Your message dated Wed, 09 Jan 2019 17:06:16 +0000
with message-id <[email protected]>
and subject line Bug#918765: fixed in hhsuite 3.0~beta3+dfsg-2
has caused the Debian Bug report #918765,
regarding hhsuite-data: does not provide
/usr/share/hhsuite/data/context_data.crf
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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--
918765: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=918765
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: hhsuite-data
Severity: important
Control: tags -1 + patch
Hello,
hhsuite-data does not provide /usr/share/hhsuite/data/context_data.crf, which
is the default context file for computing context-specific pseudocounts. This
effectively breaks hhmake and hhblits unless path to existing context_data.crf
is provided via '-contxt' command line option.
Steps to reproduce:
andrius@amalas:~$ gunzip -c /usr/share/doc/hhsuite/examples/query.a3m.gz >
query.a3m
andrius@amalas:~$ hhmake -i query.a3m
- 01:33:47.860 ERROR: Could not open file
'/usr/share/hhsuite/data/context_data.crf'
The following patch should fix the bug (was not able to try due to #917495):
diff --git a/debian/hhsuite-data.install b/debian/hhsuite-data.install
index e4403f1..f7d762c 100644
--- a/debian/hhsuite-data.install
+++ b/debian/hhsuite-data.install
@@ -1,4 +1,6 @@
usr/data/context_data.lib usr/share/hhsuite/data
+usr/data/context_data.crf usr/share/hhsuite/data
usr/data/cs219.lib usr/share/hhsuite/data
usr/data/context_data.lib usr/lib/hhsuite/data
+usr/data/context_data.crf usr/lib/hhsuite/data
usr/data/cs219.lib usr/lib/hhsuite/data
diff --git a/debian/hhsuite-data.links b/debian/hhsuite-data.links
index 4efda75..e9a226f 100644
--- a/debian/hhsuite-data.links
+++ b/debian/hhsuite-data.links
@@ -1,2 +1,3 @@
usr/share/hhsuite/data/context_data.lib usr/lib/hhsuite/data/context_data.lib
+usr/share/hhsuite/data/context_data.crf usr/lib/hhsuite/data/context_data.crf
usr/share/hhsuite/data/cs219.lib usr/lib/hhsuite/data/cs219.lib
Best,
Andrius
[#917495] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=917495
--
Andrius Merkys
Vilnius University Institute of Biotechnology, Saulėtekio al. 7, room V325
LT-10257 Vilnius, Lithuania
--- End Message ---
--- Begin Message ---
Source: hhsuite
Source-Version: 3.0~beta3+dfsg-2
We believe that the bug you reported is fixed in the latest version of
hhsuite, 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 hhsuite 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, 09 Jan 2019 17:36:27 +0100
Source: hhsuite
Binary: hhsuite hhsuite-doc hhsuite-data
Architecture: source
Version: 3.0~beta3+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
hhsuite - sensitive protein sequence searching based on HMM-HMM alignment
hhsuite-data - sensitive protein sequence searching based on HMM-HMM alignment
(
hhsuite-doc - documentation for HHsuite for HMM-HMM comparisons
Closes: 918765
Changes:
hhsuite (3.0~beta3+dfsg-2) unstable; urgency=medium
.
* Install context_data.crf (Thanks for the patch to Andrius Merkys
<[email protected]>)
Closes: #918765
* Add autopkgtest reproducing the issue of bug #918765
* debhelper 11
* Standards-Version: 4.3.0
* Secure URI in copyright format
* Remove trailing whitespace in debian/copyright
* Do not parse d/changelog
* Add versioned (Build-)Depends: ffindex
(>= 0.9.9.7.soedinglab+git20171201.74550c8)
* Adapt doc-base file to debhelper 11 location
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