[Debian-med-packaging] Bug#956136: Some investigations about bug (956136) nanopolish: FTBFS (undefined references)

[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 pdebuild (sid), then building the nanopolish with
pbuilder (sid), will succeed.
I attached the patch which resolves the problem. It should be applied
against [1].

The conclusion:
The `-flto` behaves differently from the past maybe with the recent
changes in the build tool-chain (maybe in GCC) and causes the problem.

[1]:https://salsa.debian.org/med-team/minimap2.git

Bests,
Hamid Nassiby
-------------- next part --------------
A non-text attachment was scrubbed...
Name: 0001-Remove-flto-flag.patch
Type: text/x-diff
Size: 1844 bytes
Desc: not available
URL: <http://alioth-lists.debian.net/pipermail/debian-med-packaging/attachments/20200409/53e147d8/attachment.patch>