* using log directory ‘/data/gannet/ripley/R/packages/tests-clang-SAN/GraphKit.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 ‘GraphKit/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GraphKit’ version ‘0.5’ * 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 ‘GraphKit’ can be installed ... [68s/135s] 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 examples ... ERROR Running examples in ‘GraphKit-Ex.R’ failed The error most likely occurred in: > ### Name: graph_invar > ### Title: Graph Invar > ### Aliases: graph_invar > > ### ** Examples > > > data(Xs,cov.hat,t.hat) > graph_invar(x=Xs,sigmaHat=cov.hat,thetaHat=t.hat,invar="conn") ================================================================= ==29384==ERROR: AddressSanitizer: container-overflow on address 0x604000006a10 at pc 0x7f1b07a21989 bp 0x7ffd21628370 sp 0x7ffd21628368 WRITE of size 4 at 0x604000006a10 thread T0 #0 0x7f1b07a21988 in UnionFind::UnionFind(int) /data/gannet/ripley/R/packages/tests-clang-SAN/GraphKit/src/helpers.cpp:14:19 #1 0x7f1b0798d5d1 in skipDownConnCI(arma::Mat, arma::Mat, double) /data/gannet/ripley/R/packages/tests-clang-SAN/GraphKit/src/Graph.cpp:137:28 #2 0x7f1b07a0f4ab in GraphKit_skipDownConnCI /data/gannet/ripley/R/packages/tests-clang-SAN/GraphKit/src/RcppExports.cpp:57:34 #3 0x7e58a3 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:576:17 #4 0x85d93d in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1252:11 #5 0x9c84fa in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6772:14 #6 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #7 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #8 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #9 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #10 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #11 0x9b3f74 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:747:12 #12 0xb201a3 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:258:2 #13 0xb25120 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:308:11 #14 0xb24f05 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1082:5 #15 0x52a11a in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #16 0x7f1b15466889 in __libc_start_main (/lib64/libc.so.6+0x20889) #17 0x42d8b9 in _start (/data/gannet/ripley/R/R-clang-SAN/bin/exec/R+0x42d8b9) 0x604000006a10 is located 0 bytes inside of 40-byte region [0x604000006a10,0x604000006a38) 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 0x7f1b07a23e03 in std::__1::__allocate(unsigned long) /usr/local/bin/../include/c++/v1/new:228:10 #2 0x7f1b07a23e03 in std::__1::allocator::allocate(unsigned long, void const*) /usr/local/bin/../include/c++/v1/memory:1793 #3 0x7f1b07a23e03 in std::__1::allocator_traits >::allocate(std::__1::allocator&, unsigned long) /usr/local/bin/../include/c++/v1/memory:1547 #4 0x7f1b07a23e03 in std::__1::__split_buffer&>::__split_buffer(unsigned long, unsigned long, std::__1::allocator&) /usr/local/bin/../include/c++/v1/__split_buffer:311 #5 0x7f1b07a23884 in std::__1::vector >::reserve(unsigned long) /usr/local/bin/../include/c++/v1/vector:1541:53 #6 0x7f1b07a2122d in UnionFind::UnionFind(int) /data/gannet/ripley/R/packages/tests-clang-SAN/GraphKit/src/helpers.cpp:10:12 #7 0x7f1b0798d5d1 in skipDownConnCI(arma::Mat, arma::Mat, double) /data/gannet/ripley/R/packages/tests-clang-SAN/GraphKit/src/Graph.cpp:137:28 #8 0x7f1b07a0f4ab in GraphKit_skipDownConnCI /data/gannet/ripley/R/packages/tests-clang-SAN/GraphKit/src/RcppExports.cpp:57:34 #9 0x7e58a3 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:576:17 #10 0x85d93d in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1252:11 #11 0x9c84fa in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6772:14 #12 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #13 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #14 0x9d7b68 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #15 0x9b2d9d in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:624:8 #16 0xa265fe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #17 0x9b3f74 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:747:12 #18 0xb201a3 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:258:2 #19 0xb25120 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:308:11 #20 0xb24f05 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1082:5 #21 0x52a11a in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #22 0x7f1b15466889 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 /data/gannet/ripley/R/packages/tests-clang-SAN/GraphKit/src/helpers.cpp:14:19 in UnionFind::UnionFind(int) Shadow bytes around the buggy address: 0x0c087fff8cf0: fa fa fd fd fd fd fd fd fa fa fd fd fd fd fd fd 0x0c087fff8d00: fa fa fd fd fd fd fd fd fa fa fd fd fd fd fd fd 0x0c087fff8d10: fa fa fd fd fd fd fd fd fa fa fd fd fd fd fd fd 0x0c087fff8d20: fa fa fd fd fd fd fd fd fa fa fd fd fd fd fd fd 0x0c087fff8d30: fa fa fd fd fd fd fd fd fa fa fd fd fd fd fd fd =>0x0c087fff8d40: fa fa[fc]fc fc fc fc fa fa fa fc fc fc fc fc fa 0x0c087fff8d50: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x0c087fff8d60: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x0c087fff8d70: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x0c087fff8d80: fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa fa 0x0c087fff8d90: 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 ==29384==ABORTING * DONE Status: 1 ERROR