* using log directory ‘/data/gannet/ripley/R/packages/tests-gcc-SAN/graphpcor.Rcheck’ * using R Under development (unstable) (2026-01-14 r89303) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2) GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2) * running under: Fedora Linux 42 (Workstation Edition) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘graphpcor/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘graphpcor’ version ‘0.1.15’ * package encoding: UTF-8 * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package ‘graphpcor’ can be installed ... [101s/128s] OK * used C compiler: ‘gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’ * checking package directory ... OK * checking whether the package can be loaded ... [22s/34s] OK * checking whether the package can be loaded with stated dependencies ... [22s/31s] OK * checking whether the package can be unloaded cleanly ... [22s/33s] OK * checking whether the namespace can be loaded with stated dependencies ... [19s/32s] OK * checking whether the namespace can be unloaded cleanly ... [20s/26s] OK * checking loading without being on the library search path ... [22s/31s] OK * checking compiled code ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [26s/35s] ERROR Running examples in ‘graphpcor-Ex.R’ failed The error most likely occurred in: > ### 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:116:6: runtime error: index 2 out of bounds for type 'double [*]' #0 0x7b3c5a9c6011 in cpcCholesky /data/gannet/ripley/R/packages/tests-gcc-SAN/graphpcor/src/graphpcor_utils.c:116 #1 0x7b3c5a9c6d9b in inla_cgeneric_LKJ /data/gannet/ripley/R/packages/tests-gcc-SAN/graphpcor/src/cgeneric_LKJ.c:193 #2 0x7b3de8471dfe in inla_cgeneric_element_get /tmp/RtmpgGcpoj/R.INSTALL2433587431752c/INLAtools/src/cgeneric_get.c:363 #3 0x00000074f082 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:780 #4 0x000000753bca in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1437 #5 0x0000008ceb12 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8132 #6 0x0000008bbd5b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #7 0x00000085c5b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #8 0x0000008722fa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #9 0x0000008763ba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #10 0x000000a96dd3 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #11 0x000000a96dd3 in applyMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:120 #12 0x000000a9abd0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473 #13 0x000000a9cb55 in Rf_usemethod.isra.0 /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:513 #14 0x000000a9d776 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579 #15 0x0000008dbd21 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8152 #16 0x0000008bbd5b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #17 0x00000085c5b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #18 0x0000008722fa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #19 0x0000008763ba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #20 0x00000085cc53 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #21 0x00000085cc53 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #22 0x000000a02408 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #23 0x000000a02408 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #24 0x000000a104ea in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235 #25 0x000000a10582 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242 #26 0x00000041318f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #27 0x7f3e014115f4 in __libc_start_call_main (/lib64/libc.so.6+0x35f4) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03) #28 0x7f3e014116a7 in __libc_start_main@@GLIBC_2.34 (/lib64/libc.so.6+0x36a7) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03) #29 0x000000413b74 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x413b74) (BuildId: c84ba7ce6eb358d998562f72463652524c845173) graphpcor_utils.c:116:10: runtime error: store to address 0x7ffebca445f0 with insufficient space for an object of type 'double' 0x7ffebca445f0: note: pointer points here 32 33 e3 3f 10 98 36 0c 8e 7d 00 00 30 f5 93 bf 67 0f 00 00 30 46 a4 bc fe 7f 00 00 80 a9 9f fc ^ #0 0x7b3c5a9c5f38 in cpcCholesky /data/gannet/ripley/R/packages/tests-gcc-SAN/graphpcor/src/graphpcor_utils.c:116 #1 0x7b3c5a9c6d9b in inla_cgeneric_LKJ /data/gannet/ripley/R/packages/tests-gcc-SAN/graphpcor/src/cgeneric_LKJ.c:193 #2 0x7b3de8471dfe in inla_cgeneric_element_get /tmp/RtmpgGcpoj/R.INSTALL2433587431752c/INLAtools/src/cgeneric_get.c:363 #3 0x00000074f082 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:780 #4 0x000000753bca in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1437 #5 0x0000008ceb12 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8132 #6 0x0000008bbd5b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #7 0x00000085c5b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #8 0x0000008722fa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #9 0x0000008763ba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #10 0x000000a96dd3 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #11 0x000000a96dd3 in applyMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:120 #12 0x000000a9abd0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473 #13 0x000000a9cb55 in Rf_usemethod.isra.0 /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:513 #14 0x000000a9d776 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579 #15 0x0000008dbd21 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8152 #16 0x0000008bbd5b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #17 0x00000085c5b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #18 0x0000008722fa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #19 0x0000008763ba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #20 0x00000085cc53 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #21 0x00000085cc53 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #22 0x000000a02408 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #23 0x000000a02408 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #24 0x000000a104ea in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235 #25 0x000000a10582 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242 #26 0x00000041318f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #27 0x7f3e014115f4 in __libc_start_call_main (/lib64/libc.so.6+0x35f4) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03) #28 0x7f3e014116a7 in __libc_start_main@@GLIBC_2.34 (/lib64/libc.so.6+0x36a7) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03) #29 0x000000413b74 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x413b74) (BuildId: c84ba7ce6eb358d998562f72463652524c845173) ================================================================= ==1567567==ERROR: AddressSanitizer: dynamic-stack-buffer-overflow on address 0x7ffebca445f0 at pc 0x7b3c5a9c59dc bp 0x7ffebca445b0 sp 0x7ffebca445a8 WRITE of size 8 at 0x7ffebca445f0 thread T0 #0 0x7b3c5a9c59db in cpcCholesky /data/gannet/ripley/R/packages/tests-gcc-SAN/graphpcor/src/graphpcor_utils.c:116 #1 0x7b3c5a9c6d9b in inla_cgeneric_LKJ /data/gannet/ripley/R/packages/tests-gcc-SAN/graphpcor/src/cgeneric_LKJ.c:193 #2 0x7b3de8471dfe in inla_cgeneric_element_get /tmp/RtmpgGcpoj/R.INSTALL2433587431752c/INLAtools/src/cgeneric_get.c:363 #3 0x00000074f082 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:780 #4 0x000000753bca in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1437 #5 0x0000008ceb12 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8132 #6 0x0000008bbd5b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #7 0x00000085c5b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #8 0x0000008722fa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #9 0x0000008763ba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #10 0x000000a96dd3 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #11 0x000000a96dd3 in applyMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:120 #12 0x000000a9abd0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473 #13 0x000000a9cb55 in Rf_usemethod.isra.0 /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:513 #14 0x000000a9d776 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579 #15 0x0000008dbd21 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8152 #16 0x0000008bbd5b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #17 0x00000085c5b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #18 0x0000008722fa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #19 0x0000008763ba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #20 0x00000085cc53 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #21 0x00000085cc53 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #22 0x000000a02408 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #23 0x000000a02408 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #24 0x000000a104ea in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235 #25 0x000000a10582 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242 #26 0x00000041318f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #27 0x7f3e014115f4 in __libc_start_call_main (/lib64/libc.so.6+0x35f4) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03) #28 0x7f3e014116a7 in __libc_start_main@@GLIBC_2.34 (/lib64/libc.so.6+0x36a7) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03) #29 0x000000413b74 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x413b74) (BuildId: c84ba7ce6eb358d998562f72463652524c845173) Address 0x7ffebca445f0 is located in stack of thread T0 SUMMARY: AddressSanitizer: dynamic-stack-buffer-overflow /data/gannet/ripley/R/packages/tests-gcc-SAN/graphpcor/src/graphpcor_utils.c:116 in cpcCholesky Shadow bytes around the buggy address: 0x7ffebca44300: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7ffebca44380: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7ffebca44400: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7ffebca44480: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7ffebca44500: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 =>0x7ffebca44580: 00 00 00 00 00 00 00 00 ca ca ca ca 00 00[cb]cb 0x7ffebca44600: cb cb cb cb 00 00 00 00 ca ca ca ca 00 00 00 00 0x7ffebca44680: 00 00 cb cb cb cb cb cb 00 00 00 00 00 00 00 00 0x7ffebca44700: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7ffebca44780: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7ffebca44800: ca ca ca ca 00 00 00 00 00 00 cb cb cb cb cb cb 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 ==1567567==ABORTING * checking package vignettes ... OK * checking re-building of vignette outputs ... [91s/105s] OK * DONE Status: 1 ERROR