[med-svn] [seqtools] 08/09: Use Debian packaged jsoncpp as well as get completely rid of blatSrc in automake configuration
Andreas Tille
tille at debian.org
Wed Oct 25 14:32:42 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository seqtools.
commit 1a71256c3ad0b1927a04db20eea9e8ddaa9bd626
Author: Andreas Tille <tille at debian.org>
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 <tille at debian.org>
+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
--
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