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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> -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 <[email protected]> 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 <[email protected]>) --- 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 <[email protected]> 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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
