[med-svn] r19067 - in trunk/packages/murasaki/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Thu Apr 16 09:53:36 UTC 2015
Author: tille
Date: 2015-04-16 09:53:36 +0000 (Thu, 16 Apr 2015)
New Revision: 19067
Added:
trunk/packages/murasaki/trunk/debian/patches/man_syntax.patch
trunk/packages/murasaki/trunk/debian/patches/spelling.patch
Removed:
trunk/packages/murasaki/trunk/debian/docs
Modified:
trunk/packages/murasaki/trunk/debian/patches/series
trunk/packages/murasaki/trunk/debian/rules
Log:
Polishing lintian issues
Deleted: trunk/packages/murasaki/trunk/debian/docs
===================================================================
--- trunk/packages/murasaki/trunk/debian/docs 2015-04-16 09:15:48 UTC (rev 19066)
+++ trunk/packages/murasaki/trunk/debian/docs 2015-04-16 09:53:36 UTC (rev 19067)
@@ -1,2 +0,0 @@
-doc/*.html
-doc/*.txt
Added: trunk/packages/murasaki/trunk/debian/patches/man_syntax.patch
===================================================================
--- trunk/packages/murasaki/trunk/debian/patches/man_syntax.patch (rev 0)
+++ trunk/packages/murasaki/trunk/debian/patches/man_syntax.patch 2015-04-16 09:53:36 UTC (rev 19067)
@@ -0,0 +1,26 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 15 Apr 2015 14:06:19 +0200
+Description: Fix manpage syntax
+
+--- a/qlob.pl
++++ b/qlob.pl
+@@ -204,7 +204,7 @@ __END__
+
+ =head1 NAME
+
+-qlob.pl: run quick mursaki compare
++qlob.pl -- run quick mursaki compare
+
+ =head1 SYNOPSIS
+
+--- a/substitch.pl
++++ b/substitch.pl
+@@ -465,7 +465,7 @@ __END__
+
+ =head1 NAME
+
+-substitch.pl : Split/merge stitch files into/out of stitch files
++substitch.pl -- Split/merge stitch files into/out of stitch files
+
+ =head1 SYNOPSIS
+
Modified: trunk/packages/murasaki/trunk/debian/patches/series
===================================================================
--- trunk/packages/murasaki/trunk/debian/patches/series 2015-04-16 09:15:48 UTC (rev 19066)
+++ trunk/packages/murasaki/trunk/debian/patches/series 2015-04-16 09:53:36 UTC (rev 19067)
@@ -1,3 +1,5 @@
use_proper_libboost_names.patch
include_libpstream.patch
hardening.patch
+spelling.patch
+man_syntax.patch
Added: trunk/packages/murasaki/trunk/debian/patches/spelling.patch
===================================================================
--- trunk/packages/murasaki/trunk/debian/patches/spelling.patch (rev 0)
+++ trunk/packages/murasaki/trunk/debian/patches/spelling.patch 2015-04-16 09:53:36 UTC (rev 19067)
@@ -0,0 +1,92 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 15 Apr 2015 14:06:19 +0200
+Description: Spelling fixes
+
+--- a/doc/murasaki.1
++++ b/doc/murasaki.1
+@@ -521,7 +521,7 @@ over the network (helpful for slow netwo
+ .IX Item "--mpidistro|-L <B>"
+ Toggles use of \s-1MPI\s0 to distribute sequence data over (if the sequence
+ is available on local disk on each node then turning this off may
+-potentially accerlate the intial sequence loading).
++potentially accerlate the initial sequence loading).
+ .IP "\-\-waittoanchor|\-w <B>" 4
+ .IX Item "--waittoanchor|-w <B>"
+ Postpone actual anchor computation until all location sets have been
+@@ -553,8 +553,8 @@ Assign hashers to large memory nodes fir
+ .IP "\-\-memorybalance|\-a <B>" 4
+ .IX Item "--memorybalance|-a <B>"
+ .RS 4
+-.IP "If yes (deafult): balance hash storage between nodes based on the amount of available ram." 4
+-.IX Item "If yes (deafult): balance hash storage between nodes based on the amount of available ram."
++.IP "If yes (default): balance hash storage between nodes based on the amount of available ram." 4
++.IX Item "If yes (default): balance hash storage between nodes based on the amount of available ram."
+ .IP "If no: distribute storage evently. This more likely to achieve optimal run times, but might not utilize memory as efficiently." 4
+ .IX Item "If no: distribute storage evently. This more likely to achieve optimal run times, but might not utilize memory as efficiently."
+ .RE
+--- a/doc/murasaki.html
++++ b/doc/murasaki.html
+@@ -606,7 +606,7 @@ is too high.</p>
+ <dt><strong><a name="memorybalance_a_b" class="item">--memorybalance|-a <B></a></strong></dt>
+
+ <dl>
+-<dt><strong>If yes (deafult): balance hash storage between nodes based on
++<dt><strong>If yes (default): balance hash storage between nodes based on
+ the amount of available ram.</strong></dt>
+
+ <dt><strong><a name="if_no_distribute_storage_evently_this_more_likely_to_achieve_optimal_run_times_but_might_not_utilize_memory_as_efficiently" class="item">If no: distribute storage evently. This more likely to achieve
+--- a/doc/murasaki.pod
++++ b/doc/murasaki.pod
+@@ -486,7 +486,7 @@ Assign hashers to large memory nodes fir
+
+ =over
+
+-=item If yes (deafult): balance hash storage between nodes based on
++=item If yes (default): balance hash storage between nodes based on
+ the amount of available ram.
+
+ =item If no: distribute storage evently. This more likely to achieve
+--- a/doc/murasaki.txt
++++ b/doc/murasaki.txt
+@@ -372,7 +372,7 @@ OPTIONS
+
+ --memorybalance|-a <B>
+
+- If yes (deafult): balance hash storage between nodes based on the
++ If yes (default): balance hash storage between nodes based on the
+ amount of available ram.
+ If no: distribute storage evently. This more likely to achieve
+ optimal run times, but might not utilize memory as efficiently.
+--- a/src/murasaki.cc
++++ b/src/murasaki.cc
+@@ -303,7 +303,7 @@ void MurasakiRuntime::prep(){
+ if(opt.getOptSource("quickhash")!=OPT_SRC_MANUAL){
+ int target=(opt.hashPref==OpenHash_t ? 0:3);
+ if(opt.quick_hash!=target){
+- cout << "Auto> Switching hash function to "<<target<<" to accomodate "<<opt.hashPref_s()<<endl;
++ cout << "Auto> Switching hash function to "<<target<<" to accommodate "<<opt.hashPref_s()<<endl;
+ opt.quick_hash=target;
+ }
+ }
+--- a/src/options.cc
++++ b/src/options.cc
+@@ -930,7 +930,7 @@ Adaptive has function related:\n\
+ --bigfirst|-I = assign hashers to large memory nodes first\n\
+ --hostbalance|-l = if yes (default): spread out hashers evenly among hosts\n\
+ if no: ignore host name when assigning jobs\n\
+- --memorybalance|-a = if yes (deafult): balance hash storage between nodes\n\
++ --memorybalance|-a = if yes (default): balance hash storage between nodes\n\
+ based on the amount of available ram.\n\
+ if no: distribute storage evently.\n\
+ --distmerge|-< = if yes (default): during the merge step, send seeds to\n\
+--- a/filter.pl
++++ b/filter.pl
+@@ -1682,7 +1682,7 @@ For example:
+ "--nobins" turns off binning and plots a raw (likely bumpy) histogram
+ "--showall=crop" sends all data to gnuplot even on logscale plots (by
+ default for logscale plots values <=1 at the extreme right end are
+- chopped off because they dont show up in gnuplot (1 is the baseline)
++ chopped off because they don't show up in gnuplot (1 is the baseline)
+ but they do affect the visible range, and thus causes some scrunching.
+ "--showall=scale" manually sets to the X and Y ranges to the range of the
+ data (so 1's are visibly different from 0's).
Modified: trunk/packages/murasaki/trunk/debian/rules
===================================================================
--- trunk/packages/murasaki/trunk/debian/rules 2015-04-16 09:15:48 UTC (rev 19066)
+++ trunk/packages/murasaki/trunk/debian/rules 2015-04-16 09:53:36 UTC (rev 19067)
@@ -40,3 +40,7 @@
dh_install
# using wildcards in install files is practical but it duplicates some files
find debian/$(DEBPKGNAME)/usr -name "*-mpi" -delete
+
+override_dh_fixperms:
+ dh_fixperms
+ chmod a+x debian/$(DEBPKGNAME)-common/usr/share/perl5/murasaki/config.pl
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