* using log directory ‘/home/hornik/tmp/CRAN_special_clang-san/enviGCMS.Rcheck’
* using R Under development (unstable) (2025-01-11 r87563)
* 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 ‘enviGCMS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘enviGCMS’ version ‘0.7.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Package suggested but not available for checking: ‘xcms’
* 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 ‘enviGCMS’ can be installed ... [12s/12s] OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] 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/Rtmp2EOGSM/R.INSTALL3e57ec441f4029/Rhdf5lib/src/hdf5/src/H5T.c:3848: note: H5T__close_cb defined here
    #0 0x7f7000567191 in H5I_dec_ref /home/hornik/tmp/scratch/Rtmp2EOGSM/R.INSTALL3e57ec441f4029/Rhdf5lib/src/hdf5/src/H5I.c:1261:41
    #1 0x7f70009339e3 in H5T__path_find_real /home/hornik/tmp/scratch/Rtmp2EOGSM/R.INSTALL3e57ec441f4029/Rhdf5lib/src/hdf5/src/H5T.c:4842:13
    #2 0x7f7000921faa in H5T__register /home/hornik/tmp/scratch/Rtmp2EOGSM/R.INSTALL3e57ec441f4029/Rhdf5lib/src/hdf5/src/H5T.c:2333:36
    #3 0x7f700090a3da in H5T__register_int /home/hornik/tmp/scratch/Rtmp2EOGSM/R.INSTALL3e57ec441f4029/Rhdf5lib/src/hdf5/src/H5T.c:2282:8
    #4 0x7f700090106d in H5T__init_package /home/hornik/tmp/scratch/Rtmp2EOGSM/R.INSTALL3e57ec441f4029/Rhdf5lib/src/hdf5/src/H5T.c:1048:15
    #5 0x7f70008f9e70 in H5T_init /home/hornik/tmp/scratch/Rtmp2EOGSM/R.INSTALL3e57ec441f4029/Rhdf5lib/src/hdf5/src/H5T.c:578:5
    #6 0x7f700010ee62 in H5_init_library /home/hornik/tmp/scratch/Rtmp2EOGSM/R.INSTALL3e57ec441f4029/Rhdf5lib/src/hdf5/src/H5.c:218:8
    #7 0x7f700011507c in H5open /home/hornik/tmp/scratch/Rtmp2EOGSM/R.INSTALL3e57ec441f4029/Rhdf5lib/src/hdf5/src/H5.c:930:5
    #8 0x7f7000093476 in H5::FileAccPropList::getConstant() /home/hornik/tmp/scratch/Rtmp2EOGSM/R.INSTALL3e57ec441f4029/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp:66:40
    #9 0x7f6fff79ed86 in __cxx_global_var_init /home/hornik/tmp/scratch/Rtmp2EOGSM/R.INSTALL3e57ec441f4029/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp:88:52
    #10 0x7f6fff79ed86 in _GLOBAL__sub_I_H5FaccProp.cpp /home/hornik/tmp/scratch/Rtmp2EOGSM/R.INSTALL3e57ec441f4029/Rhdf5lib/src/hdf5/c++/src/H5FaccProp.cpp
    #11 0x7f701a76329d in call_init elf/dl-init.c:74:3
    #12 0x7f701a76329d in call_init elf/dl-init.c:26:1
    #13 0x7f701a76338b in _dl_init elf/dl-init.c:121:5
    #14 0x7f701a760535 in _dl_catch_exception elf/dl-catch.c:215:7
    #15 0x7f701a769f2d in dl_open_worker elf/dl-open.c:804:5
    #16 0x7f701a7604a8 in _dl_catch_exception elf/dl-catch.c:241:8
    #17 0x7f701a76a2a7 in _dl_open elf/dl-open.c:880:17
    #18 0x7f7018fb1f97 in dlopen_doit dlfcn/dlopen.c:56:15
    #19 0x7f701a7604a8 in _dl_catch_exception elf/dl-catch.c:241:8
    #20 0x7f701a7605ce in _dl_catch_error elf/dl-catch.c:260:19
    #21 0x7f7018fb1aa6 in _dlerror_run dlfcn/dlerror.c:138:17
    #22 0x7f7018fb2048 in dlopen_implementation dlfcn/dlopen.c:71:10
    #23 0x7f7018fb2048 in dlopen dlfcn/dlopen.c:81:12
    #24 0x558c9130c2f6 in dlopen (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x8f2f6) (BuildId: ce9a0af4806c342e07ea21f487bd9584f1fffacb)
    #25 0x7f70199127cf in AddDLL /home/hornik/src/R/src/main/Rdynload.c:855:14
    #26 0x7f7019911bd7 in do_dynload /home/hornik/src/R/src/main/Rdynload.c:1229:12
    #27 0x7f7019ced889 in bcEval_loop /home/hornik/src/R/src/main/eval.c:8122:14
    #28 0x7f7019ca1ee4 in bcEval /home/hornik/src/R/src/main/eval.c:7505:16
    #29 0x7f7019ca061f in Rf_eval /home/hornik/src/R/src/main/eval.c:1167:8
    #30 0x7f7019ca251f in forcePromise /home/hornik/src/R/src/main/eval.c:976:13
    #31 0x7f7019ca074e in Rf_eval /home/hornik/src/R/src/main/eval.c:1193:2
    #32 0x7f7019cf6cc2 in bcEval_loop /home/hornik/src/R/src/main/eval.c:8016:16
    #33 0x7f7019ca1ee4 in bcEval /home/hornik/src/R/src/main/eval.c:7505:16
    #34 0x7f7019ca061f in Rf_eval /home/hornik/src/R/src/main/eval.c:1167:8
    #35 0x7f7019caad75 in R_execClosure /home/hornik/src/R/src/main/eval.c:2393:22
    #36 0x7f7019ca686c in applyClosure_core /home/hornik/src/R/src/main/eval.c:2306:16
    #37 0x7f7019ca0f9f in Rf_applyClosure /home/hornik/src/R/src/main/eval.c:2328:16
    #38 0x7f7019ca0f9f in Rf_eval /home/hornik/src/R/src/main/eval.c:1280:12
    #39 0x7f7019de4977 in Rf_ReplIteration /home/hornik/src/R/src/main/main.c:265:2
    #40 0x7f7019de7790 in R_ReplConsole /home/hornik/src/R/src/main/main.c:317:11
    #41 0x7f7019de75b4 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1219:5
    #42 0x7f7019de785a in Rf_mainloop /home/hornik/src/R/src/main/main.c:1226:5
    #43 0x558c9138bdd4 in main /home/hornik/src/R/src/main/Rmain.c:29:5
    #44 0x7f7018f4dd67 in __libc_start_call_main csu/../sysdeps/nptl/libc_start_call_main.h:58:16
    #45 0x7f7018f4de24 in __libc_start_main csu/../csu/libc-start.c:360:3
    #46 0x558c912a8370 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/Rtmp2EOGSM/R.INSTALL3e57ec441f4029/Rhdf5lib/src/hdf5/src/H5T.c:3848: note: H5T__close_cb defined here
    #0 0x7f7000562679 in H5I__clear_type_cb /home/hornik/tmp/scratch/Rtmp2EOGSM/R.INSTALL3e57ec441f4029/Rhdf5lib/src/hdf5/src/H5I.c:548:47
    #1 0x7f70008d9127 in H5SL_try_free_safe /home/hornik/tmp/scratch/Rtmp2EOGSM/R.INSTALL3e57ec441f4029/Rhdf5lib/src/hdf5/src/H5SL.c:2369:26
    #2 0x7f7000561dd7 in H5I_clear_type /home/hornik/tmp/scratch/Rtmp2EOGSM/R.INSTALL3e57ec441f4029/Rhdf5lib/src/hdf5/src/H5I.c:508:8
    #3 0x7f700090c9a2 in H5T_top_term_package /home/hornik/tmp/scratch/Rtmp2EOGSM/R.INSTALL3e57ec441f4029/Rhdf5lib/src/hdf5/src/H5T.c:1444:19
    #4 0x7f700010ff61 in H5_term_library /home/hornik/tmp/scratch/Rtmp2EOGSM/R.INSTALL3e57ec441f4029/Rhdf5lib/src/hdf5/src/H5.c:310:20
    #5 0x7f70001151a0 in H5close /home/hornik/tmp/scratch/Rtmp2EOGSM/R.INSTALL3e57ec441f4029/Rhdf5lib/src/hdf5/src/H5.c:960:5
    #6 0x7f7000092fe0 in H5::H5Library::termH5cpp() /home/hornik/tmp/scratch/Rtmp2EOGSM/R.INSTALL3e57ec441f4029/Rhdf5lib/src/hdf5/c++/src/H5Library.cpp:235:24
    #7 0x7f7018f66260 in __run_exit_handlers stdlib/exit.c:108:8
    #8 0x7f7018f66319 in exit stdlib/exit.c:138:3
    #9 0x7f701a1971bc in Rstd_CleanUp /home/hornik/src/R/src/unix/sys-std.c:1301:5
    #10 0x7f701a1a1417 in R_CleanUp /home/hornik/src/R/src/unix/system.c:87:5
    #11 0x7f7019de75e4 in end_Rmainloop /home/hornik/src/R/src/main/main.c:1209:5
    #12 0x7f7019de75e4 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1220:5
    #13 0x7f7019de785a in Rf_mainloop /home/hornik/src/R/src/main/main.c:1226:5
    #14 0x558c9138bdd4 in main /home/hornik/src/R/src/main/Rmain.c:29:5
    #15 0x7f7018f4dd67 in __libc_start_call_main csu/../sysdeps/nptl/libc_start_call_main.h:58:16
    #16 0x7f7018f4de24 in __libc_start_main csu/../csu/libc-start.c:360:3
    #17 0x558c912a8370 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 ... [29s/29s] OK
* checking Rd files ... [2s/2s] 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 ... [1s/1s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [16s/15s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [2s/2s] OK
  Running ‘testthat.R’ [1s/1s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [13s/13s] OK
* checking PDF version of manual ... [6s/6s] OK
* checking HTML version of manual ... [4s/5s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 NOTE