Package check result: ERROR Check: dependencies in R code, Result: NOTE H5I.c:1261:41: runtime error: call to function H5T__close_cb through pointer to incorrect function type 'int (*)(void *)' /home/hornik/tmp/scratch/Rtmp5xR406/R.INSTALL35bf38599e7a40/Rhdf5lib/src/hdf5/src/H5T.c:3848: note: H5T__close_cb defined here #0 0x7fcda5f67191 in H5I_dec_ref /home/hornik/tmp/scratch/Rtmp5xR406/R.INSTALL35bf38599e7a40/Rhdf5lib/src/hdf5/src/H5I.c:1261:41 #1 0x7fcda63339e3 in H5T__path_find_real /home/hornik/tmp/scratch/Rtmp5xR406/R.INSTALL35bf38599e7a40/Rhdf5lib/src/hdf5/src/H5T.c:4842:13 #2 0x7fcda6321faa in H5T__register /home/hornik/tmp/scratch/Rtmp5xR406/R.INSTALL35bf38599e7a40/Rhdf5lib/src/hdf5/src/H5T.c:2333:36 #3 0x7fcda630a3da in H5T__register_int /home/hornik/tmp/scratch/Rtmp5xR406/R.INSTALL35bf38599e7a40/Rhdf5lib/src/hdf5/src/H5T.c:2282:8 #4 0x7fcda630106d in H5T__init_package /home/hornik/tmp/scratch/Rtmp5xR406/R.INSTALL35bf38599e7a40/Rhdf5lib/src/hdf5/src/H5T.c:1048:15 #5 0x7fcda62f9e70 in H5T_init /home/hornik/tmp/scratch/Rtmp5xR406/R.INSTALL35bf38599e7a40/Rhdf5lib/src/hdf5/src/H5T.c:578:5 #6 0x7fcda5b0ee62 in H5_init_library /home/hornik/tmp/scratch/Rtmp5xR406/R.INSTALL35bf38599e7a40/Rhdf5lib/src/hdf5/src/H5.c:218:8 #7 0x7fcda5b1507c in H5open /home/hornik/tmp/scratch/Rtmp5xR406/R.INSTALL35bf38599e7a40/Rhdf5lib/src/hdf5/src/H5.c:930:5 #8 0x7fcda5a93476 in H5::FileAccPropList::getConstant() /home/hornik/tmp/scratch/Rtmp5xR406/R.INSTALL35bf38599e7a40/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp:66:40 #9 0x7fcda519ed86 in __cxx_global_var_init /home/hornik/tmp/scratch/Rtmp5xR406/R.INSTALL35bf38599e7a40/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp:88:52 #10 0x7fcda519ed86 in _GLOBAL__sub_I_H5FaccProp.cpp /home/hornik/tmp/scratch/Rtmp5xR406/R.INSTALL35bf38599e7a40/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp #11 0x7fcdc016729d in call_init elf/dl-init.c:74:3 #12 0x7fcdc016729d in call_init elf/dl-init.c:26:1 #13 0x7fcdc016738b in _dl_init elf/dl-init.c:121:5 #14 0x7fcdc0164535 in _dl_catch_exception elf/dl-catch.c:215:7 #15 0x7fcdc016df2d in dl_open_worker elf/dl-open.c:804:5 #16 0x7fcdc01644a8 in _dl_catch_exception elf/dl-catch.c:241:8 #17 0x7fcdc016e2a7 in _dl_open elf/dl-open.c:880:17 #18 0x7fcdbea97f97 in dlopen_doit dlfcn/dlopen.c:56:15 #19 0x7fcdc01644a8 in _dl_catch_exception elf/dl-catch.c:241:8 #20 0x7fcdc01645ce in _dl_catch_error elf/dl-catch.c:260:19 #21 0x7fcdbea97aa6 in _dlerror_run dlfcn/dlerror.c:138:17 #22 0x7fcdbea98048 in dlopen_implementation dlfcn/dlopen.c:71:10 #23 0x7fcdbea98048 in dlopen dlfcn/dlopen.c:81:12 #24 0x56476fce72f6 in dlopen (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x8f2f6) (BuildId: ce9a0af4806c342e07ea21f487bd9584f1fffacb) #25 0x7fcdbf3127cf in AddDLL /home/hornik/src/R/src/main/Rdynload.c:855:14 #26 0x7fcdbf311bd7 in do_dynload /home/hornik/src/R/src/main/Rdynload.c:1229:12 #27 0x7fcdbf6ed889 in bcEval_loop /home/hornik/src/R/src/main/eval.c:8122:14 #28 0x7fcdbf6a1ee4 in bcEval /home/hornik/src/R/src/main/eval.c:7505:16 #29 0x7fcdbf6a061f in Rf_eval /home/hornik/src/R/src/main/eval.c:1167:8 #30 0x7fcdbf6a251f in forcePromise /home/hornik/src/R/src/main/eval.c:976:13 #31 0x7fcdbf6a074e in Rf_eval /home/hornik/src/R/src/main/eval.c:1193:2 #32 0x7fcdbf6f6cc2 in bcEval_loop /home/hornik/src/R/src/main/eval.c:8016:16 #33 0x7fcdbf6a1ee4 in bcEval /home/hornik/src/R/src/main/eval.c:7505:16 #34 0x7fcdbf6a061f in Rf_eval /home/hornik/src/R/src/main/eval.c:1167:8 #35 0x7fcdbf6aad75 in R_execClosure /home/hornik/src/R/src/main/eval.c:2393:22 #36 0x7fcdbf6a686c in applyClosure_core /home/hornik/src/R/src/main/eval.c:2306:16 #37 0x7fcdbf6a0f9f in Rf_applyClosure /home/hornik/src/R/src/main/eval.c:2328:16 #38 0x7fcdbf6a0f9f in Rf_eval /home/hornik/src/R/src/main/eval.c:1280:12 #39 0x7fcdbf7e4977 in Rf_ReplIteration /home/hornik/src/R/src/main/main.c:265:2 #40 0x7fcdbf7e7790 in R_ReplConsole /home/hornik/src/R/src/main/main.c:317:11 #41 0x7fcdbf7e75b4 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1219:5 #42 0x7fcdbf7e785a in Rf_mainloop /home/hornik/src/R/src/main/main.c:1226:5 #43 0x56476fd66dd4 in main /home/hornik/src/R/src/main/Rmain.c:29:5 #44 0x7fcdbea33d67 in __libc_start_call_main csu/../sysdeps/nptl/libc_start_call_main.h:58:16 #45 0x7fcdbea33e24 in __libc_start_main csu/../csu/libc-start.c:360:3 #46 0x56476fc83370 in _start (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x2b370) (BuildId: ce9a0af4806c342e07ea21f487bd9584f1fffacb) SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior H5I.c:1261:41 H5I.c:548:47: runtime error: call to function H5T__close_cb through pointer to incorrect function type 'int (*)(void *)' /home/hornik/tmp/scratch/Rtmp5xR406/R.INSTALL35bf38599e7a40/Rhdf5lib/src/hdf5/src/H5T.c:3848: note: H5T__close_cb defined here #0 0x7fcda5f62679 in H5I__clear_type_cb /home/hornik/tmp/scratch/Rtmp5xR406/R.INSTALL35bf38599e7a40/Rhdf5lib/src/hdf5/src/H5I.c:548:47 #1 0x7fcda62d9127 in H5SL_try_free_safe /home/hornik/tmp/scratch/Rtmp5xR406/R.INSTALL35bf38599e7a40/Rhdf5lib/src/hdf5/src/H5SL.c:2369:26 #2 0x7fcda5f61dd7 in H5I_clear_type /home/hornik/tmp/scratch/Rtmp5xR406/R.INSTALL35bf38599e7a40/Rhdf5lib/src/hdf5/src/H5I.c:508:8 #3 0x7fcda630c9a2 in H5T_top_term_package /home/hornik/tmp/scratch/Rtmp5xR406/R.INSTALL35bf38599e7a40/Rhdf5lib/src/hdf5/src/H5T.c:1444:19 #4 0x7fcda5b0ff61 in H5_term_library /home/hornik/tmp/scratch/Rtmp5xR406/R.INSTALL35bf38599e7a40/Rhdf5lib/src/hdf5/src/H5.c:310:20 #5 0x7fcda5b151a0 in H5close /home/hornik/tmp/scratch/Rtmp5xR406/R.INSTALL35bf38599e7a40/Rhdf5lib/src/hdf5/src/H5.c:960:5 #6 0x7fcda5a92fe0 in H5::H5Library::termH5cpp() /home/hornik/tmp/scratch/Rtmp5xR406/R.INSTALL35bf38599e7a40/Rhdf5lib/src/hdf5/c++/src/H5Library.cpp:235:24 #7 0x7fcdbea4c260 in __run_exit_handlers stdlib/exit.c:108:8 #8 0x7fcdbea4c319 in exit stdlib/exit.c:138:3 #9 0x7fcdbfb971bc in Rstd_CleanUp /home/hornik/src/R/src/unix/sys-std.c:1301:5 #10 0x7fcdbfba1417 in R_CleanUp /home/hornik/src/R/src/unix/system.c:87:5 #11 0x7fcdbf7e75e4 in end_Rmainloop /home/hornik/src/R/src/main/main.c:1209:5 #12 0x7fcdbf7e75e4 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1220:5 #13 0x7fcdbf7e785a in Rf_mainloop /home/hornik/src/R/src/main/main.c:1226:5 #14 0x56476fd66dd4 in main /home/hornik/src/R/src/main/Rmain.c:29:5 #15 0x7fcdbea33d67 in __libc_start_call_main csu/../sysdeps/nptl/libc_start_call_main.h:58:16 #16 0x7fcdbea33e24 in __libc_start_main csu/../csu/libc-start.c:360:3 #17 0x56476fc83370 in _start (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x2b370) (BuildId: ce9a0af4806c342e07ea21f487bd9584f1fffacb) SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior H5I.c:548:47 Check: examples, Result: ERROR Running examples in ‘enviGCMS-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: getmass > ### Title: Get the exact mass of the isotopologues from a chemical formula > ### or reaction's isotope patterns with the highest abundances > ### Aliases: getmass > > ### ** Examples > > getmass('CH2') ================================================================= ==3569553==ERROR: AddressSanitizer: heap-buffer-overflow on address 0x50b000019398 at pc 0x7fc5058f19c6 bp 0x7fff582c2970 sp 0x7fff582c2968 READ of size 8 at 0x50b000019398 thread T0 #0 0x7fc5058f19c5 in ims::IsotopeDistribution::getAbundance(unsigned long) const /home/hornik/tmp/scratch/RtmpJlNsVO/R.INSTALL36125d62775407/Rdisop/src/./imslib/src/ims/isotopedistribution.h:249:29 #1 0x7fc5058f19c5 in ims::Element::getMass(unsigned long) const /home/hornik/tmp/scratch/RtmpJlNsVO/R.INSTALL36125d62775407/Rdisop/src/./imslib/src/ims/element.h:169:22 #2 0x7fc50591d9b6 in ims::Alphabet::getMasses(unsigned long) const /home/hornik/tmp/scratch/RtmpJlNsVO/R.INSTALL36125d62775407/Rdisop/src/imslib/src/ims/alphabet.cpp:54:25 #3 0x7fc5058ec93b in getMolecule /home/hornik/tmp/scratch/RtmpJlNsVO/R.INSTALL36125d62775407/Rdisop/src/disop.cpp:472:30 #4 0x7fc524d5115e in R_doDotCall /home/hornik/src/R/src/main/dotcode.c:766:11 #5 0x7fc524d9bb92 in do_dotcall /home/hornik/src/R/src/main/dotcode.c:1437:11 #6 0x7fc524eed889 in bcEval_loop /home/hornik/src/R/src/main/eval.c:8122:14 #7 0x7fc524ea1ee4 in bcEval /home/hornik/src/R/src/main/eval.c:7505:16 #8 0x7fc524ea061f in Rf_eval /home/hornik/src/R/src/main/eval.c:1167:8 #9 0x7fc524eaad75 in R_execClosure /home/hornik/src/R/src/main/eval.c:2393:22 #10 0x7fc524ea686c in applyClosure_core /home/hornik/src/R/src/main/eval.c:2306:16 #11 0x7fc524ea0f9f in Rf_applyClosure /home/hornik/src/R/src/main/eval.c:2328:16 #12 0x7fc524ea0f9f in Rf_eval /home/hornik/src/R/src/main/eval.c:1280:12 #13 0x7fc524fe4977 in Rf_ReplIteration /home/hornik/src/R/src/main/main.c:265:2 #14 0x7fc524fe7790 in R_ReplConsole /home/hornik/src/R/src/main/main.c:317:11 #15 0x7fc524fe75b4 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1219:5 #16 0x7fc524fe785a in Rf_mainloop /home/hornik/src/R/src/main/main.c:1226:5 #17 0x56532f640dd4 in main /home/hornik/src/R/src/main/Rmain.c:29:5 #18 0x7fc524233d67 in __libc_start_call_main csu/../sysdeps/nptl/libc_start_call_main.h:58:16 #19 0x7fc524233e24 in __libc_start_main csu/../csu/libc-start.c:360:3 #20 0x56532f55d370 in _start (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x2b370) (BuildId: ce9a0af4806c342e07ea21f487bd9584f1fffacb) 0x50b000019398 is located 8 bytes after 112-byte region [0x50b000019320,0x50b000019390) allocated by thread T0 here: #0 0x56532f63e921 in operator new(unsigned long) (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x10c921) (BuildId: ce9a0af4806c342e07ea21f487bd9584f1fffacb) #1 0x7fc5058f660a in std::__new_allocator::allocate(unsigned long, void const*) /usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/bits/new_allocator.h:151:27 #2 0x7fc5058f660a in std::allocator_traits>::allocate(std::allocator&, unsigned long) /usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/bits/alloc_traits.h:509:20 #3 0x7fc5058f660a in std::_Vector_base>::_M_allocate(unsigned long) /usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/bits/stl_vector.h:380:20 #4 0x7fc5058f660a in std::_Vector_base>::_M_create_storage(unsigned long) /usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/bits/stl_vector.h:398:33 #5 0x7fc5058f6441 in std::_Vector_base>::_Vector_base(unsigned long, std::allocator const&) /usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/bits/stl_vector.h:334:9 #6 0x7fc5058f6441 in std::vector>::vector(std::vector> const&) /usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/bits/stl_vector.h:602:9 #7 0x7fc5058f70d7 in ims::IsotopeDistribution::IsotopeDistribution(ims::IsotopeDistribution const&) /home/hornik/tmp/scratch/RtmpJlNsVO/R.INSTALL36125d62775407/Rdisop/src/./imslib/src/ims/isotopedistribution.h:165:6 #8 0x7fc5058f70d7 in ims::Element::Element(ims::Element const&) /home/hornik/tmp/scratch/RtmpJlNsVO/R.INSTALL36125d62775407/Rdisop/src/./imslib/src/ims/element.h:75:6 #9 0x7fc5058fa964 in void std::_Construct(ims::Element*, ims::Element const&) /usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/bits/stl_construct.h:119:25 #10 0x7fc5058fa964 in ims::Element* std::__do_uninit_copy(ims::Element const*, ims::Element const*, ims::Element*) /usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/bits/stl_uninitialized.h:120:6 #11 0x7fc5058fa362 in ims::Element* std::__uninitialized_copy::__uninit_copy(ims::Element const*, ims::Element const*, ims::Element*) /usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/bits/stl_uninitialized.h:137:11 #12 0x7fc5058fa362 in ims::Element* std::uninitialized_copy(ims::Element const*, ims::Element const*, ims::Element*) /usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/bits/stl_uninitialized.h:184:14 #13 0x7fc5058fa362 in ims::Element* std::__uninitialized_copy_a(ims::Element const*, ims::Element const*, ims::Element*, std::allocator&) /usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/bits/stl_uninitialized.h:373:14 #14 0x7fc5058fa362 in ims::Element* std::__uninitialized_move_if_noexcept_a>(ims::Element*, ims::Element*, ims::Element*, std::allocator&) /usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/bits/stl_uninitialized.h:398:14 #15 0x7fc5058fa362 in void std::vector>::_M_realloc_append(ims::Element const&) /usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/bits/vector.tcc:676:21 #16 0x7fc5058eb03a in initializeAlphabet(SEXPREC*, ims::Alphabet&, int) /home/hornik/tmp/scratch/RtmpJlNsVO/R.INSTALL36125d62775407/Rdisop/src/disop.cpp:839:14 #17 0x7fc5058ec401 in getMolecule /home/hornik/tmp/scratch/RtmpJlNsVO/R.INSTALL36125d62775407/Rdisop/src/disop.cpp:459:5 #18 0x7fc524d5115e in R_doDotCall /home/hornik/src/R/src/main/dotcode.c:766:11 #19 0x7fc524d9bb92 in do_dotcall /home/hornik/src/R/src/main/dotcode.c:1437:11 #20 0x7fc524eed889 in bcEval_loop /home/hornik/src/R/src/main/eval.c:8122:14 #21 0x7fc524ea1ee4 in bcEval /home/hornik/src/R/src/main/eval.c:7505:16 #22 0x7fc524ea061f in Rf_eval /home/hornik/src/R/src/main/eval.c:1167:8 #23 0x7fc524eaad75 in R_execClosure /home/hornik/src/R/src/main/eval.c:2393:22 #24 0x7fc524ea686c in applyClosure_core /home/hornik/src/R/src/main/eval.c:2306:16 #25 0x7fc524ea0f9f in Rf_applyClosure /home/hornik/src/R/src/main/eval.c:2328:16 #26 0x7fc524ea0f9f in Rf_eval /home/hornik/src/R/src/main/eval.c:1280:12 #27 0x7fc524fe4977 in Rf_ReplIteration /home/hornik/src/R/src/main/main.c:265:2 #28 0x7fc524fe7790 in R_ReplConsole /home/hornik/src/R/src/main/main.c:317:11 #29 0x7fc524fe75b4 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1219:5 #30 0x7fc524fe785a in Rf_mainloop /home/hornik/src/R/src/main/main.c:1226:5 #31 0x56532f640dd4 in main /home/hornik/src/R/src/main/Rmain.c:29:5 #32 0x7fc524233d67 in __libc_start_call_main csu/../sysdeps/nptl/libc_start_call_main.h:58:16 SUMMARY: AddressSanitizer: heap-buffer-overflow /home/hornik/tmp/scratch/RtmpJlNsVO/R.INSTALL36125d62775407/Rdisop/src/./imslib/src/ims/isotopedistribution.h:249:29 in ims::IsotopeDistribution::getAbundance(unsigned long) const Shadow bytes around the buggy address: 0x50b000019100: fa fa fd fd fd fd fd fd fd fd fd fd fd fd fd fd 0x50b000019180: fa fa fa fa fa fa fa fa fd fd fd fd fd fd fd fd 0x50b000019200: fd fd fd fd fd fd fa fa fa fa fa fa fa fa 00 00 0x50b000019280: 00 00 00 00 00 00 00 00 00 00 00 00 fa fa fa fa 0x50b000019300: fa fa fa fa 00 00 00 00 00 00 00 00 00 00 00 00 =>0x50b000019380: 00 00 fa[fa]fa fa fa fa fa fa 00 00 00 00 00 00 0x50b000019400: 00 00 00 00 00 00 00 00 fa fa fa fa fa fa fa fa 0x50b000019480: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 fa fa 0x50b000019500: fa fa fa fa fa fa 00 00 00 00 00 00 00 00 00 00 0x50b000019580: 00 00 00 00 fa fa fa fa fa fa fa fa 00 00 00 00 0x50b000019600: 00 00 00 00 00 00 00 00 00 00 fa fa fa fa fa fa Shadow byte legend (one shadow byte represents 8 application bytes): Addressable: 00 Partially addressable: 01 02 03 04 05 06 07 Heap left redzone: fa Freed heap region: fd Stack left redzone: f1 Stack mid redzone: f2 Stack right redzone: f3 Stack after return: f5 Stack use after scope: f8 Global redzone: f9 Global init order: f6 Poisoned by user: f7 Container overflow: fc Array cookie: ac Intra object redzone: bb ASan internal: fe Left alloca redzone: ca Right alloca redzone: cb ==3569553==ABORTING Post-processing issues found: File: enviGCMS-Ex.Rout ==3569553==ERROR: AddressSanitizer: heap-buffer-overflow on address 0x50b000019398 at pc 0x7fc5058f19c6 bp 0x7fff582c2970 sp 0x7fff582c2968 SUMMARY: AddressSanitizer: heap-buffer-overflow /home/hornik/tmp/scratch/RtmpJlNsVO/R.INSTALL36125d62775407/Rdisop/src/./imslib/src/ims/isotopedistribution.h:249:29 in ims::IsotopeDistribution::getAbundance(unsigned long) const ASan internal: fe File: 00check.log H5I.c:1261:41: runtime error: call to function H5T__close_cb through pointer to incorrect function type 'int (*)(void *)' H5I.c:548:47: runtime error: call to function H5T__close_cb through pointer to incorrect function type 'int (*)(void *)' ==3569553==ERROR: AddressSanitizer: heap-buffer-overflow on address 0x50b000019398 at pc 0x7fc5058f19c6 bp 0x7fff582c2970 sp 0x7fff582c2968 SUMMARY: AddressSanitizer: heap-buffer-overflow /home/hornik/tmp/scratch/RtmpJlNsVO/R.INSTALL36125d62775407/Rdisop/src/./imslib/src/ims/isotopedistribution.h:249:29 in ims::IsotopeDistribution::getAbundance(unsigned long) const ASan internal: fe