* using log directory ‘/home/hornik/tmp/CRAN_special_clang-san/rbiom.Rcheck’ * using R Under development (unstable) (2025-01-21 r87610) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.6 (1+b1) Debian flang-new version 19.1.6 (1+b1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘rbiom/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘rbiom’ version ‘2.0.12’ * package encoding: UTF-8 * 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 whether package ‘rbiom’ can be installed ... [36s/36s] OK * used C compiler: ‘Debian clang version 19.1.6 (1+b1)’ * 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 ... [4s/4s] OK * checking whether the package can be loaded with stated dependencies ... [3s/3s] OK * checking whether the package can be unloaded cleanly ... [3s/3s] OK * checking whether the namespace can be loaded with stated dependencies ... [4s/4s] OK * checking whether the namespace can be unloaded cleanly ... [4s/4s] OK * checking loading without being on the library search path ... [4s/4s] OK * checking whether startup messages can be suppressed ... [4s/4s] 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/RtmphgDXKk/R.INSTALL3807221f67f69b/Rhdf5lib/src/hdf5/src/H5T.c:3848: note: H5T__close_cb defined here #0 0x7f8f1bcbffa1 in H5I_dec_ref /home/hornik/tmp/scratch/RtmphgDXKk/R.INSTALL3807221f67f69b/Rhdf5lib/src/hdf5/src/H5I.c:1261:41 #1 0x7f8f1c079543 in H5T__path_find_real /home/hornik/tmp/scratch/RtmphgDXKk/R.INSTALL3807221f67f69b/Rhdf5lib/src/hdf5/src/H5T.c:4842:13 #2 0x7f8f1c067b0a in H5T__register /home/hornik/tmp/scratch/RtmphgDXKk/R.INSTALL3807221f67f69b/Rhdf5lib/src/hdf5/src/H5T.c:2333:36 #3 0x7f8f1c04ff3a in H5T__register_int /home/hornik/tmp/scratch/RtmphgDXKk/R.INSTALL3807221f67f69b/Rhdf5lib/src/hdf5/src/H5T.c:2282:8 #4 0x7f8f1c046bcd in H5T__init_package /home/hornik/tmp/scratch/RtmphgDXKk/R.INSTALL3807221f67f69b/Rhdf5lib/src/hdf5/src/H5T.c:1048:15 #5 0x7f8f1c03f9d0 in H5T_init /home/hornik/tmp/scratch/RtmphgDXKk/R.INSTALL3807221f67f69b/Rhdf5lib/src/hdf5/src/H5T.c:578:5 #6 0x7f8f1b8a60d2 in H5_init_library /home/hornik/tmp/scratch/RtmphgDXKk/R.INSTALL3807221f67f69b/Rhdf5lib/src/hdf5/src/H5.c:218:8 #7 0x7f8f1b8ac2ec in H5open /home/hornik/tmp/scratch/RtmphgDXKk/R.INSTALL3807221f67f69b/Rhdf5lib/src/hdf5/src/H5.c:930:5 #8 0x7f8f1b8963d6 in _H5constants /home/hornik/tmp/scratch/RtmpwhBkAm/R.INSTALL3883fa5799e0f8/rhdf5/src/H5constants.c:52:35 #9 0x7f8f4294825a in R_doDotCall /home/hornik/src/R/src/main/dotcode.c:751:11 #10 0x7f8f429a15c2 in do_dotcall /home/hornik/src/R/src/main/dotcode.c:1437:11 #11 0x7f8f42af32b9 in bcEval_loop /home/hornik/src/R/src/main/eval.c:8122:14 #12 0x7f8f42aa7914 in bcEval /home/hornik/src/R/src/main/eval.c:7505:16 #13 0x7f8f42aa604f in Rf_eval /home/hornik/src/R/src/main/eval.c:1167:8 #14 0x7f8f42ab07a5 in R_execClosure /home/hornik/src/R/src/main/eval.c:2393:22 #15 0x7f8f42aac29c in applyClosure_core /home/hornik/src/R/src/main/eval.c:2306:16 #16 0x7f8f42aa69cf in Rf_applyClosure /home/hornik/src/R/src/main/eval.c:2328:16 #17 0x7f8f42aa69cf in Rf_eval /home/hornik/src/R/src/main/eval.c:1280:12 #18 0x7f8f42bea3a7 in Rf_ReplIteration /home/hornik/src/R/src/main/main.c:265:2 #19 0x7f8f42bed1c0 in R_ReplConsole /home/hornik/src/R/src/main/main.c:317:11 #20 0x7f8f42becfe4 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1219:5 #21 0x7f8f42bed28a in Rf_mainloop /home/hornik/src/R/src/main/main.c:1226:5 #22 0x5620f6e1edd4 in main /home/hornik/src/R/src/main/Rmain.c:29:5 #23 0x7f8f41e33d67 in __libc_start_call_main csu/../sysdeps/nptl/libc_start_call_main.h:58:16 #24 0x7f8f41e33e24 in __libc_start_main csu/../csu/libc-start.c:360:3 #25 0x5620f6d3b370 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/RtmphgDXKk/R.INSTALL3807221f67f69b/Rhdf5lib/src/hdf5/src/H5T.c:3848: note: H5T__close_cb defined here #0 0x7f8f1bcbb489 in H5I__clear_type_cb /home/hornik/tmp/scratch/RtmphgDXKk/R.INSTALL3807221f67f69b/Rhdf5lib/src/hdf5/src/H5I.c:548:47 #1 0x7f8f1c01ec87 in H5SL_try_free_safe /home/hornik/tmp/scratch/RtmphgDXKk/R.INSTALL3807221f67f69b/Rhdf5lib/src/hdf5/src/H5SL.c:2369:26 #2 0x7f8f1bcbabe7 in H5I_clear_type /home/hornik/tmp/scratch/RtmphgDXKk/R.INSTALL3807221f67f69b/Rhdf5lib/src/hdf5/src/H5I.c:508:8 #3 0x7f8f1c052502 in H5T_top_term_package /home/hornik/tmp/scratch/RtmphgDXKk/R.INSTALL3807221f67f69b/Rhdf5lib/src/hdf5/src/H5T.c:1444:19 #4 0x7f8f1b8a71d1 in H5_term_library /home/hornik/tmp/scratch/RtmphgDXKk/R.INSTALL3807221f67f69b/Rhdf5lib/src/hdf5/src/H5.c:310:20 #5 0x7f8f41e4c260 in __run_exit_handlers stdlib/exit.c:108:8 #6 0x7f8f41e4c319 in exit stdlib/exit.c:138:3 #7 0x7f8f42f9cbdc in Rstd_CleanUp /home/hornik/src/R/src/unix/sys-std.c:1301:5 #8 0x7f8f42fa6e37 in R_CleanUp /home/hornik/src/R/src/unix/system.c:87:5 #9 0x7f8f42bed014 in end_Rmainloop /home/hornik/src/R/src/main/main.c:1209:5 #10 0x7f8f42bed014 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1220:5 #11 0x7f8f42bed28a in Rf_mainloop /home/hornik/src/R/src/main/main.c:1226:5 #12 0x5620f6e1edd4 in main /home/hornik/src/R/src/main/Rmain.c:29:5 #13 0x7f8f41e33d67 in __libc_start_call_main csu/../sysdeps/nptl/libc_start_call_main.h:58:16 #14 0x7f8f41e33e24 in __libc_start_main csu/../csu/libc-start.c:360:3 #15 0x5620f6d3b370 in _start (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x2b370) (BuildId: ce9a0af4806c342e07ea21f487bd9584f1fffacb) SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior H5I.c:548:47 * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [80s/80s] OK * checking Rd files ... [3s/3s] OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... [22s/22s] OK * checking LazyData ... 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 ... [138s/139s] OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed adiv_corrplot 9.307 11.658 21.227 adiv_boxplot 8.394 0.248 8.675 taxa_stats 6.634 0.148 6.798 taxa_boxplot 6.056 0.136 6.207 stats_corrplot 5.793 0.168 5.963 bdiv_heatmap 5.791 0.098 5.891 taxa_heatmap 5.495 0.120 5.619 bdiv_corrplot 5.004 0.189 5.196 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [36s/36s] OK Running ‘testthat.r’ [36s/36s] * checking PDF version of manual ... [10s/10s] OK * checking HTML version of manual ... [12s/12s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 NOTE