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Bug 896172

Summary: sci-biology/bedtools-2.30.0 fails tests (HARDENED-SYSTEM)
Product: Gentoo Linux Reporter: Agostino Sarubbo <ago>
Component: Current packagesAssignee: Gentoo Science Biology related packages <sci-biology>
Status: CONFIRMED ---    
Severity: normal    
Priority: Normal    
Version: unspecified   
Hardware: All   
OS: Linux   
Whiteboard:
Package list:
Runtime testing required: ---
Bug Depends on:    
Bug Blocks: 884417    
Attachments: build.log

Description Agostino Sarubbo gentoo-dev 2023-02-24 08:23:24 UTC
https://blogs.gentoo.org/ago/2020/07/04/gentoo-tinderbox/

Issue: sci-biology/bedtools-2.30.0 fails tests (HARDENED-SYSTEM).
Discovered on: amd64 (internal ref: hardened_tinderbox)

NOTE:
(HARDENED-SYSTEM) in the summary means that the bug was found on a machine that runs an hardened profile with -D_FORTIFY_SOURCE=3 and -D_GLIBCXX_ASSERTIONS (https://www.gentoo.org/support/news-items/2023-01-01-hardening-fortify-assertions.html) but this bug MAY or MAY NOT BE related to the changes related to hardened.
Comment 1 Agostino Sarubbo gentoo-dev 2023-02-24 08:23:26 UTC
Created attachment 854256 [details]
build.log

build log and emerge --info
Comment 2 Agostino Sarubbo gentoo-dev 2023-02-24 08:23:27 UTC
Error(s) that match a know pattern:


    expand.t1.../usr/lib/gcc/x86_64-pc-linux-gnu/12/include/g++-v12/bits/basic_string.h:1221: std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::reference std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator[](size_type) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>; reference = char&; size_type = long unsigned int]: Assertion '__pos <= size()' failed.
    getfasta.t08...index file test.iupac.fa.fai not found, generating...
    getfasta.t09...index file test.iupac.fa.fai not found, generating...
    getfasta.t10...index file test.fa.fai not found, generating...
    getfasta.t16..index file rna.fasta.fai not found, generating...
    merge.t44b...skipped - could not find vcfSVtest.2.vcf