flang_segfault_min_example

This is a minimum working example of the issue in R package sequoia, resulting in segfault when compiled with flang. No issues when compiling with gfortran, no issues detected by valgrind or ASAN.

R CMD check

R CMD check --as-cran --install-args=--configure-args=--enable-lto=check minWE_0.1.0.tar.gz

Rel_list <- GetRelA(Ped = minWE::Ped_HSg5, List=TRUE)

*** caught segfault *** address 0x7ffc7e4525c8, cause 'memory not mapped'

Traceback: 1: GetRelA(Ped = minWE::Ped_HSg5, List = TRUE) An irrecoverable exception occurred. R is aborting now ... Segmentation fault (core dumped)

Warning during installation (readelf: ..)

R Under development (unstable) (2023-12-08 r85664) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu

(...)

install.packages('minWE_0.1.0.tar.gz') Installing package into ‘/home/jisca/R/x86_64-pc-linux-gnu-library/4.4’ (as ‘lib’ is unspecified) inferring 'repos = NULL' from 'pkgs'

• installing source package ‘minWE’ ... ** using staged installation ** libs using C compiler: ‘Ubuntu clang version 17.0.6 (++20231209124227+6009708b4367-1exp120231209124336.77)’ using Fortran compiler: ‘Ubuntu flang-new version 17.0.6 (++20231209124227+6009708b4367-1exp120231209124336.77)’ flang-new-17 -fpic -g -O2 -flto -c MkRelA.f90 -o MkRelA.o clang-17 -I"/usr/local/lib64/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -flto -c init.c -o init.o clang-17 -shared -g -O2 -flto -fpic -L/usr/local/lib64 -o minWE.so MkRelA.o init.o -L/usr/lib/llvm-17/lib -lFortran_main -lFortranRuntime -lFortranDecimal -lm installing to /home/jisca/R/x86_64-pc-linux-gnu-library/4.4/00LOCK-minWE/00new/minWE/libs ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries readelf: Warning: Unrecognized form: 0x22 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path
• DONE (minWE)