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 <[email protected]> Fri, 07 Jun 2013 13:47:20 +0200 + -- Andreas Tille <[email protected]> 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@AM_LDFLAGS = $(BLOODYDARWINSTATLIBDIRHACK) -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf $(LINKEDITDIR) $(BOOST_LDFLAGS) -all-static - @BUILDMIRAMEMORC_TRUE@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@AM_LDFLAGS = $(BLOODYDARWINSTATLIBDIRHACK) -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf $(LINKEDITDIR) $(BOOST_LDFLAGS) -all-static + @BUILDMIRAMEMORC_TRUE@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 <[email protected]> -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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
