Bug#956136: Some investigations about bug (956136) nanopolish: FTBFS (undefined references)

2020-04-12 Thread Andreas Tille
Control: tags -1 pending Control: reassign -1 minimap2 Control: retitle -1 "-flto flag breaks nanopolish" Hamid, thanks a lot for your investigation. Kind regards, Andreas. -- http://fam-tille.de

Bug#956136: Some investigations about bug (956136) nanopolish: FTBFS (undefined references)

2020-04-09 Thread Hamid Nassiby
Hi all, I could find the cause. It is the `-flto` in the compile and link flags of the libminimap2-dev package. LTO is introduced recently in the following commit on the [1]: 53883a7ff8c066c14c0ea4e42299ae9958feda6a Removing `-flto` from CFLAGS and LDFLAGS, then building libminimap2-dev with pdeb

Bug#956136: Some investigations about bug (956136) nanopolish: FTBFS (undefined references)

2020-04-09 Thread Hamid Nassiby
Control: tags -1 help Hi all, The undefined reference to those functions, means that there is a problem in linking with libminimap2 which implements them. Those functions are implemented in map.c of that library. I am able to reproduce the bug with pbuilder (sid) on the buster. I made some invest

Bug#956136: nanopolish: FTBFS (undefined references)

2020-04-07 Thread Bas Couwenberg
Source: nanopolish Version: 0.12.1-1 Severity: serious Tags: ftbfs Justification: makes the package in question unusable or mostly so Control: block 954654 by -1 Dear Maintainer, Your packages fails to build in unstable: /usr/bin/ld: /tmp/nanopolish.HEB8tw.ltrans12.ltrans.o: in function `popul