* using log directory ‘/data/gannet/ripley/R/packages/tests-gcc-SAN/coil.Rcheck’ * using R Under development (unstable) (2025-01-31 r87670) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc-14 (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: Fedora Linux 36 (Workstation Edition) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘coil/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘coil’ version ‘1.2.4’ * package encoding: UTF-8 * 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 ‘coil’ can be installed ... [16s/17s] 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [139s/141s] OK * checking tests ... [417s/420s] OK Running ‘testthat.R’ [415s/418s] * checking package vignettes ... OK * checking re-building of vignette outputs ... [315s/319s] ERROR Error(s) in re-building vignettes: --- re-building ‘coil-vignette.Rmd’ using rmarkdown ================================================================= ==1669206==ERROR: AddressSanitizer: heap-buffer-overflow on address 0x52a00007d6b8 at pc 0x7fa7dddc312b bp 0x7ffc308fb2a0 sp 0x7ffc308fb298 READ of size 8 at 0x52a00007d6b8 thread T0 #0 0x7fa7dddc312a 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/Rtmpvs7aDB/R.INSTALL3bcdf75d4f68b8/aphid/src/ViterbiC.cpp:544 #1 0x7fa7ddd92742 in _aphid_ViterbiP /tmp/Rtmpvs7aDB/R.INSTALL3bcdf75d4f68b8/aphid/src/RcppExports.cpp:106 #2 0x71e24a in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:801 #3 0x73b502 in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1437 #4 0x8a7953 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8122 #5 0x878b1f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505 #6 0x83f862 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #7 0x84a832 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #8 0x83e1da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #9 0xa5401b in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #10 0xa5401b in applyMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:120 #11 0xa581d7 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473 #12 0xf4f99d in Rf_usemethod.isra.0 /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:513 #13 0xa59e46 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579 #14 0x8b49cd in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8142 #15 0x878b1f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505 #16 0x83f862 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #17 0x84a832 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #18 0x83e1da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #19 0xa5401b in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #20 0xa5401b in applyMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:120 #21 0xa581d7 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473 #22 0xf4f99d in Rf_usemethod.isra.0 /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:513 #23 0xa59e46 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579 #24 0x8b49cd in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8142 #25 0x878b1f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505 #26 0x83f862 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #27 0x84a832 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #28 0x83e1da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #29 0x83fee6 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #30 0x83fee6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #31 0x8639d6 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3571 #32 0x840316 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #33 0x86bbe9 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3945 #34 0x8a7953 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8122 #35 0x878b1f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505 #36 0x83f862 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #37 0x8fb1eb in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #38 0x840ebc in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #39 0x859f66 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3988 #40 0xa52e9a in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1411 #41 0x8b49cd in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8142 #42 0x878b1f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505 #43 0x83f862 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #44 0x8fb1eb in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #45 0x840ebc in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #46 0x8fb1eb in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #47 0x88365f in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956 #48 0x88365f in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5839 #49 0x8b6e1b in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7852 #50 0x878b1f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505 #51 0x83f862 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #52 0x84a832 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #53 0x83e1da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #54 0x83fee6 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #55 0x83fee6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #56 0x86bbe9 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3945 #57 0x8a7953 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8122 #58 0x878b1f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505 #59 0x83f862 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #60 0x84a832 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #61 0x83e1da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #62 0x83fee6 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #63 0x83fee6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #64 0x84a832 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #65 0x83e1da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #66 0x8bb815 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #67 0x8bb815 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8093 #68 0x878b1f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505 #69 0x83f862 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #70 0x84a832 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #71 0x83e1da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #72 0x83fee6 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #73 0x83fee6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #74 0x9c9d99 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #75 0x9c9d99 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #76 0x9cb29b in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1219 #77 0x9d5812 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1226 #78 0x4293ff in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #79 0x7fa7f4e2950f in __libc_start_call_main (/lib64/libc.so.6+0x2950f) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c) #80 0x7fa7f4e295c8 in __libc_start_main_alias_2 (/lib64/libc.so.6+0x295c8) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c) #81 0x429de4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x429de4) (BuildId: a84d18346db10b9f6a24beeffd63f6e34190cf95) 0x52a00007d6b8 is located 40 bytes after 21648-byte region [0x52a000078200,0x52a00007d690) allocated by thread T0 here: #0 0x7fa7f66f7997 in malloc ../../../../latest/libsanitizer/asan/asan_malloc_linux.cpp:69 #1 0xa327a7 in Rf_allocVector3 /data/gannet/ripley/R/svn/R-devel/src/main/memory.c:2890 #2 0xcc11af in Rf_allocVector /data/gannet/ripley/R/svn/R-devel/src/include/Rinlinedfuns.h:607 #3 0xcc11af in MatrixSubset /data/gannet/ripley/R/svn/R-devel/src/main/subset.c:330 #4 0xcc8f5b in do_subset_dflt /data/gannet/ripley/R/svn/R-devel/src/main/subset.c:892 #5 0x8a623d in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8269 #6 0x878b1f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505 #7 0x83f862 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #8 0x84a832 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #9 0x83e1da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #10 0x83fee6 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #11 0x83fee6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #12 0x8639d6 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3571 #13 0x840316 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #14 0x86bbe9 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3945 #15 0x8a7953 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8122 #16 0x878b1f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505 #17 0x83f862 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #18 0x8fb1eb in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #19 0x840ebc in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #20 0x859f66 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3988 #21 0xa52e9a in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1411 #22 0x8b49cd in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8142 #23 0x878b1f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505 #24 0x83f862 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #25 0x8fb1eb in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #26 0x840ebc in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #27 0x8fb1eb in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #28 0x88365f in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956 #29 0x88365f in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5839 #30 0x8b6e1b in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7852 #31 0x878b1f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505 #32 0x83f862 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 SUMMARY: AddressSanitizer: heap-buffer-overflow /tmp/Rtmpvs7aDB/R.INSTALL3bcdf75d4f68b8/aphid/src/ViterbiC.cpp:544 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: 0x52a00007d400: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x52a00007d480: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x52a00007d500: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x52a00007d580: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x52a00007d600: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 =>0x52a00007d680: 00 00 fa fa fa fa fa[fa]fa fa fa fa fa fa fa fa 0x52a00007d700: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x52a00007d780: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x52a00007d800: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x52a00007d880: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x52a00007d900: 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 ==1669206==ABORTING * DONE Status: 1 ERROR