* using log directory ‘/home/hornik/tmp/CRAN_special_clang-san/graphpcor.Rcheck’ * using R Under development (unstable) (2026-01-15 r89304) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 21.1.8 (1) Debian flang version 21.1.8 (1) * running under: Debian GNU/Linux forky/sid * using session charset: UTF-8 * checking for file ‘graphpcor/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘graphpcor’ version ‘0.1.16’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Package suggested but not available for checking: ‘INLA’ * 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 ‘graphpcor’ can be installed ... [28s/29s] OK * used C compiler: ‘Debian clang version 21.1.8 (1+b1)’ * 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 ... [6s/6s] OK * checking whether the package can be loaded with stated dependencies ... [5s/5s] OK * checking whether the package can be unloaded cleanly ... [5s/5s] OK * checking whether the namespace can be loaded with stated dependencies ... [5s/5s] OK * checking whether the namespace can be unloaded cleanly ... [5s/5s] 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 refstr.c:79:29: runtime error: member access within null pointer of type 'refstr_t' (aka 'struct refstr_t') #0 0x7b2cd6416349 in agstrdup /home/hornik/tmp/scratch/RtmpJbkx1P/R.INSTALL25622f14f6bb05/Rgraphviz/src/graphviz/lib/graph/refstr.c:79:29 #1 0x7b2cd63ff96b in agNEWgraph /home/hornik/tmp/scratch/RtmpJbkx1P/R.INSTALL25622f14f6bb05/Rgraphviz/src/graphviz/lib/graph/graph.c:243:15 #2 0x7b2cd63fee90 in agopen /home/hornik/tmp/scratch/RtmpJbkx1P/R.INSTALL25622f14f6bb05/Rgraphviz/src/graphviz/lib/graph/graph.c:291:9 #3 0x7b2cd63f6674 in initproto /home/hornik/tmp/scratch/RtmpJbkx1P/R.INSTALL25622f14f6bb05/Rgraphviz/src/graphviz/lib/graph/attribs.c:183:22 #4 0x7b2cd63f6674 in aginitlib /home/hornik/tmp/scratch/RtmpJbkx1P/R.INSTALL25622f14f6bb05/Rgraphviz/src/graphviz/lib/graph/attribs.c:332:2 #5 0x7b2cd628c907 in gvContextPlugins /home/hornik/tmp/scratch/RtmpJbkx1P/R.INSTALL25622f14f6bb05/Rgraphviz/src/graphviz/lib/gvc/gvc.c:61:5 #6 0x7b2cd6010856 in Rgraphviz_init /home/hornik/tmp/scratch/RtmpJbkx1P/R.INSTALL25622f14f6bb05/Rgraphviz/src/init.c:29:11 #7 0x7f2cfcb3bcaa in R_doDotCall /home/hornik/src/R/src/main/dotcode.c:751:11 #8 0x7f2cfcb94bec in do_dotcall /home/hornik/src/R/src/main/dotcode.c:1437:11 #9 0x7f2cfcce71d6 in bcEval_loop /home/hornik/src/R/src/main/eval.c:8132:14 #10 0x7f2cfcc9ba34 in bcEval /home/hornik/src/R/src/main/eval.c:7515:16 #11 0x7f2cfcc9a16f in Rf_eval /home/hornik/src/R/src/main/eval.c:1167:8 #12 0x7f2cfcca499b in R_execClosure /home/hornik/src/R/src/main/eval.c:2389:22 #13 0x7f2cfcca0293 in applyClosure_core /home/hornik/src/R/src/main/eval.c:2302:16 #14 0x7f2cfcc9aaef in Rf_applyClosure /home/hornik/src/R/src/main/eval.c:2324:16 #15 0x7f2cfcc9aaef in Rf_eval /home/hornik/src/R/src/main/eval.c:1280:12 #16 0x7f2cfcddf3f5 in Rf_ReplIteration /home/hornik/src/R/src/main/main.c:264:15 #17 0x7f2cfcde2550 in R_ReplConsole /home/hornik/src/R/src/main/main.c:317:11 #18 0x7f2cfcde2364 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1235:5 #19 0x7f2cfcde264a in Rf_mainloop /home/hornik/src/R/src/main/main.c:1242:5 #20 0x55df1342d004 in main /home/hornik/src/R/src/main/Rmain.c:29:5 #21 0x7f2cfbe29f74 in __libc_start_call_main csu/../sysdeps/nptl/libc_start_call_main.h:58:16 #22 0x7f2cfbe2a026 in __libc_start_main csu/../csu/libc-start.c:360:3 #23 0x55df13342380 in _start (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x2c380) (BuildId: bc88c46ef9240773c07d57c927010d00876dfe01) SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior refstr.c:79:29 * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [39s/39s] OK * 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 ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [7s/7s] ERROR Running examples in ‘graphpcor-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: cgeneric_LKJ > ### Title: Build an 'cgeneric' model for the LKG prior on correlation > ### matrix. > ### Aliases: cgeneric_LKJ > > ### ** Examples > > ## a cgeneric model for the LKJ prior > ## for theta from the CPC parametrization > cglkj <- cgeneric( + model = "LKJ", n = 3, eta = 2, + useINLAprecomp = FALSE)##!is.na(packageCheck("INLA", "25.12.16"))) > > ## correlation matrix, p = 3 > cc <- matrix(c(1,.8,-.625, 0.8,1,-.5, -0.625,-.5,1), 3) > > ## CPC parametrization: C(theta) > (bb <- basecor(cc)) Parameters (CPC parametrization): [1] 1.0986131 -0.7331689 0.0000000 Base correlation matrix: [,1] [,2] [,3] [1,] 1.000 0.8 -0.625 [2,] 0.800 1.0 -0.500 [3,] -0.625 -0.5 1.000 > th <- bb$theta > > ## p(theta | eta) > prior(cglkj, theta = th) graphpcor_utils.c:116:5: runtime error: index 2 out of bounds for type 'double[n - 1]' #0 0x7b1f2af9efeb in cpcCholesky /home/hornik/tmp/CRAN_special_clang-san/graphpcor.Rcheck/00_pkg_src/graphpcor/src/graphpcor_utils.c:116:10 #1 0x7b1f2af8e0c6 in inla_cgeneric_LKJ /home/hornik/tmp/CRAN_special_clang-san/graphpcor.Rcheck/00_pkg_src/graphpcor/src/cgeneric_LKJ.c:193:3 #2 0x7b1f2c8a0eb8 in inla_cgeneric_element_get /home/hornik/tmp/scratch/RtmpdXB8KA/R.INSTALL25a3ad7663221/INLAtools/src/cgeneric_get.c:363:10 #3 0x7f1f5554ce6e in R_doDotCall /home/hornik/src/R/src/main/dotcode.c:780:11 #4 0x7f1f55594bec in do_dotcall /home/hornik/src/R/src/main/dotcode.c:1437:11 #5 0x7f1f556e71d6 in bcEval_loop /home/hornik/src/R/src/main/eval.c:8132:14 #6 0x7f1f5569ba34 in bcEval /home/hornik/src/R/src/main/eval.c:7515:16 #7 0x7f1f5569a16f in Rf_eval /home/hornik/src/R/src/main/eval.c:1167:8 #8 0x7f1f556a499b in R_execClosure /home/hornik/src/R/src/main/eval.c:2389:22 #9 0x7f1f556a0293 in applyClosure_core /home/hornik/src/R/src/main/eval.c:2302:16 #10 0x7f1f5569e510 in Rf_applyClosure /home/hornik/src/R/src/main/eval.c:2324:16 #11 0x7f1f55839569 in dispatchMethod /home/hornik/src/R/src/main/objects.c:473:16 #12 0x7f1f55837873 in Rf_usemethod /home/hornik/src/R/src/main/objects.c:513:10 #13 0x7f1f5583a645 in do_usemethod /home/hornik/src/R/src/main/objects.c:579:9 #14 0x7f1f556d88c1 in bcEval_loop /home/hornik/src/R/src/main/eval.c:8152:15 #15 0x7f1f5569ba34 in bcEval /home/hornik/src/R/src/main/eval.c:7515:16 #16 0x7f1f5569a16f in Rf_eval /home/hornik/src/R/src/main/eval.c:1167:8 #17 0x7f1f556a499b in R_execClosure /home/hornik/src/R/src/main/eval.c:2389:22 #18 0x7f1f556a0293 in applyClosure_core /home/hornik/src/R/src/main/eval.c:2302:16 #19 0x7f1f5569aaef in Rf_applyClosure /home/hornik/src/R/src/main/eval.c:2324:16 #20 0x7f1f5569aaef in Rf_eval /home/hornik/src/R/src/main/eval.c:1280:12 #21 0x7f1f557df3f5 in Rf_ReplIteration /home/hornik/src/R/src/main/main.c:264:15 #22 0x7f1f557e2550 in R_ReplConsole /home/hornik/src/R/src/main/main.c:317:11 #23 0x7f1f557e2364 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1235:5 #24 0x7f1f557e264a in Rf_mainloop /home/hornik/src/R/src/main/main.c:1242:5 #25 0x56222be87004 in main /home/hornik/src/R/src/main/Rmain.c:29:5 #26 0x7f1f54829f74 in __libc_start_call_main csu/../sysdeps/nptl/libc_start_call_main.h:58:16 #27 0x7f1f5482a026 in __libc_start_main csu/../csu/libc-start.c:360:3 #28 0x56222bd9c380 in _start (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x2c380) (BuildId: bc88c46ef9240773c07d57c927010d00876dfe01) SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior graphpcor_utils.c:116:5 ================================================================= ==2468541==ERROR: AddressSanitizer: dynamic-stack-buffer-overflow on address 0x7ffe0208eef0 at pc 0x7b1f2af9f65d bp 0x7ffe0208eeb0 sp 0x7ffe0208eea8 WRITE of size 8 at 0x7ffe0208eef0 thread T0 #0 0x7b1f2af9f65c in cpcCholesky /home/hornik/tmp/CRAN_special_clang-san/graphpcor.Rcheck/00_pkg_src/graphpcor/src/graphpcor_utils.c:116:10 #1 0x7b1f2af8e0c6 in inla_cgeneric_LKJ /home/hornik/tmp/CRAN_special_clang-san/graphpcor.Rcheck/00_pkg_src/graphpcor/src/cgeneric_LKJ.c:193:3 #2 0x7b1f2c8a0eb8 in inla_cgeneric_element_get /home/hornik/tmp/scratch/RtmpdXB8KA/R.INSTALL25a3ad7663221/INLAtools/src/cgeneric_get.c:363:10 #3 0x7f1f5554ce6e in R_doDotCall /home/hornik/src/R/src/main/dotcode.c:780:11 #4 0x7f1f55594bec in do_dotcall /home/hornik/src/R/src/main/dotcode.c:1437:11 #5 0x7f1f556e71d6 in bcEval_loop /home/hornik/src/R/src/main/eval.c:8132:14 #6 0x7f1f5569ba34 in bcEval /home/hornik/src/R/src/main/eval.c:7515:16 #7 0x7f1f5569a16f in Rf_eval /home/hornik/src/R/src/main/eval.c:1167:8 #8 0x7f1f556a499b in R_execClosure /home/hornik/src/R/src/main/eval.c:2389:22 #9 0x7f1f556a0293 in applyClosure_core /home/hornik/src/R/src/main/eval.c:2302:16 #10 0x7f1f5569e510 in Rf_applyClosure /home/hornik/src/R/src/main/eval.c:2324:16 #11 0x7f1f55839569 in dispatchMethod /home/hornik/src/R/src/main/objects.c:473:16 #12 0x7f1f55837873 in Rf_usemethod /home/hornik/src/R/src/main/objects.c:513:10 #13 0x7f1f5583a645 in do_usemethod /home/hornik/src/R/src/main/objects.c:579:9 #14 0x7f1f556d88c1 in bcEval_loop /home/hornik/src/R/src/main/eval.c:8152:15 #15 0x7f1f5569ba34 in bcEval /home/hornik/src/R/src/main/eval.c:7515:16 #16 0x7f1f5569a16f in Rf_eval /home/hornik/src/R/src/main/eval.c:1167:8 #17 0x7f1f556a499b in R_execClosure /home/hornik/src/R/src/main/eval.c:2389:22 #18 0x7f1f556a0293 in applyClosure_core /home/hornik/src/R/src/main/eval.c:2302:16 #19 0x7f1f5569aaef in Rf_applyClosure /home/hornik/src/R/src/main/eval.c:2324:16 #20 0x7f1f5569aaef in Rf_eval /home/hornik/src/R/src/main/eval.c:1280:12 #21 0x7f1f557df3f5 in Rf_ReplIteration /home/hornik/src/R/src/main/main.c:264:15 #22 0x7f1f557e2550 in R_ReplConsole /home/hornik/src/R/src/main/main.c:317:11 #23 0x7f1f557e2364 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1235:5 #24 0x7f1f557e264a in Rf_mainloop /home/hornik/src/R/src/main/main.c:1242:5 #25 0x56222be87004 in main /home/hornik/src/R/src/main/Rmain.c:29:5 #26 0x7f1f54829f74 in __libc_start_call_main csu/../sysdeps/nptl/libc_start_call_main.h:58:16 #27 0x7f1f5482a026 in __libc_start_main csu/../csu/libc-start.c:360:3 #28 0x56222bd9c380 in _start (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x2c380) (BuildId: bc88c46ef9240773c07d57c927010d00876dfe01) Address 0x7ffe0208eef0 is located in stack of thread T0 SUMMARY: AddressSanitizer: dynamic-stack-buffer-overflow /home/hornik/tmp/CRAN_special_clang-san/graphpcor.Rcheck/00_pkg_src/graphpcor/src/graphpcor_utils.c:116:10 in cpcCholesky Shadow bytes around the buggy address: 0x7ffe0208ec00: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7ffe0208ec80: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7ffe0208ed00: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7ffe0208ed80: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7ffe0208ee00: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 =>0x7ffe0208ee80: 00 00 00 00 00 00 00 00 ca ca ca ca 00 00[cb]cb 0x7ffe0208ef00: cb cb cb cb ca ca ca ca 00 00 00 00 00 00 cb cb 0x7ffe0208ef80: cb cb cb cb 00 00 00 00 00 00 00 00 00 00 00 00 0x7ffe0208f000: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7ffe0208f080: 00 00 00 00 00 00 00 00 00 00 00 00 ca ca ca ca 0x7ffe0208f100: 00 00 00 00 00 00 cb cb cb cb cb cb ca ca ca ca Shadow byte legend (one shadow byte represents 8 application bytes): Addressable: 00 Partially addressable: 01 02 03 04 05 06 07 Heap left redzone: fa Freed heap region: fd Stack left redzone: f1 Stack mid redzone: f2 Stack right redzone: f3 Stack after return: f5 Stack use after scope: f8 Global redzone: f9 Global init order: f6 Poisoned by user: f7 Container overflow: fc Array cookie: ac Intra object redzone: bb ASan internal: fe Left alloca redzone: ca Right alloca redzone: cb ==2468541==ABORTING * checking for unstated dependencies in ‘demo’ ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [1s/1s] OK * checking PDF version of manual ... [5s/5s] OK * checking HTML version of manual ... [5s/5s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 1 NOTE