* using log directory ‘/data/gannet/ripley/R/packages/tests-gcc-SAN/cpp11bigwig.Rcheck’ * using R Under development (unstable) (2026-06-18 r90173) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7) GNU Fortran (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7) * running under: Fedora Linux 42 (Workstation Edition) * using session charset: UTF-8 * current time: 2026-06-18 19:17:48 UTC * using option ‘--no-stop-on-test-error’ * checking for file ‘cpp11bigwig/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘cpp11bigwig’ version ‘0.2.0’ * 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 ‘cpp11bigwig’ can be installed ... [97s/56s] OK * used C++ compiler: ‘g++ (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’ * checking package directory ... OK * checking whether the package can be loaded ... [12s/12s] OK * checking whether the package can be loaded with stated dependencies ... [12s/12s] OK * checking whether the package can be unloaded cleanly ... [11s/11s] OK * checking whether the namespace can be loaded with stated dependencies ... [11s/11s] OK * checking whether the namespace can be unloaded cleanly ... [12s/12s] OK * checking loading without being on the library search path ... [12s/12s] OK * checking compiled code ... OK * checking examples ... [12s/12s] ERROR Running examples in ‘cpp11bigwig-Ex.R’ failed The error most likely occurred in: > ### Name: read_bigbed > ### Title: Read data from bigBed files. > ### Aliases: read_bigbed > > ### ** Examples > > bb <- system.file("extdata", "test.bb", package = "cpp11bigwig") > > read_bigbed(bb) ================================================================= ==2131163==ERROR: AddressSanitizer: global-buffer-overflow on address 0x7b7f7e172293 at pc 0x7b7f7de7a85e bp 0x7ffce9df5f50 sp 0x7ffce9df5f48 READ of size 1 at 0x7b7f7e172293 thread T0 #0 0x7b7f7de7a85d in std::__detail::_Scanner::_M_scan_normal() /usr/include/c++/15/bits/regex_scanner.tcc:98 #1 0x7b7f7de7a85d in std::__detail::_Scanner::_M_advance() /usr/include/c++/15/bits/regex_scanner.tcc:79 #2 0x7b7f7de7d799 in std::__detail::_Compiler >::_M_match_token(std::__detail::_ScannerBase::_TokenT) /usr/include/c++/15/bits/regex_compiler.tcc:578 #3 0x7b7f7de84097 in std::__detail::_Compiler >::_M_atom() /usr/include/c++/15/bits/regex_compiler.tcc:313 #4 0x7b7f7de84097 in std::__detail::_Compiler >::_M_term() /usr/include/c++/15/bits/regex_compiler.tcc:136 #5 0x7b7f7de84097 in std::__detail::_Compiler >::_M_alternative() /usr/include/c++/15/bits/regex_compiler.tcc:118 #6 0x7b7f7de82c4a in std::__detail::_Compiler >::_M_alternative() /usr/include/c++/15/bits/regex_compiler.tcc:121 #7 0x7b7f7de82c4a in std::__detail::_Compiler >::_M_alternative() /usr/include/c++/15/bits/regex_compiler.tcc:121 #8 0x7b7f7de82c4a in std::__detail::_Compiler >::_M_alternative() /usr/include/c++/15/bits/regex_compiler.tcc:121 #9 0x7b7f7de82c4a in std::__detail::_Compiler >::_M_alternative() /usr/include/c++/15/bits/regex_compiler.tcc:121 #10 0x7b7f7de82c4a in std::__detail::_Compiler >::_M_alternative() /usr/include/c++/15/bits/regex_compiler.tcc:121 #11 0x7b7f7de82c4a in std::__detail::_Compiler >::_M_alternative() /usr/include/c++/15/bits/regex_compiler.tcc:121 #12 0x7b7f7de8c79b in std::__detail::_Compiler >::_M_disjunction() /usr/include/c++/15/bits/regex_compiler.tcc:94 #13 0x7b7f7de4a6ff in std::__detail::_Compiler >::_Compiler(char const*, char const*, std::locale const&, std::regex_constants::syntax_option_type) /usr/include/c++/15/bits/regex_compiler.tcc:79 #14 0x7b7f7de4a6ff in std::__cxx11::basic_regex >::_M_compile(char const*, char const*, std::regex_constants::syntax_option_type) [clone .constprop.0] /usr/include/c++/15/bits/regex.h:831 #15 0x7b7f7de1ed44 in std::__cxx11::basic_regex >::basic_regex(char const*, std::regex_constants::syntax_option_type) /usr/include/c++/15/bits/regex.h:495 #16 0x7b7f7de1ed44 in parse_autosql(std::__cxx11::basic_string, std::allocator > const&) /data/gannet/ripley/R/packages/tests-gcc-SAN/cpp11bigwig/src/cpp11bigwig.cpp:42 #17 0x7b7f7de2fbe1 in read_bigbed_cpp(std::__cxx11::basic_string, std::allocator >, cpp11::sexp, cpp11::sexp, cpp11::sexp) /data/gannet/ripley/R/packages/tests-gcc-SAN/cpp11bigwig/src/cpp11bigwig.cpp:164 #18 0x7b7f7de39f28 in _cpp11bigwig_read_bigbed_cpp /data/gannet/ripley/R/packages/tests-gcc-SAN/cpp11bigwig/src/cpp11.cpp:19 #19 0x000000750106 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:763 #20 0x0000008ed68a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8700 #21 0x0000008c3ee3 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #22 0x00000086296a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #23 0x00000087acaa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #24 0x00000087ec5d in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #25 0x000000863018 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #26 0x000000863018 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #27 0x000000a0b608 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #28 0x000000a0b608 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #29 0x000000a1a8fa in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235 #30 0x000000a1a992 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242 #31 0x00000041306f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #32 0x7f7f94612574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #33 0x7f7f94612627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #34 0x000000413a14 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x413a14) (BuildId: 325586472d25943af14822bd26fccd215fd271f4) 0x7b7f7e172293 is located 45 bytes before global variable '*.LC45' defined in './cpp11bigwig.so.ltrans1.ltrans' (0x7b7f7e1722c0) of size 26 '*.LC45' is ascii string 'vector::_M_realloc_append' 0x7b7f7e172293 is located 0 bytes after global variable '*.LC42' defined in './cpp11bigwig.so.ltrans1.ltrans' (0x7b7f7e172280) of size 19 '*.LC42' is ascii string '^\s*(\S+)\s+(\S+);' SUMMARY: AddressSanitizer: global-buffer-overflow /data/gannet/ripley/R/packages/tests-gcc-SAN/cpp11bigwig/src/cpp11bigwig.cpp:42 in parse_autosql(std::__cxx11::basic_string, std::allocator > const&) Shadow bytes around the buggy address: 0x7b7f7e172000: f9 f9 f9 f9 00 05 f9 f9 f9 f9 f9 f9 00 00 00 03 0x7b7f7e172080: f9 f9 f9 f9 00 00 00 06 f9 f9 f9 f9 00 00 00 00 0x7b7f7e172100: 00 00 01 f9 f9 f9 f9 f9 00 07 f9 f9 f9 f9 f9 f9 0x7b7f7e172180: 07 f9 f9 f9 f9 f9 f9 f9 00 05 f9 f9 f9 f9 f9 f9 0x7b7f7e172200: 00 f9 f9 f9 f9 f9 f9 f9 00 06 f9 f9 f9 f9 f9 f9 =>0x7b7f7e172280: 00 00[03]f9 f9 f9 f9 f9 00 00 00 02 f9 f9 f9 f9 0x7b7f7e172300: 02 f9 f9 f9 f9 f9 f9 f9 00 00 00 00 06 f9 f9 f9 0x7b7f7e172380: f9 f9 f9 f9 00 00 00 00 00 f9 f9 f9 f9 f9 f9 f9 0x7b7f7e172400: 00 00 00 00 00 02 f9 f9 f9 f9 f9 f9 00 00 00 00 0x7b7f7e172480: 07 f9 f9 f9 f9 f9 f9 f9 00 00 00 00 05 f9 f9 f9 0x7b7f7e172500: f9 f9 f9 f9 00 00 00 00 00 01 f9 f9 f9 f9 f9 f9 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 ==2131163==ABORTING * checking tests ... [14s/15s] ERROR Running ‘testthat.R’ [14s/14s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(cpp11bigwig) > > test_check("cpp11bigwig") ================================================================= ==2131238==ERROR: AddressSanitizer: global-buffer-overflow on address 0x7b7113b72293 at pc 0x7b711387a85e bp 0x7fff98fdbba0 sp 0x7fff98fdbb98 READ of size 1 at 0x7b7113b72293 thread T0 #0 0x7b711387a85d in std::__detail::_Scanner::_M_scan_normal() /usr/include/c++/15/bits/regex_scanner.tcc:98 #1 0x7b711387a85d in std::__detail::_Scanner::_M_advance() /usr/include/c++/15/bits/regex_scanner.tcc:79 #2 0x7b711387d799 in std::__detail::_Compiler >::_M_match_token(std::__detail::_ScannerBase::_TokenT) /usr/include/c++/15/bits/regex_compiler.tcc:578 #3 0x7b7113884097 in std::__detail::_Compiler >::_M_atom() /usr/include/c++/15/bits/regex_compiler.tcc:313 #4 0x7b7113884097 in std::__detail::_Compiler >::_M_term() /usr/include/c++/15/bits/regex_compiler.tcc:136 #5 0x7b7113884097 in std::__detail::_Compiler >::_M_alternative() /usr/include/c++/15/bits/regex_compiler.tcc:118 #6 0x7b7113882c4a in std::__detail::_Compiler >::_M_alternative() /usr/include/c++/15/bits/regex_compiler.tcc:121 #7 0x7b7113882c4a in std::__detail::_Compiler >::_M_alternative() /usr/include/c++/15/bits/regex_compiler.tcc:121 #8 0x7b7113882c4a in std::__detail::_Compiler >::_M_alternative() /usr/include/c++/15/bits/regex_compiler.tcc:121 #9 0x7b7113882c4a in std::__detail::_Compiler >::_M_alternative() /usr/include/c++/15/bits/regex_compiler.tcc:121 #10 0x7b7113882c4a in std::__detail::_Compiler >::_M_alternative() /usr/include/c++/15/bits/regex_compiler.tcc:121 #11 0x7b7113882c4a in std::__detail::_Compiler >::_M_alternative() /usr/include/c++/15/bits/regex_compiler.tcc:121 #12 0x7b711388c79b in std::__detail::_Compiler >::_M_disjunction() /usr/include/c++/15/bits/regex_compiler.tcc:94 #13 0x7b711384a6ff in std::__detail::_Compiler >::_Compiler(char const*, char const*, std::locale const&, std::regex_constants::syntax_option_type) /usr/include/c++/15/bits/regex_compiler.tcc:79 #14 0x7b711384a6ff in std::__cxx11::basic_regex >::_M_compile(char const*, char const*, std::regex_constants::syntax_option_type) [clone .constprop.0] /usr/include/c++/15/bits/regex.h:831 #15 0x7b711381ed44 in std::__cxx11::basic_regex >::basic_regex(char const*, std::regex_constants::syntax_option_type) /usr/include/c++/15/bits/regex.h:495 #16 0x7b711381ed44 in parse_autosql(std::__cxx11::basic_string, std::allocator > const&) /data/gannet/ripley/R/packages/tests-gcc-SAN/cpp11bigwig/src/cpp11bigwig.cpp:42 #17 0x7b711382fbe1 in read_bigbed_cpp(std::__cxx11::basic_string, std::allocator >, cpp11::sexp, cpp11::sexp, cpp11::sexp) /data/gannet/ripley/R/packages/tests-gcc-SAN/cpp11bigwig/src/cpp11bigwig.cpp:164 #18 0x7b7113839f28 in _cpp11bigwig_read_bigbed_cpp /data/gannet/ripley/R/packages/tests-gcc-SAN/cpp11bigwig/src/cpp11.cpp:19 #19 0x000000750106 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:763 #20 0x0000008ed68a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8700 #21 0x0000008c3ee3 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #22 0x00000086296a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #23 0x00000087acaa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #24 0x00000087ec5d in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #25 0x000000863018 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #26 0x000000863018 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #27 0x0000008949ae in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585 #28 0x000000863446 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #29 0x00000087721b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001 #30 0x000000863446 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230 #31 0x00000089c521 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975 #32 0x0000008d6c82 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #33 0x0000008c3ee3 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #34 0x00000086296a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #35 0x00000087acaa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #36 0x00000087ec5d in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #37 0x000000863018 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #38 0x000000863018 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #39 0x00000089d613 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3993 #40 0x0000008d6c82 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150 #41 0x0000008c3ee3 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #42 0x00000086296a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #43 0x00000087acaa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #44 0x00000087ec5d in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #45 0x00000088089a in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #46 0x00000088089a in R_forceAndCall /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2465 #47 0x000000499fd6 in do_lapply /data/gannet/ripley/R/svn/R-devel/src/main/apply.c:75 #48 0x000000a9e3b6 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1424 #49 0x0000008e3e91 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170 #50 0x0000008c3ee3 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533 #51 0x00000086296a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #52 0x00000087acaa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398 #53 0x00000087ec5d in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314 #54 0x000000863018 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333 #55 0x000000863018 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278 #56 0x000000a0b608 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #57 0x000000a0b608 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #58 0x000000a1a8fa in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235 #59 0x000000a1a992 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242 #60 0x00000041306f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #61 0x7f712a212574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #62 0x7f712a212627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #63 0x000000413a14 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x413a14) (BuildId: 325586472d25943af14822bd26fccd215fd271f4) 0x7b7113b72293 is located 45 bytes before global variable '*.LC45' defined in './cpp11bigwig.so.ltrans1.ltrans' (0x7b7113b722c0) of size 26 '*.LC45' is ascii string 'vector::_M_realloc_append' 0x7b7113b72293 is located 0 bytes after global variable '*.LC42' defined in './cpp11bigwig.so.ltrans1.ltrans' (0x7b7113b72280) of size 19 '*.LC42' is ascii string '^\s*(\S+)\s+(\S+);' SUMMARY: AddressSanitizer: global-buffer-overflow /data/gannet/ripley/R/packages/tests-gcc-SAN/cpp11bigwig/src/cpp11bigwig.cpp:42 in parse_autosql(std::__cxx11::basic_string, std::allocator > const&) Shadow bytes around the buggy address: 0x7b7113b72000: f9 f9 f9 f9 00 05 f9 f9 f9 f9 f9 f9 00 00 00 03 0x7b7113b72080: f9 f9 f9 f9 00 00 00 06 f9 f9 f9 f9 00 00 00 00 0x7b7113b72100: 00 00 01 f9 f9 f9 f9 f9 00 07 f9 f9 f9 f9 f9 f9 0x7b7113b72180: 07 f9 f9 f9 f9 f9 f9 f9 00 05 f9 f9 f9 f9 f9 f9 0x7b7113b72200: 00 f9 f9 f9 f9 f9 f9 f9 00 06 f9 f9 f9 f9 f9 f9 =>0x7b7113b72280: 00 00[03]f9 f9 f9 f9 f9 00 00 00 02 f9 f9 f9 f9 0x7b7113b72300: 02 f9 f9 f9 f9 f9 f9 f9 00 00 00 00 06 f9 f9 f9 0x7b7113b72380: f9 f9 f9 f9 00 00 00 00 00 f9 f9 f9 f9 f9 f9 f9 0x7b7113b72400: 00 00 00 00 00 02 f9 f9 f9 f9 f9 f9 00 00 00 00 0x7b7113b72480: 07 f9 f9 f9 f9 f9 f9 f9 00 00 00 00 05 f9 f9 f9 0x7b7113b72500: f9 f9 f9 f9 00 00 00 00 00 01 f9 f9 f9 f9 f9 f9 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 ==2131238==ABORTING * DONE Status: 2 ERRORs