTriangle.Rcheck/00install.out’ for details.
I noticed a bug or an error when I try to use small 'MaxArea' in the package.
I tested it with the following code:
library(RTriangle)
p <- pslg(P=rbind(c(0, 0), c(0, 1), c(0.5, 0.5), c(1, 1), c(1, 0)) * 1000,
S=rbind(c(1, 2), c(2, 3), c(3, 4), c(4, 5), c(5, 1)))
ia <- 30 * (6:1)
nc <-ia * 0
nx <- length(ia)
par(mfrow=c(3,2))
for(i in 1:nx){
## Triangulate it
tp <- triangulate(p, a=ia[i])
plot(tp, type='n')
nc[i] <- nrow(tp$T)
mtext(paste('a= ', ia[i], ' n=', nc[i]))
}
print(nc)
Printed results are:
6549 7816 9788 11469 12597 10026
When the MaxArea is larger than 120, the results are correct.
When the MaxArea is less than 120, there are some triangles whose area is larger than the threshold.
The number of triangles should become more and more, along with the increasing MaxArea threshold.
I guess that is the issue from the size of 'int' in the code. But I cannot fix it yet.
Any thoughts or suggestions? Thank you.
when I am triangulating a pslg object with attributes, the triangulate function seems to (kind of) transpose the attribute matrix.
in the example below i would expect PA to stay the same from the pslg object to the DT object. Am I misunderstanding the intended functionality?
sp_pts <- as.data.frame(matrix(nrow=4,ncol = 2))
colnames(sp_pts) <- c("latitude", "longitude")
sp_pts$latitude <- c(41,42,43,44)
sp_pts$longitude <- c(-120,-121,-122,-123)
att <- as.data.frame(matrix(nrow=4,ncol = 3))
colnames(att) <- c("att1", "att2", "att3")
att$att1 <- c(1, 1.1, 1.11, 1.111)
att$att2 <- c(2, 2.2, 2.22, 2.222)
att$att3 <- c(3, 3.3, 3.33, 3.333)
att
p <- pslg(P = sp_pts, PA = att)
p$PA[1,]
DT <- RTriangle::triangulate(p)
DT$PA[1,]
p$PA
DT$PA
The latest R-devel gives the following warning
* checking compiled code ... WARNING
File ‘RTriangle/libs/RTriangle.so’:
Found ‘sprintf’, possibly from ‘sprintf’ (C)
Object: ‘interface.o’
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