* using log directory ‘/data/gannet/ripley/R/packages/tests-gcc-SAN/Meiosis.Rcheck’ * using R Under development (unstable) (2018-02-09 r74240) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘Meiosis/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Meiosis’ version ‘1.0.2’ * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package ‘Meiosis’ can be installed ... [137s/85s] OK * checking package directory ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking contents of ‘data’ directory ... OK * checking compiled code ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking tests ... OK Running ‘testthat.R’ * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... [10s/10s] WARNING Error in re-building vignettes: ... ================================================================= ==26628==ERROR: AddressSanitizer: heap-buffer-overflow on address 0x62500a15b018 at pc 0x7f00d98c9098 bp 0x7fff6544db90 sp 0x7fff6544db80 READ of size 8 at 0x62500a15b018 thread T0 #0 0x7f00d98c9097 in double realized_ibd_ns::realized_ibd, Rcpp::Vector<14, Rcpp::PreserveStorage> >(Rcpp::Vector<13, Rcpp::PreserveStorage> const&, Rcpp::Vector<14, Rcpp::PreserveStorage> const&, Rcpp::Vector<13, Rcpp::PreserveStorage> const&, Rcpp::Vector<14, Rcpp::PreserveStorage> const&) ../inst/include/hinterface/realized_ibd.hpp:34 #1 0x7f00d98a7fe5 in realized_coancestry(Rcpp::Vector<19, Rcpp::PreserveStorage> const&, Rcpp::Nullable > const&) /data/gannet/ripley/R/packages/tests-gcc-SAN/Meiosis/src/R_interface.cpp:303 #2 0x7f00d9907c02 in Meiosis_realized_coancestry /data/gannet/ripley/R/packages/tests-gcc-SAN/Meiosis/src/RcppExports.cpp:204 #3 0x578f80 in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1252 #4 0x618d6c in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6766 #5 0x644987 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624 #6 0x649a75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1764 #7 0x62648b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6734 #8 0x644987 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624 #9 0x649a75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1764 #10 0x62648b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6734 #11 0x644987 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624 #12 0x649a75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1764 #13 0x651e79 in R_forceAndCall /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1827 #14 0x44e21a in do_lapply /data/gannet/ripley/R/svn/R-devel/src/main/apply.c:70 #15 0x6df112 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1370 #16 0x618942 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6786 #17 0x644987 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624 #18 0x649a75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1764 #19 0x62648b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6734 #20 0x644987 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624 #21 0x649a75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1764 #22 0x62648b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6734 #23 0x644987 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624 #24 0x649a75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1764 #25 0x644e76 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:747 #26 0x6466e3 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520 #27 0x64728f in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4966 #28 0x64728f in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5008 #29 0x622ae4 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6503 #30 0x644987 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624 #31 0x649a75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1764 #32 0x644e76 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:747 #33 0x6512bc in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2873 #34 0x64576b in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:718 #35 0x650ef3 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2774 #36 0x6454ec in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:699 #37 0x654097 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3153 #38 0x618d6c in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6766 #39 0x644987 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624 #40 0x649a75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1764 #41 0x62648b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6734 #42 0x644987 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624 #43 0x6466e3 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520 #44 0x645105 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:647 #45 0x6559ed in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3206 #46 0x6df112 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1370 #47 0x618942 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6786 #48 0x644987 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624 #49 0x649a75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1764 #50 0x62648b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6734 #51 0x644987 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624 #52 0x6466e3 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520 #53 0x64728f in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4966 #54 0x64728f in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5008 #55 0x622ae4 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6503 #56 0x644987 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624 #57 0x649a75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1764 #58 0x62648b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6734 #59 0x644987 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624 #60 0x6466e3 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520 #61 0x64728f in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4966 #62 0x64728f in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5008 #63 0x622ae4 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6503 #64 0x644987 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624 #65 0x649a75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1764 #66 0x62648b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6734 #67 0x644987 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624 #68 0x6466e3 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520 #69 0x64728f in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4966 #70 0x64728f in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5008 #71 0x622ae4 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6503 #72 0x644987 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624 #73 0x649a75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1764 #74 0x62648b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6734 #75 0x644987 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624 #76 0x649a75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1764 #77 0x62648b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6734 #78 0x644987 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624 #79 0x649a75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1764 #80 0x644e76 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:747 #81 0x649a75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1764 #82 0x62648b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6734 #83 0x644987 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624 #84 0x6466e3 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520 #85 0x64728f in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4966 #86 0x64728f in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5008 #87 0x622ae4 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6503 #88 0x644987 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624 #89 0x649a75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1764 #90 0x62648b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6734 #91 0x644987 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624 #92 0x649a75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1764 #93 0x62648b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6734 #94 0x644987 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624 #95 0x649a75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1764 #96 0x62648b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6734 #97 0x644987 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624 #98 0x649a75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1764 #99 0x6e4715 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:419 #100 0x6e5426 in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:459 #101 0x6e5d13 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:535 #102 0x618942 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6786 #103 0x644987 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624 #104 0x649a75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1764 #105 0x62648b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6734 #106 0x644987 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624 #107 0x6466e3 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520 #108 0x64728f in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4966 #109 0x64728f in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5008 #110 0x622ae4 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6503 #111 0x644987 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624 #112 0x649a75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1764 #113 0x62648b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6734 #114 0x644987 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624 #115 0x649a75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1764 #116 0x62648b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6734 #117 0x644987 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624 #118 0x649a75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1764 #119 0x62648b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6734 #120 0x644987 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624 #121 0x649a75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1764 #122 0x62648b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6734 #123 0x644987 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624 #124 0x649a75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1764 #125 0x62648b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6734 #126 0x644987 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624 #127 0x649a75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1764 #128 0x62648b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6734 #129 0x644987 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624 #130 0x6466e3 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520 #131 0x64728f in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4966 #132 0x64728f in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5008 #133 0x622ae4 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6503 #134 0x644987 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624 #135 0x6466e3 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520 #136 0x64728f in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4966 #137 0x64728f in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5008 #138 0x622ae4 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6503 #139 0x644987 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624 #140 0x6466e3 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520 #141 0x64728f in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4966 #142 0x64728f in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5008 #143 0x622ae4 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6503 #144 0x644987 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624 #145 0x6466e3 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520 #146 0x64728f in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4966 #147 0x64728f in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5008 #148 0x622ae4 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6503 #149 0x644987 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624 #150 0x649a75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1764 #151 0x62648b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6734 #152 0x644987 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624 #153 0x649a75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1764 #154 0x62648b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6734 #155 0x644987 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624 #156 0x649a75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1764 #157 0x62648b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6734 #158 0x644987 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624 #159 0x649a75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1764 #160 0x62648b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6734 #161 0x644987 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624 #162 0x649a75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1764 #163 0x644e76 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:747 #164 0x6b86ce in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:258 #165 0x6b90b0 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:308 #166 0x6ba7c4 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1082 #167 0x4210d8 in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #168 0x7f00ecce9889 in __libc_start_main (/lib64/libc.so.6+0x20889) #169 0x4237f9 in _start (/data/gannet/ripley/R/gcc-SAN/bin/exec/R+0x4237f9) 0x62500a15b018 is located 0 bytes to the right of 7960-byte region [0x62500a159100,0x62500a15b018) allocated by thread T0 here: #0 0x7f00f05c6850 in malloc (/lib64/libasan.so.4+0xde850) #1 0x6d722f in GetNewPage /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:888 SUMMARY: AddressSanitizer: heap-buffer-overflow ../inst/include/hinterface/realized_ibd.hpp:34 in double realized_ibd_ns::realized_ibd, Rcpp::Vector<14, Rcpp::PreserveStorage> >(Rcpp::Vector<13, Rcpp::PreserveStorage> const&, Rcpp::Vector<14, Rcpp::PreserveStorage> const&, Rcpp::Vector<13, Rcpp::PreserveStorage> const&, Rcpp::Vector<14, Rcpp::PreserveStorage> const&) Shadow bytes around the buggy address: 0x0c4a814235b0: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x0c4a814235c0: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x0c4a814235d0: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x0c4a814235e0: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x0c4a814235f0: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 =>0x0c4a81423600: 00 00 00[fa]fa fa fa fa fa fa fa fa fa fa fa fa 0x0c4a81423610: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x0c4a81423620: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x0c4a81423630: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x0c4a81423640: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x0c4a81423650: 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 ==26628==ABORTING * DONE Status: 1 WARNING