Hi,
Am Fri, Sep 30, 2022 at 01:10:27PM +0000 schrieb John Marshall:
> Andreas Tille wrote:
> > Interestingly the missing symbols are mentioned in some warnings higher up
> > in the changelog!
>
> As per the build log, those warnings were:
>
> Selecting previously unselected package libhtscodecs2:amd64.
> Preparing to unpack .../44-libhtscodecs2_1.2.2-1_amd64.deb ...
> Unpacking libhtscodecs2:amd64 (1.2.2-1) ...
> […]
> cram/cram_io.c:1725:23: warning: implicit declaration of function
> 'tok3_decode_names'; did you mean 'decode_names'?
> [-Wimplicit-function-declaration]
> 1725 | uint8_t *cp = tok3_decode_names(b->data, b->comp_size,
> &out_len);
> | ^~~~~~~~~~~~~~~~~
> | decode_names
> […]
>
> These function names (tok3_decode_names() et al) appeared in htscodecs 1.3.0
> in response to [1]. Probably the underlying problem here is that you need to
> update the requirement on the external libhtscodecs to ensure htslib 1.16 is
> built against htscodecs 1.3.0.
This should be the case, thought.
> Perhaps separately, what is the reason for [2]?
>
> Commit 2905146ffe547dd98617e32d8b834f4c802a7f77
> Fix build options to make sure symbols will remain in library
>
> It would appear from the resulting additions to debian/libhts3.symbols that
> removing -fvisibility=hidden from DEB_CFLAGS_MAINT_APPEND has caused large
> numbers of HTSlib's non-HTSLIB_EXPORT-marked internal functions to be added
> to your libhts3.symbols file. Adding these to libhts3.symbols doesn't seem
> very correct (they are not part of the ABI), and I expect the upstream HTSlib
> maintainers will be extremely uninterested in any future complaints that
> non-exported symbols have changed or disappeared.
The log specified -fvisibility=hidden twice and thus I removed one instance and
at
the same time adding -ffat-lto-objects which was due to the hint given by
lintian
to fix a lintian error. Checking the build logs[3] I realise that my attempt to
remove a duplicate of -fvisibility=hidden has removed both instances - argh!
I think this should be re-added - thanks a lot for watching me!
Strangely enough the autopkgtest is failing[4] (which was not the case in my
local build.) Could anybody have a look?
Thanks again for your valuable contributions
Andreas.
> [1] https://github.com/samtools/htscodecs/issues/36
> [2]
> https://salsa.debian.org/med-team/htslib/-/commit/2905146ffe547dd98617e32d8b834f4c802a7f77
[3] https://salsa.debian.org/med-team/htslib/-/jobs/3320177
[4] https://salsa.debian.org/med-team/htslib/-/jobs/3320185
--
http://fam-tille.de
