Package Details: gapc-fold-grammars-git 2.2.12.841.cac090a-1

Git Clone URL: https://aur.archlinux.org/gapc-fold-grammars-git.git (read-only, click to copy)
Package Base: gapc-fold-grammars-git
Description: Bielefeld RNA secondary structure prediction programs.
Upstream URL: https://bibiserv.cebitec.uni-bielefeld.de/fold-grammars/
Licenses: GPL3
Provides: Knotinframe=20.03.2015, RNAalishapes=2.4.8, RNAshapes=3.3.1, RapidShapes=18.11.2020, pAliKiss=1.0.8, pKiss=2.2.13
Submitter: RaumZeit
Maintainer: RaumZeit
Last Packager: RaumZeit
Votes: 0
Popularity: 0.000000
First Submitted: 2020-03-30 09:22
Last Updated: 2020-12-10 21:19

Dependencies (2)

Required by (1)

Sources (1)

Latest Comments

fncnt commented on 2020-08-29 14:58

At least pKiss_mfe segfaults (but I'm assuming multiple gapc-programs are affected). It's strange because a few weeks ago, everything ran fine. I'm not sure why, but apparently it's actually happening in gapc-generated code; here's a stracktrace after building gapc-git and gapc-fold-grammars-git with debug symbols:

Core was generated by `./pKiss_mfe ACG'.
Program terminated with signal SIGSEGV, Segmentation fault.
#0  Map::Pool<unsigned long, 6553600ul>::free (this=0x55bf564701bd, 
    t=<optimized out>) at /usr/include/rtlib/map_pool.hh:318
318       void free(Type *t)
(gdb) bt
#0  Map::Pool<unsigned long, 6553600ul>::free (this=0x55bf564701bd, 
    t=<optimized out>) at /usr/include/rtlib/map_pool.hh:318
#1  MultiPool<unsigned long>::free (n=<optimized out>, x=0x7fd64bc12018, 
    this=0x55ba0ce44710 <Fiber<unsigned long, unsigned char, PkAlph<unsigned long, unsigned char> >::pool>) at /usr/include/rtlib/multipool.hh:104
#2  Fiber<unsigned long, unsigned char, PkAlph<unsigned long, unsigned char> >::dealloc (n=<optimized out>, t=0x7fd64bc12018, this=0x55ba0ce44698 <closeParen>)
    at /usr/include/rtlib/shape.hh:70
#3  Fiber<unsigned long, unsigned char, PkAlph<unsigned long, unsigned char> >::~Fiber (this=0x55ba0ce44698 <closeParen>, __in_chrg=<optimized out>)
    at /usr/include/rtlib/shape.hh:130
#4  0x00007fd652054db7 in __run_exit_handlers () from /usr/lib64/libc.so.6
#5  0x00007fd652054f5e in exit () from /usr/lib64/libc.so.6
#6  0x00007fd65203d159 in __libc_start_main () from /usr/lib64/libc.so.6
#7  0x000055ba0cd9a56e in _start () at /usr/include/rtlib/pool.hh:45

Maybe it's related to a glibc update that happened a few weeks ago (2.31->2.32)? That would fit the time frame but downgrading proved to be non-trivial so I haven't actually checked that.