Your message dated Sun, 10 Dec 2017 11:00:11 +0000
with message-id <[email protected]>
and subject line Bug#881170: fixed in htslib 1.5-5
has caused the Debian Bug report #881170,
regarding htslib: please do not package cram/*.h headers
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.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
881170: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=881170
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: libhts-dev
Version: 1.5-1
X-Debbugs-CC:
[email protected]<mailto:[email protected]>,[email protected]<mailto:[email protected]>
There are several packaging infelicities in testing/unstable libhts-dev:
1. The cram/*.h headers are private and should not be packaged
Nothing outside the htslib-1.x/htslib/*.h headers is public supported HTSlib
functionality. Only items declared within those htslib/*.h headers are part of
HTSlib's supported public API and not subject to changing arbitrarily. (And for
completeness: a few items declared within htslib/*.h for technical reasons are
themselves individually documented as not being part of the public API.) By
packaging cram/*.h in libhts-dev you risk misleading Debian users into thinking
these functions are part of HTSlib's stable supported public API, which is not
true and will lead to disappointment.
debian/changelog and 44f77d57 suggest that these are installed for libseqlib's
sake. Probably upstream libseqlib bundles its own htslib, so can access these
private htslib functions in a semi-maintainable way as libseqlib controls when
its own bundled htslib is updated. But Debian would prefer to build libseqlib
against a separate htslib rather than a bundled one. Some reasonable ways to do
this would be:
(A) Maintain cram/*.h as a Debian-local patch to libseqlib, which would likely
explicitly model the version lock-step that you will have taken on by
de-bundling htslib from libseqlib.
(B) Work with upstream libseqlib to find out exactly what facilities from
cram/*.h they need, and work with upstream htslib to add equivalents to
htslib/cram.h (which is HTSlib's way of adding supported public CRAM-specific
functionality).
(C) Package cram/*.h in a separate
libhts-private-stuff-just-for-libseqlib-and-other-htslib-wrappers-dont-use-this-dev
package.
Option (B) would be the best approach as it improves both Debian-flavoured and
upstream HTSlib, though it is a long-term solution and may not be practical as
libseqlib is a C++ wrapper of htslib so may desire greater access to htslib
internals than is practically supportable.
2. debian/patches/fix_pkg-config.patch is incorrect
HTSlib's convention is that its headers are included via #include
<htslib/sam.h> etc, to avoid confusion with any other packages' headers named
sam.h. So a Cflags value of -I${includedir}/htslib is incorrect.
Presumably this has been done so that libseqlib can use #include <cram/cram.h>
etc. This is bad in general as already discussed, but it would be better to
patch libseqlib to use #include <htslib/cram/cram.h> instead or to patch
libseqlib to add -Ipath/to/include/htslib to that package only.
3. The htslib*.mk makefile fragments should not be packaged
These provide rules and dependencies that are useful when building client
software against an in-development HTSlib source tree. In particular, when you
are making changes to *both* client and htslib source code, and would like
typing "make" in the client directory to rebuild libhts.a as appropriate. This
is not necessary when building software against an already-installed HTSlib, so
these files should not be in a libhts-dev package.
debian/changelog suggests these are installed for bcftools's sake. If these are
needed when building bcftools against an installed HTSlib, either you are
configuring bcftools incorrectly or there is a bug in bcftools.
In general, upstream's "make install" rule reflects what upstream thinks should
be installed. If you find yourselves desiring to install other things too, it
would be good to contact upstream so that a solution can be reached that fixes
the problem for everyone.
John
[University of Glasgow: The Times Scottish University of the Year 2018]
--- End Message ---
--- Begin Message ---
Source: htslib
Source-Version: 1.5-5
We believe that the bug you reported is fixed in the latest version of
htslib, 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 htslib 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: SHA512
Format: 1.8
Date: Sun, 10 Dec 2017 09:00:27 +0100
Source: htslib
Binary: libhts2 libhts-dev libhts-private-dev htslib-test tabix
Architecture: source all amd64
Version: 1.5-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
htslib-test - Test data for HTSlib
libhts-dev - development files for the HTSlib
libhts-private-dev - private development files for the HTSlib (use with care)
libhts2 - C library for high-throughput sequencing data formats
tabix - generic indexer for TAB-delimited genome position files
Closes: 879885 881170 881359
Changes:
htslib (1.5-5) unstable; urgency=medium
.
[ Graham Inggs ]
* Extend i386 fix to hurd and kfreebsd
.
[ Helmut Grohne ]
* Fix FTCBFS: Let dh_auto_configure pass --host to ./configure
Closes: #879885
.
[ Andreas Tille ]
* Fix issues with private cram headers
- Provide cram headers in separate package libhts-private-dev.install
Closes: #881170
- Deactivate fix_pkg-config.patch
Closes: #881359
* Standards-Version: 4.1.2
Checksums-Sha1:
5b01f24f34966b3179ce50f74c1461044e124c2b 2343 htslib_1.5-5.dsc
502c45af22257da962fd67e9d614cefa76ecd436 14128 htslib_1.5-5.debian.tar.xz
1ffa98ecbb3fda7ba9836d1e3a4f8c465b96e7a0 798396 htslib-test_1.5-5_all.deb
25c520adc233949d1fde272d941237b4cb5b444f 7592 htslib_1.5-5_amd64.buildinfo
a794d2c47b35a74d4768205a9fdb6db493162708 375980 libhts-dev_1.5-5_amd64.deb
a2681ac839018e4ab1605f1b40e986c24a8de4da 37104 libhts-private-dev_1.5-5_all.deb
43876abeba8e40ba4e002e4a8875f9730415effd 773212 libhts2-dbgsym_1.5-5_amd64.deb
82de9d699b9534134c35642f80101a167454b602 297344 libhts2_1.5-5_amd64.deb
f3f8e165013fe3faf1152a623f9075ebf5d5c065 1905976 tabix-dbgsym_1.5-5_amd64.deb
d3227635dc3f74c5f11db0da9e7282f60bfb4f27 316872 tabix_1.5-5_amd64.deb
Checksums-Sha256:
9c7599b40e9f75e270bcfe7e001a214f25b5f8dc1df8315c92745ddbf6d37a0b 2343
htslib_1.5-5.dsc
62010d940653d8aa94c61baf7d102c54dfc61b2fd95714458ad6bf40504427a4 14128
htslib_1.5-5.debian.tar.xz
f7aa33f1cb6378d858e3ab45e6e284ad9fbea64aa2a9a42acde4a30d2bf424e1 798396
htslib-test_1.5-5_all.deb
040afa417537f1a859734e444d989efbb6db8ca64b00d9f580bd17d2a1848a2d 7592
htslib_1.5-5_amd64.buildinfo
24cff5af8fc9fa87c7603bfff39204d95c6442526f03d7236f0b524c7bdb3cfe 375980
libhts-dev_1.5-5_amd64.deb
ec5a21928f5e7cb37e7c4c443e2eb420b842bc795fb5fb651f6a07bc6186051e 37104
libhts-private-dev_1.5-5_all.deb
69b41c3ab8ba70a47ad18d932707af421a649f5409d4e40414f6db733600124f 773212
libhts2-dbgsym_1.5-5_amd64.deb
8cf015e0744a0e75a9042547555e456beaa80e6066dfe46996daec057c35a6d0 297344
libhts2_1.5-5_amd64.deb
8d94039a2dc60324eaa24bfc4900b603c15c26dc373ba7cde4ff5e58d4398d60 1905976
tabix-dbgsym_1.5-5_amd64.deb
6ae87f538045a35f8d3cade79bee61c23a05a6d37b8b5f2c082598fe52e0f0f0 316872
tabix_1.5-5_amd64.deb
Files:
e03e776414a5f78c6f45d3e13fb519f9 2343 science optional htslib_1.5-5.dsc
2090eed7767fdf9752e251aec52c3d2e 14128 science optional
htslib_1.5-5.debian.tar.xz
7130544bd66f04e5d8eb7f827f0a6d84 798396 science optional
htslib-test_1.5-5_all.deb
69642e095b3bb2a755f579bee2158630 7592 science optional
htslib_1.5-5_amd64.buildinfo
7c3ae3563018e2e5489ec69f1826c46d 375980 libdevel optional
libhts-dev_1.5-5_amd64.deb
98598ffc2e92eda0191046a70698809b 37104 libdevel optional
libhts-private-dev_1.5-5_all.deb
845d9e1eace022327b57f14a64c5c68c 773212 debug optional
libhts2-dbgsym_1.5-5_amd64.deb
007d73e2e33fa89ee5ec0b18de09205e 297344 libs optional libhts2_1.5-5_amd64.deb
52beb10fbc6bdcc8649c15de88bcb625 1905976 debug optional
tabix-dbgsym_1.5-5_amd64.deb
0bb6d2bf9e2bd7e245b2459fa151258d 316872 science optional tabix_1.5-5_amd64.deb
-----BEGIN PGP SIGNATURE-----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=+R7I
-----END PGP SIGNATURE-----
--- End Message ---
