--- re-building ‘coil-vignette.Rmd’ using rmarkdown ================================================================= ==2734821==ERROR: AddressSanitizer: heap-buffer-overflow on address 0x52a0000a76b8 at pc 0x7feb520fdaba bp 0x7ffe1af99230 sp 0x7ffe1af99228 READ of size 8 at 0x52a0000a76b8 thread T0 #0 0x7feb520fdab9 in ViterbiP(Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Matrix<14, Rcpp::PreserveStorage>, Rcpp::Matrix<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, int, Rcpp::Vector<13, Rcpp::PreserveStorage>, double, bool, bool, bool, bool) /tmp/Rtmp8XZjB6/R.INSTALL3cefbc101a950c/aphid/src/ViterbiC.cpp:544:39 #1 0x7feb520c1799 in _aphid_ViterbiP /tmp/Rtmp8XZjB6/R.INSTALL3cefbc101a950c/aphid/src/RcppExports.cpp:106:34 #2 0x55e407a654a2 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c #3 0x55e407a71a09 in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1437:11 #4 0x55e407b1bf7f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8122:14 #5 0x55e407b0e384 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505:16 #6 0x55e407b0c89a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #7 0x55e407b5636c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393:22 #8 0x55e407b55531 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306:16 #9 0x55e407b10258 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328:16 #10 0x55e407c1ffb7 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473:16 #11 0x55e407c1eab4 in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:513:10 #12 0x55e407c21223 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579:9 #13 0x55e407b21a66 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8142:15 #14 0x55e407b0e384 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505:16 #15 0x55e407b0c89a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #16 0x55e407b5636c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393:22 #17 0x55e407b55531 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306:16 #18 0x55e407b10258 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328:16 #19 0x55e407c1ffb7 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473:16 #20 0x55e407c1eab4 in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:513:10 #21 0x55e407c21223 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579:9 #22 0x55e407b21a66 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8142:15 #23 0x55e407b0e384 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505:16 #24 0x55e407b0c89a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #25 0x55e407b5636c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393:22 #26 0x55e407b55531 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306:16 #27 0x55e407b0d2e9 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328:16 #28 0x55e407b0d2e9 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280:12 #29 0x55e407b67e00 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3571:8 #30 0x55e407b0cde3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232:12 #31 0x55e407b6c78e in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3945:13 #32 0x55e407b1bf7f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8122:14 #33 0x55e407b0e384 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505:16 #34 0x55e407b0c89a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #35 0x55e407b0ec41 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #36 0x55e407b0ca94 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187:6 #37 0x55e407b6d9a3 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3988:9 #38 0x55e407c197b9 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1411:11 #39 0x55e407b21a66 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8142:15 #40 0x55e407b0e384 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505:16 #41 0x55e407b0c89a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #42 0x55e407b0ec41 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #43 0x55e407b0ca94 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187:6 #44 0x55e407b0ec41 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #45 0x55e407b3a161 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5839:6 #46 0x55e407b3a161 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7852:20 #47 0x55e407b0e384 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505:16 #48 0x55e407b0c89a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #49 0x55e407b5636c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393:22 #50 0x55e407b55531 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306:16 #51 0x55e407b0d2e9 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328:16 #52 0x55e407b0d2e9 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280:12 #53 0x55e407b6c78e in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3945:13 #54 0x55e407b1bf7f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8122:14 #55 0x55e407b0e384 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505:16 #56 0x55e407b0c89a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #57 0x55e407b5636c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393:22 #58 0x55e407b55531 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306:16 #59 0x55e407b0d2e9 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328:16 #60 0x55e407b0d2e9 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280:12 #61 0x55e407b5636c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393:22 #62 0x55e407b55531 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306:16 #63 0x55e407b32362 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328:16 #64 0x55e407b32362 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8093:16 #65 0x55e407b0e384 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505:16 #66 0x55e407b0c89a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #67 0x55e407b5636c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393:22 #68 0x55e407b55531 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306:16 #69 0x55e407b0d2e9 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328:16 #70 0x55e407b0d2e9 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280:12 #71 0x55e407be3a9a in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265:2 #72 0x55e407be61d0 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317:11 #73 0x55e407be61d0 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1219:5 #74 0x55e407be6262 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1226:5 #75 0x55e4078f020c in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #76 0x7feb68c2950f in __libc_start_call_main (/lib64/libc.so.6+0x2950f) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c) #77 0x7feb68c295c8 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x295c8) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c) #78 0x55e4078104e4 in _start (/data/gannet/ripley/R/clang-ASAN/bin/exec/R+0x1574e4) 0x52a0000a76b8 is located 40 bytes after 21648-byte region [0x52a0000a2200,0x52a0000a7690) allocated by thread T0 here: #0 0x55e4078ad2ef in malloc /data/gannet/ripley/Sources2/LLVM/19/latest/compiler-rt/lib/asan/asan_malloc_linux.cpp:68:3 #1 0x55e407beea40 in Rf_allocVector3 /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2890:7 #2 0x55e407d4857d in Rf_allocVector /data/gannet/ripley/R/svn/R-devel/src/include/Rinlinedfuns.h:607:12 #3 0x55e407d4857d in MatrixSubset /data/gannet/ripley/R/svn/R-devel/src/main/subset.c:330:14 #4 0x55e407d4857d in do_subset_dflt /data/gannet/ripley/R/svn/R-devel/src/main/subset.c:892:12 #5 0x55e407b212fc in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8269:24 #6 0x55e407b0e384 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505:16 #7 0x55e407b0c89a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #8 0x55e407b5636c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393:22 #9 0x55e407b55531 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306:16 #10 0x55e407b0d2e9 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328:16 #11 0x55e407b0d2e9 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280:12 #12 0x55e407b67e00 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3571:8 #13 0x55e407b0cde3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232:12 #14 0x55e407b6c78e in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3945:13 #15 0x55e407b1bf7f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8122:14 #16 0x55e407b0e384 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505:16 #17 0x55e407b0c89a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #18 0x55e407b0ec41 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #19 0x55e407b0ca94 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187:6 #20 0x55e407b6d9a3 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3988:9 #21 0x55e407c197b9 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1411:11 #22 0x55e407b21a66 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8142:15 #23 0x55e407b0e384 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505:16 #24 0x55e407b0c89a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #25 0x55e407b0ec41 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #26 0x55e407b0ca94 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187:6 #27 0x55e407b0ec41 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #28 0x55e407b3a161 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5839:6 #29 0x55e407b3a161 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7852:20 #30 0x55e407b0e384 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505:16 #31 0x55e407b0c89a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #32 0x55e407b5636c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393:22 #33 0x55e407b55531 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306:16 SUMMARY: AddressSanitizer: heap-buffer-overflow /tmp/Rtmp8XZjB6/R.INSTALL3cefbc101a950c/aphid/src/ViterbiC.cpp:544:39 in ViterbiP(Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Matrix<14, Rcpp::PreserveStorage>, Rcpp::Matrix<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, int, Rcpp::Vector<13, Rcpp::PreserveStorage>, double, bool, bool, bool, bool) Shadow bytes around the buggy address: 0x52a0000a7400: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x52a0000a7480: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x52a0000a7500: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x52a0000a7580: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x52a0000a7600: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 =>0x52a0000a7680: 00 00 fa fa fa fa fa[fa]fa fa fa fa fa fa fa fa 0x52a0000a7700: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x52a0000a7780: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x52a0000a7800: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x52a0000a7880: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x52a0000a7900: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 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 ==2734821==ABORTING