R Under development (unstable) (2019-11-20 r77445) -- "Unsuffered Consequences" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > pkgname <- "h5" > source(file.path(R.home("share"), "R", "examples-header.R")) > options(warn = 1) > library('h5') > > base::assign(".oldSearch", base::search(), pos = 'CheckExEnv') > base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv') > cleanEx() > nameEx("CommonFG") > ### * CommonFG > > flush(stderr()); flush(stdout()) > > ### Name: CommonFG > ### Title: The CommonFG Class > ### Aliases: CommonFG CommonFG-class h5close > ### [,CommonFG,character,ANY-method [<-,CommonFG,character,ANY-method > ### h5unlink h5unlink,CommonFG,character-method > > ### ** Examples > > file <- h5file("test.h5") > # Create new DataSet 'testset' in H5Group 'testgroup' > file["testgroup/testset"] <- matrix(1:9, nrow = 3) Group.cpp:47:35: runtime error: member call on address 0x60300001f690 which does not point to an object of type 'H5::CommonFG' 0x60300001f690: note: object is of type 'H5::H5File' 34 00 00 28 f0 2e e2 23 31 7f 00 00 40 2f e2 23 31 7f 00 00 ff ff ff ff ff ff ff ff 00 00 00 00 ^~~~~~~~~~~~~~~~~~~~~~~ vptr for 'H5::H5File' #0 0x7f3123f1db65 in ExistsGroup(Rcpp::XPtr(H5::CommonFG*)), false>, std::__1::basic_string, std::__1::allocator >) /data/gannet/ripley/R/packages/tests-clang-SAN/h5/src/Group.cpp:47:35 #1 0x7f3123f4d3fd in h5_ExistsGroup /data/gannet/ripley/R/packages/tests-clang-SAN/h5/src/RcppExports.cpp:454:34 #2 0x6ef9fb in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:597:17 #3 0x8589b1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7609:21 #4 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #5 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #6 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #7 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #8 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #9 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #10 0x8a414d in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028:11 #11 0x7f31296b0bd3 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050:19 #12 0x9d97dc in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285:13 #13 0x842f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010:12 #14 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #15 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #16 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #17 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #18 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #19 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #20 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #21 0x8a2973 in R_forceAndCall /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1919:8 #22 0x52368e in do_lapply /data/gannet/ripley/R/svn/R-devel/src/main/apply.c:70:8 #23 0x9c43ad in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1377:11 #24 0x84d77b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7073:15 #25 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #26 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #27 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #28 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #29 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #30 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #31 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #32 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #33 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #34 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #35 0x8a414d in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028:11 #36 0x7f31296b0bd3 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050:19 #37 0x9d97dc in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285:13 #38 0x842f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010:12 #39 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #40 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #41 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #42 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #43 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #44 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #45 0x8a414d in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028:11 #46 0x7f31296b0bd3 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050:19 #47 0x9d97dc in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285:13 #48 0x842f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010:12 #49 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #50 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #51 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #52 0x9db9dc in R_possible_dispatch /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1618:10 #53 0x8b5d62 in Rf_DispatchOrEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3519:14 #54 0xb65eb7 in R_DispatchOrEvalSP /data/gannet/ripley/R/svn/R-devel/src/main/subassign.c:1548:16 #55 0xb6593a in do_subassign /data/gannet/ripley/R/svn/R-devel/src/main/subassign.c:1570:8 #56 0x83d51a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763:12 #57 0x8ae895 in applydefine /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2869:18 #58 0x8ae895 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2929:9 #59 0x83d51a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763:12 #60 0x975bb6 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264:2 #61 0x97a130 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:314:11 #62 0x979f15 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1113:5 #63 0x4da35a in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #64 0x7f3134f0ff42 in __libc_start_main (/lib64/libc.so.6+0x23f42) #65 0x43036d in _start (/data/gannet/ripley/R/R-clang-SAN/bin/exec/R+0x43036d) SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior Group.cpp:47:35 in Group.cpp:10:38: runtime error: member call on address 0x60300001f690 which does not point to an object of type 'H5::CommonFG' 0x60300001f690: note: object is of type 'H5::H5File' 34 00 00 28 f0 2e e2 23 31 7f 00 00 40 2f e2 23 31 7f 00 00 ff ff ff ff ff ff ff ff 00 00 00 00 ^~~~~~~~~~~~~~~~~~~~~~~ vptr for 'H5::H5File' #0 0x7f3123f1c9b4 in CreateGroup(Rcpp::XPtr(H5::CommonFG*)), false>, std::__1::basic_string, std::__1::allocator >) /data/gannet/ripley/R/packages/tests-clang-SAN/h5/src/Group.cpp:10:38 #1 0x7f3123f4bd19 in h5_CreateGroup /data/gannet/ripley/R/packages/tests-clang-SAN/h5/src/RcppExports.cpp:419:34 #2 0x6ef9fb in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:597:17 #3 0x8589b1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7609:21 #4 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #5 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #6 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #7 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #8 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #9 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #10 0x8a414d in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028:11 #11 0x7f31296b0bd3 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050:19 #12 0x9d97dc in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285:13 #13 0x842f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010:12 #14 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #15 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #16 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #17 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #18 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #19 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #20 0x8a414d in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028:11 #21 0x7f31296b0bd3 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050:19 #22 0x9d97dc in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285:13 #23 0x842f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010:12 #24 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #25 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #26 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #27 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #28 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #29 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #30 0x8a414d in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028:11 #31 0x7f31296b0bd3 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050:19 #32 0x9d97dc in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285:13 #33 0x842f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010:12 #34 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #35 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #36 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #37 0x9db9dc in R_possible_dispatch /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1618:10 #38 0x8b5d62 in Rf_DispatchOrEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3519:14 #39 0xb65eb7 in R_DispatchOrEvalSP /data/gannet/ripley/R/svn/R-devel/src/main/subassign.c:1548:16 #40 0xb6593a in do_subassign /data/gannet/ripley/R/svn/R-devel/src/main/subassign.c:1570:8 #41 0x83d51a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763:12 #42 0x8ae895 in applydefine /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2869:18 #43 0x8ae895 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2929:9 #44 0x83d51a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763:12 #45 0x975bb6 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264:2 #46 0x97a130 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:314:11 #47 0x979f15 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1113:5 #48 0x4da35a in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #49 0x7f3134f0ff42 in __libc_start_main (/lib64/libc.so.6+0x23f42) #50 0x43036d in _start (/data/gannet/ripley/R/R-clang-SAN/bin/exec/R+0x43036d) SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior Group.cpp:10:38 in Group.cpp:25:36: runtime error: member call on address 0x60300001f690 which does not point to an object of type 'H5::CommonFG' 0x60300001f690: note: object is of type 'H5::H5File' 34 00 00 28 f0 2e e2 23 31 7f 00 00 40 2f e2 23 31 7f 00 00 ff ff ff ff ff ff ff ff 00 00 00 00 ^~~~~~~~~~~~~~~~~~~~~~~ vptr for 'H5::H5File' #0 0x7f3123f1d1bf in OpenGroup(Rcpp::XPtr(H5::CommonFG*)), false>, std::__1::basic_string, std::__1::allocator >) /data/gannet/ripley/R/packages/tests-clang-SAN/h5/src/Group.cpp:25:36 #1 0x7f3123f4c509 in h5_OpenGroup /data/gannet/ripley/R/packages/tests-clang-SAN/h5/src/RcppExports.cpp:431:34 #2 0x6ef9fb in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:597:17 #3 0x8589b1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7609:21 #4 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #5 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #6 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #7 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #8 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #9 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #10 0x8a414d in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028:11 #11 0x7f31296b0bd3 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050:19 #12 0x9d97dc in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285:13 #13 0x842f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010:12 #14 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #15 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #16 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #17 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #18 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #19 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #20 0x8a414d in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028:11 #21 0x7f31296b0bd3 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050:19 #22 0x9d97dc in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285:13 #23 0x842f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010:12 #24 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #25 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #26 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #27 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #28 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #29 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #30 0x8a414d in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028:11 #31 0x7f31296b0bd3 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050:19 #32 0x9d97dc in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285:13 #33 0x842f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010:12 #34 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #35 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #36 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #37 0x9db9dc in R_possible_dispatch /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1618:10 #38 0x8b5d62 in Rf_DispatchOrEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3519:14 #39 0xb65eb7 in R_DispatchOrEvalSP /data/gannet/ripley/R/svn/R-devel/src/main/subassign.c:1548:16 #40 0xb6593a in do_subassign /data/gannet/ripley/R/svn/R-devel/src/main/subassign.c:1570:8 #41 0x83d51a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763:12 #42 0x8ae895 in applydefine /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2869:18 #43 0x8ae895 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2929:9 #44 0x83d51a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763:12 #45 0x975bb6 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264:2 #46 0x97a130 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:314:11 #47 0x979f15 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1113:5 #48 0x4da35a in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #49 0x7f3134f0ff42 in __libc_start_main (/lib64/libc.so.6+0x23f42) #50 0x43036d in _start (/data/gannet/ripley/R/R-clang-SAN/bin/exec/R+0x43036d) SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior Group.cpp:25:36 in Group.cpp:95:28: runtime error: member call on address 0x60300000f280 which does not point to an object of type 'H5::CommonFG' 0x60300000f280: note: object is of type 'H5::Group' 35 00 00 22 30 2e e2 23 31 7f 00 00 80 2e e2 23 31 7f 00 00 01 00 00 00 00 00 00 02 00 00 00 00 ^~~~~~~~~~~~~~~~~~~~~~~ vptr for 'H5::Group' #0 0x7f3123f1ed72 in GetDataSetNames(Rcpp::XPtr(H5::CommonFG*)), false>, std::__1::basic_string, std::__1::allocator >, bool) /data/gannet/ripley/R/packages/tests-clang-SAN/h5/src/Group.cpp:95:28 #1 0x7f3123f4e461 in h5_GetDataSetNames /data/gannet/ripley/R/packages/tests-clang-SAN/h5/src/RcppExports.cpp:480:34 #2 0x6efd0a in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:600:17 #3 0x8589b1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7609:21 #4 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #5 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #6 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #7 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #8 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #9 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #10 0x8a414d in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028:11 #11 0x7f31296b0bd3 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050:19 #12 0x9d97dc in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285:13 #13 0x842f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010:12 #14 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #15 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #16 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #17 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #18 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #19 0x89bf9d in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:516:8 #20 0x8cf902 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5086:15 #21 0x8cf902 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5127:14 #22 0x86e7a9 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6805:20 #23 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #24 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #25 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #26 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #27 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #28 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #29 0x8a414d in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028:11 #30 0x7f31296b0bd3 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050:19 #31 0x9d97dc in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285:13 #32 0x842f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010:12 #33 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #34 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #35 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #36 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #37 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #38 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #39 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #40 0x83dd99 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:811:12 #41 0x8aece7 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2919:8 #42 0x83d51a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763:12 #43 0x8abc72 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2470:10 #44 0x83d51a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763:12 #45 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #46 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #47 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #48 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #49 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #50 0x8a414d in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028:11 #51 0x7f31296b0bd3 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050:19 #52 0x9d97dc in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285:13 #53 0x842f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010:12 #54 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #55 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #56 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #57 0x83dd99 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:811:12 #58 0x8abc72 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2470:10 #59 0x83d51a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763:12 #60 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #61 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #62 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #63 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #64 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #65 0x8a414d in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028:11 #66 0x7f31296b0bd3 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050:19 #67 0x9d97dc in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285:13 #68 0x842f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010:12 #69 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #70 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #71 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #72 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #73 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #74 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #75 0x8a414d in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028:11 #76 0x7f31296b0bd3 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050:19 #77 0x9d97dc in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285:13 #78 0x842f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010:12 #79 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #80 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #81 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #82 0x9db9dc in R_possible_dispatch /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1618:10 #83 0x8b5d62 in Rf_DispatchOrEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3519:14 #84 0xb65eb7 in R_DispatchOrEvalSP /data/gannet/ripley/R/svn/R-devel/src/main/subassign.c:1548:16 #85 0xb6593a in do_subassign /data/gannet/ripley/R/svn/R-devel/src/main/subassign.c:1570:8 #86 0x83d51a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763:12 #87 0x8ae895 in applydefine /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2869:18 #88 0x8ae895 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2929:9 #89 0x83d51a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763:12 #90 0x975bb6 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264:2 #91 0x97a130 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:314:11 #92 0x979f15 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1113:5 #93 0x4da35a in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #94 0x7f3134f0ff42 in __libc_start_main (/lib64/libc.so.6+0x23f42) #95 0x43036d in _start (/data/gannet/ripley/R/R-clang-SAN/bin/exec/R+0x43036d) SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior Group.cpp:95:28 in /usr/local/bin/../include/c++/v1/memory:1825:35: runtime error: nan is outside the range of representable values of type 'unsigned long long' #0 0x7f3123ef2c5d in void std::__1::allocator::construct(unsigned long long*, double&) /usr/local/bin/../include/c++/v1/memory:1825:35 #1 0x7f3123ef2c5d in void std::__1::allocator_traits >::__construct(std::__1::integral_constant, std::__1::allocator&, unsigned long long*, double&) /usr/local/bin/../include/c++/v1/memory:1717:18 #2 0x7f3123ef2c5d in void std::__1::allocator_traits >::construct(std::__1::allocator&, unsigned long long*, double&) /usr/local/bin/../include/c++/v1/memory:1560:14 #3 0x7f3123ef2765 in void std::__1::allocator_traits >::__construct_range_forward(std::__1::allocator&, double*, double*, unsigned long long*&) /usr/local/bin/../include/c++/v1/memory:1645:17 #4 0x7f3123ef201b in std::__1::enable_if<__is_forward_iterator::value, void>::type std::__1::vector >::__construct_at_end(double*, double*, unsigned long) /usr/local/bin/../include/c++/v1/vector:1074:5 #5 0x7f3123eee0b3 in std::__1::vector >::vector(double*, std::__1::enable_if<(__is_forward_iterator::value) && (is_constructible::reference>::value), double*>::type) /usr/local/bin/../include/c++/v1/vector:1222:9 #6 0x7f3123f0a5ec in CreateDataset(Rcpp::XPtr(H5::CommonFG*)), false>, std::__1::basic_string, std::__1::allocator >, char, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, int, int) /data/gannet/ripley/R/packages/tests-clang-SAN/h5/src/Dataset.cpp:96:18 #7 0x7f3123f44b58 in h5_CreateDataset /data/gannet/ripley/R/packages/tests-clang-SAN/h5/src/RcppExports.cpp:247:34 #8 0x6f5429 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:620:17 #9 0x8589b1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7609:21 #10 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #11 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #12 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #13 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #14 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #15 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #16 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #17 0x83dd99 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:811:12 #18 0x8aece7 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2919:8 #19 0x83d51a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763:12 #20 0x8abc72 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2470:10 #21 0x83d51a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763:12 #22 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #23 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #24 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #25 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #26 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #27 0x8a414d in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028:11 #28 0x7f31296b0bd3 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050:19 #29 0x9d97dc in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285:13 #30 0x842f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010:12 #31 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #32 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #33 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #34 0x83dd99 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:811:12 #35 0x8abc72 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2470:10 #36 0x83d51a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763:12 #37 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #38 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #39 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #40 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #41 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #42 0x8a414d in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028:11 #43 0x7f31296b0bd3 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050:19 #44 0x9d97dc in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285:13 #45 0x842f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010:12 #46 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #47 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #48 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #49 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #50 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #51 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #52 0x8a414d in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028:11 #53 0x7f31296b0bd3 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050:19 #54 0x9d97dc in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285:13 #55 0x842f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010:12 #56 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #57 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #58 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #59 0x9db9dc in R_possible_dispatch /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1618:10 #60 0x8b5d62 in Rf_DispatchOrEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3519:14 #61 0xb65eb7 in R_DispatchOrEvalSP /data/gannet/ripley/R/svn/R-devel/src/main/subassign.c:1548:16 #62 0xb6593a in do_subassign /data/gannet/ripley/R/svn/R-devel/src/main/subassign.c:1570:8 #63 0x83d51a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763:12 #64 0x8ae895 in applydefine /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2869:18 #65 0x8ae895 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2929:9 #66 0x83d51a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763:12 #67 0x975bb6 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264:2 #68 0x97a130 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:314:11 #69 0x979f15 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1113:5 #70 0x4da35a in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #71 0x7f3134f0ff42 in __libc_start_main (/lib64/libc.so.6+0x23f42) #72 0x43036d in _start (/data/gannet/ripley/R/R-clang-SAN/bin/exec/R+0x43036d) SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior /usr/local/bin/../include/c++/v1/memory:1825:35 in Dataset.cpp:121:35: runtime error: member call on address 0x60300000f280 which does not point to an object of type 'H5::CommonFG' 0x60300000f280: note: object is of type 'H5::Group' 35 00 00 22 30 2e e2 23 31 7f 00 00 80 2e e2 23 31 7f 00 00 01 00 00 00 00 00 00 02 00 00 00 00 ^~~~~~~~~~~~~~~~~~~~~~~ vptr for 'H5::Group' #0 0x7f3123f0b1a3 in CreateDataset(Rcpp::XPtr(H5::CommonFG*)), false>, std::__1::basic_string, std::__1::allocator >, char, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, int, int) /data/gannet/ripley/R/packages/tests-clang-SAN/h5/src/Dataset.cpp:121:35 #1 0x7f3123f44b58 in h5_CreateDataset /data/gannet/ripley/R/packages/tests-clang-SAN/h5/src/RcppExports.cpp:247:34 #2 0x6f5429 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:620:17 #3 0x8589b1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7609:21 #4 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #5 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #6 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #7 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #8 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #9 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #10 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #11 0x83dd99 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:811:12 #12 0x8aece7 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2919:8 #13 0x83d51a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763:12 #14 0x8abc72 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2470:10 #15 0x83d51a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763:12 #16 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #17 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #18 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #19 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #20 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #21 0x8a414d in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028:11 #22 0x7f31296b0bd3 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050:19 #23 0x9d97dc in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285:13 #24 0x842f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010:12 #25 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #26 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #27 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #28 0x83dd99 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:811:12 #29 0x8abc72 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2470:10 #30 0x83d51a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763:12 #31 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #32 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #33 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #34 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #35 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #36 0x8a414d in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028:11 #37 0x7f31296b0bd3 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050:19 #38 0x9d97dc in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285:13 #39 0x842f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010:12 #40 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #41 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #42 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #43 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #44 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #45 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #46 0x8a414d in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028:11 #47 0x7f31296b0bd3 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050:19 #48 0x9d97dc in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285:13 #49 0x842f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010:12 #50 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #51 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #52 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #53 0x9db9dc in R_possible_dispatch /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1618:10 #54 0x8b5d62 in Rf_DispatchOrEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3519:14 #55 0xb65eb7 in R_DispatchOrEvalSP /data/gannet/ripley/R/svn/R-devel/src/main/subassign.c:1548:16 #56 0xb6593a in do_subassign /data/gannet/ripley/R/svn/R-devel/src/main/subassign.c:1570:8 #57 0x83d51a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763:12 #58 0x8ae895 in applydefine /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2869:18 #59 0x8ae895 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2929:9 #60 0x83d51a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763:12 #61 0x975bb6 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264:2 #62 0x97a130 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:314:11 #63 0x979f15 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1113:5 #64 0x4da35a in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #65 0x7f3134f0ff42 in __libc_start_main (/lib64/libc.so.6+0x23f42) #66 0x43036d in _start (/data/gannet/ripley/R/R-clang-SAN/bin/exec/R+0x43036d) SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior Dataset.cpp:121:35 in > # Create new DataSet 'testset2' in file root > file["testset2"] <- 1:10 > # Retrieve H5Group 'testgroup' > group <- file["testgroup"] > # Retrieve DataSet 'testset' > dset <- group["testset"] Dataset.cpp:144:51: runtime error: member call on address 0x603000021ee0 which does not point to an object of type 'H5::CommonFG' 0x603000021ee0: note: object is of type 'H5::Group' 35 00 00 22 30 2e e2 23 31 7f 00 00 80 2e e2 23 31 7f 00 00 05 00 00 00 00 00 00 02 00 00 00 00 ^~~~~~~~~~~~~~~~~~~~~~~ vptr for 'H5::Group' #0 0x7f3123f0bc65 in OpenDataset(Rcpp::XPtr(H5::CommonFG*)), false>, std::__1::basic_string, std::__1::allocator >) /data/gannet/ripley/R/packages/tests-clang-SAN/h5/src/Dataset.cpp:144:51 #1 0x7f3123f454b9 in h5_OpenDataset /data/gannet/ripley/R/packages/tests-clang-SAN/h5/src/RcppExports.cpp:259:34 #2 0x6ef9fb in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:597:17 #3 0x8589b1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7609:21 #4 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #5 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #6 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #7 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #8 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #9 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #10 0x8a414d in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028:11 #11 0x7f31296b0bd3 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050:19 #12 0x9d97dc in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285:13 #13 0x842f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010:12 #14 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #15 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #16 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #17 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #18 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #19 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #20 0x8a414d in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028:11 #21 0x7f31296b0bd3 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050:19 #22 0x9d97dc in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285:13 #23 0x842f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010:12 #24 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #25 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #26 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #27 0x9db9dc in R_possible_dispatch /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1618:10 #28 0x8b5d62 in Rf_DispatchOrEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3519:14 #29 0xba8a07 in R_DispatchOrEvalSP /data/gannet/ripley/R/svn/R-devel/src/main/subset.c:633:16 #30 0xba82cb in do_subset /data/gannet/ripley/R/svn/R-devel/src/main/subset.c:652:8 #31 0x83d51a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763:12 #32 0x8aece7 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2919:8 #33 0x83d51a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763:12 #34 0x975bb6 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264:2 #35 0x97a130 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:314:11 #36 0x979f15 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1113:5 #37 0x4da35a in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #38 0x7f3134f0ff42 in __libc_start_main (/lib64/libc.so.6+0x23f42) #39 0x43036d in _start (/data/gannet/ripley/R/R-clang-SAN/bin/exec/R+0x43036d) SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior Dataset.cpp:144:51 in > h5close(dset) > h5close(group) > h5close(file) > file.remove("test.h5") [1] TRUE > > > > cleanEx() > nameEx("DataSet-Subset") > ### * DataSet-Subset > > flush(stderr()); flush(stdout()) > > ### Name: DataSet-Subset > ### Title: Operators to Subset DataSet Objects > ### Aliases: DataSet-Subset [,DataSet,ANY,ANY-method > ### [,DataSet,missing,missing-method [,DataSet,numeric,missing-method > ### [,DataSet,missing,numeric-method [<-,DataSet,missing,missing-method > ### [<-,DataSet,numeric,missing-method [<-,DataSet,missing,numeric-method > ### [<-,DataSet,ANY,ANY-method > > ### ** Examples > > # Write submatrix to sub-region of DataSet > testmat_n <- matrix(as.integer(1:90), ncol = 9) > file <- h5file("test.h5", "a") > file["testgroup/testmat_n2"] <- testmat_n > submat <- matrix(-1L:-9L, nrow = 3) > dset2 <- file["testgroup/testmat_n2"] > dset2[c(1, 3, 5), c(1, 3, 5)] <- submat > h5close(dset2) > h5close(file) > file.remove("test.h5") [1] TRUE > > > > cleanEx() > nameEx("H5File") > ### * H5File > > flush(stderr()); flush(stdout()) > > ### Name: H5File > ### Title: HDF5 File Objects > ### Aliases: H5File H5File-class h5file h5flush h5flush,H5File-method > ### h5close,H5File-method is.h5file > > ### ** Examples > > # The following examples generates a HDF5 file with the different HDF5 > # Objects and shows its contents: > file <- h5file(name = "test1.h5", mode = "a") > file["testdataset"] <- 1:10 > h5attr(file, "testattrib") <- LETTERS[1:10] > file["testgroup/testdataset2"] <- 1:10 > file H5File 'test1.h5' (mode 'a') Group.cpp:68:20: runtime error: member call on address 0x6030000244c0 which does not point to an object of type 'H5::CommonFG' 0x6030000244c0: note: object is of type 'H5::H5File' 34 00 00 28 f0 2e e2 23 31 7f 00 00 40 2f e2 23 31 7f 00 00 ff ff ff ff ff ff ff ff 02 00 00 00 ^~~~~~~~~~~~~~~~~~~~~~~ vptr for 'H5::H5File' #0 0x7f3123f1e298 in GetGroupNames(Rcpp::XPtr(H5::CommonFG*)), false>, std::__1::basic_string, std::__1::allocator >, bool) /data/gannet/ripley/R/packages/tests-clang-SAN/h5/src/Group.cpp:68:20 #1 0x7f3123f4dc31 in h5_GetGroupNames /data/gannet/ripley/R/packages/tests-clang-SAN/h5/src/RcppExports.cpp:467:34 #2 0x6efd0a in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:600:17 #3 0x8589b1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7609:21 #4 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #5 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #6 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #7 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #8 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #9 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #10 0x8a414d in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028:11 #11 0x7f31296b0bd3 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050:19 #12 0x9d97dc in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285:13 #13 0x842f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010:12 #14 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #15 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #16 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #17 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #18 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #19 0x89bf9d in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:516:8 #20 0x83dbc6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:724:6 #21 0x9ce98e in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:563:2 #22 0x84d77b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7073:15 #23 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #24 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #25 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #26 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #27 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #28 0x89bf9d in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:516:8 #29 0x83dbc6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:724:6 #30 0x89c8c3 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2978:13 #31 0x9c411d in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1373:9 #32 0x85cc45 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7016:12 #33 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #34 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #35 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #36 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #37 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #38 0x89bf9d in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:516:8 #39 0x83dbc6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:724:6 #40 0x85c2c1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6969:16 #41 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #42 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #43 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #44 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #45 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #46 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #47 0x8a414d in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028:11 #48 0x7f31296b0bd3 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050:19 #49 0x9d97dc in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285:13 #50 0x842f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010:12 #51 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #52 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #53 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #54 0x83dd99 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:811:12 #55 0xa43208 in PrintObjectS4 /data/gannet/ripley/R/svn/R-devel/src/main/print.c:339:5 #56 0xa43208 in PrintObject /data/gannet/ripley/R/svn/R-devel/src/main/print.c:374:2 #57 0xa4baf1 in PrintDispatch /data/gannet/ripley/R/svn/R-devel/src/main/print.c:384:2 #58 0xa4baf1 in Rf_PrintValueEnv /data/gannet/ripley/R/svn/R-devel/src/main/print.c:1025:9 #59 0x975c12 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:268:6 #60 0x97a130 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:314:11 #61 0x979f15 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1113:5 #62 0x4da35a in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #63 0x7f3134f0ff42 in __libc_start_main (/lib64/libc.so.6+0x23f42) #64 0x43036d in _start (/data/gannet/ripley/R/R-clang-SAN/bin/exec/R+0x43036d) SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior Group.cpp:68:20 in Attribute.cpp:180:21: runtime error: member call on address 0x6030000244c0 which does not point to an object of type 'H5::CommonFG' 0x6030000244c0: note: object is of type 'H5::H5File' 34 00 00 28 f0 2e e2 23 31 7f 00 00 40 2f e2 23 31 7f 00 00 ff ff ff ff ff ff ff ff 02 00 00 00 ^~~~~~~~~~~~~~~~~~~~~~~ vptr for 'H5::H5File' #0 0x7f3123eecc9e in GetAttributeNames_CommonFG(Rcpp::XPtr(H5::CommonFG*)), false>) /data/gannet/ripley/R/packages/tests-clang-SAN/h5/src/Attribute.cpp:180:21 #1 0x7f3123f410dc in h5_GetAttributeNames_CommonFG /data/gannet/ripley/R/packages/tests-clang-SAN/h5/src/RcppExports.cpp:156:34 #2 0x6f0bea in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:594:17 #3 0x8589b1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7609:21 #4 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #5 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #6 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #7 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #8 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #9 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #10 0x8a414d in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028:11 #11 0x7f31296b0bd3 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050:19 #12 0x9d97dc in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285:13 #13 0x842f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010:12 #14 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #15 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #16 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #17 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #18 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #19 0x89bf9d in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:516:8 #20 0x83dbc6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:724:6 #21 0x9ce98e in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:563:2 #22 0x84d77b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7073:15 #23 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #24 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #25 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #26 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #27 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #28 0x89bf9d in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:516:8 #29 0x83dbc6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:724:6 #30 0x89c8c3 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2978:13 #31 0x9c411d in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1373:9 #32 0x85cc45 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7016:12 #33 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #34 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #35 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #36 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #37 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #38 0x89bf9d in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:516:8 #39 0x83dbc6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:724:6 #40 0x85c2c1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6969:16 #41 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #42 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #43 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #44 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #45 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #46 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #47 0x8a414d in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028:11 #48 0x7f31296b0bd3 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050:19 #49 0x9d97dc in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285:13 #50 0x842f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010:12 #51 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #52 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #53 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #54 0x83dd99 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:811:12 #55 0xa43208 in PrintObjectS4 /data/gannet/ripley/R/svn/R-devel/src/main/print.c:339:5 #56 0xa43208 in PrintObject /data/gannet/ripley/R/svn/R-devel/src/main/print.c:374:2 #57 0xa4baf1 in PrintDispatch /data/gannet/ripley/R/svn/R-devel/src/main/print.c:384:2 #58 0xa4baf1 in Rf_PrintValueEnv /data/gannet/ripley/R/svn/R-devel/src/main/print.c:1025:9 #59 0x975c12 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:268:6 #60 0x97a130 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:314:11 #61 0x979f15 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1113:5 #62 0x4da35a in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #63 0x7f3134f0ff42 in __libc_start_main (/lib64/libc.so.6+0x23f42) #64 0x43036d in _start (/data/gannet/ripley/R/R-clang-SAN/bin/exec/R+0x43036d) SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior Attribute.cpp:180:21 in + testgroup D testdataset A testattrib > # Close file and delete > h5close(file) > if(file.exists("test.h5")) file.remove("test.h5") > > # The following example shows hdf5 file contents and how to use them to iterate over HDF5 elements: > file <- h5file(name = "test2.h5", mode = "a") > file["testgroup1/testset1"] <- 1:10 > file["testgroup2/testset2"] <- 11:20 > file["testgroup3/testset3"] <- 21:30 > > # Extract first 3 elements from each dataset and combine result to matrix > sapply(list.datasets(file, recursive = TRUE), function(x) file[x][1:3]) Group.cpp:92:26: runtime error: member call on address 0x603000026230 which does not point to an object of type 'H5::CommonFG' 0x603000026230: note: object is of type 'H5::H5File' 34 00 00 28 f0 2e e2 23 31 7f 00 00 40 2f e2 23 31 7f 00 00 ff ff ff ff ff ff ff ff 03 00 00 00 ^~~~~~~~~~~~~~~~~~~~~~~ vptr for 'H5::H5File' #0 0x7f3123f1ed47 in GetDataSetNames(Rcpp::XPtr(H5::CommonFG*)), false>, std::__1::basic_string, std::__1::allocator >, bool) /data/gannet/ripley/R/packages/tests-clang-SAN/h5/src/Group.cpp:92:26 #1 0x7f3123f4e461 in h5_GetDataSetNames /data/gannet/ripley/R/packages/tests-clang-SAN/h5/src/RcppExports.cpp:480:34 #2 0x6efd0a in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:600:17 #3 0x8589b1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7609:21 #4 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #5 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #6 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #7 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #8 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #9 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #10 0x8a414d in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028:11 #11 0x7f31296b0bd3 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050:19 #12 0x9d97dc in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285:13 #13 0x842f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010:12 #14 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #15 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #16 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #17 0x83dd99 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:811:12 #18 0x89bf9d in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:516:8 #19 0x8cf902 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5086:15 #20 0x8cf902 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5127:14 #21 0x86e7a9 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6805:20 #22 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #23 0x89bf9d in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:516:8 #24 0x8cf902 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5086:15 #25 0x8cf902 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5127:14 #26 0x86e7a9 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6805:20 #27 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #28 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #29 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #30 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #31 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #32 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #33 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #34 0x83dd99 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:811:12 #35 0x975bb6 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264:2 #36 0x97a130 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:314:11 #37 0x979f15 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1113:5 #38 0x4da35a in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #39 0x7f3134f0ff42 in __libc_start_main (/lib64/libc.so.6+0x23f42) #40 0x43036d in _start (/data/gannet/ripley/R/R-clang-SAN/bin/exec/R+0x43036d) SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior Group.cpp:92:26 in /testgroup1/testset1 /testgroup2/testset2 /testgroup3/testset3 [1,] 1 11 21 [2,] 2 12 22 [3,] 3 13 23 > # Add new dataset to each group in HDF5 file > for(g in list.groups(file)) { + file[paste(g, "testsetx", collapse = "/")] <- 1:10 + } Group.cpp:65:19: runtime error: member call on address 0x603000026230 which does not point to an object of type 'H5::CommonFG' 0x603000026230: note: object is of type 'H5::H5File' 34 00 00 28 f0 2e e2 23 31 7f 00 00 40 2f e2 23 31 7f 00 00 ff ff ff ff ff ff ff ff 03 00 00 00 ^~~~~~~~~~~~~~~~~~~~~~~ vptr for 'H5::H5File' #0 0x7f3123f1e26d in GetGroupNames(Rcpp::XPtr(H5::CommonFG*)), false>, std::__1::basic_string, std::__1::allocator >, bool) /data/gannet/ripley/R/packages/tests-clang-SAN/h5/src/Group.cpp:65:19 #1 0x7f3123f4dc31 in h5_GetGroupNames /data/gannet/ripley/R/packages/tests-clang-SAN/h5/src/RcppExports.cpp:467:34 #2 0x6efd0a in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:600:17 #3 0x8589b1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7609:21 #4 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #5 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #6 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #7 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #8 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #9 0x89bf9d in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:516:8 #10 0x83dbc6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:724:6 #11 0x85c2c1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6969:16 #12 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #13 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #14 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #15 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #16 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #17 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #18 0x8a414d in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028:11 #19 0x7f31296b0bd3 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050:19 #20 0x9d97dc in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285:13 #21 0x842f54 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010:12 #22 0x83cee3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688:8 #23 0x8a11c3 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #24 0x89e50f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778:16 #25 0x85ccc1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021:12 #26 0x8a9fad in R_compileAndExecute /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1479:2 #27 0x8a612b in do_for /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2259:9 #28 0x83d51a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763:12 #29 0x975bb6 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264:2 #30 0x97a130 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:314:11 #31 0x979f15 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1113:5 #32 0x4da35a in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #33 0x7f3134f0ff42 in __libc_start_main (/lib64/libc.so.6+0x23f42) #34 0x43036d in _start (/data/gannet/ripley/R/R-clang-SAN/bin/exec/R+0x43036d) SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior Group.cpp:65:19 in > list.datasets(file, recursive = TRUE) [1] "/testgroup1/testset1" "/testgroup1 testsetx" "/testgroup2/testset2" [4] "/testgroup2 testsetx" "/testgroup3/testset3" "/testgroup3 testsetx" > # Close file > h5close(file) > > > > cleanEx() > nameEx("H5Location-Attribute") > ### * H5Location-Attribute > > flush(stderr()); flush(stdout()) > > ### Name: H5Location-Attribute > ### Title: Read and Create Attributes for H5Location Objects > ### Aliases: H5Location-Attribute H5Location H5Location-class > ### createAttribute createAttribute,H5Location,character-method > ### openAttribute openAttribute,H5Location,character-method h5attr > ### h5attr,H5Location,character-method h5attr<- > ### h5attr<-,H5Location,character-method list.attributes > ### list.attributes,H5Location-method > > ### ** Examples > > # Write Attributes for H5File, H5Group and DataSet > file <- h5file("test.h5") > h5attr(file, "fileattrib") <- 1:10 > group <- file["testgroup"] > h5attr(group, "groupattrib") <- matrix(1:9, nrow = 3) > h5attr(group, "groupattrib") [,1] [,2] [,3] [1,] 1 4 7 [2,] 2 5 8 [3,] 3 6 9 > group["testdataset"] <- 1:10 > dset <- group["testdataset"] > h5attr(dset, "dsetattrib") <- LETTERS[1:10] > h5close(dset) > h5close(group) > h5close(file) > file.remove("test.h5") [1] TRUE > > > > cleanEx() > nameEx("h5-package") > ### * h5-package > > flush(stderr()); flush(stdout()) > > ### Name: h5-package > ### Title: H5 - Interface to the HDF5 API > ### Aliases: h5-package > > ### ** Examples > > # 1. Create/Open file 'test.h5' (mode set to 'a'ppend) > file <- h5file("test.h5", 'a') > > # 2. Store character vector in group '/test' and dataset 'testvec' > file["test/testvec"] <- LETTERS[1:9] > # Store integer matrix in group '/test/testmat' and dataset 'testmat' > mat <- matrix(1:9, nrow = 3) > rownames(mat) <- LETTERS[1:3] > colnames(mat) <- c("A", "BE", "BUU") > file["test/testmat/testmat"] <- mat > # Store numeric array in group '/test' and dataset 'testarray' > file["test/testarray"] <- array(as.numeric(1:45), dim = c(3, 3, 5)) > > # 3. Store rownames and column names of matrix as attributes > # Get created data set as object > dset <- file["test/testmat/testmat"] > # Store rownames in attribute 'dimnames_1' > h5attr(dset, "dimnames_1") <- rownames(mat) > # Store columnnames in attribute 'dimnames_2' > h5attr(dset, "dimnames_2") <- colnames(mat) > > # 4. Read first 3 elements of testvec > testvec <- file["test/testvec"] > testvec[1:3] [1] "A" "B" "C" > # Read first 2 rows of testmat > testmat <- file["test/testmat/testmat"] > res <- testmat[1:2, ] > # attach rownames and columnnames > rownames(res) <- attr(testmat, "rownames")[1:2] > colnames(res) <- attr(testmat, "colnames") > > # 5. Extend testvec > testvec <- c(testvec, LETTERS[10:26]) > # Retrieve entire testvec > testvec[] [1] "A" "B" "C" "D" "E" "F" "G" "H" "I" "J" "K" "L" "M" "N" "O" "P" "Q" "R" "S" [20] "T" "U" "V" "W" "X" "Y" "Z" > > # 6. Close open handles > h5close(testvec) > h5close(testmat) > h5close(file) > > > > ### *