* using log directory ‘/data/gannet/ripley/R/packages/tests-clang-SAN/largeVis.Rcheck’ * using R Under development (unstable) (2018-06-02 r74836) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘largeVis/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘largeVis’ version ‘0.2.1.1’ * 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 ‘largeVis’ can be installed ... [587s/288s] 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 compiled code ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘largeVis-Ex.R’ failed The error most likely occurred in: > ### Name: as.dendrogram.hdbscan > ### Title: as.dendrogram.hdbscan > ### Aliases: as.dendrogram.hdbscan > > ### ** Examples > > data(iris) > vis <- largeVis(t(iris[,1:4]), K = 20, sgd_batches = 1, threads = 1) > hdbscanobj <- hdbscan(vis, minPts = 10, K = 5) ================================================================= ==44638==ERROR: AddressSanitizer: container-overflow on address 0x61a00032b280 at pc 0x7f3af1da16c5 bp 0x7fff80aa5430 sp 0x7fff80aa5428 WRITE of size 8 at 0x61a00032b280 thread T0 #0 0x7f3af1da16c4 in HDBSCAN::buildHierarchy(std::__1::vector, std::__1::allocator > > const&, unsigned int const&, unsigned long long const*) /usr/local/bin/../include/c++/v1/algorithm:2186:18 #1 0x7f3af1da7b4d in HDBSCAN::build(unsigned int const&, arma::SpMat const&, unsigned int const&, Rcpp::Matrix<13, Rcpp::PreserveStorage> const&) /data/gannet/ripley/R/packages/tests-clang-SAN/largeVis/src/hdbscanobj.cpp:148:2 #2 0x7f3af1d99f7f in hdbscanc(arma::SpMat const&, Rcpp::Matrix<13, Rcpp::PreserveStorage> const&, int const&, int const&, Rcpp::Nullable >, bool) /data/gannet/ripley/R/packages/tests-clang-SAN/largeVis/src/hdbscan.cpp:18:30 #3 0x7f3af1b8d775 in largeVis_hdbscanc /data/gannet/ripley/R/packages/tests-clang-SAN/largeVis/src/RcppExports.cpp:142:34 #4 0x7eb9f9 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:586:17 #5 0x85d93d in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1252:11 #6 0x9c84fa in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6772:14 #7 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #8 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #9 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #10 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #11 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #12 0x9b3f74 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:747:12 #13 0xa355dc in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2778:8 #14 0x9b39ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:699:12 #15 0xb201a3 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:258:2 #16 0xb25120 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:308:11 #17 0xb24f05 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1082:5 #18 0x52a11a in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #19 0x7f3b03c9b889 in __libc_start_main (/lib64/libc.so.6+0x20889) #20 0x42d8b9 in _start (/data/gannet/ripley/R/R-clang-SAN/bin/exec/R+0x42d8b9) 0x61a00032b280 is located 0 bytes inside of 1200-byte region [0x61a00032b280,0x61a00032b730) allocated by thread T0 here: #0 0x525d00 in operator new(unsigned long) /data/gannet/ripley/Sources/LLVM/6.0.x/trunk/projects/compiler-rt/lib/asan/asan_new_delete.cc:92 #1 0x7f3af1db5fb3 in std::__1::__allocate(unsigned long) /usr/local/bin/../include/c++/v1/new:228:10 #2 0x7f3af1db5fb3 in std::__1::allocator::allocate(unsigned long, void const*) /usr/local/bin/../include/c++/v1/memory:1793 #3 0x7f3af1db5fb3 in std::__1::allocator_traits >::allocate(std::__1::allocator&, unsigned long) /usr/local/bin/../include/c++/v1/memory:1547 #4 0x7f3af1db5fb3 in std::__1::__split_buffer&>::__split_buffer(unsigned long, unsigned long, std::__1::allocator&) /usr/local/bin/../include/c++/v1/__split_buffer:311 #5 0x7f3af1dab694 in std::__1::vector >::reserve(unsigned long) /usr/local/bin/../include/c++/v1/vector:1541:53 #6 0x7f3af1da152a in HDBSCAN::buildHierarchy(std::__1::vector, std::__1::allocator > > const&, unsigned int const&, unsigned long long const*) /data/gannet/ripley/R/packages/tests-clang-SAN/largeVis/src/hdbscanobj.cpp:99:9 #7 0x7f3af1da7b4d in HDBSCAN::build(unsigned int const&, arma::SpMat const&, unsigned int const&, Rcpp::Matrix<13, Rcpp::PreserveStorage> const&) /data/gannet/ripley/R/packages/tests-clang-SAN/largeVis/src/hdbscanobj.cpp:148:2 #8 0x7f3af1d99f7f in hdbscanc(arma::SpMat const&, Rcpp::Matrix<13, Rcpp::PreserveStorage> const&, int const&, int const&, Rcpp::Nullable >, bool) /data/gannet/ripley/R/packages/tests-clang-SAN/largeVis/src/hdbscan.cpp:18:30 #9 0x7f3af1b8d775 in largeVis_hdbscanc /data/gannet/ripley/R/packages/tests-clang-SAN/largeVis/src/RcppExports.cpp:142:34 #10 0x7eb9f9 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:586:17 #11 0x85d93d in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1252:11 #12 0x9c84fa in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6772:14 #13 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #14 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #15 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #16 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #17 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #18 0x9b3f74 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:747:12 #19 0xa355dc in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2778:8 #20 0x9b39ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:699:12 #21 0xb201a3 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:258:2 #22 0xb25120 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:308:11 #23 0xb24f05 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1082:5 #24 0x52a11a in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #25 0x7f3b03c9b889 in __libc_start_main (/lib64/libc.so.6+0x20889) HINT: if you don't care about these errors you may set ASAN_OPTIONS=detect_container_overflow=0. If you suspect a false positive see also: https://github.com/google/sanitizers/wiki/AddressSanitizerContainerOverflow. SUMMARY: AddressSanitizer: container-overflow /usr/local/bin/../include/c++/v1/algorithm:2186:18 in HDBSCAN::buildHierarchy(std::__1::vector, std::__1::allocator > > const&, unsigned int const&, unsigned long long const*) Shadow bytes around the buggy address: 0x0c348005d600: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x0c348005d610: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x0c348005d620: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x0c348005d630: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x0c348005d640: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa =>0x0c348005d650:[fc]fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc 0x0c348005d660: fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc 0x0c348005d670: fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc 0x0c348005d680: fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc 0x0c348005d690: fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc 0x0c348005d6a0: fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc 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 ==44638==ABORTING * checking tests ... [191s/268s] ERROR Running ‘testthat.R’ [190s/266s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(largeVis) Loading required package: Matrix largeVis was compiled without OpenMP support. > > test_check("largeVis") ================================================================= ==45606==ERROR: AddressSanitizer: container-overflow on address 0x61e0008d4880 at pc 0x7f8bc76a56c5 bp 0x7ffdb3e9dbb0 sp 0x7ffdb3e9dba8 WRITE of size 8 at 0x61e0008d4880 thread T0 #0 0x7f8bc76a56c4 in HDBSCAN::buildHierarchy(std::__1::vector, std::__1::allocator > > const&, unsigned int const&, unsigned long long const*) /usr/local/bin/../include/c++/v1/algorithm:2186:18 #1 0x7f8bc76abb4d in HDBSCAN::build(unsigned int const&, arma::SpMat const&, unsigned int const&, Rcpp::Matrix<13, Rcpp::PreserveStorage> const&) /data/gannet/ripley/R/packages/tests-clang-SAN/largeVis/src/hdbscanobj.cpp:148:2 #2 0x7f8bc769df7f in hdbscanc(arma::SpMat const&, Rcpp::Matrix<13, Rcpp::PreserveStorage> const&, int const&, int const&, Rcpp::Nullable >, bool) /data/gannet/ripley/R/packages/tests-clang-SAN/largeVis/src/hdbscan.cpp:18:30 #3 0x7f8bc7491775 in largeVis_hdbscanc /data/gannet/ripley/R/packages/tests-clang-SAN/largeVis/src/RcppExports.cpp:142:34 #4 0x7eb9f9 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:586:17 #5 0x85d93d in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1252:11 #6 0x9c84fa in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6772:14 #7 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #8 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #9 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #10 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #11 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #12 0x9b3f74 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:747:12 #13 0xa355dc in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2778:8 #14 0x9b39ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:699:12 #15 0x7e54ee in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:573:17 #16 0x9cc4e3 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7280:21 #17 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #18 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #19 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #20 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #21 0xa1f3aa in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8 #22 0xa665d2 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4971:15 #23 0xa66a1b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5013:10 #24 0x9e054b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6504:20 #25 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #26 0xa1f3aa in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8 #27 0x9b40c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:647:9 #28 0xa414a8 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3210:9 #29 0xb95169 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1370:11 #30 0x9c4e9c in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6792:15 #31 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #32 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #33 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #34 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #35 0xa1f3aa in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8 #36 0xa665d2 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4971:15 #37 0xa66a1b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5013:10 #38 0x9e054b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6504:20 #39 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #40 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #41 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #42 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #43 0xa1f3aa in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8 #44 0xa665d2 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4971:15 #45 0xa66a1b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5013:10 #46 0x9e054b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6504:20 #47 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #48 0xa1f3aa in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8 #49 0xa665d2 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4971:15 #50 0xa66a1b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5013:10 #51 0x9e054b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6504:20 #52 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #53 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #54 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #55 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #56 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #57 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #58 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #59 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #60 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #61 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #62 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #63 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #64 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #65 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #66 0x9b3f74 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:747:12 #67 0xa33afd in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2395:10 #68 0x9b39ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:699:12 #69 0xa3ef4c in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3157:13 #70 0x9c84fa in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6772:14 #71 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #72 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #73 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #74 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #75 0xa1f3aa in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8 #76 0xa665d2 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4971:15 #77 0xa66a1b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5013:10 #78 0x9e054b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6504:20 #79 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #80 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #81 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #82 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #83 0xa1f3aa in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8 #84 0xa665d2 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4971:15 #85 0xa66a1b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5013:10 #86 0x9e054b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6504:20 #87 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #88 0xa1f3aa in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8 #89 0xa665d2 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4971:15 #90 0xa66a1b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5013:10 #91 0x9e054b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6504:20 #92 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #93 0xa1f3aa in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8 #94 0xa665d2 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4971:15 #95 0xa66a1b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5013:10 #96 0x9e054b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6504:20 #97 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #98 0xa1f3aa in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8 #99 0xa665d2 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4971:15 #100 0xa66a1b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5013:10 #101 0x9e054b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6504:20 #102 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #103 0xa1f3aa in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8 #104 0xa665d2 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4971:15 #105 0xa66a1b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5013:10 #106 0x9e054b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6504:20 #107 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #108 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #109 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #110 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #111 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #112 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #113 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #114 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #115 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #116 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #117 0xa1f3aa in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8 #118 0xa665d2 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4971:15 #119 0xa66a1b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5013:10 #120 0x9e054b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6504:20 #121 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #122 0xa1f3aa in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8 #123 0xa665d2 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4971:15 #124 0xa66a1b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5013:10 #125 0x9e054b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6504:20 #126 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #127 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #128 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #129 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #130 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #131 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #132 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #133 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #134 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #135 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #136 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #137 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #138 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #139 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #140 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #141 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #142 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #143 0x9b3f74 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:747:12 #144 0xa3f8c1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3181:9 #145 0x9c84fa in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6772:14 #146 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #147 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #148 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #149 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #150 0xa1f3aa in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8 #151 0xa665d2 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4971:15 #152 0xa66a1b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5013:10 #153 0x9e054b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6504:20 #154 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #155 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #156 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #157 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #158 0xa1f3aa in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8 #159 0xa665d2 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4971:15 #160 0xa66a1b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5013:10 #161 0x9e054b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6504:20 #162 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #163 0xa1f3aa in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8 #164 0xa665d2 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4971:15 #165 0xa66a1b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5013:10 #166 0x9e054b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6504:20 #167 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #168 0xa1f3aa in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8 #169 0xa665d2 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4971:15 #170 0xa66a1b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5013:10 #171 0x9e054b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6504:20 #172 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #173 0xa1f3aa in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8 #174 0xa665d2 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4971:15 #175 0xa66a1b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5013:10 #176 0x9e054b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6504:20 #177 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #178 0xa1f3aa in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8 #179 0xa665d2 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4971:15 #180 0xa66a1b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5013:10 #181 0x9e054b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6504:20 #182 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #183 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #184 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #185 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #186 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #187 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #188 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #189 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #190 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #191 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #192 0xa1f3aa in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8 #193 0xa665d2 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4971:15 #194 0xa66a1b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5013:10 #195 0x9e054b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6504:20 #196 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #197 0xa1f3aa in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8 #198 0xa665d2 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4971:15 #199 0xa66a1b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5013:10 #200 0x9e054b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6504:20 #201 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #202 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #203 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #204 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #205 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #206 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #207 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #208 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #209 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #210 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #211 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #212 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #213 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #214 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #215 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #216 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #217 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #218 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #219 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #220 0xa1f3aa in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8 #221 0xa665d2 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4971:15 #222 0xa66a1b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5013:10 #223 0x9e054b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6504:20 #224 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #225 0xa1f3aa in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8 #226 0xa665d2 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4971:15 #227 0xa66a1b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5013:10 #228 0x9e054b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6504:20 #229 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #230 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #231 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #232 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #233 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #234 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #235 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #236 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #237 0xa283d1 in R_forceAndCall /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1831:8 #238 0x588aa0 in do_lapply /data/gannet/ripley/R/svn/R-devel/src/main/apply.c:70:8 #239 0xb95169 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1370:11 #240 0x9c4e9c in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6792:15 #241 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #242 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #243 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #244 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #245 0xa1f3aa in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8 #246 0xa665d2 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4971:15 #247 0xa66a1b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5013:10 #248 0x9e054b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6504:20 #249 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #250 0xa1f3aa in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8 #251 0xa665d2 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4971:15 0x61e0008d4880 is located 0 bytes inside of 2496-byte region [0x61e0008d4880,0x61e0008d5240) allocated by thread T0 here: #0 0x525d00 in operator new(unsigned long) /data/gannet/ripley/Sources/LLVM/6.0.x/trunk/projects/compiler-rt/lib/asan/asan_new_delete.cc:92 #1 0x7f8bc76b9fb3 in std::__1::__allocate(unsigned long) /usr/local/bin/../include/c++/v1/new:228:10 #2 0x7f8bc76b9fb3 in std::__1::allocator::allocate(unsigned long, void const*) /usr/local/bin/../include/c++/v1/memory:1793 #3 0x7f8bc76b9fb3 in std::__1::allocator_traits >::allocate(std::__1::allocator&, unsigned long) /usr/local/bin/../include/c++/v1/memory:1547 #4 0x7f8bc76b9fb3 in std::__1::__split_buffer&>::__split_buffer(unsigned long, unsigned long, std::__1::allocator&) /usr/local/bin/../include/c++/v1/__split_buffer:311 #5 0x7f8bc76af694 in std::__1::vector >::reserve(unsigned long) /usr/local/bin/../include/c++/v1/vector:1541:53 #6 0x7f8bc76a552a in HDBSCAN::buildHierarchy(std::__1::vector, std::__1::allocator > > const&, unsigned int const&, unsigned long long const*) /data/gannet/ripley/R/packages/tests-clang-SAN/largeVis/src/hdbscanobj.cpp:99:9 #7 0x7f8bc76abb4d in HDBSCAN::build(unsigned int const&, arma::SpMat const&, unsigned int const&, Rcpp::Matrix<13, Rcpp::PreserveStorage> const&) /data/gannet/ripley/R/packages/tests-clang-SAN/largeVis/src/hdbscanobj.cpp:148:2 #8 0x7f8bc769df7f in hdbscanc(arma::SpMat const&, Rcpp::Matrix<13, Rcpp::PreserveStorage> const&, int const&, int const&, Rcpp::Nullable >, bool) /data/gannet/ripley/R/packages/tests-clang-SAN/largeVis/src/hdbscan.cpp:18:30 #9 0x7f8bc7491775 in largeVis_hdbscanc /data/gannet/ripley/R/packages/tests-clang-SAN/largeVis/src/RcppExports.cpp:142:34 #10 0x7eb9f9 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:586:17 #11 0x85d93d in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1252:11 #12 0x9c84fa in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6772:14 #13 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #14 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #15 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #16 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #17 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #18 0x9b3f74 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:747:12 #19 0xa355dc in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2778:8 #20 0x9b39ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:699:12 #21 0x7e54ee in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:573:17 #22 0x9cc4e3 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7280:21 #23 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #24 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #25 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #26 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #27 0xa1f3aa in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8 #28 0xa665d2 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4971:15 #29 0xa66a1b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5013:10 #30 0x9e054b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6504:20 #31 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #32 0xa1f3aa in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8 HINT: if you don't care about these errors you may set ASAN_OPTIONS=detect_container_overflow=0. If you suspect a false positive see also: https://github.com/google/sanitizers/wiki/AddressSanitizerContainerOverflow. SUMMARY: AddressSanitizer: container-overflow /usr/local/bin/../include/c++/v1/algorithm:2186:18 in HDBSCAN::buildHierarchy(std::__1::vector, std::__1::allocator > > const&, unsigned int const&, unsigned long long const*) Shadow bytes around the buggy address: 0x0c3c801128c0: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x0c3c801128d0: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x0c3c801128e0: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x0c3c801128f0: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x0c3c80112900: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa =>0x0c3c80112910:[fc]fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc 0x0c3c80112920: fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc 0x0c3c80112930: fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc 0x0c3c80112940: fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc 0x0c3c80112950: fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc 0x0c3c80112960: fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc 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 ==45606==ABORTING * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... [60s/76s] WARNING Error in re-building vignettes: ... largeVis was compiled without OpenMP support. Warning in unit(c(t, r, b, l), unit) : NAs introduced by coercion ================================================================= ==11626==ERROR: AddressSanitizer: container-overflow on address 0x61e003f08480 at pc 0x7fc274fbd6c5 bp 0x7fffb66927b0 sp 0x7fffb66927a8 WRITE of size 8 at 0x61e003f08480 thread T0 #0 0x7fc274fbd6c4 in HDBSCAN::buildHierarchy(std::__1::vector, std::__1::allocator > > const&, unsigned int const&, unsigned long long const*) /usr/local/bin/../include/c++/v1/algorithm:2186:18 #1 0x7fc274fc3b4d in HDBSCAN::build(unsigned int const&, arma::SpMat const&, unsigned int const&, Rcpp::Matrix<13, Rcpp::PreserveStorage> const&) /data/gannet/ripley/R/packages/tests-clang-SAN/largeVis/src/hdbscanobj.cpp:148:2 #2 0x7fc274fb5f7f in hdbscanc(arma::SpMat const&, Rcpp::Matrix<13, Rcpp::PreserveStorage> const&, int const&, int const&, Rcpp::Nullable >, bool) /data/gannet/ripley/R/packages/tests-clang-SAN/largeVis/src/hdbscan.cpp:18:30 #3 0x7fc274da9775 in largeVis_hdbscanc /data/gannet/ripley/R/packages/tests-clang-SAN/largeVis/src/RcppExports.cpp:142:34 #4 0x7eb9f9 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:586:17 #5 0x85d93d in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1252:11 #6 0x9c84fa in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6772:14 #7 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #8 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #9 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #10 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #11 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #12 0x9b3f74 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:747:12 #13 0xdc1a03 in R_DispatchOrEvalSP /data/gannet/ripley/R/svn/R-devel/src/main/subset.c:619:11 #14 0xdd78e0 in do_subset3 /data/gannet/ripley/R/svn/R-devel/src/main/subset.c:1207:8 #15 0x9b39ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:699:12 #16 0xa355dc in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2778:8 #17 0x9b39ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:699:12 #18 0xa33afd in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2395:10 #19 0x9b39ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:699:12 #20 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #21 0xa283d1 in R_forceAndCall /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1831:8 #22 0xb2d412 in do_mapply /data/gannet/ripley/R/svn/R-devel/src/main/mapply.c:105:13 #23 0x9c84fa in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6772:14 #24 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #25 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #26 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #27 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #28 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #29 0x9b3f74 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:747:12 #30 0xa1f3aa in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8 #31 0x9b3a52 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:660:6 #32 0x66dc07 in do_bind /data/gannet/ripley/R/svn/R-devel/src/main/bind.c:1071:2 #33 0xb95169 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1370:11 #34 0x9c4e9c in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6792:15 #35 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #36 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #37 0x9b3f74 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:747:12 #38 0xa33afd in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2395:10 #39 0x9b39ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:699:12 #40 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #41 0xa283d1 in R_forceAndCall /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1831:8 #42 0xb2d412 in do_mapply /data/gannet/ripley/R/svn/R-devel/src/main/mapply.c:105:13 #43 0x9c84fa in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6772:14 #44 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #45 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #46 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #47 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #48 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #49 0x9b3f74 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:747:12 #50 0xa1f3aa in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8 #51 0xa665d2 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4971:15 #52 0xa66a1b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5013:10 #53 0x9e054b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6504:20 #54 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #55 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #56 0x9b3f74 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:747:12 #57 0xa355dc in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2778:8 #58 0x9b39ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:699:12 #59 0xa1f3aa in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8 #60 0xa665d2 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4971:15 #61 0xa66a1b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5013:10 #62 0x9e054b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6504:20 #63 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #64 0xa1f3aa in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8 #65 0xa665d2 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4971:15 #66 0xa66a1b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5013:10 #67 0x9e054b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6504:20 #68 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #69 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #70 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #71 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #72 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #73 0x9b3f74 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:747:12 #74 0xa3ef4c in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3157:13 #75 0x9c84fa in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6772:14 #76 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #77 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #78 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #79 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #80 0xa1f3aa in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8 #81 0x9b40c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:647:9 #82 0xa414a8 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3210:9 #83 0xb95169 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1370:11 #84 0x9c4e9c in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6792:15 #85 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #86 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #87 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #88 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #89 0xa1f3aa in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8 #90 0xa665d2 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4971:15 #91 0xa66a1b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5013:10 #92 0x9e054b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6504:20 #93 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #94 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #95 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #96 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #97 0xa1f3aa in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8 #98 0xa665d2 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4971:15 #99 0xa66a1b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5013:10 #100 0x9e054b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6504:20 #101 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #102 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #103 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #104 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #105 0xa1f3aa in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8 #106 0xa665d2 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4971:15 #107 0xa66a1b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5013:10 #108 0x9e054b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6504:20 #109 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #110 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #111 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #112 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #113 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #114 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #115 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #116 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #117 0x9b3f74 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:747:12 #118 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #119 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #120 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #121 0xa1f3aa in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8 #122 0xa665d2 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4971:15 #123 0xa66a1b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5013:10 #124 0x9e054b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6504:20 #125 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #126 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #127 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #128 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #129 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #130 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #131 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #132 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #133 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #134 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #135 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #136 0xb9fa6e in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:433:16 #137 0xb9e3ad in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473:10 #138 0xba0e75 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:562:9 #139 0x9c4e9c in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6792:15 #140 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #141 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #142 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #143 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #144 0xa1f3aa in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8 #145 0xa665d2 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4971:15 #146 0xa66a1b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5013:10 #147 0x9e054b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6504:20 #148 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #149 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #150 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #151 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #152 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #153 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #154 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #155 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #156 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #157 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #158 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #159 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #160 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #161 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #162 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #163 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #164 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #165 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #166 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #167 0xa1f3aa in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8 #168 0xa665d2 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4971:15 #169 0xa66a1b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5013:10 #170 0x9e054b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6504:20 #171 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #172 0xa1f3aa in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8 #173 0xa665d2 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4971:15 #174 0xa66a1b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5013:10 #175 0x9e054b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6504:20 #176 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #177 0xa1f3aa in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8 #178 0xa665d2 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4971:15 #179 0xa66a1b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5013:10 #180 0x9e054b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6504:20 #181 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #182 0xa1f3aa in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:520:8 #183 0xa665d2 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4971:15 #184 0xa66a1b in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5013:10 #185 0x9e054b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6504:20 #186 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #187 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #188 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #189 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #190 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #191 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #192 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #193 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #194 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #195 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #196 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #197 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #198 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #199 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #200 0x9b3f74 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:747:12 #201 0xb201a3 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:258:2 #202 0xb25120 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:308:11 #203 0xb24f05 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1082:5 #204 0x52a11a in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #205 0x7fc28cc6b889 in __libc_start_main (/lib64/libc.so.6+0x20889) #206 0x42d8b9 in _start (/data/gannet/ripley/R/R-clang-SAN/bin/exec/R+0x42d8b9) 0x61e003f08480 is located 0 bytes inside of 2496-byte region [0x61e003f08480,0x61e003f08e40) allocated by thread T0 here: #0 0x525d00 in operator new(unsigned long) /data/gannet/ripley/Sources/LLVM/6.0.x/trunk/projects/compiler-rt/lib/asan/asan_new_delete.cc:92 #1 0x7fc274fd1fb3 in std::__1::__allocate(unsigned long) /usr/local/bin/../include/c++/v1/new:228:10 #2 0x7fc274fd1fb3 in std::__1::allocator::allocate(unsigned long, void const*) /usr/local/bin/../include/c++/v1/memory:1793 #3 0x7fc274fd1fb3 in std::__1::allocator_traits >::allocate(std::__1::allocator&, unsigned long) /usr/local/bin/../include/c++/v1/memory:1547 #4 0x7fc274fd1fb3 in std::__1::__split_buffer&>::__split_buffer(unsigned long, unsigned long, std::__1::allocator&) /usr/local/bin/../include/c++/v1/__split_buffer:311 #5 0x7fc274fc7694 in std::__1::vector >::reserve(unsigned long) /usr/local/bin/../include/c++/v1/vector:1541:53 #6 0x7fc274fbd52a in HDBSCAN::buildHierarchy(std::__1::vector, std::__1::allocator > > const&, unsigned int const&, unsigned long long const*) /data/gannet/ripley/R/packages/tests-clang-SAN/largeVis/src/hdbscanobj.cpp:99:9 #7 0x7fc274fc3b4d in HDBSCAN::build(unsigned int const&, arma::SpMat const&, unsigned int const&, Rcpp::Matrix<13, Rcpp::PreserveStorage> const&) /data/gannet/ripley/R/packages/tests-clang-SAN/largeVis/src/hdbscanobj.cpp:148:2 #8 0x7fc274fb5f7f in hdbscanc(arma::SpMat const&, Rcpp::Matrix<13, Rcpp::PreserveStorage> const&, int const&, int const&, Rcpp::Nullable >, bool) /data/gannet/ripley/R/packages/tests-clang-SAN/largeVis/src/hdbscan.cpp:18:30 #9 0x7fc274da9775 in largeVis_hdbscanc /data/gannet/ripley/R/packages/tests-clang-SAN/largeVis/src/RcppExports.cpp:142:34 #10 0x7eb9f9 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:586:17 #11 0x85d93d in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1252:11 #12 0x9c84fa in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6772:14 #13 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #14 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #15 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #16 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #17 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #18 0x9b3f74 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:747:12 #19 0xdc1a03 in R_DispatchOrEvalSP /data/gannet/ripley/R/svn/R-devel/src/main/subset.c:619:11 #20 0xdd78e0 in do_subset3 /data/gannet/ripley/R/svn/R-devel/src/main/subset.c:1207:8 #21 0x9b39ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:699:12 #22 0xa355dc in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2778:8 #23 0x9b39ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:699:12 #24 0xa33afd in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2395:10 #25 0x9b39ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:699:12 #26 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #27 0xa283d1 in R_forceAndCall /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1831:8 #28 0xb2d412 in do_mapply /data/gannet/ripley/R/svn/R-devel/src/main/mapply.c:105:13 #29 0x9c84fa in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6772:14 #30 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #31 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #32 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 HINT: if you don't care about these errors you may set ASAN_OPTIONS=detect_container_overflow=0. If you suspect a false positive see also: https://github.com/google/sanitizers/wiki/AddressSanitizerContainerOverflow. SUMMARY: AddressSanitizer: container-overflow /usr/local/bin/../include/c++/v1/algorithm:2186:18 in HDBSCAN::buildHierarchy(std::__1::vector, std::__1::allocator > > const&, unsigned int const&, unsigned long long const*) Shadow bytes around the buggy address: 0x0c3c807d9040: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x0c3c807d9050: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x0c3c807d9060: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x0c3c807d9070: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x0c3c807d9080: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa =>0x0c3c807d9090:[fc]fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc 0x0c3c807d90a0: fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc 0x0c3c807d90b0: fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc 0x0c3c807d90c0: fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc 0x0c3c807d90d0: fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc 0x0c3c807d90e0: fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc fc 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 ==11626==ABORTING * DONE Status: 2 ERRORs, 1 WARNING