* using log directory ‘/data/gannet/ripley/R/packages/tests-clang-ASAN/iglm.Rcheck’ * using R Under development (unstable) (2026-03-15 r89634) * using platform: x86_64-pc-linux-gnu * R was compiled by clang version 22.1.1 (https://github.com/llvm/llvm-project fef02d48c08db859ef83f84232ed78bd9d1c323a) flang version 22.1.1 (https://github.com/llvm/llvm-project fef02d48c08db859ef83f84232ed78bd9d1c323a) * running under: Fedora Linux 42 (Workstation Edition) * using session charset: UTF-8 * current time: 2026-03-16 03:25:35 UTC * using option ‘--no-stop-on-test-error’ * checking for file ‘iglm/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘iglm’ version ‘1.2’ * 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 ‘iglm’ can be installed ... [126s/93s] OK * used C++ compiler: ‘clang version 22.1.1 (https://github.com/llvm/llvm-project fef02d48c08db859ef83f84232ed78bd9d1c323a)’ * checking C++ specification ... INFO specified C++17 * checking package directory ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking compiled code ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [18s/18s] OK * checking tests ... [17s/14s] ERROR Running ‘testthat.R’ [16s/13s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(iglm) Loading required package: RcppProgress > > test_check("iglm") 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| OMP: Warning #96: Cannot form a team with 8 threads, using 2 instead. OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set). 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| ================================================================= ==1076972==ERROR: AddressSanitizer: heap-buffer-overflow on address 0x7bebdd6f0f6d at pc 0x7bcbc83721db bp 0x7ffc3d924850 sp 0x7ffc3d924848 READ of size 1 at 0x7bebdd6f0f6d thread T0 #0 0x7bcbc83721da in Network::get_val(int, int) const /data/gannet/ripley/R/packages/tests-clang-ASAN/iglm/src/../inst/include/iglm/network_class.h:160:12 #1 0x7bcbc83721da in XZ_class::initialize_overlap_counts() /data/gannet/ripley/R/packages/tests-clang-ASAN/iglm/src/../inst/include/iglm/xz_class.h:163:21 #2 0x7bcbc8375bdd in XZ_class::XZ_class(int, bool, arma::Mat, arma::Col, arma::Mat, arma::Mat, std::__1::basic_string, std::__1::allocator>, double) /data/gannet/ripley/R/packages/tests-clang-ASAN/iglm/src/../inst/include/iglm/xz_class.h:137:5 #3 0x7bcbc837479e in XYZ_class::XYZ_class(int, bool, arma::Col, arma::Col, arma::Mat, arma::Mat, arma::Mat, std::__1::basic_string, std::__1::allocator>, std::__1::basic_string, std::__1::allocator>, double, double) /data/gannet/ripley/R/packages/tests-clang-ASAN/iglm/src/../inst/include/iglm/xyz_class.h:34:5 #4 0x7bcbc829eb3a in xyz_count_global(arma::Mat const&, arma::Col const&, arma::Col const&, arma::Mat const&, arma::Mat const&, bool, std::__1::vector, std::__1::allocator>, std::__1::allocator, std::__1::allocator>>>, int, std::__1::vector, std::__1::allocator>>&, std::__1::vector>&, std::__1::basic_string, std::__1::allocator>, std::__1::basic_string, std::__1::allocator>, double, double) /data/gannet/ripley/R/packages/tests-clang-ASAN/iglm/src/xyz_sampling.cpp:224:13 #5 0x7bcbc82437a7 in _iglm_xyz_count_global /data/gannet/ripley/R/packages/tests-clang-ASAN/iglm/src/RcppExports.cpp:43:34 #6 0x55a69159b6f5 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c #7 0x55a69165d8fd in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8682:21 #8 0x55a691645164 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515:16 #9 0x55a6916436a1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #10 0x55a69168bb6c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389:39 #11 0x55a69168ad31 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302:16 #12 0x55a6916440c6 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324:16 #13 0x55a6916440c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280:12 #14 0x55a69169d1d5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3581:8 #15 0x55a691643be0 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232:12 #16 0x55a69169a379 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2992:10 #17 0x55a691643be0 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232:12 #18 0x55a6916a1c63 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955:13 #19 0x55a69165235a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8132:14 #20 0x55a691645164 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515:16 #21 0x55a6916436a1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #22 0x55a69168bb6c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389:39 #23 0x55a69168ad31 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302:16 #24 0x55a6916440c6 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324:16 #25 0x55a6916440c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280:12 #26 0x55a6916a25ca in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3973:9 #27 0x55a69165235a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8132:14 #28 0x55a691645164 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515:16 #29 0x55a6916436a1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #30 0x55a69168bb6c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389:39 #31 0x55a69168ad31 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302:16 #32 0x55a691694851 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324:16 #33 0x55a691694851 in R_forceAndCall /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2456:8 #34 0x55a69144ecf1 in do_lapply /data/gannet/ripley/R/svn/R-devel/src/main/apply.c:75:8 #35 0x55a69174a4f9 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1419:11 #36 0x55a691657b73 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8152:15 #37 0x55a691645164 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515:16 #38 0x55a6916436a1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #39 0x55a69168bb6c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389:39 #40 0x55a69168ad31 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302:16 #41 0x55a6916440c6 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324:16 #42 0x55a6916440c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280:12 #43 0x55a691713c21 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264:23 #44 0x55a691716450 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317:11 #45 0x55a691716450 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235:5 #46 0x55a6917164e2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242:5 #47 0x55a69141bd3c in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #48 0x7fcbe0012574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #49 0x7fcbe0012627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #50 0x55a6913337d4 in _start (/data/gannet/ripley/R/clang-ASAN/bin/exec/R+0x17d4) 0x7bebdd6f0f6d is located 3 bytes before 9-byte region [0x7bebdd6f0f70,0x7bebdd6f0f79) allocated by thread T0 here: #0 0x55a6913d8bb4 in malloc /home/runner/work/llvm-project/llvm-project/compiler-rt/lib/asan/asan_malloc_linux.cpp:67:3 #1 0x7fcbddc1f3fb in operator new(unsigned long) (/lib64/libstdc++.so.6+0x1f3fb) (BuildId: 51787ae23973475ac7373bc252b400c7229de8e7) #2 0x7bcbc8376915 in Network::Network(int, bool, arma::Mat) /data/gannet/ripley/R/packages/tests-clang-ASAN/iglm/src/../inst/include/iglm/network_class.h:46:13 #3 0x7bcbc8374f24 in XZ_class::XZ_class(int, bool, arma::Mat, arma::Col, arma::Mat, arma::Mat, std::__1::basic_string, std::__1::allocator>, double) /data/gannet/ripley/R/packages/tests-clang-ASAN/iglm/src/../inst/include/iglm/xz_class.h:117:5 #4 0x7bcbc837479e in XYZ_class::XYZ_class(int, bool, arma::Col, arma::Col, arma::Mat, arma::Mat, arma::Mat, std::__1::basic_string, std::__1::allocator>, std::__1::basic_string, std::__1::allocator>, double, double) /data/gannet/ripley/R/packages/tests-clang-ASAN/iglm/src/../inst/include/iglm/xyz_class.h:34:5 #5 0x7bcbc829eb3a in xyz_count_global(arma::Mat const&, arma::Col const&, arma::Col const&, arma::Mat const&, arma::Mat const&, bool, std::__1::vector, std::__1::allocator>, std::__1::allocator, std::__1::allocator>>>, int, std::__1::vector, std::__1::allocator>>&, std::__1::vector>&, std::__1::basic_string, std::__1::allocator>, std::__1::basic_string, std::__1::allocator>, double, double) /data/gannet/ripley/R/packages/tests-clang-ASAN/iglm/src/xyz_sampling.cpp:224:13 #6 0x7bcbc82437a7 in _iglm_xyz_count_global /data/gannet/ripley/R/packages/tests-clang-ASAN/iglm/src/RcppExports.cpp:43:34 #7 0x55a69159b6f5 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c #8 0x55a69165d8fd in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8682:21 #9 0x55a691645164 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515:16 #10 0x55a6916436a1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #11 0x55a69168bb6c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389:39 #12 0x55a69168ad31 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302:16 #13 0x55a6916440c6 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324:16 #14 0x55a6916440c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280:12 #15 0x55a69169d1d5 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3581:8 #16 0x55a691643be0 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232:12 #17 0x55a69169a379 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2992:10 #18 0x55a691643be0 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232:12 #19 0x55a6916a1c63 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955:13 #20 0x55a69165235a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8132:14 #21 0x55a691645164 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515:16 #22 0x55a6916436a1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #23 0x55a69168bb6c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389:39 #24 0x55a69168ad31 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302:16 #25 0x55a6916440c6 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324:16 #26 0x55a6916440c6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280:12 #27 0x55a6916a25ca in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3973:9 #28 0x55a69165235a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8132:14 #29 0x55a691645164 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515:16 #30 0x55a6916436a1 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #31 0x55a69168bb6c in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389:39 SUMMARY: AddressSanitizer: heap-buffer-overflow /data/gannet/ripley/R/packages/tests-clang-ASAN/iglm/src/../inst/include/iglm/network_class.h:160:12 in Network::get_val(int, int) const Shadow bytes around the buggy address: 0x7bebdd6f0c80: fa fa 00 04 fa fa fd fa fa fa fd fa fa fa 00 00 0x7bebdd6f0d00: fa fa fd fa fa fa 00 00 fa fa 00 00 fa fa fd fa 0x7bebdd6f0d80: fa fa fd fa fa fa fd fa fa fa fd fa fa fa fd fa 0x7bebdd6f0e00: fa fa 00 00 fa fa fd fa fa fa 00 00 fa fa 00 00 0x7bebdd6f0e80: fa fa fd fa fa fa fd fa fa fa fd fa fa fa fd fa =>0x7bebdd6f0f00: fa fa fd fa fa fa 00 01 fa fa 00 01 fa[fa]00 01 0x7bebdd6f0f80: fa fa 00 fa fa fa fd fa fa fa fd fd fa fa fd fd 0x7bebdd6f1000: fa fa fd fd fa fa fd fd fa fa fd fd fa fa fd fd 0x7bebdd6f1080: fa fa fd fd fa fa fd fd fa fa fd fd fa fa fd fd 0x7bebdd6f1100: fa fa fd fa fa fa fd fa fa fa fd fa fa fa fd fa 0x7bebdd6f1180: fa fa fd fd fa fa fd fa fa fa fd fa fa fa fd fd 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 ==1076972==ABORTING * checking package vignettes ... OK * checking re-building of vignette outputs ... [37s/37s] OK * DONE Status: 1 ERROR