[med-svn] r18797 - in trunk/packages/vsearch/trunk/debian: . patches

Andreas Tille tille at moszumanska.debian.org
Thu Feb 19 15:09:53 UTC 2015 

Author: tille
Date: 2015-02-19 15:09:53 +0000 (Thu, 19 Feb 2015)
New Revision: 18797

Removed:
   trunk/packages/vsearch/trunk/debian/patches/manpage_syntax.patch
Modified:
   trunk/packages/vsearch/trunk/debian/changelog
   trunk/packages/vsearch/trunk/debian/patches/fix_build_issue_on_hurd.patch
   trunk/packages/vsearch/trunk/debian/patches/fix_optimisation_flags.patch
   trunk/packages/vsearch/trunk/debian/patches/hardening.patch
   trunk/packages/vsearch/trunk/debian/patches/series
   trunk/packages/vsearch/trunk/debian/patches/sysconf_memory_sizing.patch
   trunk/packages/vsearch/trunk/debian/patches/x86_spezific_opts.patch
Log:
New upstream version, adapted patches


Modified: trunk/packages/vsearch/trunk/debian/changelog
===================================================================
--- trunk/packages/vsearch/trunk/debian/changelog	2015-02-19 15:07:16 UTC (rev 18796)
+++ trunk/packages/vsearch/trunk/debian/changelog	2015-02-19 15:09:53 UTC (rev 18797)
@@ -1,6 +1,15 @@
-vsearch (1.0.14+dfsg-1) UNRELEASED; urgency=medium
+vsearch (1.0.16+dfsg-1) UNRELEASED; urgency=medium
 
   * New upstream version
+  * Drop manpage syntax patch since it is a moving target
+  * Drop fix_build_issue_on_hurd.patch since applied upstream
+  * Refresh kFreeBSD patch
+
+ -- Andreas Tille <tille at debian.org>  Thu, 19 Feb 2015 15:58:50 +0100
+
+vsearch (1.0.14+dfsg-1) unstable; urgency=medium
+
+  * New upstream version
   * debian/README.source: Add proper information for data files
   * drop -msse2 flag
   * conditional use of -mtune flag

Modified: trunk/packages/vsearch/trunk/debian/patches/fix_build_issue_on_hurd.patch
===================================================================
--- trunk/packages/vsearch/trunk/debian/patches/fix_build_issue_on_hurd.patch	2015-02-19 15:07:16 UTC (rev 18796)
+++ trunk/packages/vsearch/trunk/debian/patches/fix_build_issue_on_hurd.patch	2015-02-19 15:09:53 UTC (rev 18797)
@@ -1,6 +1,7 @@
 Author: Andreas Tille <tille at debian.org>
 Last-Changed: Mon, 02 Feb 2015 07:40:07 +0100
 Bugs-Debian: http://bugs.debian.org/776815
+Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2015-February/031414.html
 Description: Fix build issue on Hurd which does not harm anywhere else
 
 --- a/src/vsearch.h

Modified: trunk/packages/vsearch/trunk/debian/patches/fix_optimisation_flags.patch
===================================================================
--- trunk/packages/vsearch/trunk/debian/patches/fix_optimisation_flags.patch	2015-02-19 15:07:16 UTC (rev 18796)
+++ trunk/packages/vsearch/trunk/debian/patches/fix_optimisation_flags.patch	2015-02-19 15:09:53 UTC (rev 18797)
@@ -1,6 +1,7 @@
 Author: Andreas Tille <tille at debian.org>
 Last-Changed: Mon, 02 Feb 2015 07:40:07 +0100
 Bugs-Debian: http://bugs.debian.org/776812
+Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2015-February/031414.html
 Description: Drop -msse2 flag
 
 --- a/src/Makefile.BZLIB

Modified: trunk/packages/vsearch/trunk/debian/patches/hardening.patch
===================================================================
--- trunk/packages/vsearch/trunk/debian/patches/hardening.patch	2015-02-19 15:07:16 UTC (rev 18796)
+++ trunk/packages/vsearch/trunk/debian/patches/hardening.patch	2015-02-19 15:09:53 UTC (rev 18797)
@@ -1,5 +1,6 @@
 Author: Andreas Tille <tille at debian.org>
 Last-Changed: Wed, 14 Jan 2015 10:40:22 +0000
+Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2015-February/031414.html
 Description: Propagate hardening options
 
 --- a/src/Makefile.BZLIB

Deleted: trunk/packages/vsearch/trunk/debian/patches/manpage_syntax.patch
===================================================================
--- trunk/packages/vsearch/trunk/debian/patches/manpage_syntax.patch	2015-02-19 15:07:16 UTC (rev 18796)
+++ trunk/packages/vsearch/trunk/debian/patches/manpage_syntax.patch	2015-02-19 15:09:53 UTC (rev 18797)
@@ -1,454 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Changed: Mon, 02 Feb 2015 07:40:07 +0100
-Description: Suppress some lintian warnings
-
---- a/doc/vsearch.1
-+++ b/doc/vsearch.1
-@@ -137,27 +137,27 @@ searching). We start with general option
- General options:
- .RS
- .TP 9
--.B --help
-+.B \-\-help
- Display a short help and exit.
- .TP
--.B --version
-+.B \-\-version
- Output version information and exit.
- .TP
--.BI --fasta_width\~ "positive integer"
-+.BI \-\-fasta_width\~ "positive integer"
- Fasta files produced by \fBvsearch\fR are wrapped (sequences are
- written on lines of \fIinteger\fR nucleotides, 80 by default). Set
- that value to 0 to eliminate the wrapping.
- .TP
--.BI --maxseqlength\~ "positive integer"
-+.BI \-\-maxseqlength\~ "positive integer"
- All \fBvsearch\fR operations will discard sequences of length equal or
- greater than \fIinteger\fR (50,000 nucleotides by default).
- .TP
--.BI --minseqlength\~ "positive integer"
-+.BI \-\-minseqlength\~ "positive integer"
- All \fBvsearch\fR operations will discard sequences of length smaller
- than \fIinteger\fR (1 nucleotide by default for sorting or shuffling,
- 32 nucleotides for clustering, dereplication or searching).
- .TP
--.B --notrunclabels
-+.B \-\-notrunclabels
- Do not truncate sequence labels at first space, use the full header in
- output files.
- .RE
-@@ -167,7 +167,7 @@ Chimera detection options:
- .PP
- .RS
- Chimera detection is based on a scoring function controlled by five
--options (--dn, --mindiffs, --mindiv, --minh, --xn). Sequences are first
-+options (\-\-dn, \-\-mindiffs, \-\-mindiv, \-\-minh, \-\-xn). Sequences are first
- sorted by decreasing abundance (if available), and compared on their
- \fIplus\fR strand only (case insensitive).
- .PP
-@@ -175,12 +175,12 @@ In \fIde novo\fR mode, input fasta file
- annotations (pattern [;]size=\fIinteger\fR[;] in the fasta
- header). The input order influences the chimera detection, so we
- recommend to sort sequences by decreasing abundance (default of
----derep_fulllength command). If your sequence set needs to be sorted,
--please see the --sortbysize command in the sorting section.
-+\-\-derep_fulllength command). If your sequence set needs to be sorted,
-+please see the \-\-sortbysize command in the sorting section.
- .PP
- .TP 9
--.BI --abskew \0real
--When using --uchime_denovo, the abundance skew is used to distinguish
-+.BI \-\-abskew \0real
-+When using \-\-uchime_denovo, the abundance skew is used to distinguish
- in a 3-way alignment which sequence is the chimera and which are the
- parents. The assumption is that chimeras appear later in the PCR
- amplification process and are therefore less abundant than their
-@@ -272,7 +272,7 @@ A: parent A sequence label.
- B: parent B sequence label.
- .IP \n+[step].
- T: top parent sequence label (i.e. parent most similar to the
--query). That field is removed when using --uchimeout5.
-+query). That field is removed when using \-\-uchimeout5.
- .IP \n+[step].
- idQM: percentage of similarity of query (Q) and model (M)
- constructed as a part of parent A and a part of parent B.
-@@ -502,9 +502,9 @@ Masking options:
- .PP
- An input sequence can be composed of lower- or uppercase
- nucleotides. Lowercase nucleotides are silently set to uppercase
--before masking, unless the --qmask soft option is used. Here are the
--results of combined masking options --qmask (or --dbmask for database
--sequences) and --hardmask, assuming each input sequences contains both
-+before masking, unless the \-\-qmask soft option is used. Here are the
-+results of combined masking options \-\-qmask (or \-\-dbmask for database
-+sequences) and \-\-hardmask, assuming each input sequences contains both
- lower and uppercase nucleotides:
- .PP
- .TS
-@@ -522,24 +522,24 @@ soft:on:lowercase symbols masked and cha
- .TE
- .PP
- .TP 9
--.B --hardmask
-+.B \-\-hardmask
- Mask low-complexity regions by replacing them with Ns instead of
- setting them to lower case.
- .TP
--.BI --maskfasta \0filename
-+.BI \-\-maskfasta \0filename
- Mask simple repeats and low-complexity regions in sequences contained
- in \fIfilename\fR. The default is to mask using \fIdust\fR (use
----qmask to modify that behavior).
-+\-\-qmask to modify that behavior).
- .TP
--.BI --output \0filename
-+.BI \-\-output \0filename
- Write the masked sequences to \fIfilename\fR, in fasta format.
- .TP
--.BI --qmask\~ "none|dust|soft"
-+.BI \-\-qmask\~ "none|dust|soft"
- Mask simple repeats and low-complexity regions in sequences using the
- \fIdust\fR or the \fIsoft\fR algorithms, or do not mask
- (\fInone\fR). The default is to mask using \fIdust\fR.
- .TP
--.BI --threads\~ "positive integer"
-+.BI \-\-threads\~ "positive integer"
- Number of computation threads to use (1 to 256). The number of threads
- should be lesser or equal to the number of available CPU cores. The
- default is to use all available ressources and to launch one thread
-@@ -582,17 +582,17 @@ per logical core.
- Searching options:
- .RS
- .TP 9
--.BI --alnout \0filename
-+.BI \-\-alnout \0filename
- Write pairwise global alignments to \fIfilename\fR using a
--human-readable format. Use --rowlen to modify alignment length. Output
-+human-readable format. Use \-\-rowlen to modify alignment length. Output
- order may vary when using multiple threads.
- .TP
--.BI --blast6out \0filename
-+.BI \-\-blast6out \0filename
- Write search results to \fIfilename\fR using a blast-like
- tab-separated format of twelve fields (listed below), with one line
--per query-target matching (or lack of matching if --output_no_hits is
-+per query-target matching (or lack of matching if \-\-output_no_hits is
- used). Output order may vary when using multiple threads. A similar
--output can be obtain with --userout \fIfilename\fR and --userfields
-+output can be obtain with \-\-userout \fIfilename\fR and \-\-userfields
- query+target+id+alnlen+mism+opens+qlo+qhi+tlo+thi+evalue+bits.
- A complete list and description is available in the section "Userfields"
- of this manual.
-@@ -714,12 +714,12 @@ default in usearch, all default scores a
- \fBvsearch\fR have been doubled to maintain equivalent penalties and
- to produce identical alignments.
- .TP
--.B --hardmask
-+.B \-\-hardmask
- Mask low-complexity regions by replacing them with Ns instead of
- setting them to lower case. For more information, please see the
- Masking section.
- .TP
--.BI --id \0real
-+.BI \-\-id \0real
- Reject the sequence match if the pairwise identity is lower than
- \fIreal\fR (value ranging from 0.0 to 1.0 included). The search
- process sorts target sequences by decreasing number of \fIk\fR-mers
-@@ -729,13 +729,13 @@ also prevent pairwise alignments with we
- there needs to be at least 6 shared \fIk\fR-mers to start the pairwise
- alignment, and at least one out of every 16 \fIk\fR-mers from the
- query needs to match the target. Consequently, using values lower than
----id 0.5 is not likely to capture more weakly matching targets. The
-+\-\-id 0.5 is not likely to capture more weakly matching targets. The
- pairwise identity is by default defined as the number of (matching columns) /
- (alignment length - terminal gaps). That definition can be modified by
----iddef.
-+\-\-iddef.
- .TP
--.BI --iddef\~ "0|1|2|3|4"
--Change the pairwise identity definition used in --id. Values accepted
-+.BI \-\-iddef\~ "0|1|2|3|4"
-+Change the pairwise identity definition used in \-\-id. Values accepted
- are:
- .RS
- .RS
-@@ -984,75 +984,75 @@ more). The default value is 8.
- Shuffling options:
- .RS
- .TP 9
--.BI --output \0filename
-+.BI \-\-output \0filename
- Write the shuffled sequences to \fIfilename\fR, in fasta format.
- .TP
--.BI --seed\~ "positive integer"
-+.BI \-\-seed\~ "positive integer"
- When shuffling sequence order, use \fIinteger\fR as seed. A given seed
- will always produce the same output order (useful for
- replicability). Set to 0 to use a pseudo-random seed (default
- behavior).
- .TP
--.BI --shuffle \0filename
-+.BI \-\-shuffle \0filename
- Pseudo-randomly shuffle the order of sequences contained in
- \fIfilename\fR.
- .TP
--.BI --topn\~ "positive integer"
-+.BI \-\-topn\~ "positive integer"
- Output only the top \fIinteger\fR sequences.
- .RE
- .PP
- .\" ----------------------------------------------------------------------------
- Sorting options:
- .RS
--Fasta entries are sorted by decreasing abundance (--sortbysize) or
--sequence length (--sortbylength). To obtain a stable sorting order,
-+Fasta entries are sorted by decreasing abundance (\-\-sortbysize) or
-+sequence length (\-\-sortbylength). To obtain a stable sorting order,
- ties are sorted by decreasing abundance and label increasing
--alpha-numerical order (--sortbylength), or just by label increasing
--alpha-numerical order (--sortbysize). Label sorting assumes that all
-+alpha-numerical order (\-\-sortbylength), or just by label increasing
-+alpha-numerical order (\-\-sortbysize). Label sorting assumes that all
- sequences have unique labels. The same applies to the automatic
--sorting performed during chimera checking (--uchime_denovo),
--dereplication (--derep_fulllength), and clustering (--cluster_fast and
----cluster_size).
-+sorting performed during chimera checking (\-\-uchime_denovo),
-+dereplication (\-\-derep_fulllength), and clustering (\-\-cluster_fast and
-+\-\-cluster_size).
- .PP
- .TP 9
--.BI --maxsize\~ "positive integer"
--When using --sortbysize, discard sequences with an abundance value
-+.BI \-\-maxsize\~ "positive integer"
-+When using \-\-sortbysize, discard sequences with an abundance value
- greater than \fIinteger\fR.
- .TP
--.BI --minsize\~ "positive integer"
--When using --sortbysize, discard sequences with an abundance value
-+.BI \-\-minsize\~ "positive integer"
-+When using \-\-sortbysize, discard sequences with an abundance value
- smaller than \fIinteger\fR.
- .TP
--.BI --output \0filename
-+.BI \-\-output \0filename
- Write the sorted sequences to \fIfilename\fR, in fasta format.
- .TP
--.BI --relabel \0string
-+.BI \-\-relabel \0string
- Relabel sequence using the prefix \fIstring\fR and a ticker (1, 2, 3,
--etc.) to construct the new headers. Use --sizeout to conserve the
-+etc.) to construct the new headers. Use \-\-sizeout to conserve the
- abundance annotations.
- .TP
--.B --sizeout
--When using --relabel, report abundance annotations to the output fasta
-+.B \-\-sizeout
-+When using \-\-relabel, report abundance annotations to the output fasta
- file (using the pattern ";size=\fIinteger\fR;").
- .TP
--.BI --sortbylength \0filename
-+.BI \-\-sortbylength \0filename
- Sort by decreasing length the sequences contained in
--\fIfilename\fR. See the general options --minseqlength and
----maxseqlength to eliminate short and long sequences.
-+\fIfilename\fR. See the general options \-\-minseqlength and
-+\-\-maxseqlength to eliminate short and long sequences.
- .TP
--.BI --sortbysize \0filename
-+.BI \-\-sortbysize \0filename
- Sort by decreasing abundance the sequences contained in \fIfilename\fR
- (the pattern "[>;]size=\fIinteger\fR[;]" has to be present). See the
--options --minsize and --maxsize to eliminate rare and dominant
-+options \-\-minsize and \-\-maxsize to eliminate rare and dominant
- sequences.
- .TP
--.BI --topn\~ "positive integer"
-+.BI \-\-topn\~ "positive integer"
- Output only the top \fIinteger\fR sequences (i.e. the longest or the
- most abundant).
- .RE
- .PP
- .\" ----------------------------------------------------------------------------
--Userfields (fields accepted by the --userfields option):
-+Userfields (fields accepted by the \-\-userfields option):
- .RS
- .TP 9
- .B aln
-@@ -1073,7 +1073,7 @@ format (Compact Idiosyncratic Gapped Ali
- (deletion) and I (insertion). Empty field if there is no alignment.
- .TP
- .B evalue
--E-value (not computed for nucleotide alignments). Always set to -1.
-+E-value (not computed for nucleotide alignments). Always set to \-1.
- .TP
- .B exts
- Number of columns containing a gap extension (zero or positive integer
-@@ -1109,7 +1109,7 @@ single difference.
- .TP
- .B id4
- BLAST definition of the percentage of identity (real value ranging
--from 0.0 to 100.0), equivalent to --iddef 2 in a context of global
-+from 0.0 to 100.0), equivalent to \-\-iddef 2 in a context of global
- pairwise alignment.
- .TP
- .B ids
-@@ -1150,7 +1150,7 @@ Internal or terminal gaps are not taken
- field is set to 0.0 if there is no alignment.
- .TP
- .B qframe
--Query frame (-3 to +3). That field only concerns coding sequences and
-+Query frame (\-3 to +3). That field only concerns coding sequences and
- is not computed by \fBvsearch\fR. Always set to +0.
- .TP
- .B qhi
-@@ -1209,7 +1209,7 @@ Internal or terminal gaps are not taken
- The field is set to 0.0 if there is no alignment.
- .TP
- .B tframe
--Target frame (-3 to +3). That field only concerns coding sequences and
-+Target frame (\-3 to +3). That field only concerns coding sequences and
- is not computed by \fBvsearch\fR. Always set to +0.
- .TP
- .B thi
-@@ -1259,31 +1259,31 @@ quirks and inconsistencies. We decided n
- and for complete transparency, to document here the deliberate changes
- we made.
- .PP
--During a search with usearch, when using the options --blast6out and
----output_no_hits, for queries with no match the number of fields
-+During a search with usearch, when using the options \-\-blast6out and
-+\-\-output_no_hits, for queries with no match the number of fields
- reported is 13, where it should be 12. This is corrected in
- \fBvsearch\fR.
- .PP
--The field raw of the --userfields option is not informative in
-+The field raw of the \-\-userfields option is not informative in
- usearch. This is corrected in \fBvsearch\fR.
- .PP
- The fields qlo, qhi, tlo, thi now have counterparts (qilo, qihi, tilo,
- tihi) reporting alignment coordinates ignoring terminal gaps.
- .PP
--In usearch, when using the option --output_no_hits, queries that
-+In usearch, when using the option \-\-output_no_hits, queries that
- receive no match are reported in blast6out file, but not in the
- alignment output file. This is corrected in \fBvsearch\fR.
- .PP
--\fBvsearch\fR introduces a new --cluster_size command that sorts
-+\fBvsearch\fR introduces a new \-\-cluster_size command that sorts
- sequences by decreasing abundance before clustering.
- .PP
--\fBvsearch\fR reintroduces --iddef alternative pairwise identity
-+\fBvsearch\fR reintroduces \-\-iddef alternative pairwise identity
- definitions that were removed from usearch.
- .PP
--\fBvsearch\fR extends the --topn option to sorting commands.
-+\fBvsearch\fR extends the \-\-topn option to sorting commands.
- .PP
--\fBvsearch\fR extends the --sizein option to dereplication
--(--derep_fulllength) and clustering (--cluster_fast).
-+\fBvsearch\fR extends the \-\-sizein option to dereplication
-+(\-\-derep_fulllength) and clustering (\-\-cluster_fast).
- .PP
- \fBvsearch\fR treats T and U as identical nucleotides during
- dereplication.
-@@ -1333,8 +1333,8 @@ Cluster with a 97% similarity threshold,
- and write cluster descriptions using a uclust-like format:
- .PP
- .RS
--\fBvsearch\fR --cluster_fast \fIqueries.fas\fR --id 0.97 --centroids
--\fIcentroids.fas\fR --uc \fIclusters.uc\fR
-+\fBvsearch\fR \-\-cluster_fast \fIqueries.fas\fR \-\-id 0.97 \-\-centroids
-+\fIcentroids.fas\fR \-\-uc \fIclusters.uc\fR
- .RE
- .PP
- Dereplicate the sequences contained in queries.fas, take into account
-@@ -1343,9 +1343,9 @@ to output with the new abundance informa
- with an abundance of 1:
- .PP
- .RS
--\fBvsearch\fR --derep_fulllength \fIqueries.fas\fR --output
--\fIqueries_masked.fas\fR --sizein --sizeout --fasta_width 0
----minuniquesize 2
-+\fBvsearch\fR \-\-derep_fulllength \fIqueries.fas\fR \-\-output
-+\fIqueries_masked.fas\fR \-\-sizein \-\-sizeout \-\-fasta_width 0
-+\-\-minuniquesize 2
- .RE
- .PP
- Mask simple repeats and low complexity regions in the input fasta file
-@@ -1362,8 +1362,8 @@ threshold, take terminal gaps into accou
- similarities:
- .PP
- .RS
--\fBvsearch\fR --usearch_global \fIqueries.fas\fR --db
--\fIreferences.fas\fR --alnout \fIresults.aln\fR --id 0.8 --iddef 1
-+\fBvsearch\fR \-\-usearch_global \fIqueries.fas\fR \-\-db
-+\fIreferences.fas\fR \-\-alnout \fIresults.aln\fR \-\-id 0.8 \-\-iddef 1
- .RE
- .PP
- Search a sequence dataset against itself (ignore self hits), get all
-@@ -1371,9 +1371,9 @@ matches with at least 60% identity, and
- blast-like tab-separated format:
- .PP
- .RS
--\fBvsearch\fR --usearch_global \fIqueries.fas\fR --db
--\fIqueries.fas\fR --id 0.6 --self --blast6out \fIresults.blast6\fR
----maxaccepts 0 --maxrejects 0
-+\fBvsearch\fR \-\-usearch_global \fIqueries.fas\fR \-\-db
-+\fIqueries.fas\fR \-\-id 0.6 \-\-self \-\-blast6out \fIresults.blast6\fR
-+\-\-maxaccepts 0 \-\-maxrejects 0
- .RE
- .PP
- Shuffle the input fasta file (change the order of sequences) in a
-@@ -1381,8 +1381,8 @@ repeatable fashion (fixed seed), and wri
- to the output file:
- .PP
- .RS
--\fBvsearch\fR --shuffle \fIqueries.fas\fR --output
--\fIqueries_shuffled.fas\fR --seed 13 --fasta_width 0
-+\fBvsearch\fR \-\-shuffle \fIqueries.fas\fR \-\-output
-+\fIqueries_shuffled.fas\fR \-\-seed 13 \-\-fasta_width 0
- .RE
- .PP
- Sort by decreasing abundance the sequences contained in queries.fas
-@@ -1469,17 +1469,17 @@ Bug fixes (ssse3/sse4.1 requirement, mem
- Bug fix (now writes help to stdout instead of stderr).
- .TP
- .BR v1.0.4\~ "released December 8th, 2014"
--Added --allpairs_global option. Reduced memory requirements
-+Added \-\-allpairs_global option. Reduced memory requirements
- slightly. Removed memory leaks.
- .TP
- .BR v1.0.5\~ "released December 9th, 2014"
--Fixes a minor bug with --allpairs_global and --acceptall options.
-+Fixes a minor bug with \-\-allpairs_global and \-\-acceptall options.
- .TP
- .BR v1.0.6\~ "released December 14th, 2014"
--Fixes a memory allocation bug in chimera detection (--uchime_ref option).
-+Fixes a memory allocation bug in chimera detection (\-\-uchime_ref option).
- .TP
- .BR v1.0.7\~ "released December 19th, 2014"
--Fixes a bug in the output from chimera detection with the --uchimeout option.
-+Fixes a bug in the output from chimera detection with the \-\-uchimeout option.
- .TP
- .BR v1.0.8\~ "released January 22nd, 2015"
- Introduces several changes and bug fixes:
-@@ -1488,7 +1488,7 @@ Introduces several changes and bug fixes
- a new linear memory aligner for alignment of sequences longer than
- 5,000 nucleotides,
- .IP -
--a new --cluster_size command that sorts sequences by decreasing
-+a new \-\-cluster_size command that sorts sequences by decreasing
- abundance before clustering,
- .IP -
- meaning of userfields qlo, qhi, tlo, thi changed for compatibility
-@@ -1511,7 +1511,7 @@ fix for lack of detection of under- or o
- .RE
- .TP
- .BR v1.0.9\~ "released January 22nd, 2015"
--Fixes a bug in the function sorting sequences by decreasing abundance (--sortbysize).
-+Fixes a bug in the function sorting sequences by decreasing abundance (\-\-sortbysize).
- .TP
- .BR v1.0.10\~ "released January 23rd, 2015"
- Fixes a bug where the sizein option was ignored and always treated as on,

Modified: trunk/packages/vsearch/trunk/debian/patches/series
===================================================================
--- trunk/packages/vsearch/trunk/debian/patches/series	2015-02-19 15:07:16 UTC (rev 18796)
+++ trunk/packages/vsearch/trunk/debian/patches/series	2015-02-19 15:09:53 UTC (rev 18797)
@@ -1,6 +1,4 @@
 fix_optimisation_flags.patch
 x86_spezific_opts.patch
 hardening.patch
-manpage_syntax.patch
-fix_build_issue_on_hurd.patch
 sysconf_memory_sizing.patch

Modified: trunk/packages/vsearch/trunk/debian/patches/sysconf_memory_sizing.patch
===================================================================
--- trunk/packages/vsearch/trunk/debian/patches/sysconf_memory_sizing.patch	2015-02-19 15:07:16 UTC (rev 18796)
+++ trunk/packages/vsearch/trunk/debian/patches/sysconf_memory_sizing.patch	2015-02-19 15:09:53 UTC (rev 18797)
@@ -1,11 +1,11 @@
-Description: <short summary of the patch>
+Description: kFreeBSD portability patch
  By using the POSIX sysconf(3) together with the nonstandard extension
  _SC_PHYS_PAGES, the system's installed memory can be queried portably on
  Linux and kFreeBSD.
 Author: Jeff Epler <jepler at unpythonic.net>
 Bug-Debian: https://bugs.debian.org/776814
-Forwarded: no
-Last-Update: Wed, 04 Feb 2015 10:26:21 -0600
+Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2015-February/031414.html
+Last-Update: Thu, 19 Feb 2015 16:07:52 +0100 (Andreas Tille <tille at debian.org>)
 
 --- a/src/arch.cc
 +++ b/src/arch.cc
@@ -18,10 +18,11 @@
  unsigned long arch_get_memused()
  {
    struct rusage r_usage;
-@@ -44,6 +46,15 @@ unsigned long arch_get_memtotal()
+@@ -63,7 +65,15 @@ unsigned long arch_get_memtotal()
    if(-1 == sysctl(mib, 2, &ram, &length, NULL, 0))
      fatal("Cannot determine amount of RAM");
    return ram;
+-
 +#elif defined(_SC_PHYS_PAGES) && defined(_SC_PAGESIZE)
 +  long phys_pages = sysconf(_SC_PHYS_PAGES),
 +       pagesize = sysconf(_SC_PAGESIZE);
@@ -32,5 +33,5 @@
 +  if( pagesize > LONG_MAX / phys_pages )  return LONG_MAX;
 +  return pagesize * phys_pages;
  #else
+ 
    struct sysinfo si;
-   if (sysinfo(&si))

Modified: trunk/packages/vsearch/trunk/debian/patches/x86_spezific_opts.patch
===================================================================
--- trunk/packages/vsearch/trunk/debian/patches/x86_spezific_opts.patch	2015-02-19 15:07:16 UTC (rev 18796)
+++ trunk/packages/vsearch/trunk/debian/patches/x86_spezific_opts.patch	2015-02-19 15:09:53 UTC (rev 18797)
@@ -1,6 +1,7 @@
 Author: Andreas Tille <tille at debian.org>
 Last-Changed: Mon, 02 Feb 2015 07:40:07 +0100
 Bugs-Debian: http://bugs.debian.org/776812
+Forwarded: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2015-February/031414.html
 Description: Conditional use of -mtune flag
 
 --- a/src/Makefile.BZLIB
@@ -10,7 +11,7 @@
  #WARN=-Weverything
  
 +ifeq ($(USEOPT),no)
-+    MTUNE:=""
++    MTUNE:=
 +else
 +    MTUNE:=-mtune=core2
 +endif
@@ -28,7 +29,7 @@
  #WARN=-Weverything
  
 +ifeq ($(USEOPT),no)
-+    MTUNE:=""
++    MTUNE:=
 +else
 +    MTUNE:=-mtune=core2
 +endif
@@ -46,7 +47,7 @@
  #WARN=-Weverything
  
 +ifeq ($(USEOPT),no)
-+    MTUNE:=""
++    MTUNE:=
 +else
 +    MTUNE:=-mtune=core2
 +endif

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