[med-svn] r21949 - in trunk/packages/prank/trunk/debian: . patches
Sascha Steinbiss
sascha-guest at moszumanska.debian.org
Fri May 13 22:19:25 UTC 2016
Author: sascha-guest
Date: 2016-05-13 22:19:22 +0000 (Fri, 13 May 2016)
New Revision: 21949
Added:
trunk/packages/prank/trunk/debian/patches/fix-gcc6.patch
Modified:
trunk/packages/prank/trunk/debian/changelog
trunk/packages/prank/trunk/debian/control
trunk/packages/prank/trunk/debian/patches/hardening.patch
trunk/packages/prank/trunk/debian/patches/series
trunk/packages/prank/trunk/debian/rules
Log:
bug fixes and housekeeping
Modified: trunk/packages/prank/trunk/debian/changelog
===================================================================
--- trunk/packages/prank/trunk/debian/changelog 2016-05-13 11:43:22 UTC (rev 21948)
+++ trunk/packages/prank/trunk/debian/changelog 2016-05-13 22:19:22 UTC (rev 21949)
@@ -1,11 +1,21 @@
prank (0.0.150803-2) UNRELEASED; urgency=medium
+ * Team upload.
+
+ [ Andreas Tille ]
* New homepage
* d/watch: Adapt to new location
* d/copyright: Upstream-Contact
- -- Andreas Tille <tille at debian.org> Wed, 20 Jan 2016 10:50:28 +0100
+ [ Sascha Steinbiss ]
+ * Fix building with GCC 6
+ Closes: #811827
+ * Enable full hardening.
+ * Bump Standards-Version.
+ * Use secure Vcs-*.
+ -- Sascha Steinbiss <sascha at steinbiss.name> Fri, 13 May 2016 21:57:42 +0000
+
prank (0.0.150803-1) unstable; urgency=medium
* New upstream version.
Modified: trunk/packages/prank/trunk/debian/control
===================================================================
--- trunk/packages/prank/trunk/debian/control 2016-05-13 11:43:22 UTC (rev 21948)
+++ trunk/packages/prank/trunk/debian/control 2016-05-13 22:19:22 UTC (rev 21949)
@@ -5,8 +5,8 @@
Section: science
Priority: optional
Build-Depends: debhelper (>= 9)
-Standards-Version: 3.9.6
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/prank/trunk/
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/prank/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/prank/trunk/
Homepage: http://wasabiapp.org/software/prank/
Added: trunk/packages/prank/trunk/debian/patches/fix-gcc6.patch
===================================================================
--- trunk/packages/prank/trunk/debian/patches/fix-gcc6.patch (rev 0)
+++ trunk/packages/prank/trunk/debian/patches/fix-gcc6.patch 2016-05-13 22:19:22 UTC (rev 21949)
@@ -0,0 +1,21 @@
+Description: fix building with GCC 6
+ This patch enables support for an older C++ standard, as a newer one
+ (breaking some compatibility) is apparently the default now in GCC6.
+Author: Sascha Steinbiss <sascha at steinbiss.name>
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -4,11 +4,11 @@
+
+ ####### Compiler, tools and options
+
+-CC = gcc
+-CXX = g++
++CC ?= gcc
++CXX ?= g++
+ DEFINES =
+ CFLAGS += -pipe -O3 $(DEFINES)
+-CXXFLAGS += -pipe -O3 $(DEFINES)
++CXXFLAGS += -std=gnu++98 -pipe -O3 $(DEFINES)
+ INCPATH = -I. -I/usr/include
+ LINK = g++
+ #LFLAGS = -m64
Modified: trunk/packages/prank/trunk/debian/patches/hardening.patch
===================================================================
--- trunk/packages/prank/trunk/debian/patches/hardening.patch 2016-05-13 11:43:22 UTC (rev 21948)
+++ trunk/packages/prank/trunk/debian/patches/hardening.patch 2016-05-13 22:19:22 UTC (rev 21949)
@@ -19,7 +19,32 @@
LIBS = $(SUBLIBS)
AR = ar cqs
RANLIB =
-@@ -136,7 +136,7 @@ first: all
+@@ -116,19 +116,19 @@
+ .SUFFIXES: .o .c .cpp .cc .cxx .C
+
+ .cpp.o:
+- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o "$@" "$<"
++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o "$@" "$<"
+
+ .cc.o:
+- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o "$@" "$<"
++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o "$@" "$<"
+
+ .cxx.o:
+- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o "$@" "$<"
++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o "$@" "$<"
+
+ .C.o:
+- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o "$@" "$<"
++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o "$@" "$<"
+
+ .c.o:
+- $(CC) -c $(CFLAGS) $(INCPATH) -o "$@" "$<"
++ $(CC) -c $(CPPFLAGS) $(CFLAGS) $(INCPATH) -o "$@" "$<"
+
+ ####### Build rules
+
+@@ -136,7 +136,7 @@
all: Makefile $(TARGET) $(MANPAGES)
$(TARGET): $(OBJECTS)
@@ -28,3 +53,257 @@
clean:compiler_clean
+@@ -167,7 +167,7 @@
+ dbmatrix.h \
+ boolmatrix.h \
+ ancestralsequence.h
+- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o writefile.o writefile.cpp
++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o writefile.o writefile.cpp
+
+ treenode.o: treenode.cpp config.h \
+ hmmodel.h \
+@@ -187,7 +187,7 @@
+ fullprobability.h \
+ postprobability.h \
+ characterprobability.h
+- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o treenode.o treenode.cpp
++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o treenode.o treenode.cpp
+
+ translatesequences.o: translatesequences.cpp translatesequences.h \
+ config.h \
+@@ -201,7 +201,7 @@
+ site.h \
+ boolmatrix.h \
+ ancestralsequence.h
+- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o translatesequences.o translatesequences.cpp
++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o translatesequences.o translatesequences.cpp
+
+ terminalsequence.o: terminalsequence.cpp terminalsequence.h \
+ sequence.h \
+@@ -215,7 +215,7 @@
+ ancestralnode.h \
+ treenode.h \
+ ancestralsequence.h
+- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o terminalsequence.o terminalsequence.cpp
++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o terminalsequence.o terminalsequence.cpp
+
+ terminalnode.o: terminalnode.cpp terminalnode.h \
+ treenode.h \
+@@ -230,7 +230,7 @@
+ hmmodel.h \
+ ancestralnode.h \
+ ancestralsequence.h
+- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o terminalnode.o terminalnode.cpp
++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o terminalnode.o terminalnode.cpp
+
+ site.o: site.cpp site.h \
+ intmatrix.h \
+@@ -242,7 +242,7 @@
+ treenode.h \
+ sequence.h \
+ ancestralsequence.h
+- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o site.o site.cpp
++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o site.o site.cpp
+
+ sequence.o: sequence.cpp sequence.h \
+ site.h \
+@@ -250,7 +250,7 @@
+ flmatrix.h \
+ dbmatrix.h \
+ boolmatrix.h
+- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o sequence.o sequence.cpp
++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o sequence.o sequence.cpp
+
+ readnewick.o: readnewick.cpp readnewick.h \
+ treenode.h \
+@@ -263,10 +263,10 @@
+ ancestralnode.h \
+ ancestralsequence.h \
+ node.h
+- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o readnewick.o readnewick.cpp
++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o readnewick.o readnewick.cpp
+
+ readfile.o: readfile.cpp readfile.h
+- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o readfile.o readfile.cpp
++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o readfile.o readfile.cpp
+
+ readalignment.o: readalignment.cpp readalignment.h \
+ sequence.h \
+@@ -282,12 +282,12 @@
+ config.h \
+ hmmodel.h \
+ ancestralnode.h
+- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o readalignment.o readalignment.cpp
++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o readalignment.o readalignment.cpp
+
+ pwsite.o: pwsite.cpp pwsite.h \
+ flmatrix.h \
+ intmatrix.h
+- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o pwsite.o pwsite.cpp
++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o pwsite.o pwsite.cpp
+
+ pwhirschberg.o: pwhirschberg.cpp config.h \
+ hmmodel.h \
+@@ -303,7 +303,7 @@
+ pwhirschberg.h \
+ pwsite.h \
+ exonerate_reads.h
+- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o pwhirschberg.o pwhirschberg.cpp
++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o pwhirschberg.o pwhirschberg.cpp
+
+ progressivealignment.o: progressivealignment.cpp readnewick.h \
+ treenode.h \
+@@ -330,7 +330,7 @@
+ readalignment.h \
+ exonerate_reads.h \
+ bppancestors.h
+- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o progressivealignment.o progressivealignment.cpp
++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o progressivealignment.o progressivealignment.cpp
+
+ prank.o: prank.cpp progressivealignment.h \
+ config.h \
+@@ -353,7 +353,7 @@
+ mafft_alignment.h \
+ check_version.h \
+ prank.h
+- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o prank.o prank.cpp
++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o prank.o prank.cpp
+
+ postprobability.o: postprobability.cpp config.h \
+ hmmodel.h \
+@@ -369,7 +369,7 @@
+ postprobability.h \
+ phylomatchscore.h \
+ terminalsequence.h
+- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o postprobability.o postprobability.cpp
++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o postprobability.o postprobability.cpp
+
+ phylomatchscore.o: phylomatchscore.cpp config.h \
+ hmmodel.h \
+@@ -384,13 +384,13 @@
+ ancestralsequence.h \
+ phylomatchscore.h \
+ terminalsequence.h
+- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o phylomatchscore.o phylomatchscore.cpp
++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o phylomatchscore.o phylomatchscore.cpp
+
+ node.o: node.cpp node.h
+- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o node.o node.cpp
++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o node.o node.cpp
+
+ intmatrix.o: intmatrix.cpp intmatrix.h
+- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o intmatrix.o intmatrix.cpp
++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o intmatrix.o intmatrix.cpp
+
+ hmmodel.o: hmmodel.cpp hmmodel.h \
+ dbmatrix.h \
+@@ -403,7 +403,7 @@
+ boolmatrix.h \
+ ancestralsequence.h \
+ eigen.h
+- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o hmmodel.o hmmodel.cpp
++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o hmmodel.o hmmodel.cpp
+
+ hirschberg.o: hirschberg.cpp config.h \
+ hmmodel.h \
+@@ -420,7 +420,7 @@
+ hirschberg.h \
+ phylomatchscore.h \
+ terminalsequence.h
+- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o hirschberg.o hirschberg.cpp
++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o hirschberg.o hirschberg.cpp
+
+ guidetree.o: guidetree.cpp guidetree.h \
+ flmatrix.h \
+@@ -437,7 +437,7 @@
+ boolmatrix.h \
+ ancestralsequence.h \
+ translatesequences.h
+- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o guidetree.o guidetree.cpp
++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o guidetree.o guidetree.cpp
+
+ fullprobability.o: fullprobability.cpp config.h \
+ hmmodel.h \
+@@ -453,16 +453,16 @@
+ fullprobability.h \
+ phylomatchscore.h \
+ terminalsequence.h
+- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o fullprobability.o fullprobability.cpp
++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o fullprobability.o fullprobability.cpp
+
+ flmatrix.o: flmatrix.cpp flmatrix.h
+- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o flmatrix.o flmatrix.cpp
++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o flmatrix.o flmatrix.cpp
+
+ eigen.o: eigen.cpp eigen.h
+- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o eigen.o eigen.cpp
++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o eigen.o eigen.cpp
+
+ dbmatrix.o: dbmatrix.cpp dbmatrix.h
+- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o dbmatrix.o dbmatrix.cpp
++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o dbmatrix.o dbmatrix.cpp
+
+ characterprobability.o: characterprobability.cpp config.h \
+ hmmodel.h \
+@@ -477,10 +477,10 @@
+ ancestralsequence.h \
+ characterprobability.h \
+ terminalsequence.h
+- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o characterprobability.o characterprobability.cpp
++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o characterprobability.o characterprobability.cpp
+
+ boolmatrix.o: boolmatrix.cpp boolmatrix.h
+- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o boolmatrix.o boolmatrix.cpp
++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o boolmatrix.o boolmatrix.cpp
+
+ ancestralsequence.o: ancestralsequence.cpp ancestralsequence.h \
+ sequence.h \
+@@ -493,7 +493,7 @@
+ hmmodel.h \
+ ancestralnode.h \
+ treenode.h
+- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o ancestralsequence.o ancestralsequence.cpp
++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o ancestralsequence.o ancestralsequence.cpp
+
+ ancestralnode.o: ancestralnode.cpp config.h \
+ hmmodel.h \
+@@ -515,10 +515,10 @@
+ characterprobability.h \
+ terminalnode.h \
+ readalignment.h
+- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o ancestralnode.o ancestralnode.cpp
++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o ancestralnode.o ancestralnode.cpp
+
+ check_version.o: check_version.cpp check_version.h
+- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o check_version.o check_version.cpp
++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o check_version.o check_version.cpp
+
+ exonerate_reads.o: exonerate_reads.cpp exonerate_reads.h \
+ config.h \
+@@ -533,7 +533,7 @@
+ boolmatrix.h \
+ ancestralsequence.h \
+ translatesequences.h
+- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o exonerate_reads.o exonerate_reads.cpp
++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o exonerate_reads.o exonerate_reads.cpp
+
+ mafft_alignment.o: mafft_alignment.cpp mafft_alignment.h \
+ config.h \
+@@ -547,7 +547,7 @@
+ site.h \
+ boolmatrix.h \
+ ancestralsequence.h
+- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o mafft_alignment.o mafft_alignment.cpp
++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o mafft_alignment.o mafft_alignment.cpp
+
+ bppancestors.o: bppancestors.cpp bppancestors.h \
+ ancestralnode.h \
+@@ -563,7 +563,7 @@
+ hmmodel.h \
+ readfile.h \
+ readnewick.h
+- $(CXX) -c $(CXXFLAGS) $(INCPATH) -o bppancestors.o bppancestors.cpp
++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(INCPATH) -o bppancestors.o bppancestors.cpp
+
+ ####### Manpages
+
Modified: trunk/packages/prank/trunk/debian/patches/series
===================================================================
--- trunk/packages/prank/trunk/debian/patches/series 2016-05-13 11:43:22 UTC (rev 21948)
+++ trunk/packages/prank/trunk/debian/patches/series 2016-05-13 22:19:22 UTC (rev 21949)
@@ -1 +1,2 @@
hardening.patch
+fix-gcc6.patch
Modified: trunk/packages/prank/trunk/debian/rules
===================================================================
--- trunk/packages/prank/trunk/debian/rules 2016-05-13 11:43:22 UTC (rev 21948)
+++ trunk/packages/prank/trunk/debian/rules 2016-05-13 22:19:22 UTC (rev 21949)
@@ -2,6 +2,8 @@
SRCDIR=src
+export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+
%:
dh $@ --sourcedirectory=$(SRCDIR) --parallel
More information about the debian-med-commit
mailing list