R Under development (unstable) (2019-11-18 r77434) -- "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:47:43: runtime error: member call on address 0x60300001ec40 which does not point to an object of type 'CommonFG' 0x60300001ec40: note: object is of type 'H5::H5File' 04 00 80 11 78 ad 3c e1 ea 7f 00 00 28 ae 3c e1 ea 7f 00 00 ff ff ff ff 00 00 00 01 00 00 00 00 ^~~~~~~~~~~~~~~~~~~~~~~ vptr for 'H5::H5File' #0 0x7feae173aab0 in ExistsGroup(Rcpp::XPtr(H5::CommonFG*)), false>, std::__cxx11::basic_string, std::allocator >) /data/gannet/ripley/R/packages/tests-gcc-SAN/h5/src/Group.cpp:47 #1 0x7feae178d612 in h5_ExistsGroup /data/gannet/ripley/R/packages/tests-gcc-SAN/h5/src/RcppExports.cpp:454 #2 0x57880b in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:597 #3 0x6350f9 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7609 #4 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #5 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #6 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #7 0x63be41 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021 #8 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #9 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #10 0x6720f6 in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028 #11 0x7feae6bf0323 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050 #12 0x71f584 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285 #13 0x63aca5 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010 #14 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #15 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #16 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #17 0x63be41 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021 #18 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #19 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #20 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #21 0x6785cd in R_forceAndCall /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1919 #22 0x44a6ca in do_lapply /data/gannet/ripley/R/svn/R-devel/src/main/apply.c:70 #23 0x712e0f in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1377 #24 0x62c5c1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7073 #25 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #26 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #27 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #28 0x63be41 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021 #29 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #30 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #31 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #32 0x63be41 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021 #33 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #34 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #35 0x6720f6 in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028 #36 0x7feae6bf0323 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050 #37 0x71f584 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285 #38 0x63aca5 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010 #39 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #40 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #41 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #42 0x63be41 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021 #43 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #44 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #45 0x6720f6 in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028 #46 0x7feae6bf0323 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050 #47 0x71f584 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285 #48 0x63aca5 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010 #49 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #50 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #51 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #52 0x72090a in R_possible_dispatch /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1618 #53 0x67d8ca in Rf_DispatchOrEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3519 #54 0x819d58 in R_DispatchOrEvalSP /data/gannet/ripley/R/svn/R-devel/src/main/subassign.c:1548 #55 0x819d58 in do_subassign /data/gannet/ripley/R/svn/R-devel/src/main/subassign.c:1570 #56 0x66a1bc in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763 #57 0x676639 in applydefine /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2869 #58 0x66a1bc in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763 #59 0x6e662d in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #60 0x6e662d in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:200 #61 0x6e6d28 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:314 #62 0x6e6e74 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1113 #63 0x419378 in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #64 0x7feaf21ebf42 in __libc_start_main (/lib64/libc.so.6+0x23f42) #65 0x41babd in _start (/data/gannet/ripley/R/gcc-SAN/bin/exec/R+0x41babd) Group.cpp:10:46: runtime error: member call on address 0x60300001ec40 which does not point to an object of type 'CommonFG' 0x60300001ec40: note: object is of type 'H5::H5File' 04 00 80 11 78 ad 3c e1 ea 7f 00 00 28 ae 3c e1 ea 7f 00 00 ff ff ff ff 00 00 00 01 00 00 00 00 ^~~~~~~~~~~~~~~~~~~~~~~ vptr for 'H5::H5File' #0 0x7feae173c8d5 in CreateGroup(Rcpp::XPtr(H5::CommonFG*)), false>, std::__cxx11::basic_string, std::allocator >) /data/gannet/ripley/R/packages/tests-gcc-SAN/h5/src/Group.cpp:10 #1 0x7feae17828b8 in h5_CreateGroup /data/gannet/ripley/R/packages/tests-gcc-SAN/h5/src/RcppExports.cpp:419 #2 0x57880b in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:597 #3 0x6350f9 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7609 #4 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #5 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #6 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #7 0x63be41 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021 #8 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #9 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #10 0x6720f6 in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028 #11 0x7feae6bf0323 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050 #12 0x71f584 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285 #13 0x63aca5 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010 #14 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #15 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #16 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #17 0x63be41 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021 #18 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #19 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #20 0x6720f6 in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028 #21 0x7feae6bf0323 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050 #22 0x71f584 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285 #23 0x63aca5 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010 #24 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #25 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #26 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #27 0x63be41 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021 #28 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #29 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #30 0x6720f6 in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028 #31 0x7feae6bf0323 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050 #32 0x71f584 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285 #33 0x63aca5 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010 #34 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #35 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #36 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #37 0x72090a in R_possible_dispatch /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1618 #38 0x67d8ca in Rf_DispatchOrEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3519 #39 0x819d58 in R_DispatchOrEvalSP /data/gannet/ripley/R/svn/R-devel/src/main/subassign.c:1548 #40 0x819d58 in do_subassign /data/gannet/ripley/R/svn/R-devel/src/main/subassign.c:1570 #41 0x66a1bc in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763 #42 0x676639 in applydefine /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2869 #43 0x66a1bc in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763 #44 0x6e662d in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #45 0x6e662d in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:200 #46 0x6e6d28 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:314 #47 0x6e6e74 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1113 #48 0x419378 in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #49 0x7feaf21ebf42 in __libc_start_main (/lib64/libc.so.6+0x23f42) #50 0x41babd in _start (/data/gannet/ripley/R/gcc-SAN/bin/exec/R+0x41babd) Group.cpp:25:44: runtime error: member call on address 0x60300001ec40 which does not point to an object of type 'CommonFG' 0x60300001ec40: note: object is of type 'H5::H5File' 04 00 80 11 78 ad 3c e1 ea 7f 00 00 28 ae 3c e1 ea 7f 00 00 ff ff ff ff 00 00 00 01 00 00 00 00 ^~~~~~~~~~~~~~~~~~~~~~~ vptr for 'H5::H5File' #0 0x7feae173c035 in OpenGroup(Rcpp::XPtr(H5::CommonFG*)), false>, std::__cxx11::basic_string, std::allocator >) /data/gannet/ripley/R/packages/tests-gcc-SAN/h5/src/Group.cpp:25 #1 0x7feae1783118 in h5_OpenGroup /data/gannet/ripley/R/packages/tests-gcc-SAN/h5/src/RcppExports.cpp:431 #2 0x57880b in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:597 #3 0x6350f9 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7609 #4 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #5 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #6 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #7 0x63be41 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021 #8 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #9 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #10 0x6720f6 in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028 #11 0x7feae6bf0323 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050 #12 0x71f584 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285 #13 0x63aca5 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010 #14 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #15 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #16 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #17 0x63be41 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021 #18 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #19 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #20 0x6720f6 in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028 #21 0x7feae6bf0323 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050 #22 0x71f584 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285 #23 0x63aca5 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010 #24 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #25 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #26 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #27 0x63be41 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021 #28 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #29 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #30 0x6720f6 in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028 #31 0x7feae6bf0323 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050 #32 0x71f584 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285 #33 0x63aca5 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010 #34 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #35 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #36 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #37 0x72090a in R_possible_dispatch /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1618 #38 0x67d8ca in Rf_DispatchOrEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3519 #39 0x819d58 in R_DispatchOrEvalSP /data/gannet/ripley/R/svn/R-devel/src/main/subassign.c:1548 #40 0x819d58 in do_subassign /data/gannet/ripley/R/svn/R-devel/src/main/subassign.c:1570 #41 0x66a1bc in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763 #42 0x676639 in applydefine /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2869 #43 0x66a1bc in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763 #44 0x6e662d in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #45 0x6e662d in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:200 #46 0x6e6d28 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:314 #47 0x6e6e74 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1113 #48 0x419378 in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #49 0x7feaf21ebf42 in __libc_start_main (/lib64/libc.so.6+0x23f42) #50 0x41babd in _start (/data/gannet/ripley/R/gcc-SAN/bin/exec/R+0x41babd) Group.cpp:95:36: runtime error: member call on address 0x60300001f8a0 which does not point to an object of type 'CommonFG' 0x60300001f8a0: note: object is of type 'H5::Group' 04 00 80 6a 78 ac 3c e1 ea 7f 00 00 28 ad 3c e1 ea 7f 00 00 01 00 00 02 be be be be 00 00 00 00 ^~~~~~~~~~~~~~~~~~~~~~~ vptr for 'H5::Group' #0 0x7feae173e541 in GetDataSetNames(Rcpp::XPtr(H5::CommonFG*)), false>, std::__cxx11::basic_string, std::allocator >, bool) /data/gannet/ripley/R/packages/tests-gcc-SAN/h5/src/Group.cpp:95 #1 0x7feae1787486 in h5_GetDataSetNames /data/gannet/ripley/R/packages/tests-gcc-SAN/h5/src/RcppExports.cpp:480 #2 0x5787c0 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:600 #3 0x6350f9 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7609 #4 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #5 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #6 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #7 0x63be41 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021 #8 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #9 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #10 0x6720f6 in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028 #11 0x7feae6bf0323 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050 #12 0x71f584 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285 #13 0x63aca5 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010 #14 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #15 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #16 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #17 0x63be41 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021 #18 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #19 0x66b692 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:516 #20 0x66c0f7 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5086 #21 0x66c0f7 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5127 #22 0x632498 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6805 #23 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #24 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #25 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #26 0x63be41 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021 #27 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #28 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #29 0x6720f6 in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028 #30 0x7feae6bf0323 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050 #31 0x71f584 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285 #32 0x63aca5 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010 #33 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #34 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #35 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #36 0x63be41 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021 #37 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #38 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #39 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #40 0x669cc8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:811 #41 0x677681 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2919 #42 0x66a1bc in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763 #43 0x673a38 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2470 #44 0x66a1bc in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763 #45 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #46 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #47 0x63be41 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021 #48 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #49 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #50 0x6720f6 in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028 #51 0x7feae6bf0323 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050 #52 0x71f584 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285 #53 0x63aca5 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010 #54 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #55 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #56 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #57 0x669cc8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:811 #58 0x673a38 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2470 #59 0x66a1bc in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763 #60 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #61 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #62 0x63be41 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021 #63 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #64 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #65 0x6720f6 in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028 #66 0x7feae6bf0323 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050 #67 0x71f584 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285 #68 0x63aca5 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010 #69 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #70 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #71 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #72 0x63be41 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021 #73 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #74 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #75 0x6720f6 in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028 #76 0x7feae6bf0323 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050 #77 0x71f584 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285 #78 0x63aca5 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010 #79 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #80 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #81 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #82 0x72090a in R_possible_dispatch /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1618 #83 0x67d8ca in Rf_DispatchOrEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3519 #84 0x819d58 in R_DispatchOrEvalSP /data/gannet/ripley/R/svn/R-devel/src/main/subassign.c:1548 #85 0x819d58 in do_subassign /data/gannet/ripley/R/svn/R-devel/src/main/subassign.c:1570 #86 0x66a1bc in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763 #87 0x676639 in applydefine /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2869 #88 0x66a1bc in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763 #89 0x6e662d in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #90 0x6e662d in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:200 #91 0x6e6d28 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:314 #92 0x6e6e74 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1113 #93 0x419378 in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #94 0x7feaf21ebf42 in __libc_start_main (/lib64/libc.so.6+0x23f42) #95 0x41babd in _start (/data/gannet/ripley/R/gcc-SAN/bin/exec/R+0x41babd) Dataset.cpp:121:43: runtime error: member call on address 0x60300001f8a0 which does not point to an object of type 'CommonFG' 0x60300001f8a0: note: object is of type 'H5::Group' 04 00 80 6a 78 ac 3c e1 ea 7f 00 00 28 ad 3c e1 ea 7f 00 00 01 00 00 02 be be be be 00 00 00 00 ^~~~~~~~~~~~~~~~~~~~~~~ vptr for 'H5::Group' #0 0x7feae1703a3f in CreateDataset(Rcpp::XPtr(H5::CommonFG*)), false>, std::__cxx11::basic_string, std::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-gcc-SAN/h5/src/Dataset.cpp:121 #1 0x7feae1785f6f in h5_CreateDataset /data/gannet/ripley/R/packages/tests-gcc-SAN/h5/src/RcppExports.cpp:247 #2 0x578557 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:620 #3 0x6350f9 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7609 #4 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #5 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #6 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #7 0x63be41 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021 #8 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #9 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #10 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #11 0x669cc8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:811 #12 0x677681 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2919 #13 0x66a1bc in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763 #14 0x673a38 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2470 #15 0x66a1bc in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763 #16 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #17 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #18 0x63be41 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021 #19 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #20 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #21 0x6720f6 in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028 #22 0x7feae6bf0323 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050 #23 0x71f584 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285 #24 0x63aca5 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010 #25 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #26 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #27 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #28 0x669cc8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:811 #29 0x673a38 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2470 #30 0x66a1bc in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763 #31 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #32 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #33 0x63be41 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021 #34 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #35 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #36 0x6720f6 in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028 #37 0x7feae6bf0323 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050 #38 0x71f584 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285 #39 0x63aca5 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010 #40 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #41 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #42 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #43 0x63be41 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021 #44 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #45 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #46 0x6720f6 in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028 #47 0x7feae6bf0323 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050 #48 0x71f584 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285 #49 0x63aca5 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010 #50 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #51 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #52 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #53 0x72090a in R_possible_dispatch /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1618 #54 0x67d8ca in Rf_DispatchOrEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3519 #55 0x819d58 in R_DispatchOrEvalSP /data/gannet/ripley/R/svn/R-devel/src/main/subassign.c:1548 #56 0x819d58 in do_subassign /data/gannet/ripley/R/svn/R-devel/src/main/subassign.c:1570 #57 0x66a1bc in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763 #58 0x676639 in applydefine /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2869 #59 0x66a1bc in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763 #60 0x6e662d in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #61 0x6e662d in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:200 #62 0x6e6d28 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:314 #63 0x6e6e74 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1113 #64 0x419378 in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #65 0x7feaf21ebf42 in __libc_start_main (/lib64/libc.so.6+0x23f42) #66 0x41babd in _start (/data/gannet/ripley/R/gcc-SAN/bin/exec/R+0x41babd) > # 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:144:59: runtime error: member call on address 0x603000021100 which does not point to an object of type 'CommonFG' 0x603000021100: note: object is of type 'H5::Group' 04 00 80 6a 78 ac 3c e1 ea 7f 00 00 28 ad 3c e1 ea 7f 00 00 02 00 00 02 be be be be 00 00 00 00 ^~~~~~~~~~~~~~~~~~~~~~~ vptr for 'H5::Group' #0 0x7feae16f8ba5 in OpenDataset(Rcpp::XPtr(H5::CommonFG*)), false>, std::__cxx11::basic_string, std::allocator >) /data/gannet/ripley/R/packages/tests-gcc-SAN/h5/src/Dataset.cpp:144 #1 0x7feae1780cc8 in h5_OpenDataset /data/gannet/ripley/R/packages/tests-gcc-SAN/h5/src/RcppExports.cpp:259 #2 0x57880b in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:597 #3 0x6350f9 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7609 #4 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #5 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #6 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #7 0x63be41 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021 #8 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #9 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #10 0x6720f6 in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028 #11 0x7feae6bf0323 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050 #12 0x71f584 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285 #13 0x63aca5 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010 #14 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #15 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #16 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #17 0x63be41 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021 #18 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #19 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #20 0x6720f6 in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028 #21 0x7feae6bf0323 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050 #22 0x71f584 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285 #23 0x63aca5 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010 #24 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #25 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #26 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #27 0x72090a in R_possible_dispatch /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1618 #28 0x67d8ca in Rf_DispatchOrEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3519 #29 0x837458 in R_DispatchOrEvalSP /data/gannet/ripley/R/svn/R-devel/src/main/subset.c:633 #30 0x837458 in do_subset /data/gannet/ripley/R/svn/R-devel/src/main/subset.c:652 #31 0x66a1bc in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763 #32 0x677681 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2919 #33 0x66a1bc in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763 #34 0x6e662d in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #35 0x6e662d in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:200 #36 0x6e6d28 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:314 #37 0x6e6e74 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1113 #38 0x419378 in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #39 0x7feaf21ebf42 in __libc_start_main (/lib64/libc.so.6+0x23f42) #40 0x41babd in _start (/data/gannet/ripley/R/gcc-SAN/bin/exec/R+0x41babd) > 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:68:28: runtime error: member call on address 0x6030000233e0 which does not point to an object of type 'CommonFG' 0x6030000233e0: note: object is of type 'H5::H5File' 04 00 80 11 78 ad 3c e1 ea 7f 00 00 28 ae 3c e1 ea 7f 00 00 ff ff ff ff 00 00 00 01 00 00 00 00 ^~~~~~~~~~~~~~~~~~~~~~~ vptr for 'H5::H5File' #0 0x7feae173d54d in GetGroupNames(Rcpp::XPtr(H5::CommonFG*)), false>, std::__cxx11::basic_string, std::allocator >, bool) /data/gannet/ripley/R/packages/tests-gcc-SAN/h5/src/Group.cpp:68 #1 0x7feae1786b86 in h5_GetGroupNames /data/gannet/ripley/R/packages/tests-gcc-SAN/h5/src/RcppExports.cpp:467 #2 0x5787c0 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:600 #3 0x6350f9 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7609 #4 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #5 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #6 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #7 0x63be41 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021 #8 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #9 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #10 0x6720f6 in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028 #11 0x7feae6bf0323 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050 #12 0x71f584 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285 #13 0x63aca5 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010 #14 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #15 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #16 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #17 0x63be41 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021 #18 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #19 0x66b692 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:516 #20 0x669a40 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:724 #21 0x71a235 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:563 #22 0x62c5c1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7073 #23 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #24 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #25 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #26 0x63be41 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021 #27 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #28 0x66b692 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:516 #29 0x669a40 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:724 #30 0x677dd4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2978 #31 0x712ed6 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1373 #32 0x63aead in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7016 #33 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #34 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #35 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #36 0x63be41 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021 #37 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #38 0x66b692 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:516 #39 0x669a40 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:724 #40 0x64ba51 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6969 #41 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #42 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #43 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #44 0x63be41 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021 #45 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #46 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #47 0x6720f6 in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028 #48 0x7feae6bf0323 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050 #49 0x71f584 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285 #50 0x63aca5 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010 #51 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #52 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #53 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #54 0x669cc8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:811 #55 0x768faf in PrintObjectS4 /data/gannet/ripley/R/svn/R-devel/src/main/print.c:339 #56 0x768faf in PrintObject /data/gannet/ripley/R/svn/R-devel/src/main/print.c:374 #57 0x772492 in Rf_PrintValueEnv /data/gannet/ripley/R/svn/R-devel/src/main/print.c:1025 #58 0x6e6751 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:268 #59 0x6e6751 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:200 #60 0x6e6d28 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:314 #61 0x6e6e74 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1113 #62 0x419378 in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #63 0x7feaf21ebf42 in __libc_start_main (/lib64/libc.so.6+0x23f42) #64 0x41babd in _start (/data/gannet/ripley/R/gcc-SAN/bin/exec/R+0x41babd) Attribute.cpp:180:29: runtime error: member call on address 0x6030000233e0 which does not point to an object of type 'CommonFG' 0x6030000233e0: note: object is of type 'H5::H5File' 04 00 80 11 78 ad 3c e1 ea 7f 00 00 28 ae 3c e1 ea 7f 00 00 ff ff ff ff 00 00 00 01 00 00 00 00 ^~~~~~~~~~~~~~~~~~~~~~~ vptr for 'H5::H5File' #0 0x7feae16c57e4 in GetAttributeNames_CommonFG(Rcpp::XPtr(H5::CommonFG*)), false>) /data/gannet/ripley/R/packages/tests-gcc-SAN/h5/src/Attribute.cpp:180 #1 0x7feae1778fc6 in h5_GetAttributeNames_CommonFG /data/gannet/ripley/R/packages/tests-gcc-SAN/h5/src/RcppExports.cpp:156 #2 0x57952f in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:594 #3 0x6350f9 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7609 #4 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #5 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #6 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #7 0x63be41 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021 #8 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #9 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #10 0x6720f6 in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028 #11 0x7feae6bf0323 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050 #12 0x71f584 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285 #13 0x63aca5 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010 #14 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #15 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #16 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #17 0x63be41 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021 #18 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #19 0x66b692 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:516 #20 0x669a40 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:724 #21 0x71a235 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:563 #22 0x62c5c1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7073 #23 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #24 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #25 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #26 0x63be41 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021 #27 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #28 0x66b692 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:516 #29 0x669a40 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:724 #30 0x677dd4 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2978 #31 0x712ed6 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1373 #32 0x63aead in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7016 #33 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #34 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #35 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #36 0x63be41 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021 #37 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #38 0x66b692 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:516 #39 0x669a40 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:724 #40 0x64ba51 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6969 #41 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #42 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #43 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #44 0x63be41 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021 #45 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #46 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #47 0x6720f6 in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028 #48 0x7feae6bf0323 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050 #49 0x71f584 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285 #50 0x63aca5 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010 #51 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #52 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #53 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #54 0x669cc8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:811 #55 0x768faf in PrintObjectS4 /data/gannet/ripley/R/svn/R-devel/src/main/print.c:339 #56 0x768faf in PrintObject /data/gannet/ripley/R/svn/R-devel/src/main/print.c:374 #57 0x772492 in Rf_PrintValueEnv /data/gannet/ripley/R/svn/R-devel/src/main/print.c:1025 #58 0x6e6751 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:268 #59 0x6e6751 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:200 #60 0x6e6d28 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:314 #61 0x6e6e74 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1113 #62 0x419378 in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #63 0x7feaf21ebf42 in __libc_start_main (/lib64/libc.so.6+0x23f42) #64 0x41babd in _start (/data/gannet/ripley/R/gcc-SAN/bin/exec/R+0x41babd) + 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:92:34: runtime error: member call on address 0x603000024eb0 which does not point to an object of type 'CommonFG' 0x603000024eb0: note: object is of type 'H5::H5File' 04 00 80 11 78 ad 3c e1 ea 7f 00 00 28 ae 3c e1 ea 7f 00 00 ff ff ff ff 00 00 00 01 00 00 00 00 ^~~~~~~~~~~~~~~~~~~~~~~ vptr for 'H5::H5File' #0 0x7feae173e5ea in GetDataSetNames(Rcpp::XPtr(H5::CommonFG*)), false>, std::__cxx11::basic_string, std::allocator >, bool) /data/gannet/ripley/R/packages/tests-gcc-SAN/h5/src/Group.cpp:92 #1 0x7feae1787486 in h5_GetDataSetNames /data/gannet/ripley/R/packages/tests-gcc-SAN/h5/src/RcppExports.cpp:480 #2 0x5787c0 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:600 #3 0x6350f9 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7609 #4 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #5 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #6 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #7 0x63be41 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021 #8 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #9 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #10 0x6720f6 in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028 #11 0x7feae6bf0323 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050 #12 0x71f584 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285 #13 0x63aca5 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010 #14 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #15 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #16 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #17 0x669cc8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:811 #18 0x66b692 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:516 #19 0x66c0f7 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5086 #20 0x66c0f7 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5127 #21 0x632498 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6805 #22 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #23 0x66b692 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:516 #24 0x66c0f7 in FORCE_PROMISE /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5086 #25 0x66c0f7 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5127 #26 0x632498 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6805 #27 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #28 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #29 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #30 0x63be41 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021 #31 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #32 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #33 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #34 0x669cc8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:811 #35 0x6e662d in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #36 0x6e662d in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:200 #37 0x6e6d28 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:314 #38 0x6e6e74 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1113 #39 0x419378 in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #40 0x7feaf21ebf42 in __libc_start_main (/lib64/libc.so.6+0x23f42) #41 0x41babd in _start (/data/gannet/ripley/R/gcc-SAN/bin/exec/R+0x41babd) /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:65:27: runtime error: member call on address 0x603000024eb0 which does not point to an object of type 'CommonFG' 0x603000024eb0: note: object is of type 'H5::H5File' 04 00 80 11 78 ad 3c e1 ea 7f 00 00 28 ae 3c e1 ea 7f 00 00 ff ff ff ff 00 00 00 01 00 00 00 00 ^~~~~~~~~~~~~~~~~~~~~~~ vptr for 'H5::H5File' #0 0x7feae173d61e in GetGroupNames(Rcpp::XPtr(H5::CommonFG*)), false>, std::__cxx11::basic_string, std::allocator >, bool) /data/gannet/ripley/R/packages/tests-gcc-SAN/h5/src/Group.cpp:65 #1 0x7feae1786b86 in h5_GetGroupNames /data/gannet/ripley/R/packages/tests-gcc-SAN/h5/src/RcppExports.cpp:467 #2 0x5787c0 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:600 #3 0x6350f9 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7609 #4 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #5 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #6 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #7 0x63be41 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021 #8 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #9 0x66b692 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:516 #10 0x669a40 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:724 #11 0x64ba51 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6969 #12 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #13 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #14 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #15 0x63be41 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021 #16 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #17 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #18 0x6720f6 in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2028 #19 0x7feae6bf0323 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1050 #20 0x71f584 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1285 #21 0x63aca5 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7010 #22 0x66987f in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:688 #23 0x66ec75 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1852 #24 0x671394 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1778 #25 0x63be41 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7021 #26 0x67f3b5 in R_compileAndExecute /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1479 #27 0x67fc69 in do_for /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2259 #28 0x66a1bc in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:763 #29 0x6e662d in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #30 0x6e662d in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:200 #31 0x6e6d28 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:314 #32 0x6e6e74 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1113 #33 0x419378 in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #34 0x7feaf21ebf42 in __libc_start_main (/lib64/libc.so.6+0x23f42) #35 0x41babd in _start (/data/gannet/ripley/R/gcc-SAN/bin/exec/R+0x41babd) > 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) > > > > ### *