[med-svn] r17966 - in trunk/packages/hhsuite/tags: . 2.0.16-2/debian
Laszlo Kajan
lkajan at moszumanska.debian.org
Mon Sep 8 19:46:09 UTC 2014
Author: lkajan
Date: 2014-09-08 19:46:09 +0000 (Mon, 08 Sep 2014)
New Revision: 17966
Added:
trunk/packages/hhsuite/tags/2.0.16-2/
trunk/packages/hhsuite/tags/2.0.16-2/debian/README.source
trunk/packages/hhsuite/tags/2.0.16-2/debian/changelog
trunk/packages/hhsuite/tags/2.0.16-2/debian/control
trunk/packages/hhsuite/tags/2.0.16-2/debian/docs
trunk/packages/hhsuite/tags/2.0.16-2/debian/hhsuite-doc.doc-base
trunk/packages/hhsuite/tags/2.0.16-2/debian/hhsuite.docs
trunk/packages/hhsuite/tags/2.0.16-2/debian/rules
Removed:
trunk/packages/hhsuite/tags/2.0.16-2/debian/README.source
trunk/packages/hhsuite/tags/2.0.16-2/debian/changelog
trunk/packages/hhsuite/tags/2.0.16-2/debian/control
trunk/packages/hhsuite/tags/2.0.16-2/debian/docs
trunk/packages/hhsuite/tags/2.0.16-2/debian/hhsuite-doc.doc-base
trunk/packages/hhsuite/tags/2.0.16-2/debian/hhsuite.docs
trunk/packages/hhsuite/tags/2.0.16-2/debian/rules
Log:
[svn-buildpackage] Tagging hhsuite 2.0.16-2
Deleted: trunk/packages/hhsuite/tags/2.0.16-2/debian/README.source
===================================================================
--- trunk/packages/hhsuite/trunk/debian/README.source 2014-09-08 10:04:41 UTC (rev 17963)
+++ trunk/packages/hhsuite/tags/2.0.16-2/debian/README.source 2014-09-08 19:46:09 UTC (rev 17966)
@@ -1,8 +0,0 @@
-hhsuite for Debian
-------------------
-
-Patches
-.......
-Patches are documented in their headers.
-
-# vim:et:ts=2:
Copied: trunk/packages/hhsuite/tags/2.0.16-2/debian/README.source (from rev 17964, trunk/packages/hhsuite/trunk/debian/README.source)
===================================================================
--- trunk/packages/hhsuite/tags/2.0.16-2/debian/README.source (rev 0)
+++ trunk/packages/hhsuite/tags/2.0.16-2/debian/README.source 2014-09-08 19:46:09 UTC (rev 17966)
@@ -0,0 +1,13 @@
+hhsuite for Debian
+------------------
+
+Patches
+.......
+Patches are documented in their headers.
+
+Not architecture independent documentation
+..........................................
+This is to help Ubuntu developers, see [1].
+[1] https://launchpad.net/ubuntu/+source/hhsuite/2.0.16-1ubuntu1
+
+# vim:et:ts=2:
Deleted: trunk/packages/hhsuite/tags/2.0.16-2/debian/changelog
===================================================================
--- trunk/packages/hhsuite/trunk/debian/changelog 2014-09-08 10:04:41 UTC (rev 17963)
+++ trunk/packages/hhsuite/tags/2.0.16-2/debian/changelog 2014-09-08 19:46:09 UTC (rev 17966)
@@ -1,58 +0,0 @@
-hhsuite (2.0.16-2) UNRELEASED; urgency=low
-
- [Steffen Moeller]
- * Bumped standard to 3.9.4.
- * Removed DMUA flag.
- * Created new -doc package and moved user guide to it
- * Moved scripts directory from hhsuite-data to hhsuite
- * Added CHANGES file to .docs
- * joined hardening patch with rest1
-
- -- Steffen Moeller <moeller at debian.org> Thu, 25 Jul 2013 16:05:49 +0200
-
-hhsuite (2.0.16-1) unstable; urgency=low
-
- [Laszlo Kajan]
- * New upstream release.
- * Updated debian/watch file.
-
- -- Laszlo Kajan <lkajan at rostlab.org> Mon, 24 Sep 2012 09:32:14 +0200
-
-hhsuite (2.0.15-1) unstable; urgency=low
-
- * New upstream release.
-
- -- Laszlo Kajan <lkajan at rostlab.org> Wed, 27 Jun 2012 14:17:05 +0200
-
-hhsuite (2.0.14-1) unstable; urgency=low
-
- * [Andreas Tille <tille at debian.org>]
- debian/upstream: Enhanced author values
- * [Laszlo Kajan <lkajan at rostlab.org>]
- New upstream release.
-
- -- Laszlo Kajan <lkajan at rostlab.org> Wed, 23 May 2012 10:52:40 +0200
-
-hhsuite (2.0.13-2) unstable; urgency=low
-
- * [Andreas Tille <tille at debian.org>]
- debian/upstream:
- - it is (now) possible to support more than one citation
- - more verbose citation information
- * [Laszlo Kajan <lkajan at rostlab.org]
- Added #include <unistd.h> to src/hhsearch.C in order to fix compilation
- issue with g++-4.7. (Closes: #667201)
-
- -- Laszlo Kajan <lkajan at rostlab.org> Wed, 04 Apr 2012 13:45:49 +0200
-
-hhsuite (2.0.13-1) unstable; urgency=low
-
- * New upstream release
-
- -- Laszlo Kajan <lkajan at rostlab.org> Wed, 07 Mar 2012 09:35:48 +0100
-
-hhsuite (2.0.12-1) unstable; urgency=low
-
- * Initial release (Closes: #656626)
-
- -- Laszlo Kajan <lkajan at rostlab.org> Wed, 22 Feb 2012 10:03:00 +0100
Copied: trunk/packages/hhsuite/tags/2.0.16-2/debian/changelog (from rev 17964, trunk/packages/hhsuite/trunk/debian/changelog)
===================================================================
--- trunk/packages/hhsuite/tags/2.0.16-2/debian/changelog (rev 0)
+++ trunk/packages/hhsuite/tags/2.0.16-2/debian/changelog 2014-09-08 19:46:09 UTC (rev 17966)
@@ -0,0 +1,65 @@
+hhsuite (2.0.16-2) unstable; urgency=low
+
+ [Steffen Moeller]
+ * Bumped standard to 3.9.4.
+ * Removed DMUA flag.
+ * Created new -doc package and moved user guide to it
+ * Moved scripts directory from hhsuite-data to hhsuite
+ * Added CHANGES file to .docs
+ * joined hardening patch with rest1
+
+ [Laszlo Kajan]
+ * Bumped standard to 3.9.5.
+ * Pulled 2.0.16-1 -> 2.0.16-1u1 changes from Ubuntu: arch all packages are
+ now amd64, since all arch dep packages are also amd64.
+ * Completed Steffen's changes.
+ * Removed libpng12-dev dependency by disabling png feature. (Closes: #742579)
+
+ -- Laszlo Kajan <lkajan at debian.org> Mon, 08 Sep 2014 19:32:43 +0200
+
+hhsuite (2.0.16-1) unstable; urgency=low
+
+ [Laszlo Kajan]
+ * New upstream release.
+ * Updated debian/watch file.
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Mon, 24 Sep 2012 09:32:14 +0200
+
+hhsuite (2.0.15-1) unstable; urgency=low
+
+ * New upstream release.
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Wed, 27 Jun 2012 14:17:05 +0200
+
+hhsuite (2.0.14-1) unstable; urgency=low
+
+ * [Andreas Tille <tille at debian.org>]
+ debian/upstream: Enhanced author values
+ * [Laszlo Kajan <lkajan at rostlab.org>]
+ New upstream release.
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Wed, 23 May 2012 10:52:40 +0200
+
+hhsuite (2.0.13-2) unstable; urgency=low
+
+ * [Andreas Tille <tille at debian.org>]
+ debian/upstream:
+ - it is (now) possible to support more than one citation
+ - more verbose citation information
+ * [Laszlo Kajan <lkajan at rostlab.org]
+ Added #include <unistd.h> to src/hhsearch.C in order to fix compilation
+ issue with g++-4.7. (Closes: #667201)
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Wed, 04 Apr 2012 13:45:49 +0200
+
+hhsuite (2.0.13-1) unstable; urgency=low
+
+ * New upstream release
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Wed, 07 Mar 2012 09:35:48 +0100
+
+hhsuite (2.0.12-1) unstable; urgency=low
+
+ * Initial release (Closes: #656626)
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Wed, 22 Feb 2012 10:03:00 +0100
Deleted: trunk/packages/hhsuite/tags/2.0.16-2/debian/control
===================================================================
--- trunk/packages/hhsuite/trunk/debian/control 2014-09-08 10:04:41 UTC (rev 17963)
+++ trunk/packages/hhsuite/tags/2.0.16-2/debian/control 2014-09-08 19:46:09 UTC (rev 17966)
@@ -1,59 +0,0 @@
-Source: hhsuite
-Section: science
-Priority: extra
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Laszlo Kajan <lkajan at rostlab.org>
-Build-Depends: debhelper (>= 8.0.0), libffindex0-dev (>= 0.9.6.1), help2man, libpng12-dev
-Standards-Version: 3.9.4
-Homepage: http://toolkit.genzentrum.lmu.de/sections/search
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/hhsuite/trunk/
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/hhsuite/trunk/
-
-Package: hhsuite
-Architecture: amd64
-Depends: ${shlibs:Depends}, ${misc:Depends}, ffindex (>= 0.9.6.1),
- hhsuite-data (= ${source:Version})
-Description: sensitive protein sequence searching based on HMM-HMM alignment
- HH-suite is an open-source software package for sensitive protein sequence
- searching based on the pairwise alignment of hidden Markov models (HMMs).
- .
- This package contains HHsearch and HHblits among other programs and utilities.
- .
- HHsearch takes as input a multiple sequence alignment (MSA) or profile HMM
- and searches a database of HMMs (e.g. PDB, Pfam, or InterPro) for homologous
- proteins. HHsearch is often used for protein structure prediction to detect
- homologous templates and to build highly accurate query-template pairwise
- alignments for homology modeling.
- .
- HHblits can build high-quality MSAs starting from single sequences or from
- MSAs. It transforms these into a query HMM and, using an iterative search
- strategy, adds significantly similar sequences from the previous search to
- the updated query HMM for the next search iteration. Compared to PSI-BLAST,
- HHblits is faster, up to twice as sensitive and produces more accurate
- alignments.
-
-Package: hhsuite-doc
-Architecture: all
-Depends: ${shlibs:Depends}, ${misc:Depends}
-Recommends: hhsuite
-Description: documentation for HHsuite for HMM-HMM comparisons
- This package provides a PDF with the user guide for the HH-suite.
-
-Package: hhsuite-data
-Architecture: all
-Depends: ${misc:Depends}
-Description: sensitive protein sequence searching based on HMM-HMM alignment (data)
- HH-suite is an open-source software package for sensitive protein sequence
- searching based on the pairwise alignment of hidden Markov models (HMMs).
- .
- This package contains architecture independent scripts and data files.
-
-Package: hhsuite-dbg
-Architecture: amd64
-Section: debug
-Depends: hhsuite (= ${binary:Version}), ${shlibs:Depends}, ${misc:Depends}
-Description: sensitive protein sequence searching based on HMM-HMM alignment (debug)
- HH-suite is an open-source software package for sensitive protein sequence
- searching based on the pairwise alignment of hidden Markov models (HMMs).
- .
- This package contains the debugging symbols.
Copied: trunk/packages/hhsuite/tags/2.0.16-2/debian/control (from rev 17965, trunk/packages/hhsuite/trunk/debian/control)
===================================================================
--- trunk/packages/hhsuite/tags/2.0.16-2/debian/control (rev 0)
+++ trunk/packages/hhsuite/tags/2.0.16-2/debian/control 2014-09-08 19:46:09 UTC (rev 17966)
@@ -0,0 +1,63 @@
+Source: hhsuite
+Section: science
+Priority: extra
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Laszlo Kajan <lkajan at debian.org>
+Build-Depends: debhelper (>= 8.0.0), libffindex0-dev (>= 0.9.6.1), help2man
+Standards-Version: 3.9.5
+Homepage: http://toolkit.genzentrum.lmu.de/sections/search
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/hhsuite/trunk/
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/hhsuite/trunk/
+
+Package: hhsuite
+Architecture: amd64
+Depends: ${shlibs:Depends}, ${misc:Depends}, ffindex (>= 0.9.6.1),
+ hhsuite-data (= ${binary:Version})
+Description: sensitive protein sequence searching based on HMM-HMM alignment
+ HH-suite is an open-source software package for sensitive protein sequence
+ searching based on the pairwise alignment of hidden Markov models (HMMs).
+ .
+ This package contains HHsearch and HHblits among other programs and utilities.
+ .
+ HHsearch takes as input a multiple sequence alignment (MSA) or profile HMM
+ and searches a database of HMMs (e.g. PDB, Pfam, or InterPro) for homologous
+ proteins. HHsearch is often used for protein structure prediction to detect
+ homologous templates and to build highly accurate query-template pairwise
+ alignments for homology modeling.
+ .
+ HHblits can build high-quality MSAs starting from single sequences or from
+ MSAs. It transforms these into a query HMM and, using an iterative search
+ strategy, adds significantly similar sequences from the previous search to
+ the updated query HMM for the next search iteration. Compared to PSI-BLAST,
+ HHblits is faster, up to twice as sensitive and produces more accurate
+ alignments.
+
+Package: hhsuite-doc
+Section: doc
+Architecture: amd64
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Recommends: hhsuite
+Description: documentation for HHsuite for HMM-HMM comparisons
+ HH-suite is an open-source software package for sensitive protein sequence
+ searching based on the pairwise alignment of hidden Markov models (HMMs).
+ .
+ This package provides a PDF with the user guide for HH-suite.
+
+Package: hhsuite-data
+Architecture: amd64
+Depends: ${misc:Depends}
+Description: sensitive protein sequence searching based on HMM-HMM alignment (data)
+ HH-suite is an open-source software package for sensitive protein sequence
+ searching based on the pairwise alignment of hidden Markov models (HMMs).
+ .
+ This package contains architecture independent scripts and data files.
+
+Package: hhsuite-dbg
+Architecture: amd64
+Section: debug
+Depends: hhsuite (= ${binary:Version}), ${shlibs:Depends}, ${misc:Depends}
+Description: sensitive protein sequence searching based on HMM-HMM alignment (debug)
+ HH-suite is an open-source software package for sensitive protein sequence
+ searching based on the pairwise alignment of hidden Markov models (HMMs).
+ .
+ This package contains the debugging symbols.
Deleted: trunk/packages/hhsuite/tags/2.0.16-2/debian/docs
===================================================================
--- trunk/packages/hhsuite/trunk/debian/docs 2014-09-08 10:04:41 UTC (rev 17963)
+++ trunk/packages/hhsuite/tags/2.0.16-2/debian/docs 2014-09-08 19:46:09 UTC (rev 17966)
@@ -1,2 +0,0 @@
-README
-hhsuite-userguide.pdf
Copied: trunk/packages/hhsuite/tags/2.0.16-2/debian/docs (from rev 17964, trunk/packages/hhsuite/trunk/debian/docs)
===================================================================
--- trunk/packages/hhsuite/tags/2.0.16-2/debian/docs (rev 0)
+++ trunk/packages/hhsuite/tags/2.0.16-2/debian/docs 2014-09-08 19:46:09 UTC (rev 17966)
@@ -0,0 +1 @@
+README
Deleted: trunk/packages/hhsuite/tags/2.0.16-2/debian/hhsuite-doc.doc-base
===================================================================
--- trunk/packages/hhsuite/trunk/debian/hhsuite-doc.doc-base 2014-09-08 10:04:41 UTC (rev 17963)
+++ trunk/packages/hhsuite/tags/2.0.16-2/debian/hhsuite-doc.doc-base 2014-09-08 19:46:09 UTC (rev 17966)
@@ -1,8 +0,0 @@
-Document: hhsuite
-Title: HH-suite User Guide
-Author: Johannes Söding, Michael Remmert, Andreas Hauser
-Abstract: HH-suite for sensitive sequence searching based on HMM-HMM alignment.
-Section: Science/Biology
-
-Format: PDF
-Files: /usr/share/doc/hhsuite/hhsuite-userguide.pdf.gz
Copied: trunk/packages/hhsuite/tags/2.0.16-2/debian/hhsuite-doc.doc-base (from rev 17964, trunk/packages/hhsuite/trunk/debian/hhsuite-doc.doc-base)
===================================================================
--- trunk/packages/hhsuite/tags/2.0.16-2/debian/hhsuite-doc.doc-base (rev 0)
+++ trunk/packages/hhsuite/tags/2.0.16-2/debian/hhsuite-doc.doc-base 2014-09-08 19:46:09 UTC (rev 17966)
@@ -0,0 +1,8 @@
+Document: hhsuite
+Title: HH-suite User Guide
+Author: Johannes Söding, Michael Remmert, Andreas Hauser
+Abstract: HH-suite for sensitive sequence searching based on HMM-HMM alignment.
+Section: Science/Biology
+
+Format: PDF
+Files: /usr/share/doc/hhsuite-doc/hhsuite-userguide.pdf.gz
Deleted: trunk/packages/hhsuite/tags/2.0.16-2/debian/hhsuite.docs
===================================================================
--- trunk/packages/hhsuite/trunk/debian/hhsuite.docs 2014-09-08 10:04:41 UTC (rev 17963)
+++ trunk/packages/hhsuite/tags/2.0.16-2/debian/hhsuite.docs 2014-09-08 19:46:09 UTC (rev 17966)
@@ -1,2 +0,0 @@
-README
-CHANGES
Copied: trunk/packages/hhsuite/tags/2.0.16-2/debian/hhsuite.docs (from rev 17964, trunk/packages/hhsuite/trunk/debian/hhsuite.docs)
===================================================================
--- trunk/packages/hhsuite/tags/2.0.16-2/debian/hhsuite.docs (rev 0)
+++ trunk/packages/hhsuite/tags/2.0.16-2/debian/hhsuite.docs 2014-09-08 19:46:09 UTC (rev 17966)
@@ -0,0 +1 @@
+README
Deleted: trunk/packages/hhsuite/tags/2.0.16-2/debian/rules
===================================================================
--- trunk/packages/hhsuite/trunk/debian/rules 2014-09-08 10:04:41 UTC (rev 17963)
+++ trunk/packages/hhsuite/tags/2.0.16-2/debian/rules 2014-09-08 19:46:09 UTC (rev 17966)
@@ -1,46 +0,0 @@
-#!/usr/bin/make -f
-
-export CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)
-export CFLAGS:=$(shell dpkg-buildflags --get CFLAGS)
-export CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS)
-export LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)
-
-# Uncomment this to turn on verbose mode.
-#export DH_VERBOSE=1
-
-VERSION=$(shell sed --posix -n -e '/VERSION_AND_DATE/{ s/.*version \([0-9][0-9.]*\).*/\1/; p; }' src/hhdecl.C)
-
-HHMANPAGES = hhalign.1 hhblits.1 hhconsensus.1 hhfilter.1 hhmake.1 hhsearch.1
-
-export n_hhalign=align a query alignment/HMM to a template alignment/HMM
-export n_hhblits=fast homology detection method to iteratively search a HMM database
-export n_hhconsensus=calculate the consensus sequence for an A3M/FASTA input file
-export n_hhfilter=filter an alignment by maximum sequence identity of match states and minimum coverage
-export n_hhmake=build an HMM from an input alignment or convert between HMMER format and HHsearch format
-export n_hhsearch=search a database of HMMs with a query alignment or query HMM
-
-.PHONY: hhmanpages
-hhmanpages: $(HHMANPAGES)
-
-.PHONY: override_dh_strip
-override_dh_strip:
- dh_strip --dbg-package=hhsuite-dbg -Xlibffindex.a -Xlibffindex.so
-
-.PHONY: override_dh_installman
-override_dh_installman: $(HHMANPAGES)
- dh_installman
-
-$(HHMANPAGES): %.1 : debian/tmp/usr/bin/%
- unset LD_PRELOAD && export LD_LIBRARY_PATH=debian/tmp/usr/lib && export HHLIB=/usr/share/hhsuite && help2man --no-info --help-option '-h all' --version-string $(VERSION) -n "$$n_$*" '$<' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > '$@'
-
-.PHONY: override_dh_clean
-override_dh_clean:
- rm -f $(HHMANPAGES)
- dh_clean
-
-get-orig-source:
- mkdir -p ../tarballs
- uscan --verbose --force-download --destdir=../tarballs
-
-%:
- dh $@ --parallel
Copied: trunk/packages/hhsuite/tags/2.0.16-2/debian/rules (from rev 17964, trunk/packages/hhsuite/trunk/debian/rules)
===================================================================
--- trunk/packages/hhsuite/tags/2.0.16-2/debian/rules (rev 0)
+++ trunk/packages/hhsuite/tags/2.0.16-2/debian/rules 2014-09-08 19:46:09 UTC (rev 17966)
@@ -0,0 +1,50 @@
+#!/usr/bin/make -f
+
+export CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)
+export CFLAGS:=$(shell dpkg-buildflags --get CFLAGS)
+export CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS)
+export LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+VERSION=$(shell sed --posix -n -e '/VERSION_AND_DATE/{ s/.*version \([0-9][0-9.]*\).*/\1/; p; }' src/hhdecl.C)
+
+HHMANPAGES = hhalign.1 hhblits.1 hhconsensus.1 hhfilter.1 hhmake.1 hhsearch.1
+
+export n_hhalign=align a query alignment/HMM to a template alignment/HMM
+export n_hhblits=fast homology detection method to iteratively search a HMM database
+export n_hhconsensus=calculate the consensus sequence for an A3M/FASTA input file
+export n_hhfilter=filter an alignment by maximum sequence identity of match states and minimum coverage
+export n_hhmake=build an HMM from an input alignment or convert between HMMER format and HHsearch format
+export n_hhsearch=search a database of HMMs with a query alignment or query HMM
+
+.PHONY: hhmanpages
+hhmanpages: $(HHMANPAGES)
+
+.PHONY: override_dh_strip
+override_dh_strip:
+ dh_strip --dbg-package=hhsuite-dbg -Xlibffindex.a -Xlibffindex.so
+
+.PHONY: override_dh_installman
+override_dh_installman: $(HHMANPAGES)
+ dh_installman
+
+$(HHMANPAGES): %.1 : debian/tmp/usr/bin/%
+ unset LD_PRELOAD && export LD_LIBRARY_PATH=debian/tmp/usr/lib && export HHLIB=. && help2man --no-info --help-option '-h all' --version-string $(VERSION) -n "$$n_$*" '$<' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > '$@'
+
+.PHONY: override_dh_clean
+override_dh_clean:
+ rm -f $(HHMANPAGES)
+ dh_clean
+
+.PHONY: override_dh_auto_build
+override_dh_auto_build:
+ dh_auto_build -- NO_PNG=1
+
+get-orig-source:
+ mkdir -p ../tarballs
+ uscan --verbose --force-download --destdir=../tarballs
+
+%:
+ dh $@ --parallel
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