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R crashes due the use of sc_striated2() #15

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TengMCing opened this issue Dec 3, 2023 · 2 comments
Closed

R crashes due the use of sc_striated2() #15

TengMCing opened this issue Dec 3, 2023 · 2 comments

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@TengMCing
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The entire R program will crash while running sc_striated2() with the dataset provided below. Other functions such as sc_clumpy2() will raise an error "Error: unspecified error -10 in shull!" or "Error: shull: cannot triangulate this set", but they will not crash the program.

Crash report

The crash report shows that there is invalid pointer access.

*** Error in `/usr/local/r/4.0.5/lib64/R/bin/exec/R': munmap_chunk(): invalid pointer: 0x00000000110c33d0 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x7f474)[0x7f6195277474]
/fs03/sk54/wlii0039/r_libs/interp/libs/interp.so(_ZN9__gnu_cxx13new_allocatorI3ShxE10deallocateEPS1_m+0x20)[0x7f616c00f9fa]
/fs03/sk54/wlii0039/r_libs/interp/libs/interp.so(_ZNSt16allocator_traitsISaI3ShxEE10deallocateERS1_PS0_m+0x2b)[0x7f616c00ecee]
/fs03/sk54/wlii0039/r_libs/interp/libs/interp.so(_ZNSt12_Vector_baseI3ShxSaIS0_EE13_M_deallocateEPS0_m+0x32)[0x7f616c00daf0]
/fs03/sk54/wlii0039/r_libs/interp/libs/interp.so(_ZNSt12_Vector_baseI3ShxSaIS0_EED1Ev+0x4f)[0x7f616c00ca05]
/fs03/sk54/wlii0039/r_libs/interp/libs/interp.so(_ZNSt6vectorI3ShxSaIS0_EED2Ev+0x41)[0x7f616c00b8e3]
/fs03/sk54/wlii0039/r_libs/interp/libs/interp.so(_Z10s_hull_proRSt6vectorI3ShxSaIS0_EERS_I5TriadSaIS4_EEi+0x28ba)[0x7f616c006b14]
/fs03/sk54/wlii0039/r_libs/interp/libs/interp.so(_Z4shDtSt6vectorIdSaIdEES1_ddi+0x19c)[0x7f616c016473]
/fs03/sk54/wlii0039/r_libs/interp/libs/interp.so(_Z11shullDeltriN4Rcpp6VectorILi14ENS_15PreserveStorageEEES2_NS0_ILi10ES1_EE+0x38f)[0x7f616c012946]
/fs03/sk54/wlii0039/r_libs/interp/libs/interp.so(_interp_shullDeltri+0x161)[0x7f616beec0be]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(+0xee88c)[0x7f6195afe88c]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(+0xf99ab)[0x7f6195b099ab]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(+0x147e6e)[0x7f6195b57e6e]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(Rf_eval+0x245)[0x7f6195b4423e]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(+0x136dd7)[0x7f6195b46dd7]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(Rf_applyClosure+0x2b6)[0x7f6195b46abe]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(+0x147ab5)[0x7f6195b57ab5]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(Rf_eval+0x245)[0x7f6195b4423e]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(+0x136dd7)[0x7f6195b46dd7]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(Rf_applyClosure+0x2b6)[0x7f6195b46abe]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(+0x147ab5)[0x7f6195b57ab5]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(Rf_eval+0x245)[0x7f6195b4423e]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(+0x136dd7)[0x7f6195b46dd7]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(Rf_applyClosure+0x2b6)[0x7f6195b46abe]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(+0x147ab5)[0x7f6195b57ab5]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(Rf_eval+0x245)[0x7f6195b4423e]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(+0x136dd7)[0x7f6195b46dd7]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(Rf_applyClosure+0x2b6)[0x7f6195b46abe]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(+0x147ab5)[0x7f6195b57ab5]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(Rf_eval+0x245)[0x7f6195b4423e]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(+0x136dd7)[0x7f6195b46dd7]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(Rf_applyClosure+0x2b6)[0x7f6195b46abe]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(+0x19c52b)[0x7f6195bac52b]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(+0x19d1cf)[0x7f6195bad1cf]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(+0x19d4a2)[0x7f6195bad4a2]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(+0x19d84c)[0x7f6195bad84c]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(+0x1480dd)[0x7f6195b580dd]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(Rf_eval+0x245)[0x7f6195b4423e]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(+0x136dd7)[0x7f6195b46dd7]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(Rf_applyClosure+0x2b6)[0x7f6195b46abe]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(+0x147ab5)[0x7f6195b57ab5]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(Rf_eval+0x245)[0x7f6195b4423e]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(+0x133dc9)[0x7f6195b43dc9]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(+0x13e4d2)[0x7f6195b4e4d2]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(+0x13e68d)[0x7f6195b4e68d]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(+0x145042)[0x7f6195b55042]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(Rf_eval+0x245)[0x7f6195b4423e]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(+0x133dc9)[0x7f6195b43dc9]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(+0x13e4d2)[0x7f6195b4e4d2]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(+0x13e68d)[0x7f6195b4e68d]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(+0x145042)[0x7f6195b55042]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(Rf_eval+0x245)[0x7f6195b4423e]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(+0x133dc9)[0x7f6195b43dc9]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(+0x13e4d2)[0x7f6195b4e4d2]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(+0x13e68d)[0x7f6195b4e68d]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(+0x145042)[0x7f6195b55042]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(Rf_eval+0x245)[0x7f6195b4423e]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(+0x133dc9)[0x7f6195b43dc9]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(+0x13e4d2)[0x7f6195b4e4d2]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(+0x13e68d)[0x7f6195b4e68d]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(+0x145042)[0x7f6195b55042]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(Rf_eval+0x245)[0x7f6195b4423e]
/usr/local/r/4.0.5/lib64/R/lib/libR.so(+0x133dc9)[0x7f6195b43dc9]
======= Memory map: ========
00400000-00401000 r-xp 00000000 00:2d 16328621141                        /usr/local/r/4.0.5/lib64/R/bin/exec/R
00600000-00601000 r--p 00000000 00:2d 16328621141                        /usr/local/r/4.0.5/lib64/R/bin/exec/R
00601000-00602000 rw-p 00001000 00:2d 16328621141                        /usr/local/r/4.0.5/lib64/R/bin/exec/R
01603000-21039000 rw-p 00000000 00:00 0                                  [heap]
7f616917a000-7f61691bb000 r-xp 00000000 a2:41038 144121439082021691      /fs03/sk54/wlii0039/r_libs/energy/libs/energy.so
7f61691bb000-7f61693bb000 ---p 00041000 a2:41038 144121439082021691      /fs03/sk54/wlii0039/r_libs/energy/libs/energy.so
7f61693bb000-7f61693bc000 r--p 00041000 a2:41038 144121439082021691      /fs03/sk54/wlii0039/r_libs/energy/libs/energy.so
7f61693bc000-7f61693be000 rw-p 00042000 a2:41038 144121439082021691      /fs03/sk54/wlii0039/r_libs/energy/libs/energy.so
7f61693be000-7f61693c0000 rw-p 00000000 00:00 0
7f61693c0000-7f61693fc000 r-xp 00000000 00:2d 4519590250                 /usr/local/gsl/2.2-system/lib/libgslcblas.so.0.0.0
7f61693fc000-7f61695fb000 ---p 0003c000 00:2d 4519590250                 /usr/local/gsl/2.2-system/lib/libgslcblas.so.0.0.0
7f61695fb000-7f61695fc000 r--p 0003b000 00:2d 4519590250                 /usr/local/gsl/2.2-system/lib/libgslcblas.so.0.0.0
7f61695fc000-7f61695fd000 rw-p 0003c000 00:2d 4519590250                 /usr/local/gsl/2.2-system/lib/libgslcblas.so.0.0.0
7f61695fd000-7f616984b000 r-xp 00000000 00:2d 4519590247                 /usr/local/gsl/2.2-system/lib/libgsl.so.19.1.0
7f616984b000-7f6169a4b000 ---p 0024e000 00:2d 4519590247                 /usr/local/gsl/2.2-system/lib/libgsl.so.19.1.0
7f6169a4b000-7f6169a4e000 r--p 0024e000 00:2d 4519590247                 /usr/local/gsl/2.2-system/lib/libgsl.so.19.1.0
7f6169a4e000-7f6169a5f000 rw-p 00251000 00:2d 4519590247                 /usr/local/gsl/2.2-system/lib/libgsl.so.19.1.0
7f6169a5f000-7f6169a7d000 r-xp 00000000 00:2d 7366452422                 /usr/local/r/4.0.5/lib64/R/library/gsl/libs/gsl.so
7f6169a7d000-7f6169c7c000 ---p 0001e000 00:2d 7366452422                 /usr/local/r/4.0.5/lib64/R/library/gsl/libs/gsl.so
7f6169c7c000-7f6169c7f000 r--p 0001d000 00:2d 7366452422                 /usr/local/r/4.0.5/lib64/R/library/gsl/libs/gsl.so
7f6169c7f000-7f6169c80000 rw-p 00020000 00:2d 7366452422                 /usr/local/r/4.0.5/lib64/R/library/gsl/libs/gsl.so
7f6169c80000-7f6169dde000 r-xp 00000000 fd:02 1205418                    /usr/lib64/libxml2.so.2.9.1
7f6169dde000-7f6169fde000 ---p 0015e000 fd:02 1205418                    /usr/lib64/libxml2.so.2.9.1
7f6169fde000-7f6169fe6000 r--p 0015e000 fd:02 1205418                    /usr/lib64/libxml2.so.2.9.1
7f6169fe6000-7f6169fe8000 rw-p 00166000 fd:02 1205418                    /usr/lib64/libxml2.so.2.9.1
7f6169fe8000-7f6169fea000 rw-p 00000000 00:00 0
7f6169fea000-7f616a473000 r-xp 00000000 00:2d 7366378529                 /usr/local/r/4.0.5/lib64/R/library/igraph/libs/igraph.so
7f616a473000-7f616a673000 ---p 00489000 00:2d 7366378529                 /usr/local/r/4.0.5/lib64/R/library/igraph/libs/igraph.so
7f616a673000-7f616a677000 r--p 00489000 00:2d 7366378529                 /usr/local/r/4.0.5/lib64/R/library/igraph/libs/igraph.so
7f616a677000-7f616a684000 rw-p 0048d000 00:2d 7366378529                 /usr/local/r/4.0.5/lib64/R/library/igraph/libs/igraph.so
7f616a684000-7f616a689000 rw-p 00000000 00:00 0
7f616a689000-7f616a6ca000 r-xp 00000000 a2:41038 144121439082021945      /fs03/sk54/wlii0039/r_libs/spatstat.random/libs/spatstat.random.so
7f616a6ca000-7f616a8c9000 ---p 00041000 a2:41038 144121439082021945      /fs03/sk54/wlii0039/r_libs/spatstat.random/libs/spatstat.random.so
7f616a8c9000-7f616a8ca000 r--p 00040000 a2:41038 144121439082021945      /fs03/sk54/wlii0039/r_libs/spatstat.random/libs/spatstat.random.so
7f616a8ca000-7f616a8cb000 rw-p 00041000 a2:41038 144121439082021945      /fs03/sk54/wlii0039/r_libs/spatstat.random/libs/spatstat.random.so
7f616a8cb000-7f616a912000 r-xp 00000000 a2:41038 144121439082021902      /fs03/sk54/wlii0039/r_libs/spatstat.geom/libs/spatstat.geom.so
7f616a912000-7f616ab11000 ---p 00047000 a2:41038 144121439082021902      /fs03/sk54/wlii0039/r_libs/spatstat.geom/libs/spatstat.geom.so
7f616ab11000-7f616ab13000 r--p 00046000 a2:41038 144121439082021902      /fs03/sk54/wlii0039/r_libs/spatstat.geom/libs/spatstat.geom.so
7f616ab13000-7f616ab14000 rw-p 00048000 a2:41038 144121439082021902      /fs03/sk54/wlii0039/r_libs/spatstat.geom/libs/spatstat.geom.so
7f616ab14000-7f616ab73000 r-xp 00000000 00:2d 18338556894                /usr/local/r/4.0.5/lib64/R/library/polyclip/libs/polyclip.so
7f616ab73000-7f616ad72000 ---p 0005f000 00:2d 18338556894                /usr/local/r/4.0.5/lib64/R/library/polyclip/libs/polyclip.so
7f616ad72000-7f616ad73000 r--p 0005e000 00:2d 18338556894                /usr/local/r/4.0.5/lib64/R/library/polyclip/libs/polyclip.so
7f616ad73000-7f616ad76000 rw-p 0005f000 00:2d 18338556894                /usr/local/r/4.0.5/lib64/R/library/polyclip/libs/polyclip.so
7f616ad76000-7f616af40000 r-xp 00000000 a2:41038 144121099762886045      /fs03/sk54/wlii0039/r_libs/Matrix/libs/Matrix.so
7f616af40000-7f616b13f000 ---p 001ca000 a2:41038 144121099762886045      /fs03/sk54/wlii0039/r_libs/Matrix/libs/Matrix.so
7f616b13f000-7f616b140000 r--p 001c9000 a2:41038 144121099762886045      /fs03/sk54/wlii0039/r_libs/Matrix/libs/Matrix.so
7f616b140000-7f616b146000 rw-p 001ca000 a2:41038 144121099762886045      /fs03/sk54/wlii0039/r_libs/Matrix/libs/Matrix.so
7f616b146000-7f616b147000 rw-p 00000000 00:00 0
7f616b147000-7f616b14f000 r-xp 00000000 a2:41038 144121439082021654      /fs03/sk54/wlii0039/r_libs/spatstat.utils/libs/spatstat.utils.so
7f616b14f000-7f616b34e000 ---p 00008000 a2:41038 144121439082021654      /fs03/sk54/wlii0039/r_libs/spatstat.utils/libs/spatstat.utils.so
7f616b34e000-7f616b34f000 r--p 00007000 a2:41038 144121439082021654      /fs03/sk54/wlii0039/r_libs/spatstat.utils/libs/spatstat.utils.so
7f616b34f000-7f616b351000 rw-p 00008000 a2:41038 144121439082021654      /fs03/sk54/wlii0039/r_libs/spatstat.utils/libs/spatstat.utils.so
7f616b351000-7f616b35b000 r-xp 00000000 00:2d 19908110032                /usr/local/r/4.0.5/lib64/R/library/splancs/libs/splancs.so
7f616b35b000-7f616b55b000 ---p 0000a000 00:2d 19908110032                /usr/local/r/4.0.5/lib64/R/library/splancs/libs/splancs.so
7f616b55b000-7f616b55c000 r--p 0000a000 00:2d 19908110032                /usr/local/r/4.0.5/lib64/R/library/splancs/libs/splancs.so
7f616b55c000-7f616b55d000 rw-p 0000b000 00:2d 19908110032                /usr/local/r/4.0.5/lib64/R/library/splancs/libs/splancs.so
7f616b55d000-7f616b561000 rw-p 00000000 00:00 0
7f616b561000-7f616b56a000 r-xp 00000000 00:2d 3052347333                 /usr/local/r/4.0.5/lib64/R/library/sp/libs/sp.so
7f616b56a000-7f616b769000 ---p 00009000 00:2d 3052347333                 /usr/local/r/4.0.5/lib64/R/library/sp/libs/sp.so
7f616b769000-7f616b76a000 r--p 00008000 00:2d 3052347333                 /usr/local/r/4.0.5/lib64/R/library/sp/libs/sp.so
7f616b76a000-7f616b76b000 rw-p 00009000 00:2d 3052347333                 /usr/local/r/4.0.5/lib64/R/library/sp/libs/sp.so
7f616b76b000-7f616b76f000 r-xp 00000000 00:2d 18338409174                /usr/local/r/4.0.5/lib64/R/library/lattice/libs/lattice.so
7f616b76f000-7f616b96e000 ---p 00004000 00:2d 18338409174                /usr/local/r/4.0.5/lib64/R/library/lattice/libs/lattice.so
7f616b96e000-7f616b96f000 r--p 00003000 00:2d 18338409174                /usr/local/r/4.0.5/lib64/R/library/lattice/libs/lattice.so
7f616b96f000-7f616b970000 rw-p 00004000 00:2d 18338409174                /usr/local/r/4.0.5/lib64/R/library/lattice/libs/lattice.so
7f616b970000-7f616b971000 r-xp 00000000 00:2d 3052434384                 /usr/local/r/4.0.5/lib64/R/library/sgeostat/libs/sgeostat.so
7f616b971000-7f616bb70000 ---p 00001000 00:2d 3052434384                 /usr/local/r/4.0.5/lib64/R/library/sgeostat/libs/sgeostat.so
7f616bb70000-7f616bb71000 r--p 00000000 00:2d 3052434384                 /usr/local/r/4.0.5/lib64/R/library/sgeostat/libs/sgeostat.so
7f616bb71000-7f616bb72000 rw-p 00001000 00:2d 3052434384                 /usr/local/r/4.0.5/lib64/R/library/sgeostat/libs/sgeostat.so
7f616bb72000-7f616c0a0000 r-xp 00000000 a2:41038 144121439082021849      /fs03/sk54/wlii0039/r_libs/interp/libs/interp.so
7f616c0a0000-7f616c2a0000 ---p 0052e000 a2:41038 144121439082021849      /fs03/sk54/wlii0039/r_libs/interp/libs/interp.so
7f616c2a0000-7f616c2a1000 r--p 0052e000 a2:41038 144121439082021849      /fs03/sk54/wlii0039/r_libs/interp/libs/interp.so
7f616c2a1000-7f616c2b9000 rw-p 0052f000 a2:41038 144121439082021849      /fs03/sk54/wlii0039/r_libs/interp/libs/interp.so
7f616c2b9000-7f616c2bb000 rw-p 00000000 00:00 0
7f616c2bb000-7f616c2c2000 r-xp 00000000 a2:41038 144121439082021592      /fs03/sk54/wlii0039/r_libs/deldir/libs/deldir.so
7f616c2c2000-7f616c4c1000 ---p 00007000 a2:41038 144121439082021592      /fs03/sk54/wlii0039/r_libs/deldir/libs/deldir.so
7f616c4c1000-7f616c4c2000 r--p 00006000 a2:41038 144121439082021592      /fs03/sk54/wlii0039/r_libs/deldir/libs/deldir.so
7f616c4c2000-7f616c4c3000 rw-p 00007000 a2:41038 144121439082021592      /fs03/sk54/wlii0039/r_libs/deldir/libs/deldir.so
7f616c4c3000-7f616c4c4000 ---p 00000000 00:00 0
7f616c4c4000-7f616ccc4000 rw-p 00000000 00:00 0
7f616d5ad000-7f616dfac000 rw-p 00000000 00:00 0
7f616dfac000-7f616e0b7000 r-xp 00000000 00:2d 7366374028                 /usr/local/r/4.0.5/lib64/R/library/farver/libs/farver.so
7f616e0b7000-7f616e2b7000 ---p 0010b000 00:2d 7366374028                 /usr/local/r/4.0.5/lib64/R/library/farver/libs/farver.so
7f616e2b7000-7f616e2b8000 r--p 0010b000 00:2d 7366374028                 /usr/local/r/4.0.5/lib64/R/library/farver/libs/farver.so
7f616e2b8000-7f616e2bb000 rw-p 0010c000 00:2d 7366374028                 /usr/local/r/4.0.5/lib64/R/library/farver/libs/farver.so
7f616e2bb000-7f616e2c4000 r-xp 00000000 fd:02 1206429                    /usr/lib64/libjbig.so.2.0
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7f618eaf6000-7f618eaf7000 rw-p 00101000 fd:02 1198509                    /usr/lib64/libm-2.17.so
7f618eaf7000-7f618ed62000 r-xp 00000000 00:2d 19499663796                /usr/local/gcc/8.1.0/lib64/libgfortran.so.5.0.0
7f618ed62000-7f618ef61000 ---p 0026b000 00:2d 19499663796                /usr/local/gcc/8.1.0/lib64/libgfortran.so.5.0.0
7f618ef61000-7f618ef62000 r--p 0026a000 00:2d 19499663796                /usr/local/gcc/8.1.0/lib64/libgfortran.so.5.0.0
7f618ef62000-7f618ef64000 rw-p 0026b000 00:2d 19499663796                /usr/local/gcc/8.1.0/lib64/libgfortran.so.5.0.0
7f618ef64000-7f6192d4f000 r-xp 00000000 00:2d 225804220                  /usr/local/intel/2018u3/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64_lin/libmkl_core.so
7f6192d4f000-7f6192f4e000 ---p 03deb000 00:2d 225804220                  /usr/local/intel/2018u3/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64_lin/libmkl_core.so
7f6192f4e000-7f6192f55000 r--p 03dea000 00:2d 225804220                  /usr/local/intel/2018u3/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64_lin/libmkl_core.so
7f6192f55000-7f6192f82000 rw-p 03df1000 00:2d 225804220                  /usr/local/intel/2018u3/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64_lin/libmkl_core.so
7f6192f82000-7f6192f96000 rw-p 00000000 00:00 0
7f6192f96000-7f61944d3000 r-xp 00000000 00:2d 225804227                  /usr/local/intel/2018u3/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64_lin/libmkl_gnu_thread.so
7f61944d3000-7f61946d3000 ---p 0153d000 00:2d 225804227                  /usr/local/intel/2018u3/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64_lin/libmkl_gnu_thread.so
7f61946d3000-7f61946d6000 r--p 0153d000 00:2d 225804227                  /usr/local/intel/2018u3/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64_lin/libmkl_gnu_thread.so
7f61946d6000-7f61946ed000 rw-p 01540000 00:2d 225804227                  /usr/local/intel/2018u3/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64_lin/libmkl_gnu_thread.so
7f61946ed000-7f6194fdf000 r-xp 00000000 00:2d 225804225                  /usr/local/intel/2018u3/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64_lin/libmkl_gf_lp64.so
7f6194fdf000-7f61951de000 ---p 008f2000 00:2d 225804225                  /usr/local/intel/2018u3/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64_lin/libmkl_gf_lp64.so
7f61951de000-7f61951e0000 r--p 008f1000 00:2d 225804225                  /usr/local/intel/2018u3/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64_lin/libmkl_gf_lp64.so
7f61951e0000-7f61951f2000 rw-p 008f3000 00:2d 225804225                  /usr/local/intel/2018u3/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64_lin/libmkl_gf_lp64.so
7f61951f2000-7f61951f8000 rw-p 00000000 00:00 0
7f61951f8000-7f61953bc000 r-xp 00000000 fd:02 1198501                    /usr/lib64/libc-2.17.so
7f61953bc000-7f61955bb000 ---p 001c4000 fd:02 1198501                    /usr/lib64/libc-2.17.so
7f61955bb000-7f61955bf000 r--p 001c3000 fd:02 1198501                    /usr/lib64/libc-2.17.so
7f61955bf000-7f61955c1000 rw-p 001c7000 fd:02 1198501                    /usr/lib64/libc-2.17.so
7f61955c1000-7f61955c6000 rw-p 00000000 00:00 0
7f61955c6000-7f61955dd000 r-xp 00000000 fd:02 1198527                    /usr/lib64/libpthread-2.17.so
7f61955dd000-7f61957dc000 ---p 00017000 fd:02 1198527                    /usr/lib64/libpthread-2.17.so
7f61957dc000-7f61957dd000 r--p 00016000 fd:02 1198527                    /usr/lib64/libpthread-2.17.so
7f61957dd000-7f61957de000 rw-p 00017000 fd:02 1198527                    /usr/lib64/libpthread-2.17.so
7f61957de000-7f61957e2000 rw-p 00000000 00:00 0
7f61957e2000-7f619580f000 r-xp 00000000 00:2d 19499663800                /usr/local/gcc/8.1.0/lib64/libgomp.so.1.0.0
7f619580f000-7f6195a0e000 ---p 0002d000 00:2d 19499663800                /usr/local/gcc/8.1.0/lib64/libgomp.so.1.0.0
7f6195a0e000-7f6195a0f000 r--p 0002c000 00:2d 19499663800                /usr/local/gcc/8.1.0/lib64/libgomp.so.1.0.0
7f6195a0f000-7f6195a10000 rw-p 0002d000 00:2d 19499663800                /usr/local/gcc/8.1.0/lib64/libgomp.so.1.0.0
7f6195a10000-7f6195d3d000 r-xp 00000000 00:2d 18338406731                /usr/local/r/4.0.5/lib64/R/lib/libR.so
7f6195d3d000-7f6195f3d000 ---p 0032d000 00:2d 18338406731                /usr/local/r/4.0.5/lib64/R/lib/libR.so
7f6195f3d000-7f6195f59000 r--p 0032d000 00:2d 18338406731                /usr/local/r/4.0.5/lib64/R/lib/libR.so
7f6195f59000-7f6195f6a000 rw-p 00349000 00:2d 18338406731                /usr/local/r/4.0.5/lib64/R/lib/libR.so
7f6195f6a000-7f61960ba000 rw-p 00000000 00:00 0
7f61960ba000-7f61960dc000 r-xp 00000000 fd:02 1190777                    /usr/lib64/ld-2.17.so
7f6196161000-7f61961c2000 rw-p 00000000 00:00 0
7f6196243000-7f61962b4000 rw-p 00000000 00:00 0
7f61962d3000-7f61962d6000 rw-p 00000000 00:00 0
7f61962d6000-7f61962d7000 r--p 00000000 00:2d 24480032481                /usr/local/r/4.0.5/lib64/R/library/translations/en/LC_MESSAGES/R.mo
7f61962d7000-7f61962db000 rw-p 00000000 00:00 0
7f61962db000-7f61962dc000 r--p 00021000 fd:02 1190777                    /usr/lib64/ld-2.17.so
7f61962dc000-7f61962dd000 rw-p 00022000 fd:02 1190777                    /usr/lib64/ld-2.17.so
7f61962dd000-7f61962de000 rw-p 00000000 00:00 0
7fff22458000-7fff22581000 rw-p 00000000 00:00 0                          [stack]
7fff225ca000-7fff225cc000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
/opt/slurm/var/spool/job32763837/slurm_script: line 16: 134738 Aborted                 (core dumped) Rscript scripts/data_preparation/phn_residual_plots.R

This could be due to

  1. double free() the dynamically allocated memory.
  2. free() memory that is not dynamically allocated.
  3. other memory management issues.

Dataset

6_crash.csv

Session Info

R version 4.2.2 (2022-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.3.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] forcats_0.5.2    stringr_1.5.0    dplyr_1.1.3      purrr_1.0.2      readr_2.1.4      tidyr_1.3.0     
 [7] tibble_3.2.1     ggplot2_3.4.0    tidyverse_1.3.2  cassowaryr_2.0.1

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.9            lubridate_1.9.3       lattice_0.20-45       deldir_2.0-2          prettyunits_1.2.0    
 [6] assertthat_0.2.1      utf8_1.2.4            R6_2.5.1              cellranger_1.1.0      backports_1.4.1      
[11] reprex_2.0.2          httr_1.4.7            pillar_1.9.0          rlang_1.1.1           progress_1.2.2       
[16] googlesheets4_1.1.1   readxl_1.4.1          rstudioapi_0.15.0     R.utils_2.12.3        R.oo_1.25.0          
[21] Matrix_1.5-1          googledrive_2.1.1     polyclip_1.10-4       bit_4.0.5             munsell_0.5.0        
[26] spatstat.data_3.0-3   broom_1.0.1           compiler_4.2.2        modelr_0.1.9          pkgconfig_2.0.3      
[31] tidyselect_1.2.0      spatstat.random_3.2-2 fansi_1.0.5           crayon_1.5.2          tzdb_0.4.0           
[36] dbplyr_2.2.1          withr_2.5.1           R.methodsS3_1.8.2     grid_4.2.2            jsonlite_1.8.7       
[41] gtable_0.3.1          lifecycle_1.0.3       DBI_1.1.3             magrittr_2.0.3        scales_1.2.1         
[46] cli_3.6.1             stringi_1.7.12        vroom_1.6.4           fs_1.6.3              sp_1.5-1             
[51] xml2_1.3.3            generics_0.1.3        vctrs_0.6.4           spatstat.utils_3.0-4  tools_4.2.2          
[56] interp_1.1-5          bit64_4.0.5           alphahull_2.5         glue_1.6.2            splancs_2.01-44      
[61] hms_1.1.3             parallel_4.2.2        timechange_0.2.0      colorspace_2.1-0      gargle_1.5.2         
[66] rvest_1.0.3           sgeostat_1.0-27       spatstat.geom_3.2-7   haven_2.5.1
@TengMCing
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After checking the crash report and using lldb to debug the program, I believe it is related to the use of interp::tri.mesh() in alphahull::delvor().

I have sent an email to the maintainer of interp:

Dear Professor Albrecht Gebhardt,

I hope this message finds you well. My name is Weihao (Patrick) Li, and I am a PhD student affiliated with the Department of Econometrics and Business Statistics at Monash University, Australia.

I am reaching out to bring attention to a significant issue I have encountered while using the interp 1.1.5 package with R 4.2.2. Unfortunately, I couldn't locate a corresponding GitHub repository for your package on the CRAN website, so I decided to reach out via email.

Upon executing the command provided below in a terminal, I observed a critical bug that led to a segmentation fault, causing the R program to crash. To assist in resolving this issue, I have attached two crash reports generated by macOS. These reports pinpoint potential problem areas in the code, specifically highlighting the T_flip_pro() function at line 809 and the Cline_Renka_test() function at line 1167 of the s_hull_pro.cpp file.

Rscript -e "library(interp); dat <- readRDS('interp-tri_mesh_crash.rds'); for (i in 1:1000) {try(tri.mesh(dat)); print(i)}"

In the example code, I have incorporated a for loop to illustrate that the tri.mesh() function occasionally functions correctly but may also result in various error messages, such as "shull: cannot triangulate this set" and "unspecified error -10 in shull!".

I appreciate your attention to this matter and would be grateful for any assistance or guidance you can provide to address and resolve this critical bug. Please let me know if you require any additional information or clarification.

Thank you for your time and consideration.

Cheers,
Patrick

Attachments

bugsintherpackageinterp1_1_5.zip

Suggestions

Harriet,

I'm uncertain if it's possible to predict whether certain combinations of x and y are invalid and will crash R. To handle this, consider using the stop() function to raise errors safely. Given the potential delay in the interp package bug fix, exploring other alpha hull implementations might be worthwhile. Additionally, reaching out to the author of the alphahull package (although lacking a GitHub repo) to address the bug could be another option.

This is the same data set that will crash alphahull::delvor:
alphahull-delvor_crash.rds.zip

@TengMCing
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solved by updated version of interp

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