[med-svn] r14410 - in trunk/packages/mira/trunk/debian: . patches
Andreas Tille
tille at alioth.debian.org
Fri Aug 9 12:17:44 UTC 2013
Author: tille
Date: 2013-08-09 12:17:44 +0000 (Fri, 09 Aug 2013)
New Revision: 14410
Added:
trunk/packages/mira/trunk/debian/patches/boost-minimal.patch
Removed:
trunk/packages/mira/trunk/debian/patches/add_shebang_lines
trunk/packages/mira/trunk/debian/patches/boost-minimal
trunk/packages/mira/trunk/debian/patches/spelling.patch
trunk/packages/mira/trunk/debian/patches/xsltproc_nonet_for_doc_build
Modified:
trunk/packages/mira/trunk/debian/changelog
trunk/packages/mira/trunk/debian/patches/series
Log:
New upstream version - upstream applied most of the patches
Modified: trunk/packages/mira/trunk/debian/changelog
===================================================================
--- trunk/packages/mira/trunk/debian/changelog 2013-08-08 21:15:53 UTC (rev 14409)
+++ trunk/packages/mira/trunk/debian/changelog 2013-08-09 12:17:44 UTC (rev 14410)
@@ -1,8 +1,9 @@
-mira (3.9.17-2) UNRELEASED; urgency=low
+mira (3.9.18-1) UNRELEASED; urgency=low
+ * New upstream version (most patches applied by upstream)
* debian/copyright: Add Upstream-Contact
- -- Andreas Tille <tille at debian.org> Fri, 07 Jun 2013 13:47:20 +0200
+ -- Andreas Tille <tille at debian.org> Fri, 09 Aug 2013 13:59:24 +0200
mira (3.9.17-1) unstable; urgency=low
Deleted: trunk/packages/mira/trunk/debian/patches/add_shebang_lines
===================================================================
--- trunk/packages/mira/trunk/debian/patches/add_shebang_lines 2013-08-08 21:15:53 UTC (rev 14409)
+++ trunk/packages/mira/trunk/debian/patches/add_shebang_lines 2013-08-09 12:17:44 UTC (rev 14410)
@@ -1,27 +0,0 @@
-#Add a missing #! line to 2 demo scripts just to please Lintian
---- mira-3.4.0.1.orig/minidemo/solexa1/runme.sh
-+++ mira-3.4.0.1/minidemo/solexa1/runme.sh
-@@ -1,7 +1,8 @@
-+#!/bin/sh
-
- ln -s ../data/solexa_eco_art/ecoli_* .
-
- mira --project=ecoli --job=mapping,genome,normal,solexa --fasta -AS:nop=1 -SB:bsn=ecoli_k12_mg1655 -SB:lsd=yes:bft=gbf SOLEXA_SETTINGS -AL:mrs=60:shme=5 | tee log_assembly.txt
-
- echo
--echo "Please read the README to know what is in the results."
-\ No newline at end of file
-+echo "Please read the README to know what is in the results."
---- mira-3.4.0.1.orig/minidemo/solexa2/runme.sh
-+++ mira-3.4.0.1/minidemo/solexa2/runme.sh
-@@ -1,7 +1,8 @@
-+#!/bin/sh
-
- ln -s ../data/solexa_eco_art/ecoli_*fasta* .
-
- mira --project=ecoli --job=denovo,genome,normal,solexa --fasta | tee log_assembly.txt
-
- echo
--echo "This was a de-novo assembly of Solexa reads."
-\ No newline at end of file
-+echo "This was a de-novo assembly of Solexa reads."
Deleted: trunk/packages/mira/trunk/debian/patches/boost-minimal
===================================================================
--- trunk/packages/mira/trunk/debian/patches/boost-minimal 2013-08-08 21:15:53 UTC (rev 14409)
+++ trunk/packages/mira/trunk/debian/patches/boost-minimal 2013-08-09 12:17:44 UTC (rev 14410)
@@ -1,13 +0,0 @@
-Description: boost minimal
-
---- mira-3.9.17.orig/src/progs/Makefile.in
-+++ mira-3.9.17/src/progs/Makefile.in
-@@ -265,7 +265,7 @@ noinst_HEADERS = quirks.H
- # EdIt_abi373 EdIt_alf skimmer
- @BUILDMIRASTATIC_TRUE at AM_LDFLAGS = $(BLOODYDARWINSTATLIBDIRHACK) -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf $(LINKEDITDIR) $(BOOST_LDFLAGS) -all-static
- @BUILDMIRAMEMORC_TRUE at MEMORC = -lmemorc
--MIRALIBS = -lmiradebuggersupport $(MEMORC) -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport $(LINKEDITLIB)
-+MIRALIBS = -lmiradebuggersupport $(MEMORC) -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lboost_filesystem -lboost_iostreams -lboost_regex -lboost_thread -lboost_system $(LINKEDITLIB)
- sw_SOURCES = sw.C
- sw_LDADD = $(MIRALIBS)
- mira_SOURCES = mira.C
Added: trunk/packages/mira/trunk/debian/patches/boost-minimal.patch
===================================================================
--- trunk/packages/mira/trunk/debian/patches/boost-minimal.patch (rev 0)
+++ trunk/packages/mira/trunk/debian/patches/boost-minimal.patch 2013-08-09 12:17:44 UTC (rev 14410)
@@ -0,0 +1,11 @@
+--- a/src/progs/Makefile.in
++++ b/src/progs/Makefile.in
+@@ -256,7 +256,7 @@ noinst_HEADERS = quirks.H
+ # EdIt_abi373 EdIt_alf skimmer
+ @BUILDMIRASTATIC_TRUE at AM_LDFLAGS = $(BLOODYDARWINSTATLIBDIRHACK) -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf $(LINKEDITDIR) $(BOOST_LDFLAGS) -all-static
+ @BUILDMIRAMEMORC_TRUE at MEMORC = -lmemorc
+-MIRALIBS = -lmiradebuggersupport $(MEMORC) -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport $(LINKEDITLIB)
++MIRALIBS = -lmiradebuggersupport $(MEMORC) -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lboost_filesystem -lboost_iostreams -lboost_regex -lboost_thread -lboost_system $(LINKEDITLIB)
+ mira_SOURCES = mira.C
+ mira_LDADD = $(MIRALIBS)
+ convert_project_SOURCES = convert_project.C
Modified: trunk/packages/mira/trunk/debian/patches/series
===================================================================
--- trunk/packages/mira/trunk/debian/patches/series 2013-08-08 21:15:53 UTC (rev 14409)
+++ trunk/packages/mira/trunk/debian/patches/series 2013-08-09 12:17:44 UTC (rev 14410)
@@ -1,5 +1 @@
-xsltproc_nonet_for_doc_build
-add_shebang_lines
-spelling.patch
-boost-minimal
-
+boost-minimal.patch
Deleted: trunk/packages/mira/trunk/debian/patches/spelling.patch
===================================================================
--- trunk/packages/mira/trunk/debian/patches/spelling.patch 2013-08-08 21:15:53 UTC (rev 14409)
+++ trunk/packages/mira/trunk/debian/patches/spelling.patch 2013-08-09 12:17:44 UTC (rev 14410)
@@ -1,67 +0,0 @@
-Author: Thorsten Alteholz <debian at alteholz.de>
-Description: lintian complains about some spelling errors
-Index: mira-3.9.17/src/mira/assembly.C
-===================================================================
---- mira-3.9.17.orig/src/mira/assembly.C 2013-05-21 20:10:33.000000000 +0200
-+++ mira-3.9.17/src/mira/assembly.C 2013-06-06 11:20:57.000000000 +0200
-@@ -555,7 +555,7 @@
- cerr << "\n\nOUCH! something strange ... tried more than 100 deletes of " << basename << " ... list size is " << AS_usedtmpfiles.size() << '\n';
- }
- if(numdeleted>1200) {
-- cerr << "\n\nOUCH! something wierd ... tried more than 1200 deletes of " << basename << " ... list size is " << AS_usedtmpfiles.size() << '\n';
-+ cerr << "\n\nOUCH! something weird ... tried more than 1200 deletes of " << basename << " ... list size is " << AS_usedtmpfiles.size() << '\n';
- cerr << "We'll stop that here.\n";
- return numdeleted;
- }
-Index: mira-3.9.17/src/mira/maf_parse.C
-===================================================================
---- mira-3.9.17.orig/src/mira/maf_parse.C 2013-05-21 20:10:33.000000000 +0200
-+++ mira-3.9.17/src/mira/maf_parse.C 2013-06-06 11:26:01.000000000 +0200
-@@ -985,7 +985,7 @@
- MAF_read_seqtype=ReadGroupLib::stringToSeqType(actline);
-
- if(MAF_read_seqtype==ReadGroupLib::SEQTYPE_END){
-- MIRANOTIFY(Notify::FATAL, "Error in " << MAF_read_name << " in tag " << acttoken << ": unkown sequencing type '" << actline << "'?");
-+ MIRANOTIFY(Notify::FATAL, "Error in " << MAF_read_name << " in tag " << acttoken << ": unknown sequencing type '" << actline << "'?");
- }
- FUNCEND();
- }
-Index: mira-3.9.17/src/progs/mira.C
-===================================================================
---- mira-3.9.17.orig/src/progs/mira.C 2013-05-21 20:10:33.000000000 +0200
-+++ mira-3.9.17/src/progs/mira.C 2013-06-06 11:20:16.000000000 +0200
-@@ -558,7 +558,7 @@
- cout << "\nOptions:\n";
- cout <<
- " -c / --cwd=\t\tdirectory\tChange working directory\n"
-- " -r / --resume\t\t\t\tResume an interupted assembly\n"
-+ " -r / --resume\t\t\t\tResume an interrupted assembly\n"
- " -h / --help\t\t\t\tPrint short help and exit\n"
- " -v / --version\t\t\tPrint version and exit\n"
- ;
-Index: mira-3.9.17/src/io/gap4_ft_so_map.xxd
-===================================================================
---- mira-3.9.17.orig/src/io/gap4_ft_so_map.xxd 2013-05-21 20:10:33.000000000 +0200
-+++ mira-3.9.17/src/io/gap4_ft_so_map.xxd 2013-06-06 11:34:24.000000000 +0200
-@@ -46,7 +46,7 @@
- Fm-R misc_RNA transcript SO:0000673 any transcript or RNA product that cannot be defined by other RNA keys (prim_transcript, precursor_RNA, mRNA, 5'clip, 3'clip, 5'UTR, 3'UTR, exon, CDS, sig_peptide, transit_peptide, mat_peptide, intron, polyA_site, rRNA, tRNA, scRNA, and snRNA); An RNA synthesized on a DNA or RNA template by an RNA polymerase.
- Fm-b misc_binding binding_site SO:0000409 site in nucleic acid which covalently or non-covalently binds another moiety that cannot be described by any other binding key (primer_bind or protein_bind); A region on the surface of a molecule that may interact with another molecule.
- Fm-d misc_difference sequence_difference SO:0000413 feature sequence is different from that presented in the entry and cannot be described by any other Difference key (conflict, unsure, old_sequence, variation, or modified_base); A region where the sequences differs from that of a specified sequence.
--Fm-f misc_feature region SO:0000001 region of biological interest which cannot be described by any other feature key; a new or rare feature; Continous sequence.
-+Fm-f misc_feature region SO:0000001 region of biological interest which cannot be described by any other feature key; a new or rare feature; Continuous sequence.
- Fm-r misc_recomb recombination_feature SO:0000298 site of any generalized, site-specific or replicative recombination event where there is a breakage and reunion of duplex DNA that cannot be described by other recombination keys or qualifiers of source key (/insertion_seq, /transposon, /proviral);
- Fm-S misc_signal regulatory_region SO:0005836 any region containing a signal controlling or altering gene function or expression that cannot be described by other signal keys (promoter, CAAT_signal, TATA_signal, -35_signal, -10_signal, GC_signal, RBS, polyA_signal, enhancer, attenuator, terminator, and rep_origin). A DNA sequence that controls the expression of a gene.
- Fm-s misc_structure sequence_secondary_structure SO:0000002 any secondary or tertiary nucleotide structure or conformation that cannot be described by other Structure keys (stem_loop and D-loop); A folded sequence.
-Index: mira-3.9.17/src/mira/sam_collect.C
-===================================================================
---- mira-3.9.17.orig/src/mira/sam_collect.C 2013-05-21 20:10:33.000000000 +0200
-+++ mira-3.9.17/src/mira/sam_collect.C 2013-06-06 11:33:31.000000000 +0200
-@@ -445,7 +445,7 @@
- SAMC_contiglengths.push_back(mafline.size());
- }else if(maftoken==cpsEC){
- if(actcontigid==0){
-- errorMsgMAFFormat(mafname,linenumber,mafline,"found EC token without preceeding CO token?");
-+ errorMsgMAFFormat(mafname,linenumber,mafline,"found EC token without preceding CO token?");
- }
- actcontigid=0;
- }else if(maftoken==cpsHReadGroupShort
Deleted: trunk/packages/mira/trunk/debian/patches/xsltproc_nonet_for_doc_build
===================================================================
--- trunk/packages/mira/trunk/debian/patches/xsltproc_nonet_for_doc_build 2013-08-08 21:15:53 UTC (rev 14409)
+++ trunk/packages/mira/trunk/debian/patches/xsltproc_nonet_for_doc_build 2013-08-09 12:17:44 UTC (rev 14410)
@@ -1,30 +0,0 @@
-Author: Tim Booth
-Description: Do not use the Internet to fetch DTDs, entities or documents.
- Makes sure the documentation builds without needing network access.
- This magically works if docbook-xsl is installed, otherwise it fails
- complaining that it needs to access http://docbook.sourceforge.net/release/xsl/current/html/docbook.xsl
-
-Index: mira-3.9.17/doc/docbook/Makefile.in
-===================================================================
---- mira-3.9.17.orig/doc/docbook/Makefile.in 2013-05-21 20:17:52.000000000 +0200
-+++ mira-3.9.17/doc/docbook/Makefile.in 2013-06-05 09:57:40.000000000 +0200
-@@ -405,16 +405,16 @@
-
- %_part.html: %_part.xml
- @echo "Making .html out of _part.xml" $@
-- @$(SHELL) -ec 'xsltproc --xinclude --output $@ $(top_srcdir)/doc/docbook/mira.xsl $<'
-+ @$(SHELL) -ec 'xsltproc --nonet --xinclude --output $@ $(top_srcdir)/doc/docbook/mira.xsl $<'
-
- chapters: ${CHAP_HTML} versionfile
-
- book_3rdparty: versionfile ${CHAP_XML} book_3rdparty.xml
-- xsltproc --xinclude --output 3rdparty_MIRA.html $(top_srcdir)/doc/docbook/book.xsl $(top_srcdir)/doc/docbook/book_3rdparty.xml
-+ xsltproc --nonet --xinclude --output 3rdparty_MIRA.html $(top_srcdir)/doc/docbook/book.xsl $(top_srcdir)/doc/docbook/book_3rdparty.xml
- dblatex --xslt-opts=--nonet --output=3rdparty_MIRA.pdf $(top_srcdir)/doc/docbook/book_3rdparty.xml
-
- book_definitive: versionfile ${CHAP_XML} book_definitiveguide.xml
-- xsltproc --xinclude --output DefinitiveGuideToMIRA.html $(top_srcdir)/doc/docbook/book.xsl $(top_srcdir)/doc/docbook/book_definitiveguide.xml
-+ xsltproc --nonet --xinclude --output DefinitiveGuideToMIRA.html $(top_srcdir)/doc/docbook/book.xsl $(top_srcdir)/doc/docbook/book_definitiveguide.xml
- dblatex --xslt-opts=--nonet --output=DefinitiveGuideToMIRA.pdf $(top_srcdir)/doc/docbook/book_definitiveguide.xml
-
- books: versionfile book_definitive book_3rdparty
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