Package check result: ERROR Check: examples, Result: ERROR Running examples in ‘onemap-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: add_marker > ### Title: Creates a new sequence by adding markers. > ### Aliases: add_marker > > ### ** Examples > > data(onemap_example_out) > twopt <- rf_2pts(onemap_example_out) Computing 435 recombination fractions ... ================================================================= ==4013797==ERROR: AddressSanitizer: heap-buffer-overflow on address 0x514000795bcc at pc 0x7f73deed272b bp 0x7ffc708cdbb0 sp 0x7ffc708cdba8 READ of size 4 at 0x514000795bcc thread T0 #0 0x7f73deed272a in est_rf_out(Rcpp::Vector<14, Rcpp::PreserveStorage>, int, Rcpp::Vector<13, Rcpp::PreserveStorage>, int, int) /home/hornik/tmp/CRAN_special_clang-san/onemap.Rcheck/00_pkg_src/onemap/src/twopts_out.cpp:113:11 #1 0x7f73deec5620 in est_rf_out_wrap /home/hornik/tmp/CRAN_special_clang-san/onemap.Rcheck/00_pkg_src/onemap/src/twopts_out.cpp:53:12 #2 0x7f7403357a5e in R_doDotCall /home/hornik/src/R/src/main/dotcode.c:766:11 #3 0x7f74033a2492 in do_dotcall /home/hornik/src/R/src/main/dotcode.c:1437:11 #4 0x7f74034f4429 in bcEval_loop /home/hornik/src/R/src/main/eval.c:8118:14 #5 0x7f74034a89a4 in bcEval /home/hornik/src/R/src/main/eval.c:7501:16 #6 0x7f74034a70df in Rf_eval /home/hornik/src/R/src/main/eval.c:1167:8 #7 0x7f74034b1835 in R_execClosure /home/hornik/src/R/src/main/eval.c:2393:22 #8 0x7f74034ad32c in applyClosure_core /home/hornik/src/R/src/main/eval.c:2306:16 #9 0x7f74034a7a5f in Rf_applyClosure /home/hornik/src/R/src/main/eval.c:2328:16 #10 0x7f74034a7a5f in Rf_eval /home/hornik/src/R/src/main/eval.c:1280:12 #11 0x7f74034c04d5 in do_set /home/hornik/src/R/src/main/eval.c:3567:8 #12 0x7f74034a74ab in Rf_eval /home/hornik/src/R/src/main/eval.c:1232:12 #13 0x7f74035eb567 in Rf_ReplIteration /home/hornik/src/R/src/main/main.c:265:2 #14 0x7f74035ee4f0 in R_ReplConsole /home/hornik/src/R/src/main/main.c:317:11 #15 0x7f74035ee304 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1234:5 #16 0x7f74035ee5ea in Rf_mainloop /home/hornik/src/R/src/main/main.c:1241:5 #17 0x564414cc2dd4 in main /home/hornik/src/R/src/main/Rmain.c:29:5 #18 0x7f7402743ca7 in __libc_start_call_main csu/../sysdeps/nptl/libc_start_call_main.h:58:16 #19 0x7f7402743d64 in __libc_start_main csu/../csu/libc-start.c:360:3 #20 0x564414bdf370 in _start (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x2b370) (BuildId: cb572fc433d0ad213d4bcc3b6ed58fac2d1ab683) 0x514000795bcc is located 0 bytes after 396-byte region [0x514000795a40,0x514000795bcc) allocated by thread T0 here: #0 0x564414cc0921 in operator new(unsigned long) (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0x10c921) (BuildId: cb572fc433d0ad213d4bcc3b6ed58fac2d1ab683) #1 0x7f73deec83cf in std::__new_allocator::allocate(unsigned long, void const*) /usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/bits/new_allocator.h:151:27 #2 0x7f73deec83cf in std::allocator_traits>::allocate(std::allocator&, unsigned long) /usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/bits/alloc_traits.h:515:20 #3 0x7f73deec83cf in std::_Vector_base>::_M_allocate(unsigned long) /usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/bits/stl_vector.h:380:20 #4 0x7f73deec83cf in void std::vector>::_M_range_initialize(double*, double*, std::forward_iterator_tag) /usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/bits/stl_vector.h:1694:14 #5 0x7f73deec83cf in std::vector>::vector(double*, double*, std::allocator const&) /usr/lib/gcc/x86_64-linux-gnu/14/../../../../include/c++/14/bits/stl_vector.h:711:4 #6 0x7f73deec83cf in est_rf_out(Rcpp::Vector<14, Rcpp::PreserveStorage>, int, Rcpp::Vector<13, Rcpp::PreserveStorage>, int, int) /home/hornik/tmp/CRAN_special_clang-san/onemap.Rcheck/00_pkg_src/onemap/src/twopts_out.cpp:107:21 #7 0x7f73deec5620 in est_rf_out_wrap /home/hornik/tmp/CRAN_special_clang-san/onemap.Rcheck/00_pkg_src/onemap/src/twopts_out.cpp:53:12 #8 0x7f7403357a5e in R_doDotCall /home/hornik/src/R/src/main/dotcode.c:766:11 #9 0x7f74033a2492 in do_dotcall /home/hornik/src/R/src/main/dotcode.c:1437:11 #10 0x7f74034f4429 in bcEval_loop /home/hornik/src/R/src/main/eval.c:8118:14 #11 0x7f74034a89a4 in bcEval /home/hornik/src/R/src/main/eval.c:7501:16 #12 0x7f74034a70df in Rf_eval /home/hornik/src/R/src/main/eval.c:1167:8 #13 0x7f74034b1835 in R_execClosure /home/hornik/src/R/src/main/eval.c:2393:22 #14 0x7f74034ad32c in applyClosure_core /home/hornik/src/R/src/main/eval.c:2306:16 #15 0x7f74034a7a5f in Rf_applyClosure /home/hornik/src/R/src/main/eval.c:2328:16 #16 0x7f74034a7a5f in Rf_eval /home/hornik/src/R/src/main/eval.c:1280:12 #17 0x7f74034c04d5 in do_set /home/hornik/src/R/src/main/eval.c:3567:8 #18 0x7f74034a74ab in Rf_eval /home/hornik/src/R/src/main/eval.c:1232:12 #19 0x7f74035eb567 in Rf_ReplIteration /home/hornik/src/R/src/main/main.c:265:2 #20 0x7f74035ee4f0 in R_ReplConsole /home/hornik/src/R/src/main/main.c:317:11 #21 0x7f74035ee304 in run_Rmainloop /home/hornik/src/R/src/main/main.c:1234:5 #22 0x7f74035ee5ea in Rf_mainloop /home/hornik/src/R/src/main/main.c:1241:5 #23 0x564414cc2dd4 in main /home/hornik/src/R/src/main/Rmain.c:29:5 #24 0x7f7402743ca7 in __libc_start_call_main csu/../sysdeps/nptl/libc_start_call_main.h:58:16 SUMMARY: AddressSanitizer: heap-buffer-overflow /home/hornik/tmp/CRAN_special_clang-san/onemap.Rcheck/00_pkg_src/onemap/src/twopts_out.cpp:113:11 in est_rf_out(Rcpp::Vector<14, Rcpp::PreserveStorage>, int, Rcpp::Vector<13, Rcpp::PreserveStorage>, int, int) Shadow bytes around the buggy address: 0x514000795900: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x514000795980: 00 00 00 00 00 00 00 00 00 04 fa fa fa fa fa fa 0x514000795a00: fa fa fa fa fa fa fa fa 00 00 00 00 00 00 00 00 0x514000795a80: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x514000795b00: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 =>0x514000795b80: 00 00 00 00 00 00 00 00 00[04]fa fa fa fa fa fa 0x514000795c00: fa fa fa fa fa fa fa fa 00 00 00 00 00 00 00 00 0x514000795c80: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x514000795d00: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x514000795d80: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 fa fa 0x514000795e00: fa fa fa fa fa fa fa fa 00 00 00 00 00 00 00 00 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 ==4013797==ABORTING Post-processing issues found: File: onemap-Ex.Rout ==4013797==ERROR: AddressSanitizer: heap-buffer-overflow on address 0x514000795bcc at pc 0x7f73deed272b bp 0x7ffc708cdbb0 sp 0x7ffc708cdba8 SUMMARY: AddressSanitizer: heap-buffer-overflow /home/hornik/tmp/CRAN_special_clang-san/onemap.Rcheck/00_pkg_src/onemap/src/twopts_out.cpp:113:11 in est_rf_out(Rcpp::Vector<14, Rcpp::PreserveStorage>, int, Rcpp::Vector<13, Rcpp::PreserveStorage>, int, int) ASan internal: fe File: 00check.log ==4013797==ERROR: AddressSanitizer: heap-buffer-overflow on address 0x514000795bcc at pc 0x7f73deed272b bp 0x7ffc708cdbb0 sp 0x7ffc708cdba8 SUMMARY: AddressSanitizer: heap-buffer-overflow /home/hornik/tmp/CRAN_special_clang-san/onemap.Rcheck/00_pkg_src/onemap/src/twopts_out.cpp:113:11 in est_rf_out(Rcpp::Vector<14, Rcpp::PreserveStorage>, int, Rcpp::Vector<13, Rcpp::PreserveStorage>, int, int) ASan internal: fe