--- re-building ‘phmm_poisson_df.Rmd’ using rmarkdown Loading required package: survival Loading required package: lattice Loading required package: Matrix phmm.c:501:8: runtime error: index 4 out of bounds for type 'double *[*]' #0 0x7fddbd8f20f0 in Estep /data/gannet/ripley/R/packages/tests-gcc-SAN/phmm/src/phmm.c:501 #1 0x7fddbd8f2c36 in EM /data/gannet/ripley/R/packages/tests-gcc-SAN/phmm/src/phmm.c:380 #2 0x7fddbd8fe05a in phmm /data/gannet/ripley/R/packages/tests-gcc-SAN/phmm/src/phmm.c:181 #3 0x596d85 in do_dotCode /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1950 #4 0x61f3f1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7090 #5 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #6 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #7 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #8 0x66c8f8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:846 #9 0x67a351 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2956 #10 0x66cdec in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:798 #11 0x67d216 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3331 #12 0x61f3f1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7090 #13 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #14 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #15 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #16 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #17 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #18 0x66e362 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:551 #19 0x66d5bf in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:746 #20 0x67ee3c in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3383 #21 0x717e0f in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1384 #22 0x62f1f1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7110 #23 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #24 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #25 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #26 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #27 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #28 0x66e362 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:551 #29 0x66edc7 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5123 #30 0x66edc7 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5164 #31 0x6350c8 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6842 #32 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #33 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #34 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #35 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #36 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #37 0x66e362 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:551 #38 0x66edc7 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5123 #39 0x66edc7 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5164 #40 0x6350c8 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6842 #41 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #42 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #43 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #44 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #45 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #46 0x66e362 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:551 #47 0x66edc7 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5123 #48 0x66edc7 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5164 #49 0x6350c8 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6842 #50 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #51 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #52 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #53 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #54 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #55 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #56 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #57 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #58 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #59 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #60 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #61 0x66c8f8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:846 #62 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #63 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #64 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #65 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #66 0x66e362 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:551 #67 0x66edc7 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5123 #68 0x66edc7 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5164 #69 0x6350c8 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6842 #70 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #71 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #72 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #73 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #74 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #75 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #76 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #77 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #78 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #79 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #80 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #81 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #82 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #83 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #84 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #85 0x71d75b in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:436 #86 0x71e256 in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:476 #87 0x71edb3 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:565 #88 0x62f1f1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7110 #89 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #90 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #91 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #92 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #93 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #94 0x66e362 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:551 #95 0x66edc7 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5123 #96 0x66edc7 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5164 #97 0x6350c8 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6842 #98 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #99 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #100 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #101 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #102 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #103 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #104 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #105 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #106 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #107 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #108 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #109 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #110 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #111 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #112 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #113 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #114 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #115 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #116 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #117 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #118 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #119 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #120 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #121 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #122 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #123 0x66e362 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:551 #124 0x66edc7 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5123 #125 0x66edc7 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5164 #126 0x6350c8 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6842 #127 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #128 0x66e362 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:551 #129 0x66edc7 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5123 #130 0x66edc7 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5164 #131 0x6350c8 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6842 #132 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #133 0x66e362 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:551 #134 0x66edc7 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5123 #135 0x66edc7 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5164 #136 0x6350c8 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6842 #137 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #138 0x66e362 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:551 #139 0x66edc7 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5123 #140 0x66edc7 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5164 #141 0x6350c8 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6842 #142 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #143 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #144 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #145 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #146 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #147 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #148 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #149 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #150 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #151 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #152 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #153 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #154 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #155 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #156 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #157 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #158 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #159 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #160 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #161 0x66c8f8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:846 #162 0x6eb2dd in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #163 0x6eb2dd in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:200 #164 0x6eb9d8 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:314 #165 0x6ebb24 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1113 #166 0x419388 in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #167 0x7fddd1534f42 in __libc_start_main (/lib64/libc.so.6+0x23f42) #168 0x41bacd in _start (/data/gannet/ripley/R/gcc-SAN/bin/exec/R+0x41bacd) ================================================================= ==16957==ERROR: AddressSanitizer: dynamic-stack-buffer-overflow on address 0x7fff03e5e7e0 at pc 0x7fddbd8f20cf bp 0x7fff03e5e790 sp 0x7fff03e5e780 WRITE of size 8 at 0x7fff03e5e7e0 thread T0 #0 0x7fddbd8f20ce in Estep /data/gannet/ripley/R/packages/tests-gcc-SAN/phmm/src/phmm.c:501 #1 0x7fddbd8f2c36 in EM /data/gannet/ripley/R/packages/tests-gcc-SAN/phmm/src/phmm.c:380 #2 0x7fddbd8fe05a in phmm /data/gannet/ripley/R/packages/tests-gcc-SAN/phmm/src/phmm.c:181 #3 0x596d85 in do_dotCode /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1950 #4 0x61f3f1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7090 #5 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #6 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #7 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #8 0x66c8f8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:846 #9 0x67a351 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2956 #10 0x66cdec in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:798 #11 0x67d216 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3331 #12 0x61f3f1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7090 #13 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #14 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #15 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #16 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #17 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #18 0x66e362 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:551 #19 0x66d5bf in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:746 #20 0x67ee3c in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3383 #21 0x717e0f in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1384 #22 0x62f1f1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7110 #23 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #24 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #25 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #26 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #27 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #28 0x66e362 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:551 #29 0x66edc7 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5123 #30 0x66edc7 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5164 #31 0x6350c8 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6842 #32 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #33 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #34 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #35 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #36 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #37 0x66e362 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:551 #38 0x66edc7 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5123 #39 0x66edc7 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5164 #40 0x6350c8 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6842 #41 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #42 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #43 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #44 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #45 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #46 0x66e362 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:551 #47 0x66edc7 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5123 #48 0x66edc7 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5164 #49 0x6350c8 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6842 #50 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #51 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #52 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #53 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #54 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #55 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #56 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #57 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #58 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #59 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #60 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #61 0x66c8f8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:846 #62 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #63 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #64 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #65 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #66 0x66e362 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:551 #67 0x66edc7 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5123 #68 0x66edc7 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5164 #69 0x6350c8 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6842 #70 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #71 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #72 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #73 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #74 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #75 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #76 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #77 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #78 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #79 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #80 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #81 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #82 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #83 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #84 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #85 0x71d75b in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:436 #86 0x71e256 in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:476 #87 0x71edb3 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:565 #88 0x62f1f1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7110 #89 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #90 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #91 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #92 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #93 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #94 0x66e362 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:551 #95 0x66edc7 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5123 #96 0x66edc7 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5164 #97 0x6350c8 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6842 #98 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #99 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #100 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #101 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #102 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #103 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #104 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #105 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #106 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #107 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #108 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #109 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #110 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #111 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #112 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #113 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #114 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #115 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #116 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #117 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #118 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #119 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #120 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #121 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #122 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #123 0x66e362 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:551 #124 0x66edc7 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5123 #125 0x66edc7 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5164 #126 0x6350c8 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6842 #127 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #128 0x66e362 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:551 #129 0x66edc7 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5123 #130 0x66edc7 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5164 #131 0x6350c8 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6842 #132 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #133 0x66e362 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:551 #134 0x66edc7 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5123 #135 0x66edc7 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5164 #136 0x6350c8 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6842 #137 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #138 0x66e362 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:551 #139 0x66edc7 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5123 #140 0x66edc7 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5164 #141 0x6350c8 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6842 #142 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #143 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #144 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #145 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #146 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #147 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #148 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #149 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #150 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #151 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #152 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #153 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #154 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #155 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #156 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #157 0x63ea71 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7058 #158 0x66c4af in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:723 #159 0x671945 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1888 #160 0x674064 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1814 #161 0x66c8f8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:846 #162 0x6eb2dd in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #163 0x6eb2dd in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:200 #164 0x6eb9d8 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:314 #165 0x6ebb24 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1113 #166 0x419388 in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #167 0x7fddd1534f42 in __libc_start_main (/lib64/libc.so.6+0x23f42) #168 0x41bacd in _start (/data/gannet/ripley/R/gcc-SAN/bin/exec/R+0x41bacd) Address 0x7fff03e5e7e0 is located in stack of thread T0 SUMMARY: AddressSanitizer: dynamic-stack-buffer-overflow /data/gannet/ripley/R/packages/tests-gcc-SAN/phmm/src/phmm.c:501 in Estep Shadow bytes around the buggy address: 0x1000607c3ca0: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x1000607c3cb0: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x1000607c3cc0: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x1000607c3cd0: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x1000607c3ce0: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 =>0x1000607c3cf0: 00 00 00 00 ca ca ca ca 00 00 00 00[cb]cb cb cb 0x1000607c3d00: 00 00 00 00 00 00 00 00 ca ca ca ca 00 00 00 00 0x1000607c3d10: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x1000607c3d20: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x1000607c3d30: 00 00 00 00 cb cb cb cb 00 00 00 00 00 00 00 00 0x1000607c3d40: ca ca ca ca 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 Shadow gap: cc ==16957==ABORTING