Bug 896172

Summary:	sci-biology/bedtools-2.30.0 fails tests (HARDENED-SYSTEM)
Product:	Gentoo Linux	Reporter:	Agostino Sarubbo <ago>
Component:	Current packages	Assignee:	Gentoo Science Biology related packages <sci-biology>
Status:	CONFIRMED ---
Severity:	normal
Priority:	Normal
Version:	unspecified
Hardware:	All
OS:	Linux
See Also:	https://github.com/arq5x/bedtools2/issues/1088
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