[med-svn] [Git][med-team/vmatch][master] initial packaging
Sascha Steinbiss
gitlab at salsa.debian.org
Mon Dec 30 14:06:01 GMT 2019
Sascha Steinbiss pushed to branch master at Debian Med / vmatch
Commits:
365ac97a by Sascha Steinbiss at 2019-12-30T13:51:32Z
initial packaging
- - - - -
15 changed files:
- + debian/changelog
- + debian/control
- + debian/copyright
- + debian/libvmatch-dev.install
- + debian/patches/common-distdir.patch
- + debian/patches/hardening.patch
- + debian/patches/no-symlink.patch
- + debian/patches/remove-hardcoded-includepaths.patch
- + debian/patches/series
- + debian/patches/skip-doc-installation.patch
- + debian/patches/use-shared-gt-lib.patch
- + debian/rules
- + debian/source/format
- + debian/vmatch.install
- + debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -0,0 +1,5 @@
+vmatch (2.3.0+dfsg-1) unstable; urgency=medium
+
+ * Initial release (Closes: #)
+
+ -- Sascha Steinbiss <satta at debian.org> Mon, 30 Dec 2019 14:49:09 +0100
=====================================
debian/control
=====================================
@@ -0,0 +1,35 @@
+Source: vmatch
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Sascha Steinbiss <satta at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 12),
+ debhelper-compat (= 12),
+ genometools,
+ libgenometools0-dev,
+ zlib1g-dev,
+ libbz2-dev,
+ asciidoctor
+Standards-Version: 4.4.1
+Vcs-Browser: https://salsa.debian.org/med-team/vmatch
+Vcs-Git: https://salsa.debian.org/med-team/vmatch.git
+Homepage: http://www.vmatch.de
+
+Package: vmatch
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: large scale sequence analysis software
+ Vmatch is a versatile software tool for efficiently solving large scale
+ sequence matching tasks. It subsumes the software tool REPuter, but is
+ much more general, with a very flexible user interface, and improved space
+ and time requirements.
+
+Package: libvmatch-dev
+Architecture: any
+Section: libdevel
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: development headers and static library for Vmatch
+ This package contains C development headers and a static library to
+ build custom programs utilizing Vmatch.
=====================================
debian/copyright
=====================================
@@ -0,0 +1,25 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: Vmatch
+Source: https://github.com/genometools/vstree
+Files-Excluded: src/lib-homann
+ src/include/libpssm.h
+ src/Makedef
+ src/doc/WWW/distributions
+ src/doc/*.so.*
+
+Files: *
+Copyright: © 2000-2006 Stefan Kurtz <kurtz at zbh.uni-hamburg.de>
+License: ISC
+
+License: ISC
+ Permission to use, copy, modify, and distribute this software for any
+ purpose with or without fee is hereby granted, provided that the above
+ copyright notice and this permission notice appear in all copies.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
+ WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
+ MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
+ ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
+ WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
+ ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
+ OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE
=====================================
debian/libvmatch-dev.install
=====================================
@@ -0,0 +1,3 @@
+src/lib/libfiles/*.a /usr/lib
+src/include/*.h /usr/include/vmatch
+src/include/*.pr /usr/include/vmatch
=====================================
debian/patches/common-distdir.patch
=====================================
@@ -0,0 +1,40 @@
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -6,9 +6,8 @@
+ BIT=32bit
+ endif
+ VERSION:="`cat $(CURDIR)/VERSION`"
+-SYSTEMNAME:="$(SYSTEM)_$(MACHINE)"
+-VMATCHDISTBASENAME:="vmatch-$(VERSION)-$(SYSTEMNAME)-$(BIT)"
+-DISTDIR:="$(CURDIR)/dist/$(SYSTEMNAME)"
++VMATCHDISTBASENAME:="vmatch"
++DISTDIR:="$(CURDIR)/dist"
+ VMATCHDISTDIR:="$(DISTDIR)/$(VMATCHDISTBASENAME)"
+
+ SELECTDIR=SELECT
+--- a/src/Makedef-linux-gcc
++++ b/src/Makedef-linux-gcc
+@@ -57,8 +57,8 @@
+
+ # the libraries implemented in the vstree package
+
+-PATHEND=32bit
+-LIBBASEDIR=lib/${CONFIGGUESS}/${PATHEND}
++PATHEND=libfiles
++LIBBASEDIR=lib/${PATHEND}
+ COMPILEDIRPREFIX=../${LIBBASEDIR}
+ EXECDIRPREFIX=../${LIBBASEDIR}
+ LIBDIR=${VSTREEBASEDIR}/${LIBBASEDIR}
+--- a/src/Makedef-linux-gcc-64
++++ b/src/Makedef-linux-gcc-64
+@@ -61,8 +61,8 @@
+
+ # the libraries implemented in the vstree package
+
+-PATHEND=64bit
+-LIBBASEDIR=lib/${CONFIGGUESS}/${PATHEND}
++PATHEND=libfiles
++LIBBASEDIR=lib/${PATHEND}
+ COMPILEDIRPREFIX=../${LIBBASEDIR}
+ EXECDIRPREFIX=../${LIBBASEDIR}
+ LIBDIR=${VSTREEBASEDIR}/${LIBBASEDIR}
=====================================
debian/patches/hardening.patch
=====================================
@@ -0,0 +1,356 @@
+--- a/src/bin/mkfilegoals.pl
++++ b/src/bin/mkfilegoals.pl
+@@ -225,7 +225,7 @@
+ }
+ if($kind eq 'o')
+ {
+- printf("\t\${CC} \${CFLAGS} -c \$< -o \$@ -MT \$@ -MMD -MP -MF \$(\@:.o=.d)\n\n");
++ printf("\t\${CC} \${CFLAGS} ${CPPFLAGS} -c \$< -o \$@ -MT \$@ -MMD -MP -MF \$(\@:.o=.d)\n\n");
+ } elsif($kind eq 'splint')
+ {
+ printf("\tsplint \${SPLINTFLAGS} \$<\n");
+@@ -235,20 +235,20 @@
+ printf("\tskproto \$< > \$@\n\n");
+ } elsif($kind eq 'prepro')
+ {
+- printf("\t\${CC} -E -g3 \${CFLAGS} -DDEBUG -c \$< -o \$@\n");
++ printf("\t\${CC} -E -g3 \${CFLAGS} ${CPPFLAGS} -DDEBUG -c \$< -o \$@\n");
+ printf("\tindent \$@\n\n");
+ } elsif($kind eq 'dbg4')
+ {
+- printf("\t\${CC} \${CFLAGS} -DDEBUG -DSYMBOLBYTES=4 -c \$< -o \$@\n\n");
++ printf("\t\${CC} \${CFLAGS} ${CPPFLAGS} -DDEBUG -DSYMBOLBYTES=4 -c \$< -o \$@\n\n");
+ } elsif($kind eq '4')
+ {
+- printf("\t\${CC} \${CFLAGS} -DSYMBOLBYTES=4 -c \$< -o \$@\n\n");
++ printf("\t\${CC} \${CFLAGS} ${CPPFLAGS} -DSYMBOLBYTES=4 -c \$< -o \$@\n\n");
+ } elsif($kind eq 'dbg')
+ {
+- printf("\t\${CC} \${CFLAGS} -DDEBUG -c \$< -o \$@\n\n");
++ printf("\t\${CC} \${CFLAGS} ${CPPFLAGS} -DDEBUG -c \$< -o \$@\n\n");
+ } elsif($kind eq 'so')
+ {
+- printf("\t\${CC} \${CFLAGS} \${SHARED} \$< -o \$@\n\n");
++ printf("\t\${CC} \${CFLAGS} ${CPPFLAGS} \${SHARED} \$< -o \$@\n\n");
+ } else
+ {
+ printf("illegal kind value \"%s\"\n",$kind);
+--- a/src/bin/mklink.sh
++++ b/src/bin/mklink.sh
+@@ -31,7 +31,7 @@
+ cmd="make -f ${TMPFILE}"
+ CFLAGS=`${cmd}`
+
+-cmd="vmrelease.sh ${CFLAGS}"
++cmd="vmrelease.sh ${CFLAGS} ${CPPFLAGS}"
+ ${cmd} > ${WORKVSTREESRC}/include/vmrelease.h
+
+ rm -f ${TMPFILE}
+--- a/src/doc/Fpiccompile
++++ b/src/doc/Fpiccompile
+@@ -2,10 +2,10 @@
+ one C-file:
+
+ mycode.o:
+- gcc ${CFLAGS} -fPIC -c mycode.c
++ gcc ${CFLAGS} ${CPPFLAGS} -fPIC -c mycode.c
+
+ selstartend.o:
+- gcc ${CFLAGS} -fPIC -c selstartend.c
++ gcc ${CFLAGS} ${CPPFLAGS} -fPIC -c selstartend.c
+
+ selstartend.so:selstartend.o mycode.o
+ ld -G -o selstartend.so selstartend.o mycode.o
+--- a/src/kurtz-basic/Filegoals.mf
++++ b/src/kurtz-basic/Filegoals.mf
+@@ -2,13 +2,13 @@
+ rm -f ${COMPILEDIR}*.[ox]
+
+ ${COMPILEDIR}%.o:%.c
+- ${CC} ${CFLAGS} -c $< -o $@
++ ${CC} ${CFLAGS} ${CPPFLAGS} -c $< -o $@
+
+ ${COMPILEDIR}%.dbg.o:%.c
+- ${CC} ${CFLAGS} -DDEBUG -c $< -o $@
++ ${CC} ${CFLAGS} ${CPPFLAGS} -DDEBUG -c $< -o $@
+
+ %.prepro:%.c
+- ${CC} -E -g3 ${CFLAGS} -DDEBUG -c $< -o $@
++ ${CC} -E -g3 ${CFLAGS} ${CPPFLAGS} -DDEBUG -c $< -o $@
+ indent $@
+
+ %.splint:%.c
+--- a/src/kurtz-basic/Makefile
++++ b/src/kurtz-basic/Makefile
+@@ -28,17 +28,17 @@
+ $(RANLIB) $@
+
+ release:
+- vmrelease.sh VMATCH ${CFLAGS} > ../include/vmrelease.h
++ vmrelease.sh VMATCH ${CFLAGS} ${CPPFLAGS} > ../include/vmrelease.h
+
+ chain2dim2.o:chain2dim.c
+- ${CC} ${CFLAGS} -DREVERSEDIM -c $< -o $@
++ ${CC} ${CFLAGS} ${CPPFLAGS} -DREVERSEDIM -c $< -o $@
+
+ .PHONY:clean
+ clean:splintclean
+ rm -f *.[oa] *.dbg.o *.inc *.aux *.dvi *.log
+
+ cflagsstring:
+- @echo "${CFLAGS}"
++ @echo "${CFLAGS} ${CPPFLAGS}"
+
+ .PHONY:prototypes
+ prototypes:${PROTOTYPES}
+--- a/src/kurtz/Filegoals.mf
++++ b/src/kurtz/Filegoals.mf
+@@ -2,13 +2,13 @@
+ rm -f ${COMPILEDIR}*.[ox]
+
+ ${COMPILEDIR}%.o:%.c
+- ${CC} ${CFLAGS} -c $< -o $@ -MT $@ -MMD -MP -MF $(@:.o=.d)
++ ${CC} ${CFLAGS} ${CPPFLAGS} -c $< -o $@ -MT $@ -MMD -MP -MF $(@:.o=.d)
+
+ ${COMPILEDIR}%.dbg.o:%.c
+- ${CC} ${CFLAGS} -DDEBUG -c $< -o $@
++ ${CC} ${CFLAGS} ${CPPFLAGS} -DDEBUG -c $< -o $@
+
+ %.prepro:%.c
+- ${CC} -E -g3 ${CFLAGS} -DDEBUG -c $< -o $@
++ ${CC} -E -g3 ${CFLAGS} ${CPPFLAGS} -DDEBUG -c $< -o $@
+ indent $@
+
+ %.splint:%.c
+--- a/src/kurtz/libtest/Filegoals.mf
++++ b/src/kurtz/libtest/Filegoals.mf
+@@ -34,16 +34,16 @@
+ rm -f ${COMPILEDIR}*.[ox]
+
+ ${COMPILEDIR}%.o:%.c
+- ${CC} ${CFLAGS} -c $< -o $@ -MT $@ -MMD -MP -MF $(@:.o=.d)
++ ${CC} ${CFLAGS} ${CPPFLAGS} -c $< -o $@ -MT $@ -MMD -MP -MF $(@:.o=.d)
+
+ ${COMPILEDIR}%.dbg.o:%.c
+- ${CC} ${CFLAGS} -DDEBUG -c $< -o $@
++ ${CC} ${CFLAGS} ${CPPFLAGS} -DDEBUG -c $< -o $@
+
+ %.so:%.c
+- ${CC} ${CFLAGS} ${SHARED} $< -o $@
++ ${CC} ${CFLAGS} ${CPPFLAGS} ${SHARED} $< -o $@
+
+ %.prepro:%.c
+- ${CC} -E -g3 ${CFLAGS} -DDEBUG -c $< -o $@
++ ${CC} -E -g3 ${CFLAGS} ${CPPFLAGS} -DDEBUG -c $< -o $@
+ indent $@
+
+ %.pr:%.c
+--- a/src/kurtz/libtest/Makefile
++++ b/src/kurtz/libtest/Makefile
+@@ -50,7 +50,7 @@
+ ${LD} ${LDFLAGS} strmfna.o ${LIBS} ${LDLIBS} -o $@
+
+ readdb.o:readdb.c
+- ${CC} -c ${CFLAGS} readdb.c
++ ${CC} -c ${CFLAGS} ${CPPFLAGS} readdb.c
+
+ suffixprefix.x:suffixprefix.o
+ ${LD} ${LDFLAGS} suffixprefix.o ${LIBSDBG} ${LDLIBS} -o $@
+@@ -151,6 +151,6 @@
+ cleanpp.sh
+
+ cflagsstring:
+- @echo "${CFLAGS}"
++ @echo "${CFLAGS} ${CPPFLAGS}"
+
+ -include $(wildcard *.d)
+--- a/src/kurtz/Makefile
++++ b/src/kurtz/Makefile
+@@ -25,14 +25,14 @@
+ $(RANLIB) $@
+
+ release:
+- vmrelease.sh VMATCH ${CFLAGS} > ../include/vmrelease.h
++ vmrelease.sh VMATCH ${CFLAGS} ${CPPFLAGS} > ../include/vmrelease.h
+
+ .PHONY:clean
+ clean:splintclean
+ rm -f *.[oa] *.dbg.o *.inc *.aux *.dvi *.log
+
+ cflagsstring:
+- @echo "${CFLAGS}"
++ @echo "${CFLAGS} ${CPPFLAGS}"
+
+ libtest:$(LIBKURTZ) $(LIBKURTZDBG)
+ ${MAKE} -C libtest
+--- a/src/Mkvtree/Filegoals.mf
++++ b/src/Mkvtree/Filegoals.mf
+@@ -30,16 +30,16 @@
+ rm -f ${COMPILEDIR}*.[ox]
+
+ ${COMPILEDIR}%.o:%.c
+- ${CC} ${CFLAGS} -c $< -o $@ -MT $@ -MMD -MP -MF $(@:.o=.d)
++ ${CC} ${CFLAGS} ${CPPFLAGS} -c $< -o $@ -MT $@ -MMD -MP -MF $(@:.o=.d)
+
+ ${COMPILEDIR}%.dbg.o:%.c
+- ${CC} ${CFLAGS} -DDEBUG -c $< -o $@
++ ${CC} ${CFLAGS} ${CPPFLAGS} -DDEBUG -c $< -o $@
+
+ %.so:%.c
+- ${CC} ${CFLAGS} ${SHARED} $< -o $@
++ ${CC} ${CFLAGS} ${CPPFLAGS} ${SHARED} $< -o $@
+
+ %.prepro:%.c
+- ${CC} -E -g3 ${CFLAGS} -DDEBUG -c $< -o $@
++ ${CC} -E -g3 ${CFLAGS} ${CPPFLAGS} -DDEBUG -c $< -o $@
+ indent $@
+
+ %.pr:%.c
+--- a/src/Mkvtree/Makefile
++++ b/src/Mkvtree/Makefile
+@@ -180,10 +180,10 @@
+ ${LD} ${LDFLAGS} ${COMPILEDIR}mkdna6idx.dbg.o ${LIBSDBG} ${LDLIBS} -o $@
+
+ ${COMPILEDIR}besespecial.o:besespecial.c
+- ${CC} ${CFLAGS} -DSPECIAL -c besespecial.c -o $@
++ ${CC} ${CFLAGS} ${CPPFLAGS} -DSPECIAL -c besespecial.c -o $@
+
+ ${COMPILEDIR}besespecial.dbg.o:besespecial.c
+- ${CC} ${CFLAGS} -DSPECIAL -DDEBUG -c besespecial.c -o $@
++ ${CC} ${CFLAGS} ${CPPFLAGS} -DSPECIAL -DDEBUG -c besespecial.c -o $@
+
+ besespecial.splint:besespecial.c
+ splint ${SPLINTFLAGS} -DSPECIAL -DDEBUG besespecial.c
+@@ -221,6 +221,6 @@
+ cleanpp.sh
+
+ cflagsstring:
+- @echo "${CFLAGS}"
++ @echo "${CFLAGS} ${CPPFLAGS}"
+
+ -include $(wildcard ${COMPILEDIR}/*.d)
+--- a/src/Vmatch/Filegoals.mf
++++ b/src/Vmatch/Filegoals.mf
+@@ -58,16 +58,16 @@
+ rm -f ${COMPILEDIR}*.[ox]
+
+ ${COMPILEDIR}%.o:%.c
+- ${CC} ${CFLAGS} -c $< -o $@ -MT $@ -MMD -MP -MF $(@:.o=.d)
++ ${CC} ${CFLAGS} ${CPPFLAGS} -c $< -o $@ -MT $@ -MMD -MP -MF $(@:.o=.d)
+
+ ${COMPILEDIR}%.dbg.o:%.c
+- ${CC} ${CFLAGS} -DDEBUG -c $< -o $@
++ ${CC} ${CFLAGS} ${CPPFLAGS} -DDEBUG -c $< -o $@
+
+ %.so:%.c
+- ${CC} ${CFLAGS} ${SHARED} $< -o $@
++ ${CC} ${CFLAGS} ${CPPFLAGS} ${SHARED} $< -o $@
+
+ %.prepro:%.c
+- ${CC} -E -g3 ${CFLAGS} -DDEBUG -c $< -o $@
++ ${CC} -E -g3 ${CFLAGS} ${CPPFLAGS} -DDEBUG -c $< -o $@
+ indent $@
+
+ %.pr:%.c
+--- a/src/Vmatch/Makefile
++++ b/src/Vmatch/Makefile
+@@ -220,10 +220,10 @@
+ $(RANLIB) $@
+
+ vmotif-demo.o:vmotif-demo.c
+- ${CC} ${CFLAGS} -fPIC -c $< -o $@
++ ${CC} ${CFLAGS} ${CPPFLAGS} -fPIC -c $< -o $@
+
+ cpridxps-demo.o:cpridxps-demo.c
+- ${CC} ${CFLAGS} -fPIC -c $< -o $@
++ ${CC} ${CFLAGS} ${CPPFLAGS} -fPIC -c $< -o $@
+
+ vmotif-demo.so:vmotif-demo.o ${LIBKURTZ}
+ ${CC} ${SHARED} $< ${LIBKURTZ} -o $@
+@@ -280,6 +280,6 @@
+ -include Filegoals.mf
+
+ cflagsstring:
+- @echo "${CFLAGS} -DALPHABETSIZE=4"
++ @echo "${CFLAGS} ${CPPFLAGS} -DALPHABETSIZE=4"
+
+ -include $(wildcard ${COMPILEDIR}/*.d)
+--- a/src/Vmatch/SELECT/makefile
++++ b/src/Vmatch/SELECT/makefile
+@@ -43,21 +43,21 @@
+ # on most platforms the shared objects have a suffix .so
+
+ %.so:%.c Shareddef
+- ${CC} ${CFLAGS} ${SHARED} $< -o $@
++ ${CC} ${CFLAGS} ${CPPFLAGS} ${SHARED} $< -o $@
+
+ mergematches-dbg.so:mergematches.c Shareddef
+- ${CC} ${CFLAGS} -DDEBUG ${SHARED} $< -o $@
++ ${CC} ${CFLAGS} ${CPPFLAGS} -DDEBUG ${SHARED} $< -o $@
+
+ # on HP-UX the shared objects have a suffix .sl
+
+ %.sl:%.c Shareddef
+- @${CC} ${CFLAGS} ${SHARED} $< -o $@
++ @${CC} ${CFLAGS} ${CPPFLAGS} ${SHARED} $< -o $@
+
+ # the following goal generates the output of the C-preprocessor
+ # applied to the given C-file.
+
+ %.prepro:%.c Shareddef
+- @${CC} -E -g3 ${CFLAGS} -c $< -o $@
++ @${CC} -E -g3 ${CFLAGS} ${CPPFLAGS} -c $< -o $@
+
+ %.splint:%.c Shareddef
+ splint ${SPLINTFLAGS} -DDEBUG -DALPHABETSIZE=4 $<
+--- a/src/Vmengine/Filegoals.mf
++++ b/src/Vmengine/Filegoals.mf
+@@ -2,13 +2,13 @@
+ rm -f ${COMPILEDIR}*.[ox]
+
+ ${COMPILEDIR}%.o:%.c
+- ${CC} ${CFLAGS} -c $< -o $@ -MT $@ -MMD -MP -MF $(@:.o=.d)
++ ${CC} ${CFLAGS} ${CPPFLAGS} -c $< -o $@ -MT $@ -MMD -MP -MF $(@:.o=.d)
+
+ ${COMPILEDIR}%.dbg.o:%.c
+- ${CC} ${CFLAGS} -DDEBUG -c $< -o $@
++ ${CC} ${CFLAGS} ${CPPFLAGS} -DDEBUG -c $< -o $@
+
+ %.prepro:%.c
+- ${CC} -E -g3 ${CFLAGS} -DDEBUG -c $< -o $@
++ ${CC} -E -g3 ${CFLAGS} ${CPPFLAGS} -DDEBUG -c $< -o $@
+ indent $@
+
+ %.splint:%.c
+--- a/src/Vmengine/Makefile
++++ b/src/Vmengine/Makefile
+@@ -43,7 +43,7 @@
+ rm -f *.[oa] *.dbg.o *.inc *.aux *.dvi *.log
+
+ cflagsstring:
+- @echo "${CFLAGS}"
++ @echo "${CFLAGS} ${CPPFLAGS}"
+
+ libtest:${LIBVMENGINE} ${LIBVMENGINEDBG}
+ ${MAKE} -C libtest
+@@ -52,16 +52,16 @@
+ cat ${VMENGINEKERN} | skproto > $@
+
+ ${COMPILEDIR}vmatfind-dyn.o:vmatfind.c ../include/virtualdef.h
+- ${CC} ${CFLAGS} -DDYNAMICALPHABET -c vmatfind.c -o $@
++ ${CC} ${CFLAGS} ${CPPFLAGS} -DDYNAMICALPHABET -c vmatfind.c -o $@
+
+ ${COMPILEDIR}vmatfind-strm.o:vmatfind.c ../include/esastream.h
+- ${CC} ${CFLAGS} -DDYNAMICALPHABET -DESASTREAMACCESS -c vmatfind.c -o $@
++ ${CC} ${CFLAGS} ${CPPFLAGS} -DDYNAMICALPHABET -DESASTREAMACCESS -c vmatfind.c -o $@
+
+ ${COMPILEDIR}vmatfind-dyn.dbg.o:vmatfind.c ../include/virtualdef.h
+- ${CC} ${CFLAGS} -DDEBUG -DDYNAMICALPHABET -c vmatfind.c -o $@
++ ${CC} ${CFLAGS} ${CPPFLAGS} -DDEBUG -DDYNAMICALPHABET -c vmatfind.c -o $@
+
+ ${COMPILEDIR}vmatfind-strm.dbg.o:vmatfind.c ../include/esastream.h
+- ${CC} ${CFLAGS} -DDEBUG -DDYNAMICALPHABET -DESASTREAMACCESS -c vmatfind.c -o $@
++ ${CC} ${CFLAGS} ${CPPFLAGS} -DDEBUG -DDYNAMICALPHABET -DESASTREAMACCESS -c vmatfind.c -o $@
+
+ vmatfind4.splint:vmatfind.c
+ splint ${SPLINTFLAGS} -DDEBUG -DALPHABETSIZE=4 vmatfind.c
=====================================
debian/patches/no-symlink.patch
=====================================
@@ -0,0 +1,11 @@
+--- a/src/bin/mklink.sh
++++ b/src/bin/mklink.sh
+@@ -17,7 +17,7 @@
+ echo "${destfile} does not exist"
+ exit 1
+ fi
+-cmd="ln -sf ${destfile} Makedef"
++cmd="cp ${destfile} Makedef"
+ ${cmd}
+
+ TMPFILE=makefile.$$
=====================================
debian/patches/remove-hardcoded-includepaths.patch
=====================================
@@ -0,0 +1,26 @@
+--- a/src/Makedef-linux-gcc
++++ b/src/Makedef-linux-gcc
+@@ -15,9 +15,7 @@
+
+ # the include directory path
+
+-INCLUDEOPT=-I${VSTREEBASEDIR}/include\
+- -I${VSTREEBASEDIR}/../../genometools/src/external/zlib-1.2.8 \
+- -I${VSTREEBASEDIR}/../../genometools/src/external/bzip2-1.0.6
++INCLUDEOPT=-I${VSTREEBASEDIR}/include
+
+ # the following should be used to define the CFLAGS
+
+--- a/src/Makedef-linux-gcc-64
++++ b/src/Makedef-linux-gcc-64
+@@ -15,9 +15,7 @@
+
+ # the include directory path
+
+-INCLUDEOPT=-I${VSTREEBASEDIR}/include \
+- -I${VSTREEBASEDIR}/../../genometools/src/external/zlib-1.2.8 \
+- -I../../../genometools/src/external/bzip2-1.0.6
++INCLUDEOPT=-I${VSTREEBASEDIR}/include
+
+ # the following should be used to define the CFLAGS
+
=====================================
debian/patches/series
=====================================
@@ -0,0 +1,6 @@
+no-symlink.patch
+use-shared-gt-lib.patch
+remove-hardcoded-includepaths.patch
+common-distdir.patch
+skip-doc-installation.patch
+hardening.patch
=====================================
debian/patches/skip-doc-installation.patch
=====================================
@@ -0,0 +1,15 @@
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -187,9 +187,9 @@
+ @cp Mkvtree/TRANS/Trans* $(VMATCHDISTDIR)/${SMAPDIR}
+ @cp bin/cleanpp.sh $(VMATCHDISTDIR)
+ @cp bin/Vmatchtrans.pl $(VMATCHDISTDIR)
+- @cp doc/virtman.pdf $(VMATCHDISTDIR)
+- @cp doc/chain2dim.pdf $(VMATCHDISTDIR)
+- @cp doc/matchcluster.pdf $(VMATCHDISTDIR)
++ #@cp doc/virtman.pdf $(VMATCHDISTDIR)
++ #@cp doc/chain2dim.pdf $(VMATCHDISTDIR)
++ #@cp doc/matchcluster.pdf $(VMATCHDISTDIR)
+ @cp ../LICENSE $(VMATCHDISTDIR)
+ @cp README.distrib $(VMATCHDISTDIR)
+ @cp CHANGELOG $(VMATCHDISTDIR)
=====================================
debian/patches/use-shared-gt-lib.patch
=====================================
@@ -0,0 +1,61 @@
+--- a/src/Mkvtree/Makefile
++++ b/src/Mkvtree/Makefile
+@@ -1,10 +1,10 @@
+ include ../Makedef
+
+ MAINFLAGS=-DWITHLCP # ${DEFINESUFFIXPTR}
+-CFLAGS=${DEFINECFLAGS} ${DEFINECPPFLAGS} ${MAINFLAGS}
++CFLAGS+=${DEFINECFLAGS} ${DEFINECPPFLAGS} ${MAINFLAGS}
+ SPLINTFLAGS=${MAINFLAGS} ${DEFINESPLINTFLAGS}
+ VPATH=${COMPILEDIRPREFIX}
+-LDFLAGS=-L${COMPILEDIRPREFIX} ${DEFINELDFLAGS}
++LDFLAGS+=-L${COMPILEDIRPREFIX} ${DEFINELDFLAGS}
+ LDLIBS=${DEFINELDLIBS}
+ COMPILEDIR=${COMPILEDIRPREFIX}/Mkvtree/
+ #EXECDIR=${EXECDIRPREFIX}/Mkvtree/
+@@ -13,12 +13,10 @@
+ CFLAGS += -I../../../licensemanager/src \
+ -I../../../genometools/src
+ LDLIBS = ${CURDIR}/../../../licensemanager/lib/$(BIT)/liblicensemanager.a \
+- ${CURDIR}/../../../genometools/lib/libgenometools.a \
+- ${DEFINELDLIBS}
++ ${DEFINELDLIBS} -lgenometools -lz -lbz2
+ else
+ CFLAGS += -DNOLICENSEMANAGER
+- LDLIBS = ${CURDIR}/../../../genometools/lib/libgenometools.a \
+- ${DEFINELDLIBS}
++ LDLIBS = ${DEFINELDLIBS} -lgenometools -lz -lbz2
+ endif
+
+ MKVTREEOBJ=${COMPILEDIR}mkvtree.o\
+--- a/src/Vmatch/Makefile
++++ b/src/Vmatch/Makefile
+@@ -2,11 +2,11 @@
+
+ #DEFINEVMATCHDB=-DVMATCHDB
+ #DISTRIBUTEDDFS=-DDISTRIBUTEDDFS
+-CFLAGS=${DEFINECFLAGS} ${DEFINECPPFLAGS} -I../Vmengine ${DEFINEVMATCHDB} ${DISTRIBUTEDDFS}
++CFLAGS+=${DEFINECFLAGS} ${DEFINECPPFLAGS} -I../Vmengine ${DEFINEVMATCHDB} ${DISTRIBUTEDDFS}
+ SPLINTFLAGS=${DEFINESPLINTFLAGS} -I../Vmengine
+ #CFLAGS=-DCOUNT
+ #LIBELECTRICFENCE=-lefence
+-LDFLAGS=${DEFINELDFLAGS} ${LIBELECTRICFENCE}
++LDFLAGS+=${DEFINELDFLAGS} ${LIBELECTRICFENCE}
+ LDLIBS=${DEFINELDLIBS}
+ COMPILEDIR=${COMPILEDIRPREFIX}/Vmatch/
+ #EXECDIR=${EXECDIRPREFIX}/Vmatch/
+@@ -15,12 +15,10 @@
+ CFLAGS += -I../../../licensemanager/src \
+ -I../../../genometools/src
+ LDLIBS = ${CURDIR}/../../../licensemanager/lib/$(BIT)/liblicensemanager.a \
+- ${CURDIR}/../../../genometools/lib/libgenometools.a \
+- ${DEFINELDLIBS}
++ ${DEFINELDLIBS} -lgenometools -lz -lbz2
+ else
+ CFLAGS += -DNOLICENSEMANAGER
+- LDLIBS = ${CURDIR}/../../../genometools/lib/libgenometools.a \
+- ${DEFINELDLIBS}
++ LDLIBS = ${DEFINELDLIBS} -lgenometools -lz -lbz2
+ endif
+
+ LIBS=${LIBVMATCH}\
=====================================
debian/rules
=====================================
@@ -0,0 +1,24 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+export LC_ALL=C.UTF-8
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+export PATH:=$(PATH):$(CURDIR)/src/bin
+export WORKVSTREESRC=$(CURDIR)/src
+
+%:
+ dh $@
+
+override_dh_auto_build:
+ cd src && mklink.sh linux-gcc-64
+ cd src && make licensemanager=no $*
+
+override_dh_auto_install:
+ cd src && make licensemanager=no dist
+ dh_auto_install
+
+override_dh_installman:
+ #mkdir -p $(CURDIR)/debian/man
+ #asciidoctor -a docdate='' -b manpage $(CURDIR)/debian/man_src/*.adoc
+ #cp $(CURDIR)/debian/man_src/*.? $(CURDIR)/debian/man
+ dh_installman --
=====================================
debian/source/format
=====================================
@@ -0,0 +1 @@
+3.0 (quilt)
=====================================
debian/vmatch.install
=====================================
@@ -0,0 +1,14 @@
+src/dist/vmatch/chain2dim /usr/bin
+#src/dist/vmatch/cleanpp.sh /usr/bin
+src/dist/vmatch/matchcluster /usr/bin
+src/dist/vmatch/mkdna6idx /usr/bin
+src/dist/vmatch/mkvtree /usr/bin
+src/dist/vmatch/vendian /usr/bin
+src/dist/vmatch/vmatch /usr/bin
+src/dist/vmatch/vmatchselect /usr/bin
+#src/dist/vmatch/vmigrate.sh /usr/bin
+src/dist/vmatch/vseqinfo /usr/bin
+src/dist/vmatch/vseqselect /usr/bin
+src/dist/vmatch/vstree2tex /usr/bin
+src/dist/vmatch/vsubseqselect /usr/bin
+src/dist/vmatch/TRANS /usr/share/vmatch
=====================================
debian/watch
=====================================
@@ -0,0 +1,4 @@
+version=3
+
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
+https://github.com/genometools/vstree/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
View it on GitLab: https://salsa.debian.org/med-team/vmatch/commit/365ac97ac74d2f233fc20d2a5f9625b226a9d63c
--
View it on GitLab: https://salsa.debian.org/med-team/vmatch/commit/365ac97ac74d2f233fc20d2a5f9625b226a9d63c
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