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commit 1a71256c3ad0b1927a04db20eea9e8ddaa9bd626 Author: Andreas Tille <[email protected]> Date: Wed Oct 25 16:07:58 2017 +0200 Use Debian packaged jsoncpp as well as get completely rid of blatSrc in automake configuration --- debian/patches/series | 1 + debian/patches/use_debian_packaged_jsoncpp.patch | 292 +++++++++++++++++++++++ 2 files changed, 293 insertions(+) diff --git a/debian/patches/series b/debian/patches/series index c6bf00c..d1b5196 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,2 +1,3 @@ dynamic-lib.patch prevent_usage_of_blatsrc.patch +use_debian_packaged_jsoncpp.patch diff --git a/debian/patches/use_debian_packaged_jsoncpp.patch b/debian/patches/use_debian_packaged_jsoncpp.patch new file mode 100644 index 0000000..4fd8e05 --- /dev/null +++ b/debian/patches/use_debian_packaged_jsoncpp.patch @@ -0,0 +1,292 @@ +Author: Andreas Tille <[email protected]> +Last-Update: Thu, 19 Oct 2017 16:27:56 +0200 +Description: Use Debian packaged jsoncpp as well as get completely rid + of blatSrc in automake configuration + +--- a/gbtools/Makefile.am ++++ b/gbtools/Makefile.am +@@ -10,11 +10,7 @@ libgbtools_la_SOURCES = + + libgbtools_la_LIBADD = src/gbtoolsGUI/libgbtoolsGUI.la src/gbtoolsUtils/libgbtoolsUtils.la + +-if USE_BLATSRC +-libgbtools_la_LIBADD += src/blatSrc/libblatSrc.la +-endif +- +-libgbtools_la_LIBADD += src/jsoncpp/libjsoncpp.la ++libgbtools_la_LIBADD += -ljsoncpp + + if USE_LIBCURL + libgbtools_la_LIBADD += src/gbtoolsCurl/libgbtoolsCurl.la src/gbtoolsPfetch/libgbtoolsPfetch.la +--- a/gbtools/configure.ac ++++ b/gbtools/configure.ac +@@ -19,8 +19,6 @@ src/gbtoolsGUI/Makefile + src/gbtoolsCurl/Makefile + src/gbtoolsTrackhub/Makefile + src/gbtoolsPfetch/Makefile +-src/jsoncpp/Makefile +-src/blatSrc/Makefile + ]) + + +--- a/gbtools/src/Makefile.am ++++ b/gbtools/src/Makefile.am +@@ -1,12 +1,6 @@ + + SUBDIRS = include gbtoolsUtils gbtoolsGUI + +-SUBDIRS += jsoncpp +- +-if USE_BLATSRC +-SUBDIRS += blatSrc +-endif +- + if USE_LIBCURL + SUBDIRS += gbtoolsCurl gbtoolsPfetch + SUBDIRS += gbtoolsTrackhub +--- a/gbtools/src/include/Makefile.am ++++ b/gbtools/src/include/Makefile.am +@@ -6,210 +6,6 @@ gbtools/gbtoolsTrackhub.hpp \ + gbtools/gbtoolsGUI.hpp \ + gbtools/gbtoolsPfetch.hpp \ + gbtools/gbtoolsUtils.hpp \ +-json/json.h \ +-json/json-forwards.h \ +-blatSrc/ace.h \ +-blatSrc/aliType.h \ +-blatSrc/annoAssembly.h \ +-blatSrc/annoFilter.h \ +-blatSrc/annoFormatTab.h \ +-blatSrc/annoFormatter.h \ +-blatSrc/annoGrateWig.h \ +-blatSrc/annoGrator.h \ +-blatSrc/annoGratorQuery.h \ +-blatSrc/annoOption.h \ +-blatSrc/annoRow.h \ +-blatSrc/annoStreamBigBed.h \ +-blatSrc/annoStreamBigWig.h \ +-blatSrc/annoStreamTab.h \ +-blatSrc/annoStreamVcf.h \ +-blatSrc/annoStreamer.h \ +-blatSrc/apacheLog.h \ +-blatSrc/asParse.h \ +-blatSrc/axt.h \ +-blatSrc/bPlusTree.h \ +-blatSrc/bamFile.h \ +-blatSrc/bandExt.h \ +-blatSrc/base64.h \ +-blatSrc/basicBed.h \ +-blatSrc/bbiFile.h \ +-blatSrc/bigBed.h \ +-blatSrc/bigWig.h \ +-blatSrc/binRange.h \ +-blatSrc/bits.h \ +-blatSrc/blastParse.h \ +-blatSrc/boxClump.h \ +-blatSrc/boxLump.h \ +-blatSrc/bwgInternal.h \ +-blatSrc/cda.h \ +-blatSrc/cgi_build_rules.mk \ +-blatSrc/chain.h \ +-blatSrc/chainBlock.h \ +-blatSrc/chainConnect.h \ +-blatSrc/chainToAxt.h \ +-blatSrc/chainToPsl.h \ +-blatSrc/cheapcgi.h \ +-blatSrc/cirTree.h \ +-blatSrc/codebias.h \ +-blatSrc/common.h \ +-blatSrc/common.mk \ +-blatSrc/correlate.h \ +-blatSrc/crTree.h \ +-blatSrc/crudeali.h \ +-blatSrc/diGraph.h \ +-blatSrc/diGraph.h.97 \ +-blatSrc/dlist.h \ +-blatSrc/dnaLoad.h \ +-blatSrc/dnaMarkov.h \ +-blatSrc/dnaMotif.h \ +-blatSrc/dnaseq.h \ +-blatSrc/dnautil.h \ +-blatSrc/dtdParse.h \ +-blatSrc/dyOut.h \ +-blatSrc/dystring.h \ +-blatSrc/elmTree.h \ +-blatSrc/emblParse.h \ +-blatSrc/ens.h \ +-blatSrc/errAbort.h \ +-blatSrc/errCatch.h \ +-blatSrc/fa.h \ +-blatSrc/fieldedTable.h \ +-blatSrc/filePath.h \ +-blatSrc/flydna.h \ +-blatSrc/fof.h \ +-blatSrc/fq.h \ +-blatSrc/fuzzyFind.h \ +-blatSrc/gapCalc.h \ +-blatSrc/gdf.h \ +-blatSrc/genoFind.h \ +-blatSrc/genomeRangeTree.h \ +-blatSrc/gfClientLib.h \ +-blatSrc/gfPcrLib.h \ +-blatSrc/gfWebLib.h \ +-blatSrc/gff.h \ +-blatSrc/gff3.h \ +-blatSrc/gfxPoly.h \ +-blatSrc/gifLabel.h \ +-blatSrc/hacTree.h \ +-blatSrc/hash.h \ +-blatSrc/hex.h \ +-blatSrc/hgGene.h \ +-blatSrc/hgap.h \ +-blatSrc/hgdb.h \ +-blatSrc/histogram.h \ +-blatSrc/hmac.h \ +-blatSrc/hmmPfamParse.h \ +-blatSrc/hmmstats.h \ +-blatSrc/htmlPage.h \ +-blatSrc/htmshell.h \ +-blatSrc/https.h \ +-blatSrc/intValTree.h \ +-blatSrc/internet.h \ +-blatSrc/itsa.h \ +-blatSrc/iupac.h \ +-blatSrc/jointalign.h \ +-blatSrc/jpegSize.h \ +-blatSrc/jsonParse.h \ +-blatSrc/jsonWrite.h \ +-blatSrc/keys.h \ +-blatSrc/knetUdc.h \ +-blatSrc/kxTok.h \ +-blatSrc/linefile.h \ +-blatSrc/localEnvironment.mk \ +-blatSrc/localmem.h \ +-blatSrc/log.h \ +-blatSrc/longToList.h \ +-blatSrc/maDbRep.h \ +-blatSrc/maToFf.h \ +-blatSrc/maf.h \ +-blatSrc/mailViaPipe.h \ +-blatSrc/md5.h \ +-blatSrc/memalloc.h \ +-blatSrc/memgfx.h \ +-blatSrc/meta.h \ +-blatSrc/metaWig.h \ +-blatSrc/mime.h \ +-blatSrc/net.h \ +-blatSrc/nib.h \ +-blatSrc/nibTwo.h \ +-blatSrc/nt4.h \ +-blatSrc/obscure.h \ +-blatSrc/oldGff.h \ +-blatSrc/oligoTm.h \ +-blatSrc/ooc.h \ +-blatSrc/options.h \ +-blatSrc/pairDistance.h \ +-blatSrc/pairHmm.h \ +-blatSrc/paraFetch.h \ +-blatSrc/patSpace.h \ +-blatSrc/peakCluster.h \ +-blatSrc/phyloTree.h \ +-blatSrc/pipeline.h \ +-blatSrc/portable.h \ +-blatSrc/psGfx.h \ +-blatSrc/psPoly.h \ +-blatSrc/pscmGfx.h \ +-blatSrc/psl.h \ +-blatSrc/pslTbl.h \ +-blatSrc/pslTransMap.h \ +-blatSrc/pthreadDoList.h \ +-blatSrc/pthreadWrap.h \ +-blatSrc/qa.h \ +-blatSrc/quickHeap.h \ +-blatSrc/quotedP.h \ +-blatSrc/ra.h \ +-blatSrc/raToStruct.h \ +-blatSrc/rainbow.h \ +-blatSrc/rangeTree.h \ +-blatSrc/rbTree.h \ +-blatSrc/regexHelper.h \ +-blatSrc/repMask.h \ +-blatSrc/rle.h \ +-blatSrc/rnautil.h \ +-blatSrc/rql.h \ +-blatSrc/rudp.h \ +-blatSrc/scoreWindow.h \ +-blatSrc/seg.h \ +-blatSrc/seqOut.h \ +-blatSrc/seqStats.h \ +-blatSrc/shaRes.h \ +-blatSrc/sig.h \ +-blatSrc/slog.h \ +-blatSrc/snof.h \ +-blatSrc/snofmake.h \ +-blatSrc/spaceSaver.h \ +-blatSrc/spacedColumn.h \ +-blatSrc/spacedSeed.h \ +-blatSrc/splatAli.h \ +-blatSrc/splix.h \ +-blatSrc/sqlList.h \ +-blatSrc/sqlNum.h \ +-blatSrc/subText.h \ +-blatSrc/sufa.h \ +-blatSrc/sufx.h \ +-blatSrc/supStitch.h \ +-blatSrc/synQueue.h \ +-blatSrc/tabRow.h \ +-blatSrc/textOut.h \ +-blatSrc/tokenizer.h \ +-blatSrc/trans3.h \ +-blatSrc/trix.h \ +-blatSrc/twoBit.h \ +-blatSrc/udc.h \ +-blatSrc/unfin.h \ +-blatSrc/userApp.mk \ +-blatSrc/vGfx.h \ +-blatSrc/vcf.h \ +-blatSrc/vcfBits.h \ +-blatSrc/verbose.h \ +-blatSrc/wormdna.h \ +-blatSrc/xAli.h \ +-blatSrc/xa.h \ +-blatSrc/xap.h \ +-blatSrc/xenalign.h \ +-blatSrc/xmlEscape.h \ +-blatSrc/xp.h \ +-blatSrc/zlibFace.h \ + $(NULL) + + # Extra files to remove for the maintainer-clean target. +--- a/gbtools/src/Makefile.am.common ++++ b/gbtools/src/Makefile.am.common +@@ -4,7 +4,7 @@ + AM_CPPFLAGS = \ + $(DEPS_CFLAGS) \ + -I$(top_srcdir)/src/include \ +--I$(top_srcdir)/src/include/blatSrc ++-I/usr/include/jsoncpp + + AM_CXXFLAGS = -std=c++11 -g -Wall + +--- a/doc/Design_notes/Makefile ++++ b/doc/Design_notes/Makefile +@@ -185,7 +185,7 @@ CXXFLAGS = -g -O2 + CYGPATH_W = echo + DEFS = -DHAVE_CONFIG_H + DEPDIR = .deps +-DEPS_CFLAGS = -pthread -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/x86_64-linux-gnu/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/gio-unix-2.0/ -I/usr/include/freetype2 -I/usr/include/pixman-1 -I/usr/include/libpng12 -I/usr/include/harfbuzz ++DEPS_CFLAGS = -pthread -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/x86_64-linux-gnu/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/gio-unix-2.0/ -I/usr/include/freetype2 -I/usr/include/pixman-1 -I/usr/include/libpng12 -I/usr/include/harfbuzz + DEPS_LIBS = -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfontconfig -lgobject-2.0 -lglib-2.0 -lfreetype + DEPS_SQLITE3_CFLAGS = + DEPS_SQLITE3_LIBS = -lsqlite3 +--- a/doc/Design_notes/modules/Makefile ++++ b/doc/Design_notes/modules/Makefile +@@ -185,7 +185,7 @@ CXXFLAGS = -g -O2 + CYGPATH_W = echo + DEFS = -DHAVE_CONFIG_H + DEPDIR = .deps +-DEPS_CFLAGS = -pthread -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/x86_64-linux-gnu/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/gio-unix-2.0/ -I/usr/include/freetype2 -I/usr/include/pixman-1 -I/usr/include/libpng12 -I/usr/include/harfbuzz ++DEPS_CFLAGS = -pthread -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/x86_64-linux-gnu/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/gio-unix-2.0/ -I/usr/include/freetype2 -I/usr/include/pixman-1 -I/usr/include/libpng12 -I/usr/include/harfbuzz + DEPS_LIBS = -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfontconfig -lgobject-2.0 -lglib-2.0 -lfreetype + DEPS_SQLITE3_CFLAGS = + DEPS_SQLITE3_LIBS = -lsqlite3 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/seqtools.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
