* using log directory ‘/home/hornik/tmp/CRAN_special_clang-san/onemap.Rcheck’
* using R Under development (unstable) (2025-04-08 r88126)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.7 (1+b1)
    Debian flang-new version 19.1.7 (1+b1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘onemap/DESCRIPTION’ ... OK
* this is package ‘onemap’ version ‘3.2.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘onemap’ can be installed ... [157s/158s] OK
* used C compiler: ‘Debian clang version 19.1.7 (3)’
* used C++ compiler: ‘Debian clang version 19.1.7 (3)’
* 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 ... [14s/14s] OK
* checking whether the package can be loaded with stated dependencies ... [13s/13s] OK
* checking whether the package can be unloaded cleanly ... [12s/12s] OK
* checking whether the namespace can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the namespace can be unloaded cleanly ... [14s/14s] OK
* checking loading without being on the library search path ... [14s/14s] OK
* checking whether startup messages can be suppressed ... [13s/13s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [224s/224s] OK
* checking Rd files ... [4s/4s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [1s/1s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... 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 ... [14s/15s] 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<int>::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<std::allocator<int>>::allocate(std::allocator<int>&, 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<int, std::allocator<int>>::_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<int, std::allocator<int>>::_M_range_initialize<double*>(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<int, std::allocator<int>>::vector<double*, void>(double*, double*, std::allocator<int> 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
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [15s/15s] OK
* checking HTML version of manual ... [15s/16s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR