* using log directory ‘/home/hornik/tmp/CRAN_special_clang-san/apLCMS.Rcheck’ * using R Under development (unstable) (2025-09-03 r88788) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (3+b1) Debian flang-new version 19.1.7 (3+b1) * running under: Debian GNU/Linux forky/sid * using session charset: UTF-8 * checking for file ‘apLCMS/DESCRIPTION’ ... OK * this is package ‘apLCMS’ version ‘6.8.4’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking serialization versions ... OK * checking whether package ‘apLCMS’ can be installed ... [45s/45s] OK * used C++ compiler: ‘Debian clang version 19.1.7 (3+b2)’ * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [6s/6s] OK * checking whether the package can be loaded with stated dependencies ... [6s/6s] OK * checking whether the package can be unloaded cleanly ... [6s/6s] OK * checking whether the namespace can be loaded with stated dependencies ... [6s/6s] OK * checking whether the namespace can be unloaded cleanly ... [6s/6s] OK * checking loading without being on the library search path ... [6s/6s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... 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/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:3848: note: H5T__close_cb defined here #0 0x7f9e87d736c1 in H5I_dec_ref /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5I.c:1261:41 #1 0x7f9e8813ff13 in H5T__path_find_real /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:4842:13 #2 0x7f9e8812e4da in H5T__register /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:2333:36 #3 0x7f9e8811690a in H5T__register_int /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:2282:8 #4 0x7f9e8810d59d in H5T__init_package /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:1048:15 #5 0x7f9e881063a0 in H5T_init /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:578:5 #6 0x7f9e8791b392 in H5_init_library /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:218:8 #7 0x7f9e879215ac in H5open /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:930:5 #8 0x7f9e8789f8a6 in H5::FileAccPropList::getConstant() /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp:66:40 #9 0x7f9e86fb5446 in __cxx_global_var_init /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp:88:52 #10 0x7f9e86fb5446 in _GLOBAL__sub_I_H5FaccProp.cpp /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp #11 0x7f9f206d6fad in call_init elf/dl-init.c:74:3 #12 0x7f9f206d6fad in call_init elf/dl-init.c:26:1 #13 0x7f9f206d707b in _dl_init elf/dl-init.c:121:5 #14 0x7f9f206d4425 in _dl_catch_exception elf/dl-catch.c:215:7 #15 0x7f9f206dda27 in dl_open_worker elf/dl-open.c:799:3 #16 0x7f9f206d4398 in _dl_catch_exception elf/dl-catch.c:241:8 #17 0x7f9f206ddda7 in _dl_open elf/dl-open.c:874:17 #18 0x7f9f1efa9257 in dlopen_doit dlfcn/dlopen.c:56:15 #19 0x7f9f206d4398 in _dl_catch_exception elf/dl-catch.c:241:8 #20 0x7f9f206d44be in _dl_catch_error elf/dl-catch.c:260:19 #21 0x7f9f1efa8d66 in _dlerror_run dlfcn/dlerror.c:138:17 #22 0x7f9f1efa9308 in dlopen_implementation dlfcn/dlopen.c:71:10 #23 0x7f9f1efa9308 in dlopen dlfcn/dlopen.c:81:12 #24 0x55e4dfbf52f6 in dlopen (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x8f2f6) (BuildId: 8b69897b2fcd08f10a8fcf1956a30782b1479dfd) #25 0x7f9f1f9159ff in AddDLL /home/hornik/src/R/src/main/Rdynload.c:874:14 #26 0x7f9f1f914e07 in do_dynload /home/hornik/src/R/src/main/Rdynload.c:1248:12 #27 0x7f9f1fcf7739 in bcEval_loop /home/hornik/src/R/src/main/eval.c:8114:14 #28 0x7f9f1fcabfd4 in bcEval /home/hornik/src/R/src/main/eval.c:7497:16 #29 0x7f9f1fcaa70f in Rf_eval /home/hornik/src/R/src/main/eval.c:1167:8 #30 0x7f9f1fcb4b45 in R_execClosure /home/hornik/src/R/src/main/eval.c:2389:22 #31 0x7f9f1fcb063c in applyClosure_core /home/hornik/src/R/src/main/eval.c:2302:16 #32 0x7f9f1fcab08f in Rf_applyClosure /home/hornik/src/R/src/main/eval.c:2324:16 #33 0x7f9f1fcab08f in Rf_eval /home/hornik/src/R/src/main/eval.c:1280:12 #34 0x7f9f1fdee896 in Rf_ReplIteration /home/hornik/src/R/src/main/main.c:264:15 #35 0x7f9f1fdf18a0 in R_ReplConsole /home/hornik/src/R/src/main/main.c:317:11 #36 0x7f9f1fdf16b4 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1235:5 #37 0x7f9f1fdf199a in Rf_mainloop /home/hornik/src/R/src/main/main.c:1242:5 #38 0x55e4dfc74dd4 in main /home/hornik/src/R/src/main/Rmain.c:29:5 #39 0x7f9f1ef43ca7 in __libc_start_call_main csu/../sysdeps/nptl/libc_start_call_main.h:58:16 #40 0x7f9f1ef43d64 in __libc_start_main csu/../csu/libc-start.c:360:3 #41 0x55e4dfb91370 in _start (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x2b370) (BuildId: 8b69897b2fcd08f10a8fcf1956a30782b1479dfd) 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/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:3848: note: H5T__close_cb defined here #0 0x7f9e87d6eba9 in H5I__clear_type_cb /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5I.c:548:47 #1 0x7f9e880e5657 in H5SL_try_free_safe /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5SL.c:2369:26 #2 0x7f9e87d6e307 in H5I_clear_type /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5I.c:508:8 #3 0x7f9e88118ed2 in H5T_top_term_package /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:1444:19 #4 0x7f9e8791c491 in H5_term_library /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:310:20 #5 0x7f9e879216d0 in H5close /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:960:5 #6 0x7f9e8789f410 in H5::H5Library::termH5cpp() /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5Library.cpp:235:24 #7 0x7f9f1ef5c290 in __run_exit_handlers stdlib/exit.c:118:8 #8 0x7f9f1ef5c359 in exit stdlib/exit.c:148:3 #9 0x7f9f201a0b4c in Rstd_CleanUp /home/hornik/src/R/src/unix/sys-std.c:1300:5 #10 0x7f9f201aadd7 in R_CleanUp /home/hornik/src/R/src/unix/system.c:87:5 #11 0x7f9f1fdf16e4 in end_Rmainloop /home/hornik/src/R/src/main/main.c:1225:5 #12 0x7f9f1fdf16e4 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1236:5 #13 0x7f9f1fdf199a in Rf_mainloop /home/hornik/src/R/src/main/main.c:1242:5 #14 0x55e4dfc74dd4 in main /home/hornik/src/R/src/main/Rmain.c:29:5 #15 0x7f9f1ef43ca7 in __libc_start_call_main csu/../sysdeps/nptl/libc_start_call_main.h:58:16 #16 0x7f9f1ef43d64 in __libc_start_main csu/../csu/libc-start.c:360:3 #17 0x55e4dfb91370 in _start (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x2b370) (BuildId: 8b69897b2fcd08f10a8fcf1956a30782b1479dfd) SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior H5I.c:548:47 * checking S3 generic/method consistency ... WARNING H5I.c:1261:41: runtime error: call to function H5T__close_cb through pointer to incorrect function type 'int (*)(void *)' /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:3848: note: H5T__close_cb defined here #0 0x7f0cb67736c1 in H5I_dec_ref /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5I.c:1261:41 #1 0x7f0cb6b3ff13 in H5T__path_find_real /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:4842:13 #2 0x7f0cb6b2e4da in H5T__register /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:2333:36 #3 0x7f0cb6b1690a in H5T__register_int /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:2282:8 #4 0x7f0cb6b0d59d in H5T__init_package /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:1048:15 #5 0x7f0cb6b063a0 in H5T_init /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:578:5 #6 0x7f0cb631b392 in H5_init_library /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:218:8 #7 0x7f0cb63215ac in H5open /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:930:5 #8 0x7f0cb629f8a6 in H5::FileAccPropList::getConstant() /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp:66:40 #9 0x7f0cb59b5446 in __cxx_global_var_init /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp:88:52 #10 0x7f0cb59b5446 in _GLOBAL__sub_I_H5FaccProp.cpp /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp #11 0x7f0d4f088fad in call_init elf/dl-init.c:74:3 #12 0x7f0d4f088fad in call_init elf/dl-init.c:26:1 #13 0x7f0d4f08907b in _dl_init elf/dl-init.c:121:5 #14 0x7f0d4f086425 in _dl_catch_exception elf/dl-catch.c:215:7 #15 0x7f0d4f08fa27 in dl_open_worker elf/dl-open.c:799:3 #16 0x7f0d4f086398 in _dl_catch_exception elf/dl-catch.c:241:8 #17 0x7f0d4f08fda7 in _dl_open elf/dl-open.c:874:17 #18 0x7f0d4d899257 in dlopen_doit dlfcn/dlopen.c:56:15 #19 0x7f0d4f086398 in _dl_catch_exception elf/dl-catch.c:241:8 #20 0x7f0d4f0864be in _dl_catch_error elf/dl-catch.c:260:19 #21 0x7f0d4d898d66 in _dlerror_run dlfcn/dlerror.c:138:17 #22 0x7f0d4d899308 in dlopen_implementation dlfcn/dlopen.c:71:10 #23 0x7f0d4d899308 in dlopen dlfcn/dlopen.c:81:12 #24 0x5615f43122f6 in dlopen (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x8f2f6) (BuildId: 8b69897b2fcd08f10a8fcf1956a30782b1479dfd) #25 0x7f0d4e1159ff in AddDLL /home/hornik/src/R/src/main/Rdynload.c:874:14 #26 0x7f0d4e114e07 in do_dynload /home/hornik/src/R/src/main/Rdynload.c:1248:12 #27 0x7f0d4e4f7739 in bcEval_loop /home/hornik/src/R/src/main/eval.c:8114:14 #28 0x7f0d4e4abfd4 in bcEval /home/hornik/src/R/src/main/eval.c:7497:16 #29 0x7f0d4e4aa70f in Rf_eval /home/hornik/src/R/src/main/eval.c:1167:8 #30 0x7f0d4e4b4b45 in R_execClosure /home/hornik/src/R/src/main/eval.c:2389:22 #31 0x7f0d4e4b063c in applyClosure_core /home/hornik/src/R/src/main/eval.c:2302:16 #32 0x7f0d4e4ab08f in Rf_applyClosure /home/hornik/src/R/src/main/eval.c:2324:16 #33 0x7f0d4e4ab08f in Rf_eval /home/hornik/src/R/src/main/eval.c:1280:12 #34 0x7f0d4e5ee896 in Rf_ReplIteration /home/hornik/src/R/src/main/main.c:264:15 #35 0x7f0d4e5f18a0 in R_ReplConsole /home/hornik/src/R/src/main/main.c:317:11 #36 0x7f0d4e5f16b4 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1235:5 #37 0x7f0d4e5f199a in Rf_mainloop /home/hornik/src/R/src/main/main.c:1242:5 #38 0x5615f4391dd4 in main /home/hornik/src/R/src/main/Rmain.c:29:5 #39 0x7f0d4d833ca7 in __libc_start_call_main csu/../sysdeps/nptl/libc_start_call_main.h:58:16 #40 0x7f0d4d833d64 in __libc_start_main csu/../csu/libc-start.c:360:3 #41 0x5615f42ae370 in _start (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x2b370) (BuildId: 8b69897b2fcd08f10a8fcf1956a30782b1479dfd) 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/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:3848: note: H5T__close_cb defined here #0 0x7f0cb676eba9 in H5I__clear_type_cb /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5I.c:548:47 #1 0x7f0cb6ae5657 in H5SL_try_free_safe /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5SL.c:2369:26 #2 0x7f0cb676e307 in H5I_clear_type /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5I.c:508:8 #3 0x7f0cb6b18ed2 in H5T_top_term_package /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:1444:19 #4 0x7f0cb631c491 in H5_term_library /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:310:20 #5 0x7f0cb63216d0 in H5close /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:960:5 #6 0x7f0cb629f410 in H5::H5Library::termH5cpp() /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5Library.cpp:235:24 #7 0x7f0d4d84c290 in __run_exit_handlers stdlib/exit.c:118:8 #8 0x7f0d4d84c359 in exit stdlib/exit.c:148:3 #9 0x7f0d4e9a0b4c in Rstd_CleanUp /home/hornik/src/R/src/unix/sys-std.c:1300:5 #10 0x7f0d4e9aadd7 in R_CleanUp /home/hornik/src/R/src/unix/system.c:87:5 #11 0x7f0d4e5f16e4 in end_Rmainloop /home/hornik/src/R/src/main/main.c:1225:5 #12 0x7f0d4e5f16e4 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1236:5 #13 0x7f0d4e5f199a in Rf_mainloop /home/hornik/src/R/src/main/main.c:1242:5 #14 0x5615f4391dd4 in main /home/hornik/src/R/src/main/Rmain.c:29:5 #15 0x7f0d4d833ca7 in __libc_start_call_main csu/../sysdeps/nptl/libc_start_call_main.h:58:16 #16 0x7f0d4d833d64 in __libc_start_main csu/../csu/libc-start.c:360:3 #17 0x5615f42ae370 in _start (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x2b370) (BuildId: 8b69897b2fcd08f10a8fcf1956a30782b1479dfd) SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior H5I.c:548:47 See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... WARNING H5I.c:1261:41: runtime error: call to function H5T__close_cb through pointer to incorrect function type 'int (*)(void *)' /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:3848: note: H5T__close_cb defined here #0 0x7f30d89736c1 in H5I_dec_ref /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5I.c:1261:41 #1 0x7f30d8d3ff13 in H5T__path_find_real /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:4842:13 #2 0x7f30d8d2e4da in H5T__register /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:2333:36 #3 0x7f30d8d1690a in H5T__register_int /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:2282:8 #4 0x7f30d8d0d59d in H5T__init_package /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:1048:15 #5 0x7f30d8d063a0 in H5T_init /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:578:5 #6 0x7f30d851b392 in H5_init_library /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:218:8 #7 0x7f30d85215ac in H5open /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:930:5 #8 0x7f30d849f8a6 in H5::FileAccPropList::getConstant() /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp:66:40 #9 0x7f30d7bb5446 in __cxx_global_var_init /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp:88:52 #10 0x7f30d7bb5446 in _GLOBAL__sub_I_H5FaccProp.cpp /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp #11 0x7f317128afad in call_init elf/dl-init.c:74:3 #12 0x7f317128afad in call_init elf/dl-init.c:26:1 #13 0x7f317128b07b in _dl_init elf/dl-init.c:121:5 #14 0x7f3171288425 in _dl_catch_exception elf/dl-catch.c:215:7 #15 0x7f3171291a27 in dl_open_worker elf/dl-open.c:799:3 #16 0x7f3171288398 in _dl_catch_exception elf/dl-catch.c:241:8 #17 0x7f3171291da7 in _dl_open elf/dl-open.c:874:17 #18 0x7f316fa99257 in dlopen_doit dlfcn/dlopen.c:56:15 #19 0x7f3171288398 in _dl_catch_exception elf/dl-catch.c:241:8 #20 0x7f31712884be in _dl_catch_error elf/dl-catch.c:260:19 #21 0x7f316fa98d66 in _dlerror_run dlfcn/dlerror.c:138:17 #22 0x7f316fa99308 in dlopen_implementation dlfcn/dlopen.c:71:10 #23 0x7f316fa99308 in dlopen dlfcn/dlopen.c:81:12 #24 0x558d6333d2f6 in dlopen (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x8f2f6) (BuildId: 8b69897b2fcd08f10a8fcf1956a30782b1479dfd) #25 0x7f31703159ff in AddDLL /home/hornik/src/R/src/main/Rdynload.c:874:14 #26 0x7f3170314e07 in do_dynload /home/hornik/src/R/src/main/Rdynload.c:1248:12 #27 0x7f31706f7739 in bcEval_loop /home/hornik/src/R/src/main/eval.c:8114:14 #28 0x7f31706abfd4 in bcEval /home/hornik/src/R/src/main/eval.c:7497:16 #29 0x7f31706aa70f in Rf_eval /home/hornik/src/R/src/main/eval.c:1167:8 #30 0x7f31706b4b45 in R_execClosure /home/hornik/src/R/src/main/eval.c:2389:22 #31 0x7f31706b063c in applyClosure_core /home/hornik/src/R/src/main/eval.c:2302:16 #32 0x7f31706ab08f in Rf_applyClosure /home/hornik/src/R/src/main/eval.c:2324:16 #33 0x7f31706ab08f in Rf_eval /home/hornik/src/R/src/main/eval.c:1280:12 #34 0x7f31707ee896 in Rf_ReplIteration /home/hornik/src/R/src/main/main.c:264:15 #35 0x7f31707f18a0 in R_ReplConsole /home/hornik/src/R/src/main/main.c:317:11 #36 0x7f31707f16b4 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1235:5 #37 0x7f31707f199a in Rf_mainloop /home/hornik/src/R/src/main/main.c:1242:5 #38 0x558d633bcdd4 in main /home/hornik/src/R/src/main/Rmain.c:29:5 #39 0x7f316fa33ca7 in __libc_start_call_main csu/../sysdeps/nptl/libc_start_call_main.h:58:16 #40 0x7f316fa33d64 in __libc_start_main csu/../csu/libc-start.c:360:3 #41 0x558d632d9370 in _start (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x2b370) (BuildId: 8b69897b2fcd08f10a8fcf1956a30782b1479dfd) 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/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:3848: note: H5T__close_cb defined here #0 0x7f30d896eba9 in H5I__clear_type_cb /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5I.c:548:47 #1 0x7f30d8ce5657 in H5SL_try_free_safe /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5SL.c:2369:26 #2 0x7f30d896e307 in H5I_clear_type /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5I.c:508:8 #3 0x7f30d8d18ed2 in H5T_top_term_package /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:1444:19 #4 0x7f30d851c491 in H5_term_library /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:310:20 #5 0x7f30d85216d0 in H5close /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:960:5 #6 0x7f30d849f410 in H5::H5Library::termH5cpp() /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5Library.cpp:235:24 #7 0x7f316fa4c290 in __run_exit_handlers stdlib/exit.c:118:8 #8 0x7f316fa4c359 in exit stdlib/exit.c:148:3 #9 0x7f3170ba0b4c in Rstd_CleanUp /home/hornik/src/R/src/unix/sys-std.c:1300:5 #10 0x7f3170baadd7 in R_CleanUp /home/hornik/src/R/src/unix/system.c:87:5 #11 0x7f31707f16e4 in end_Rmainloop /home/hornik/src/R/src/main/main.c:1225:5 #12 0x7f31707f16e4 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1236:5 #13 0x7f31707f199a in Rf_mainloop /home/hornik/src/R/src/main/main.c:1242:5 #14 0x558d633bcdd4 in main /home/hornik/src/R/src/main/Rmain.c:29:5 #15 0x7f316fa33ca7 in __libc_start_call_main csu/../sysdeps/nptl/libc_start_call_main.h:58:16 #16 0x7f316fa33d64 in __libc_start_main csu/../csu/libc-start.c:360:3 #17 0x558d632d9370 in _start (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x2b370) (BuildId: 8b69897b2fcd08f10a8fcf1956a30782b1479dfd) SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior H5I.c:548:47 The argument of a replacement function which corresponds to the right hand side must be named ‘value’. * checking foreign function calls ... 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/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:3848: note: H5T__close_cb defined here #0 0x7f9d171736c1 in H5I_dec_ref /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5I.c:1261:41 #1 0x7f9d1753ff13 in H5T__path_find_real /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:4842:13 #2 0x7f9d1752e4da in H5T__register /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:2333:36 #3 0x7f9d1751690a in H5T__register_int /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:2282:8 #4 0x7f9d1750d59d in H5T__init_package /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:1048:15 #5 0x7f9d175063a0 in H5T_init /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:578:5 #6 0x7f9d16d1b392 in H5_init_library /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:218:8 #7 0x7f9d16d215ac in H5open /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:930:5 #8 0x7f9d16c9f8a6 in H5::FileAccPropList::getConstant() /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp:66:40 #9 0x7f9d163b5446 in __cxx_global_var_init /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp:88:52 #10 0x7f9d163b5446 in _GLOBAL__sub_I_H5FaccProp.cpp /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp #11 0x7f9dafb42fad in call_init elf/dl-init.c:74:3 #12 0x7f9dafb42fad in call_init elf/dl-init.c:26:1 #13 0x7f9dafb4307b in _dl_init elf/dl-init.c:121:5 #14 0x7f9dafb40425 in _dl_catch_exception elf/dl-catch.c:215:7 #15 0x7f9dafb49a27 in dl_open_worker elf/dl-open.c:799:3 #16 0x7f9dafb40398 in _dl_catch_exception elf/dl-catch.c:241:8 #17 0x7f9dafb49da7 in _dl_open elf/dl-open.c:874:17 #18 0x7f9dae3a9257 in dlopen_doit dlfcn/dlopen.c:56:15 #19 0x7f9dafb40398 in _dl_catch_exception elf/dl-catch.c:241:8 #20 0x7f9dafb404be in _dl_catch_error elf/dl-catch.c:260:19 #21 0x7f9dae3a8d66 in _dlerror_run dlfcn/dlerror.c:138:17 #22 0x7f9dae3a9308 in dlopen_implementation dlfcn/dlopen.c:71:10 #23 0x7f9dae3a9308 in dlopen dlfcn/dlopen.c:81:12 #24 0x556253bb62f6 in dlopen (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x8f2f6) (BuildId: 8b69897b2fcd08f10a8fcf1956a30782b1479dfd) #25 0x7f9daed159ff in AddDLL /home/hornik/src/R/src/main/Rdynload.c:874:14 #26 0x7f9daed14e07 in do_dynload /home/hornik/src/R/src/main/Rdynload.c:1248:12 #27 0x7f9daf0f7739 in bcEval_loop /home/hornik/src/R/src/main/eval.c:8114:14 #28 0x7f9daf0abfd4 in bcEval /home/hornik/src/R/src/main/eval.c:7497:16 #29 0x7f9daf0aa70f in Rf_eval /home/hornik/src/R/src/main/eval.c:1167:8 #30 0x7f9daf0b4b45 in R_execClosure /home/hornik/src/R/src/main/eval.c:2389:22 #31 0x7f9daf0b063c in applyClosure_core /home/hornik/src/R/src/main/eval.c:2302:16 #32 0x7f9daf0ab08f in Rf_applyClosure /home/hornik/src/R/src/main/eval.c:2324:16 #33 0x7f9daf0ab08f in Rf_eval /home/hornik/src/R/src/main/eval.c:1280:12 #34 0x7f9daf1ee896 in Rf_ReplIteration /home/hornik/src/R/src/main/main.c:264:15 #35 0x7f9daf1f18a0 in R_ReplConsole /home/hornik/src/R/src/main/main.c:317:11 #36 0x7f9daf1f16b4 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1235:5 #37 0x7f9daf1f199a in Rf_mainloop /home/hornik/src/R/src/main/main.c:1242:5 #38 0x556253c35dd4 in main /home/hornik/src/R/src/main/Rmain.c:29:5 #39 0x7f9dae343ca7 in __libc_start_call_main csu/../sysdeps/nptl/libc_start_call_main.h:58:16 #40 0x7f9dae343d64 in __libc_start_main csu/../csu/libc-start.c:360:3 #41 0x556253b52370 in _start (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x2b370) (BuildId: 8b69897b2fcd08f10a8fcf1956a30782b1479dfd) 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/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:3848: note: H5T__close_cb defined here #0 0x7f9d1716eba9 in H5I__clear_type_cb /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5I.c:548:47 #1 0x7f9d174e5657 in H5SL_try_free_safe /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5SL.c:2369:26 #2 0x7f9d1716e307 in H5I_clear_type /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5I.c:508:8 #3 0x7f9d17518ed2 in H5T_top_term_package /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:1444:19 #4 0x7f9d16d1c491 in H5_term_library /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:310:20 #5 0x7f9d16d216d0 in H5close /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:960:5 #6 0x7f9d16c9f410 in H5::H5Library::termH5cpp() /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5Library.cpp:235:24 #7 0x7f9dae35c290 in __run_exit_handlers stdlib/exit.c:118:8 #8 0x7f9dae35c359 in exit stdlib/exit.c:148:3 #9 0x7f9daf5a0b4c in Rstd_CleanUp /home/hornik/src/R/src/unix/sys-std.c:1300:5 #10 0x7f9daf5aadd7 in R_CleanUp /home/hornik/src/R/src/unix/system.c:87:5 #11 0x7f9daf1f16e4 in end_Rmainloop /home/hornik/src/R/src/main/main.c:1225:5 #12 0x7f9daf1f16e4 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1236:5 #13 0x7f9daf1f199a in Rf_mainloop /home/hornik/src/R/src/main/main.c:1242:5 #14 0x556253c35dd4 in main /home/hornik/src/R/src/main/Rmain.c:29:5 #15 0x7f9dae343ca7 in __libc_start_call_main csu/../sysdeps/nptl/libc_start_call_main.h:58:16 #16 0x7f9dae343d64 in __libc_start_main csu/../csu/libc-start.c:360:3 #17 0x556253b52370 in _start (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x2b370) (BuildId: 8b69897b2fcd08f10a8fcf1956a30782b1479dfd) SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior H5I.c:548:47 See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... [77s/78s] 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/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:3848: note: H5T__close_cb defined here #0 0x7f90bff736c1 in H5I_dec_ref /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5I.c:1261:41 #1 0x7f90c033ff13 in H5T__path_find_real /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:4842:13 #2 0x7f90c032e4da in H5T__register /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:2333:36 #3 0x7f90c031690a in H5T__register_int /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:2282:8 #4 0x7f90c030d59d in H5T__init_package /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:1048:15 #5 0x7f90c03063a0 in H5T_init /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:578:5 #6 0x7f90bfb1b392 in H5_init_library /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:218:8 #7 0x7f90bfb215ac in H5open /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:930:5 #8 0x7f90bfa9f8a6 in H5::FileAccPropList::getConstant() /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp:66:40 #9 0x7f90bf1b5446 in __cxx_global_var_init /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp:88:52 #10 0x7f90bf1b5446 in _GLOBAL__sub_I_H5FaccProp.cpp /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp #11 0x7f915891efad in call_init elf/dl-init.c:74:3 #12 0x7f915891efad in call_init elf/dl-init.c:26:1 #13 0x7f915891f07b in _dl_init elf/dl-init.c:121:5 #14 0x7f915891c425 in _dl_catch_exception elf/dl-catch.c:215:7 #15 0x7f9158925a27 in dl_open_worker elf/dl-open.c:799:3 #16 0x7f915891c398 in _dl_catch_exception elf/dl-catch.c:241:8 #17 0x7f9158925da7 in _dl_open elf/dl-open.c:874:17 #18 0x7f91571a9257 in dlopen_doit dlfcn/dlopen.c:56:15 #19 0x7f915891c398 in _dl_catch_exception elf/dl-catch.c:241:8 #20 0x7f915891c4be in _dl_catch_error elf/dl-catch.c:260:19 #21 0x7f91571a8d66 in _dlerror_run dlfcn/dlerror.c:138:17 #22 0x7f91571a9308 in dlopen_implementation dlfcn/dlopen.c:71:10 #23 0x7f91571a9308 in dlopen dlfcn/dlopen.c:81:12 #24 0x555a3e0092f6 in dlopen (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x8f2f6) (BuildId: 8b69897b2fcd08f10a8fcf1956a30782b1479dfd) #25 0x7f9157b159ff in AddDLL /home/hornik/src/R/src/main/Rdynload.c:874:14 #26 0x7f9157b14e07 in do_dynload /home/hornik/src/R/src/main/Rdynload.c:1248:12 #27 0x7f9157ef7739 in bcEval_loop /home/hornik/src/R/src/main/eval.c:8114:14 #28 0x7f9157eabfd4 in bcEval /home/hornik/src/R/src/main/eval.c:7497:16 #29 0x7f9157eaa70f in Rf_eval /home/hornik/src/R/src/main/eval.c:1167:8 #30 0x7f9157eb4b45 in R_execClosure /home/hornik/src/R/src/main/eval.c:2389:22 #31 0x7f9157eb063c in applyClosure_core /home/hornik/src/R/src/main/eval.c:2302:16 #32 0x7f9157eab08f in Rf_applyClosure /home/hornik/src/R/src/main/eval.c:2324:16 #33 0x7f9157eab08f in Rf_eval /home/hornik/src/R/src/main/eval.c:1280:12 #34 0x7f9157fee896 in Rf_ReplIteration /home/hornik/src/R/src/main/main.c:264:15 #35 0x7f9157ff18a0 in R_ReplConsole /home/hornik/src/R/src/main/main.c:317:11 #36 0x7f9157ff16b4 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1235:5 #37 0x7f9157ff199a in Rf_mainloop /home/hornik/src/R/src/main/main.c:1242:5 #38 0x555a3e088dd4 in main /home/hornik/src/R/src/main/Rmain.c:29:5 #39 0x7f9157143ca7 in __libc_start_call_main csu/../sysdeps/nptl/libc_start_call_main.h:58:16 #40 0x7f9157143d64 in __libc_start_main csu/../csu/libc-start.c:360:3 #41 0x555a3dfa5370 in _start (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x2b370) (BuildId: 8b69897b2fcd08f10a8fcf1956a30782b1479dfd) 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/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:3848: note: H5T__close_cb defined here #0 0x7f90bff6eba9 in H5I__clear_type_cb /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5I.c:548:47 #1 0x7f90c02e5657 in H5SL_try_free_safe /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5SL.c:2369:26 #2 0x7f90bff6e307 in H5I_clear_type /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5I.c:508:8 #3 0x7f90c0318ed2 in H5T_top_term_package /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:1444:19 #4 0x7f90bfb1c491 in H5_term_library /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:310:20 #5 0x7f90bfb216d0 in H5close /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:960:5 #6 0x7f90bfa9f410 in H5::H5Library::termH5cpp() /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5Library.cpp:235:24 #7 0x7f915715c290 in __run_exit_handlers stdlib/exit.c:118:8 #8 0x7f915715c359 in exit stdlib/exit.c:148:3 #9 0x7f91583a0b4c in Rstd_CleanUp /home/hornik/src/R/src/unix/sys-std.c:1300:5 #10 0x7f91583aadd7 in R_CleanUp /home/hornik/src/R/src/unix/system.c:87:5 #11 0x7f9157ff16e4 in end_Rmainloop /home/hornik/src/R/src/main/main.c:1225:5 #12 0x7f9157ff16e4 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1236:5 #13 0x7f9157ff199a in Rf_mainloop /home/hornik/src/R/src/main/main.c:1242:5 #14 0x555a3e088dd4 in main /home/hornik/src/R/src/main/Rmain.c:29:5 #15 0x7f9157143ca7 in __libc_start_call_main csu/../sysdeps/nptl/libc_start_call_main.h:58:16 #16 0x7f9157143d64 in __libc_start_main csu/../csu/libc-start.c:360:3 #17 0x555a3dfa5370 in _start (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x2b370) (BuildId: 8b69897b2fcd08f10a8fcf1956a30782b1479dfd) SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior H5I.c:548:47 H5I.c:1261:41: runtime error: call to function H5T__close_cb through pointer to incorrect function type 'int (*)(void *)' /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:3848: note: H5T__close_cb defined here #0 0x7f402b7736c1 in H5I_dec_ref /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5I.c:1261:41 #1 0x7f402bb3ff13 in H5T__path_find_real /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:4842:13 #2 0x7f402bb2e4da in H5T__register /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:2333:36 #3 0x7f402bb1690a in H5T__register_int /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:2282:8 #4 0x7f402bb0d59d in H5T__init_package /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:1048:15 #5 0x7f402bb063a0 in H5T_init /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:578:5 #6 0x7f402b31b392 in H5_init_library /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:218:8 #7 0x7f402b3215ac in H5open /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:930:5 #8 0x7f402b29f8a6 in H5::FileAccPropList::getConstant() /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp:66:40 #9 0x7f402a9b5446 in __cxx_global_var_init /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp:88:52 #10 0x7f402a9b5446 in _GLOBAL__sub_I_H5FaccProp.cpp /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp #11 0x7f40c408bfad in call_init elf/dl-init.c:74:3 #12 0x7f40c408bfad in call_init elf/dl-init.c:26:1 #13 0x7f40c408c07b in _dl_init elf/dl-init.c:121:5 #14 0x7f40c4089425 in _dl_catch_exception elf/dl-catch.c:215:7 #15 0x7f40c4092a27 in dl_open_worker elf/dl-open.c:799:3 #16 0x7f40c4089398 in _dl_catch_exception elf/dl-catch.c:241:8 #17 0x7f40c4092da7 in _dl_open elf/dl-open.c:874:17 #18 0x7f40c29a9257 in dlopen_doit dlfcn/dlopen.c:56:15 #19 0x7f40c4089398 in _dl_catch_exception elf/dl-catch.c:241:8 #20 0x7f40c40894be in _dl_catch_error elf/dl-catch.c:260:19 #21 0x7f40c29a8d66 in _dlerror_run dlfcn/dlerror.c:138:17 #22 0x7f40c29a9308 in dlopen_implementation dlfcn/dlopen.c:71:10 #23 0x7f40c29a9308 in dlopen dlfcn/dlopen.c:81:12 #24 0x5581770232f6 in dlopen (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x8f2f6) (BuildId: 8b69897b2fcd08f10a8fcf1956a30782b1479dfd) #25 0x7f40c33159ff in AddDLL /home/hornik/src/R/src/main/Rdynload.c:874:14 #26 0x7f40c3314e07 in do_dynload /home/hornik/src/R/src/main/Rdynload.c:1248:12 #27 0x7f40c36f7739 in bcEval_loop /home/hornik/src/R/src/main/eval.c:8114:14 #28 0x7f40c36abfd4 in bcEval /home/hornik/src/R/src/main/eval.c:7497:16 #29 0x7f40c36aa70f in Rf_eval /home/hornik/src/R/src/main/eval.c:1167:8 #30 0x7f40c36b4b45 in R_execClosure /home/hornik/src/R/src/main/eval.c:2389:22 #31 0x7f40c36b063c in applyClosure_core /home/hornik/src/R/src/main/eval.c:2302:16 #32 0x7f40c36ab08f in Rf_applyClosure /home/hornik/src/R/src/main/eval.c:2324:16 #33 0x7f40c36ab08f in Rf_eval /home/hornik/src/R/src/main/eval.c:1280:12 #34 0x7f40c37ee896 in Rf_ReplIteration /home/hornik/src/R/src/main/main.c:264:15 #35 0x7f40c37f18a0 in R_ReplConsole /home/hornik/src/R/src/main/main.c:317:11 #36 0x7f40c37f16b4 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1235:5 #37 0x7f40c37f199a in Rf_mainloop /home/hornik/src/R/src/main/main.c:1242:5 #38 0x5581770a2dd4 in main /home/hornik/src/R/src/main/Rmain.c:29:5 #39 0x7f40c2943ca7 in __libc_start_call_main csu/../sysdeps/nptl/libc_start_call_main.h:58:16 #40 0x7f40c2943d64 in __libc_start_main csu/../csu/libc-start.c:360:3 #41 0x558176fbf370 in _start (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x2b370) (BuildId: 8b69897b2fcd08f10a8fcf1956a30782b1479dfd) 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/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:3848: note: H5T__close_cb defined here #0 0x7f402b76eba9 in H5I__clear_type_cb /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5I.c:548:47 #1 0x7f402bae5657 in H5SL_try_free_safe /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5SL.c:2369:26 #2 0x7f402b76e307 in H5I_clear_type /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5I.c:508:8 #3 0x7f402bb18ed2 in H5T_top_term_package /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:1444:19 #4 0x7f402b31c491 in H5_term_library /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:310:20 #5 0x7f402b3216d0 in H5close /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:960:5 #6 0x7f402b29f410 in H5::H5Library::termH5cpp() /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5Library.cpp:235:24 #7 0x7f40c295c290 in __run_exit_handlers stdlib/exit.c:118:8 #8 0x7f40c295c359 in exit stdlib/exit.c:148:3 #9 0x7f40c3ba0b4c in Rstd_CleanUp /home/hornik/src/R/src/unix/sys-std.c:1300:5 #10 0x7f40c3baadd7 in R_CleanUp /home/hornik/src/R/src/unix/system.c:87:5 #11 0x7f40c37f16e4 in end_Rmainloop /home/hornik/src/R/src/main/main.c:1225:5 #12 0x7f40c37f16e4 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1236:5 #13 0x7f40c37f199a in Rf_mainloop /home/hornik/src/R/src/main/main.c:1242:5 #14 0x5581770a2dd4 in main /home/hornik/src/R/src/main/Rmain.c:29:5 #15 0x7f40c2943ca7 in __libc_start_call_main csu/../sysdeps/nptl/libc_start_call_main.h:58:16 #16 0x7f40c2943d64 in __libc_start_main csu/../csu/libc-start.c:360:3 #17 0x558176fbf370 in _start (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x2b370) (BuildId: 8b69897b2fcd08f10a8fcf1956a30782b1479dfd) SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior H5I.c:548:47 H5I.c:1261:41: runtime error: call to function H5T__close_cb through pointer to incorrect function type 'int (*)(void *)' /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:3848: note: H5T__close_cb defined here #0 0x7fedefd736c1 in H5I_dec_ref /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5I.c:1261:41 #1 0x7fedf013ff13 in H5T__path_find_real /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:4842:13 #2 0x7fedf012e4da in H5T__register /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:2333:36 #3 0x7fedf011690a in H5T__register_int /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:2282:8 #4 0x7fedf010d59d in H5T__init_package /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:1048:15 #5 0x7fedf01063a0 in H5T_init /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:578:5 #6 0x7fedef91b392 in H5_init_library /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:218:8 #7 0x7fedef9215ac in H5open /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:930:5 #8 0x7fedef89f8a6 in H5::FileAccPropList::getConstant() /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp:66:40 #9 0x7fedeefb5446 in __cxx_global_var_init /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp:88:52 #10 0x7fedeefb5446 in _GLOBAL__sub_I_H5FaccProp.cpp /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp #11 0x7fee886d7fad in call_init elf/dl-init.c:74:3 #12 0x7fee886d7fad in call_init elf/dl-init.c:26:1 #13 0x7fee886d807b in _dl_init elf/dl-init.c:121:5 #14 0x7fee886d5425 in _dl_catch_exception elf/dl-catch.c:215:7 #15 0x7fee886dea27 in dl_open_worker elf/dl-open.c:799:3 #16 0x7fee886d5398 in _dl_catch_exception elf/dl-catch.c:241:8 #17 0x7fee886deda7 in _dl_open elf/dl-open.c:874:17 #18 0x7fee86fa9257 in dlopen_doit dlfcn/dlopen.c:56:15 #19 0x7fee886d5398 in _dl_catch_exception elf/dl-catch.c:241:8 #20 0x7fee886d54be in _dl_catch_error elf/dl-catch.c:260:19 #21 0x7fee86fa8d66 in _dlerror_run dlfcn/dlerror.c:138:17 #22 0x7fee86fa9308 in dlopen_implementation dlfcn/dlopen.c:71:10 #23 0x7fee86fa9308 in dlopen dlfcn/dlopen.c:81:12 #24 0x561269d8d2f6 in dlopen (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x8f2f6) (BuildId: 8b69897b2fcd08f10a8fcf1956a30782b1479dfd) #25 0x7fee879159ff in AddDLL /home/hornik/src/R/src/main/Rdynload.c:874:14 #26 0x7fee87914e07 in do_dynload /home/hornik/src/R/src/main/Rdynload.c:1248:12 #27 0x7fee87cf7739 in bcEval_loop /home/hornik/src/R/src/main/eval.c:8114:14 #28 0x7fee87cabfd4 in bcEval /home/hornik/src/R/src/main/eval.c:7497:16 #29 0x7fee87caa70f in Rf_eval /home/hornik/src/R/src/main/eval.c:1167:8 #30 0x7fee87cb4b45 in R_execClosure /home/hornik/src/R/src/main/eval.c:2389:22 #31 0x7fee87cb063c in applyClosure_core /home/hornik/src/R/src/main/eval.c:2302:16 #32 0x7fee87cab08f in Rf_applyClosure /home/hornik/src/R/src/main/eval.c:2324:16 #33 0x7fee87cab08f in Rf_eval /home/hornik/src/R/src/main/eval.c:1280:12 #34 0x7fee87dee896 in Rf_ReplIteration /home/hornik/src/R/src/main/main.c:264:15 #35 0x7fee87df18a0 in R_ReplConsole /home/hornik/src/R/src/main/main.c:317:11 #36 0x7fee87df16b4 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1235:5 #37 0x7fee87df199a in Rf_mainloop /home/hornik/src/R/src/main/main.c:1242:5 #38 0x561269e0cdd4 in main /home/hornik/src/R/src/main/Rmain.c:29:5 #39 0x7fee86f43ca7 in __libc_start_call_main csu/../sysdeps/nptl/libc_start_call_main.h:58:16 #40 0x7fee86f43d64 in __libc_start_main csu/../csu/libc-start.c:360:3 #41 0x561269d29370 in _start (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x2b370) (BuildId: 8b69897b2fcd08f10a8fcf1956a30782b1479dfd) 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/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:3848: note: H5T__close_cb defined here #0 0x7fedefd6eba9 in H5I__clear_type_cb /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5I.c:548:47 #1 0x7fedf00e5657 in H5SL_try_free_safe /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5SL.c:2369:26 #2 0x7fedefd6e307 in H5I_clear_type /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5I.c:508:8 #3 0x7fedf0118ed2 in H5T_top_term_package /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:1444:19 #4 0x7fedef91c491 in H5_term_library /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:310:20 #5 0x7fedef9216d0 in H5close /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:960:5 #6 0x7fedef89f410 in H5::H5Library::termH5cpp() /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5Library.cpp:235:24 #7 0x7fee86f5c290 in __run_exit_handlers stdlib/exit.c:118:8 #8 0x7fee86f5c359 in exit stdlib/exit.c:148:3 #9 0x7fee881a0b4c in Rstd_CleanUp /home/hornik/src/R/src/unix/sys-std.c:1300:5 #10 0x7fee881aadd7 in R_CleanUp /home/hornik/src/R/src/unix/system.c:87:5 #11 0x7fee87df16e4 in end_Rmainloop /home/hornik/src/R/src/main/main.c:1225:5 #12 0x7fee87df16e4 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1236:5 #13 0x7fee87df199a in Rf_mainloop /home/hornik/src/R/src/main/main.c:1242:5 #14 0x561269e0cdd4 in main /home/hornik/src/R/src/main/Rmain.c:29:5 #15 0x7fee86f43ca7 in __libc_start_call_main csu/../sysdeps/nptl/libc_start_call_main.h:58:16 #16 0x7fee86f43d64 in __libc_start_main csu/../csu/libc-start.c:360:3 #17 0x561269d29370 in _start (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x2b370) (BuildId: 8b69897b2fcd08f10a8fcf1956a30782b1479dfd) SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior H5I.c:548:47 * checking Rd files ... [1s/1s] OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING H5I.c:1261:41: runtime error: call to function H5T__close_cb through pointer to incorrect function type 'int (*)(void *)' /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:3848: note: H5T__close_cb defined here #0 0x7fc5707736c1 in H5I_dec_ref /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5I.c:1261:41 #1 0x7fc570b3ff13 in H5T__path_find_real /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:4842:13 #2 0x7fc570b2e4da in H5T__register /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:2333:36 #3 0x7fc570b1690a in H5T__register_int /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:2282:8 #4 0x7fc570b0d59d in H5T__init_package /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:1048:15 #5 0x7fc570b063a0 in H5T_init /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:578:5 #6 0x7fc57031b392 in H5_init_library /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:218:8 #7 0x7fc5703215ac in H5open /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:930:5 #8 0x7fc57029f8a6 in H5::FileAccPropList::getConstant() /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp:66:40 #9 0x7fc56f9b5446 in __cxx_global_var_init /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp:88:52 #10 0x7fc56f9b5446 in _GLOBAL__sub_I_H5FaccProp.cpp /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp #11 0x7fc6091c0fad in call_init elf/dl-init.c:74:3 #12 0x7fc6091c0fad in call_init elf/dl-init.c:26:1 #13 0x7fc6091c107b in _dl_init elf/dl-init.c:121:5 #14 0x7fc6091be425 in _dl_catch_exception elf/dl-catch.c:215:7 #15 0x7fc6091c7a27 in dl_open_worker elf/dl-open.c:799:3 #16 0x7fc6091be398 in _dl_catch_exception elf/dl-catch.c:241:8 #17 0x7fc6091c7da7 in _dl_open elf/dl-open.c:874:17 #18 0x7fc607a99257 in dlopen_doit dlfcn/dlopen.c:56:15 #19 0x7fc6091be398 in _dl_catch_exception elf/dl-catch.c:241:8 #20 0x7fc6091be4be in _dl_catch_error elf/dl-catch.c:260:19 #21 0x7fc607a98d66 in _dlerror_run dlfcn/dlerror.c:138:17 #22 0x7fc607a99308 in dlopen_implementation dlfcn/dlopen.c:71:10 #23 0x7fc607a99308 in dlopen dlfcn/dlopen.c:81:12 #24 0x5643cfe952f6 in dlopen (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x8f2f6) (BuildId: 8b69897b2fcd08f10a8fcf1956a30782b1479dfd) #25 0x7fc6083159ff in AddDLL /home/hornik/src/R/src/main/Rdynload.c:874:14 #26 0x7fc608314e07 in do_dynload /home/hornik/src/R/src/main/Rdynload.c:1248:12 #27 0x7fc6086f7739 in bcEval_loop /home/hornik/src/R/src/main/eval.c:8114:14 #28 0x7fc6086abfd4 in bcEval /home/hornik/src/R/src/main/eval.c:7497:16 #29 0x7fc6086aa70f in Rf_eval /home/hornik/src/R/src/main/eval.c:1167:8 #30 0x7fc6086b4b45 in R_execClosure /home/hornik/src/R/src/main/eval.c:2389:22 #31 0x7fc6086b063c in applyClosure_core /home/hornik/src/R/src/main/eval.c:2302:16 #32 0x7fc6086ab08f in Rf_applyClosure /home/hornik/src/R/src/main/eval.c:2324:16 #33 0x7fc6086ab08f in Rf_eval /home/hornik/src/R/src/main/eval.c:1280:12 #34 0x7fc6087ee896 in Rf_ReplIteration /home/hornik/src/R/src/main/main.c:264:15 #35 0x7fc6087f18a0 in R_ReplConsole /home/hornik/src/R/src/main/main.c:317:11 #36 0x7fc6087f16b4 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1235:5 #37 0x7fc6087f199a in Rf_mainloop /home/hornik/src/R/src/main/main.c:1242:5 #38 0x5643cff14dd4 in main /home/hornik/src/R/src/main/Rmain.c:29:5 #39 0x7fc607a33ca7 in __libc_start_call_main csu/../sysdeps/nptl/libc_start_call_main.h:58:16 #40 0x7fc607a33d64 in __libc_start_main csu/../csu/libc-start.c:360:3 #41 0x5643cfe31370 in _start (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x2b370) (BuildId: 8b69897b2fcd08f10a8fcf1956a30782b1479dfd) 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/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:3848: note: H5T__close_cb defined here #0 0x7fc57076eba9 in H5I__clear_type_cb /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5I.c:548:47 #1 0x7fc570ae5657 in H5SL_try_free_safe /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5SL.c:2369:26 #2 0x7fc57076e307 in H5I_clear_type /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5I.c:508:8 #3 0x7fc570b18ed2 in H5T_top_term_package /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:1444:19 #4 0x7fc57031c491 in H5_term_library /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:310:20 #5 0x7fc5703216d0 in H5close /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:960:5 #6 0x7fc57029f410 in H5::H5Library::termH5cpp() /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5Library.cpp:235:24 #7 0x7fc607a4c290 in __run_exit_handlers stdlib/exit.c:118:8 #8 0x7fc607a4c359 in exit stdlib/exit.c:148:3 #9 0x7fc608ba0b4c in Rstd_CleanUp /home/hornik/src/R/src/unix/sys-std.c:1300:5 #10 0x7fc608baadd7 in R_CleanUp /home/hornik/src/R/src/unix/system.c:87:5 #11 0x7fc6087f16e4 in end_Rmainloop /home/hornik/src/R/src/main/main.c:1225:5 #12 0x7fc6087f16e4 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1236:5 #13 0x7fc6087f199a in Rf_mainloop /home/hornik/src/R/src/main/main.c:1242:5 #14 0x5643cff14dd4 in main /home/hornik/src/R/src/main/Rmain.c:29:5 #15 0x7fc607a33ca7 in __libc_start_call_main csu/../sysdeps/nptl/libc_start_call_main.h:58:16 #16 0x7fc607a33d64 in __libc_start_main csu/../csu/libc-start.c:360:3 #17 0x5643cfe31370 in _start (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x2b370) (BuildId: 8b69897b2fcd08f10a8fcf1956a30782b1479dfd) SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior H5I.c:548:47 All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... WARNING H5I.c:1261:41: runtime error: call to function H5T__close_cb through pointer to incorrect function type 'int (*)(void *)' /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:3848: note: H5T__close_cb defined here #0 0x7f069b7736c1 in H5I_dec_ref /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5I.c:1261:41 #1 0x7f069bb3ff13 in H5T__path_find_real /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:4842:13 #2 0x7f069bb2e4da in H5T__register /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:2333:36 #3 0x7f069bb1690a in H5T__register_int /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:2282:8 #4 0x7f069bb0d59d in H5T__init_package /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:1048:15 #5 0x7f069bb063a0 in H5T_init /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:578:5 #6 0x7f069b31b392 in H5_init_library /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:218:8 #7 0x7f069b3215ac in H5open /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:930:5 #8 0x7f069b29f8a6 in H5::FileAccPropList::getConstant() /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp:66:40 #9 0x7f069a9b5446 in __cxx_global_var_init /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp:88:52 #10 0x7f069a9b5446 in _GLOBAL__sub_I_H5FaccProp.cpp /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp #11 0x7f0734018fad in call_init elf/dl-init.c:74:3 #12 0x7f0734018fad in call_init elf/dl-init.c:26:1 #13 0x7f073401907b in _dl_init elf/dl-init.c:121:5 #14 0x7f0734016425 in _dl_catch_exception elf/dl-catch.c:215:7 #15 0x7f073401fa27 in dl_open_worker elf/dl-open.c:799:3 #16 0x7f0734016398 in _dl_catch_exception elf/dl-catch.c:241:8 #17 0x7f073401fda7 in _dl_open elf/dl-open.c:874:17 #18 0x7f0732899257 in dlopen_doit dlfcn/dlopen.c:56:15 #19 0x7f0734016398 in _dl_catch_exception elf/dl-catch.c:241:8 #20 0x7f07340164be in _dl_catch_error elf/dl-catch.c:260:19 #21 0x7f0732898d66 in _dlerror_run dlfcn/dlerror.c:138:17 #22 0x7f0732899308 in dlopen_implementation dlfcn/dlopen.c:71:10 #23 0x7f0732899308 in dlopen dlfcn/dlopen.c:81:12 #24 0x562cb329d2f6 in dlopen (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x8f2f6) (BuildId: 8b69897b2fcd08f10a8fcf1956a30782b1479dfd) #25 0x7f07331159ff in AddDLL /home/hornik/src/R/src/main/Rdynload.c:874:14 #26 0x7f0733114e07 in do_dynload /home/hornik/src/R/src/main/Rdynload.c:1248:12 #27 0x7f07334f7739 in bcEval_loop /home/hornik/src/R/src/main/eval.c:8114:14 #28 0x7f07334abfd4 in bcEval /home/hornik/src/R/src/main/eval.c:7497:16 #29 0x7f07334aa70f in Rf_eval /home/hornik/src/R/src/main/eval.c:1167:8 #30 0x7f07334b4b45 in R_execClosure /home/hornik/src/R/src/main/eval.c:2389:22 #31 0x7f07334b063c in applyClosure_core /home/hornik/src/R/src/main/eval.c:2302:16 #32 0x7f07334ab08f in Rf_applyClosure /home/hornik/src/R/src/main/eval.c:2324:16 #33 0x7f07334ab08f in Rf_eval /home/hornik/src/R/src/main/eval.c:1280:12 #34 0x7f07335ee896 in Rf_ReplIteration /home/hornik/src/R/src/main/main.c:264:15 #35 0x7f07335f18a0 in R_ReplConsole /home/hornik/src/R/src/main/main.c:317:11 #36 0x7f07335f16b4 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1235:5 #37 0x7f07335f199a in Rf_mainloop /home/hornik/src/R/src/main/main.c:1242:5 #38 0x562cb331cdd4 in main /home/hornik/src/R/src/main/Rmain.c:29:5 #39 0x7f0732833ca7 in __libc_start_call_main csu/../sysdeps/nptl/libc_start_call_main.h:58:16 #40 0x7f0732833d64 in __libc_start_main csu/../csu/libc-start.c:360:3 #41 0x562cb3239370 in _start (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x2b370) (BuildId: 8b69897b2fcd08f10a8fcf1956a30782b1479dfd) 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/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:3848: note: H5T__close_cb defined here #0 0x7f069b76eba9 in H5I__clear_type_cb /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5I.c:548:47 #1 0x7f069bae5657 in H5SL_try_free_safe /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5SL.c:2369:26 #2 0x7f069b76e307 in H5I_clear_type /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5I.c:508:8 #3 0x7f069bb18ed2 in H5T_top_term_package /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:1444:19 #4 0x7f069b31c491 in H5_term_library /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:310:20 #5 0x7f069b3216d0 in H5close /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:960:5 #6 0x7f069b29f410 in H5::H5Library::termH5cpp() /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5Library.cpp:235:24 #7 0x7f073284c290 in __run_exit_handlers stdlib/exit.c:118:8 #8 0x7f073284c359 in exit stdlib/exit.c:148:3 #9 0x7f07339a0b4c in Rstd_CleanUp /home/hornik/src/R/src/unix/sys-std.c:1300:5 #10 0x7f07339aadd7 in R_CleanUp /home/hornik/src/R/src/unix/system.c:87:5 #11 0x7f07335f16e4 in end_Rmainloop /home/hornik/src/R/src/main/main.c:1225:5 #12 0x7f07335f16e4 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1236:5 #13 0x7f07335f199a in Rf_mainloop /home/hornik/src/R/src/main/main.c:1242:5 #14 0x562cb331cdd4 in main /home/hornik/src/R/src/main/Rmain.c:29:5 #15 0x7f0732833ca7 in __libc_start_call_main csu/../sysdeps/nptl/libc_start_call_main.h:58:16 #16 0x7f0732833d64 in __libc_start_main csu/../csu/libc-start.c:360:3 #17 0x562cb3239370 in _start (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x2b370) (BuildId: 8b69897b2fcd08f10a8fcf1956a30782b1479dfd) SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior H5I.c:548:47 H5I.c:1261:41: runtime error: call to function H5T__close_cb through pointer to incorrect function type 'int (*)(void *)' /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:3848: note: H5T__close_cb defined here #0 0x7fe4a11736c1 in H5I_dec_ref /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5I.c:1261:41 #1 0x7fe4a153ff13 in H5T__path_find_real /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:4842:13 #2 0x7fe4a152e4da in H5T__register /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:2333:36 #3 0x7fe4a151690a in H5T__register_int /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:2282:8 #4 0x7fe4a150d59d in H5T__init_package /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:1048:15 #5 0x7fe4a15063a0 in H5T_init /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:578:5 #6 0x7fe4a0d1b392 in H5_init_library /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:218:8 #7 0x7fe4a0d215ac in H5open /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:930:5 #8 0x7fe4a0c9f8a6 in H5::FileAccPropList::getConstant() /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp:66:40 #9 0x7fe4a03b5446 in __cxx_global_var_init /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp:88:52 #10 0x7fe4a03b5446 in _GLOBAL__sub_I_H5FaccProp.cpp /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp #11 0x7fe539ac5fad in call_init elf/dl-init.c:74:3 #12 0x7fe539ac5fad in call_init elf/dl-init.c:26:1 #13 0x7fe539ac607b in _dl_init elf/dl-init.c:121:5 #14 0x7fe539ac3425 in _dl_catch_exception elf/dl-catch.c:215:7 #15 0x7fe539acca27 in dl_open_worker elf/dl-open.c:799:3 #16 0x7fe539ac3398 in _dl_catch_exception elf/dl-catch.c:241:8 #17 0x7fe539accda7 in _dl_open elf/dl-open.c:874:17 #18 0x7fe5383a9257 in dlopen_doit dlfcn/dlopen.c:56:15 #19 0x7fe539ac3398 in _dl_catch_exception elf/dl-catch.c:241:8 #20 0x7fe539ac34be in _dl_catch_error elf/dl-catch.c:260:19 #21 0x7fe5383a8d66 in _dlerror_run dlfcn/dlerror.c:138:17 #22 0x7fe5383a9308 in dlopen_implementation dlfcn/dlopen.c:71:10 #23 0x7fe5383a9308 in dlopen dlfcn/dlopen.c:81:12 #24 0x556b4fe702f6 in dlopen (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x8f2f6) (BuildId: 8b69897b2fcd08f10a8fcf1956a30782b1479dfd) #25 0x7fe538d159ff in AddDLL /home/hornik/src/R/src/main/Rdynload.c:874:14 #26 0x7fe538d14e07 in do_dynload /home/hornik/src/R/src/main/Rdynload.c:1248:12 #27 0x7fe5390f7739 in bcEval_loop /home/hornik/src/R/src/main/eval.c:8114:14 #28 0x7fe5390abfd4 in bcEval /home/hornik/src/R/src/main/eval.c:7497:16 #29 0x7fe5390aa70f in Rf_eval /home/hornik/src/R/src/main/eval.c:1167:8 #30 0x7fe5390b4b45 in R_execClosure /home/hornik/src/R/src/main/eval.c:2389:22 #31 0x7fe5390b063c in applyClosure_core /home/hornik/src/R/src/main/eval.c:2302:16 #32 0x7fe5390ab08f in Rf_applyClosure /home/hornik/src/R/src/main/eval.c:2324:16 #33 0x7fe5390ab08f in Rf_eval /home/hornik/src/R/src/main/eval.c:1280:12 #34 0x7fe5391ee896 in Rf_ReplIteration /home/hornik/src/R/src/main/main.c:264:15 #35 0x7fe5391f18a0 in R_ReplConsole /home/hornik/src/R/src/main/main.c:317:11 #36 0x7fe5391f16b4 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1235:5 #37 0x7fe5391f199a in Rf_mainloop /home/hornik/src/R/src/main/main.c:1242:5 #38 0x556b4feefdd4 in main /home/hornik/src/R/src/main/Rmain.c:29:5 #39 0x7fe538343ca7 in __libc_start_call_main csu/../sysdeps/nptl/libc_start_call_main.h:58:16 #40 0x7fe538343d64 in __libc_start_main csu/../csu/libc-start.c:360:3 #41 0x556b4fe0c370 in _start (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x2b370) (BuildId: 8b69897b2fcd08f10a8fcf1956a30782b1479dfd) 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/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:3848: note: H5T__close_cb defined here #0 0x7fe4a116eba9 in H5I__clear_type_cb /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5I.c:548:47 #1 0x7fe4a14e5657 in H5SL_try_free_safe /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5SL.c:2369:26 #2 0x7fe4a116e307 in H5I_clear_type /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5I.c:508:8 #3 0x7fe4a1518ed2 in H5T_top_term_package /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:1444:19 #4 0x7fe4a0d1c491 in H5_term_library /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:310:20 #5 0x7fe4a0d216d0 in H5close /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:960:5 #6 0x7fe4a0c9f410 in H5::H5Library::termH5cpp() /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5Library.cpp:235:24 #7 0x7fe53835c290 in __run_exit_handlers stdlib/exit.c:118:8 #8 0x7fe53835c359 in exit stdlib/exit.c:148:3 #9 0x7fe5395a0b4c in Rstd_CleanUp /home/hornik/src/R/src/unix/sys-std.c:1300:5 #10 0x7fe5395aadd7 in R_CleanUp /home/hornik/src/R/src/unix/system.c:87:5 #11 0x7fe5391f16e4 in end_Rmainloop /home/hornik/src/R/src/main/main.c:1225:5 #12 0x7fe5391f16e4 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1236:5 #13 0x7fe5391f199a in Rf_mainloop /home/hornik/src/R/src/main/main.c:1242:5 #14 0x556b4feefdd4 in main /home/hornik/src/R/src/main/Rmain.c:29:5 #15 0x7fe538343ca7 in __libc_start_call_main csu/../sysdeps/nptl/libc_start_call_main.h:58:16 #16 0x7fe538343d64 in __libc_start_main csu/../csu/libc-start.c:360:3 #17 0x556b4fe0c370 in _start (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x2b370) (BuildId: 8b69897b2fcd08f10a8fcf1956a30782b1479dfd) SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior H5I.c:548:47 H5I.c:1261:41: runtime error: call to function H5T__close_cb through pointer to incorrect function type 'int (*)(void *)' /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:3848: note: H5T__close_cb defined here #0 0x7f02f4b736c1 in H5I_dec_ref /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5I.c:1261:41 #1 0x7f02f4f3ff13 in H5T__path_find_real /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:4842:13 #2 0x7f02f4f2e4da in H5T__register /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:2333:36 #3 0x7f02f4f1690a in H5T__register_int /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:2282:8 #4 0x7f02f4f0d59d in H5T__init_package /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:1048:15 #5 0x7f02f4f063a0 in H5T_init /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:578:5 #6 0x7f02f471b392 in H5_init_library /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:218:8 #7 0x7f02f47215ac in H5open /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:930:5 #8 0x7f02f469f8a6 in H5::FileAccPropList::getConstant() /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp:66:40 #9 0x7f02f3db5446 in __cxx_global_var_init /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp:88:52 #10 0x7f02f3db5446 in _GLOBAL__sub_I_H5FaccProp.cpp /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp #11 0x7f038d469fad in call_init elf/dl-init.c:74:3 #12 0x7f038d469fad in call_init elf/dl-init.c:26:1 #13 0x7f038d46a07b in _dl_init elf/dl-init.c:121:5 #14 0x7f038d467425 in _dl_catch_exception elf/dl-catch.c:215:7 #15 0x7f038d470a27 in dl_open_worker elf/dl-open.c:799:3 #16 0x7f038d467398 in _dl_catch_exception elf/dl-catch.c:241:8 #17 0x7f038d470da7 in _dl_open elf/dl-open.c:874:17 #18 0x7f038bc99257 in dlopen_doit dlfcn/dlopen.c:56:15 #19 0x7f038d467398 in _dl_catch_exception elf/dl-catch.c:241:8 #20 0x7f038d4674be in _dl_catch_error elf/dl-catch.c:260:19 #21 0x7f038bc98d66 in _dlerror_run dlfcn/dlerror.c:138:17 #22 0x7f038bc99308 in dlopen_implementation dlfcn/dlopen.c:71:10 #23 0x7f038bc99308 in dlopen dlfcn/dlopen.c:81:12 #24 0x559c50a052f6 in dlopen (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x8f2f6) (BuildId: 8b69897b2fcd08f10a8fcf1956a30782b1479dfd) #25 0x7f038c5159ff in AddDLL /home/hornik/src/R/src/main/Rdynload.c:874:14 #26 0x7f038c514e07 in do_dynload /home/hornik/src/R/src/main/Rdynload.c:1248:12 #27 0x7f038c8f7739 in bcEval_loop /home/hornik/src/R/src/main/eval.c:8114:14 #28 0x7f038c8abfd4 in bcEval /home/hornik/src/R/src/main/eval.c:7497:16 #29 0x7f038c8aa70f in Rf_eval /home/hornik/src/R/src/main/eval.c:1167:8 #30 0x7f038c8b4b45 in R_execClosure /home/hornik/src/R/src/main/eval.c:2389:22 #31 0x7f038c8b063c in applyClosure_core /home/hornik/src/R/src/main/eval.c:2302:16 #32 0x7f038c8ab08f in Rf_applyClosure /home/hornik/src/R/src/main/eval.c:2324:16 #33 0x7f038c8ab08f in Rf_eval /home/hornik/src/R/src/main/eval.c:1280:12 #34 0x7f038c9ee896 in Rf_ReplIteration /home/hornik/src/R/src/main/main.c:264:15 #35 0x7f038c9f18a0 in R_ReplConsole /home/hornik/src/R/src/main/main.c:317:11 #36 0x7f038c9f16b4 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1235:5 #37 0x7f038c9f199a in Rf_mainloop /home/hornik/src/R/src/main/main.c:1242:5 #38 0x559c50a84dd4 in main /home/hornik/src/R/src/main/Rmain.c:29:5 #39 0x7f038bc33ca7 in __libc_start_call_main csu/../sysdeps/nptl/libc_start_call_main.h:58:16 #40 0x7f038bc33d64 in __libc_start_main csu/../csu/libc-start.c:360:3 #41 0x559c509a1370 in _start (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x2b370) (BuildId: 8b69897b2fcd08f10a8fcf1956a30782b1479dfd) 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/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:3848: note: H5T__close_cb defined here #0 0x7f02f4b6eba9 in H5I__clear_type_cb /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5I.c:548:47 #1 0x7f02f4ee5657 in H5SL_try_free_safe /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5SL.c:2369:26 #2 0x7f02f4b6e307 in H5I_clear_type /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5I.c:508:8 #3 0x7f02f4f18ed2 in H5T_top_term_package /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:1444:19 #4 0x7f02f471c491 in H5_term_library /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:310:20 #5 0x7f02f47216d0 in H5close /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:960:5 #6 0x7f02f469f410 in H5::H5Library::termH5cpp() /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5Library.cpp:235:24 #7 0x7f038bc4c290 in __run_exit_handlers stdlib/exit.c:118:8 #8 0x7f038bc4c359 in exit stdlib/exit.c:148:3 #9 0x7f038cda0b4c in Rstd_CleanUp /home/hornik/src/R/src/unix/sys-std.c:1300:5 #10 0x7f038cdaadd7 in R_CleanUp /home/hornik/src/R/src/unix/system.c:87:5 #11 0x7f038c9f16e4 in end_Rmainloop /home/hornik/src/R/src/main/main.c:1225:5 #12 0x7f038c9f16e4 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1236:5 #13 0x7f038c9f199a in Rf_mainloop /home/hornik/src/R/src/main/main.c:1242:5 #14 0x559c50a84dd4 in main /home/hornik/src/R/src/main/Rmain.c:29:5 #15 0x7f038bc33ca7 in __libc_start_call_main csu/../sysdeps/nptl/libc_start_call_main.h:58:16 #16 0x7f038bc33d64 in __libc_start_main csu/../csu/libc-start.c:360:3 #17 0x559c509a1370 in _start (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x2b370) (BuildId: 8b69897b2fcd08f10a8fcf1956a30782b1479dfd) SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior H5I.c:548:47 * checking Rd \usage sections ... 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/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:3848: note: H5T__close_cb defined here #0 0x7f3d737736c1 in H5I_dec_ref /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5I.c:1261:41 #1 0x7f3d73b3ff13 in H5T__path_find_real /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:4842:13 #2 0x7f3d73b2e4da in H5T__register /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:2333:36 #3 0x7f3d73b1690a in H5T__register_int /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:2282:8 #4 0x7f3d73b0d59d in H5T__init_package /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:1048:15 #5 0x7f3d73b063a0 in H5T_init /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:578:5 #6 0x7f3d7331b392 in H5_init_library /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:218:8 #7 0x7f3d733215ac in H5open /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:930:5 #8 0x7f3d7329f8a6 in H5::FileAccPropList::getConstant() /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp:66:40 #9 0x7f3d729b5446 in __cxx_global_var_init /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp:88:52 #10 0x7f3d729b5446 in _GLOBAL__sub_I_H5FaccProp.cpp /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp #11 0x7f3e0c087fad in call_init elf/dl-init.c:74:3 #12 0x7f3e0c087fad in call_init elf/dl-init.c:26:1 #13 0x7f3e0c08807b in _dl_init elf/dl-init.c:121:5 #14 0x7f3e0c085425 in _dl_catch_exception elf/dl-catch.c:215:7 #15 0x7f3e0c08ea27 in dl_open_worker elf/dl-open.c:799:3 #16 0x7f3e0c085398 in _dl_catch_exception elf/dl-catch.c:241:8 #17 0x7f3e0c08eda7 in _dl_open elf/dl-open.c:874:17 #18 0x7f3e0a899257 in dlopen_doit dlfcn/dlopen.c:56:15 #19 0x7f3e0c085398 in _dl_catch_exception elf/dl-catch.c:241:8 #20 0x7f3e0c0854be in _dl_catch_error elf/dl-catch.c:260:19 #21 0x7f3e0a898d66 in _dlerror_run dlfcn/dlerror.c:138:17 #22 0x7f3e0a899308 in dlopen_implementation dlfcn/dlopen.c:71:10 #23 0x7f3e0a899308 in dlopen dlfcn/dlopen.c:81:12 #24 0x564626c872f6 in dlopen (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x8f2f6) (BuildId: 8b69897b2fcd08f10a8fcf1956a30782b1479dfd) #25 0x7f3e0b1159ff in AddDLL /home/hornik/src/R/src/main/Rdynload.c:874:14 #26 0x7f3e0b114e07 in do_dynload /home/hornik/src/R/src/main/Rdynload.c:1248:12 #27 0x7f3e0b4f7739 in bcEval_loop /home/hornik/src/R/src/main/eval.c:8114:14 #28 0x7f3e0b4abfd4 in bcEval /home/hornik/src/R/src/main/eval.c:7497:16 #29 0x7f3e0b4aa70f in Rf_eval /home/hornik/src/R/src/main/eval.c:1167:8 #30 0x7f3e0b4b4b45 in R_execClosure /home/hornik/src/R/src/main/eval.c:2389:22 #31 0x7f3e0b4b063c in applyClosure_core /home/hornik/src/R/src/main/eval.c:2302:16 #32 0x7f3e0b4ab08f in Rf_applyClosure /home/hornik/src/R/src/main/eval.c:2324:16 #33 0x7f3e0b4ab08f in Rf_eval /home/hornik/src/R/src/main/eval.c:1280:12 #34 0x7f3e0b5ee896 in Rf_ReplIteration /home/hornik/src/R/src/main/main.c:264:15 #35 0x7f3e0b5f18a0 in R_ReplConsole /home/hornik/src/R/src/main/main.c:317:11 #36 0x7f3e0b5f16b4 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1235:5 #37 0x7f3e0b5f199a in Rf_mainloop /home/hornik/src/R/src/main/main.c:1242:5 #38 0x564626d06dd4 in main /home/hornik/src/R/src/main/Rmain.c:29:5 #39 0x7f3e0a833ca7 in __libc_start_call_main csu/../sysdeps/nptl/libc_start_call_main.h:58:16 #40 0x7f3e0a833d64 in __libc_start_main csu/../csu/libc-start.c:360:3 #41 0x564626c23370 in _start (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x2b370) (BuildId: 8b69897b2fcd08f10a8fcf1956a30782b1479dfd) 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/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:3848: note: H5T__close_cb defined here #0 0x7f3d7376eba9 in H5I__clear_type_cb /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5I.c:548:47 #1 0x7f3d73ae5657 in H5SL_try_free_safe /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5SL.c:2369:26 #2 0x7f3d7376e307 in H5I_clear_type /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5I.c:508:8 #3 0x7f3d73b18ed2 in H5T_top_term_package /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5T.c:1444:19 #4 0x7f3d7331c491 in H5_term_library /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:310:20 #5 0x7f3d733216d0 in H5close /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/src/H5.c:960:5 #6 0x7f3d7329f410 in H5::H5Library::termH5cpp() /home/hornik/tmp/scratch/RtmpB78nVN/R.INSTALL3dae194002b20d/Rhdf5lib/src/hdf5/c++/src/H5Library.cpp:235:24 #7 0x7f3e0a84c290 in __run_exit_handlers stdlib/exit.c:118:8 #8 0x7f3e0a84c359 in exit stdlib/exit.c:148:3 #9 0x7f3e0b9a0b4c in Rstd_CleanUp /home/hornik/src/R/src/unix/sys-std.c:1300:5 #10 0x7f3e0b9aadd7 in R_CleanUp /home/hornik/src/R/src/unix/system.c:87:5 #11 0x7f3e0b5f16e4 in end_Rmainloop /home/hornik/src/R/src/main/main.c:1225:5 #12 0x7f3e0b5f16e4 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1236:5 #13 0x7f3e0b5f199a in Rf_mainloop /home/hornik/src/R/src/main/main.c:1242:5 #14 0x564626d06dd4 in main /home/hornik/src/R/src/main/Rmain.c:29:5 #15 0x7f3e0a833ca7 in __libc_start_call_main csu/../sysdeps/nptl/libc_start_call_main.h:58:16 #16 0x7f3e0a833d64 in __libc_start_main csu/../csu/libc-start.c:360:3 #17 0x564626c23370 in _start (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x2b370) (BuildId: 8b69897b2fcd08f10a8fcf1956a30782b1479dfd) SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior H5I.c:548:47 The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... [1s/1s] OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking examples ... [12s/12s] OK * checking PDF version of manual ... [6s/6s] OK * checking HTML version of manual ... [3s/3s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 4 WARNINGs, 4 NOTEs