Your message dated Wed, 18 Dec 2019 14:38:59 +0000
with message-id <[email protected]>
and subject line Bug#946924: fixed in libseqlib 1.1.2+dfsg-5
has caused the Debian Bug report #946924,
regarding Patch to remove any need for libhts-private-dev
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
946924: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=946924
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: libseqlib
Version: 1.1.2+dfsg-4
SeqLib uses private HTSlib headers that HTSlib would prefer were not installed,
and at last count SeqLib was the only package desiring these private HTSlib
cram/*.h headers. The attached patch recodes to avoid the need for these
headers. See bug #881170 for background; this patch is option (B) from the
initial message on that bug, and it turns out that the changes required are
trivial.
This has also been proposed upstream as
<https://github.com/walaj/SeqLib/pull/53>. However as upstream releases are
infrequent and the problem was caused by Debian's desire to build against a
non-bundled HTSlib, it would be appropriate for Debian to apply this patch now
rather than wait for upstream to incorporate it and make a new release.
Please apply the attached patch, which is also available at
<https://github.com/walaj/SeqLib/commit/3fc64616a64adfcaf5271ae24f35e443ce822faf.patch>.
You will also want to remove the existing use_private_htslib_headers.patch as
it is superseded by this.
Once this has been done, if libseqlib was still the only Debian package using
libhts-private-dev then it will be appropriate to remove that bodge from htslib
-- for which I am happy to submit another bug as appropriate.
John
fix_private_htslib_usage.patch
Description: fix_private_htslib_usage.patch
--- End Message ---
--- Begin Message ---
Source: libseqlib
Source-Version: 1.1.2+dfsg-5
We believe that the bug you reported is fixed in the latest version of
libseqlib, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated libseqlib package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Wed, 18 Dec 2019 14:17:13 +0100
Source: libseqlib
Architecture: source
Version: 1.1.2+dfsg-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Closes: 946924
Changes:
libseqlib (1.1.2+dfsg-5) unstable; urgency=medium
.
* Avoid using non-public HTSlib headers and functions
and do not (Build-)Depend libhts-private-dev
Closes: #946924
* Standards-Version: 4.4.1
* Set upstream metadata fields: Bug-Database.
* Refresh symbols
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