[med-svn] [augustus] 01/06: more sanitization
Sascha Steinbiss
satta at debian.org
Sat Jul 29 05:14:01 UTC 2017
This is an automated email from the git hooks/post-receive script.
satta pushed a commit to branch master
in repository augustus.
commit effa00aafabb4be86bebbc4664d33774a346a92f
Author: Sascha Steinbiss <satta at debian.org>
Date: Sat Jul 22 10:05:31 2017 +0200
more sanitization
---
debian/changelog | 10 +++-
debian/control | 1 +
debian/patches/buildflags.patch | 106 +++++++++++++++++++++++++++++++++++---
debian/patches/search_config_path | 2 +-
debian/patches/spelling.patch | 4 +-
debian/rules | 16 +++++-
6 files changed, 126 insertions(+), 13 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 3aa2697..e25abd2 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,10 +1,16 @@
-augustus (3.3+dfsg-2) UNRELEASED; urgency=medium
+augustus (3.3+dfsg-2) unstable; urgency=medium
[ Steffen Moeller ]
* Added registry entries for bio.tools and OMICtools.
[ Sascha Steinbiss ]
- * Use new htslib.
+ * Make sure dynamic linking is used throughout the package.
+ One exception is a package still using the legacy samtools
+ API, for which it links statically against the libbam.a provided
+ by libbam-dev. Added a Built-Using entry for that.
+ Thanks to Mattia Rizzolo for the hint.
+ * Sanitize runtime dependencies.
+ * Add missing auxtools to package.
-- Sascha Steinbiss <satta at debian.org> Fri, 21 Jul 2017 10:05:49 +0200
diff --git a/debian/control b/debian/control
index 5a908be..7fd1674 100644
--- a/debian/control
+++ b/debian/control
@@ -18,6 +18,7 @@ Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
augustus-data
+Built-Using: libbam-dev (= 0.1.19-2)
Description: gene prediction in eukaryotic genomes
AUGUSTUS is a software for gene prediction in eukaryotic genomic sequences
that is based on a generalized hidden Markov model (HMM), a probabilistic
diff --git a/debian/patches/buildflags.patch b/debian/patches/buildflags.patch
index d035d2c..8f30392 100644
--- a/debian/patches/buildflags.patch
+++ b/debian/patches/buildflags.patch
@@ -5,12 +5,12 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
@@ -1,8 +1,9 @@
compileSpliceCands : compileSpliceCands.o list.h list.o
- gcc $(LDFLAGS) -o compileSpliceCands compileSpliceCands.o list.o;
-+ gcc -o compileSpliceCands compileSpliceCands.o list.o $(LDFLAGS);
++ $(CC) -o compileSpliceCands compileSpliceCands.o list.o $(CFLAGS) $(LDFLAGS);
# cp compileSpliceCands ../../bin
+
compileSpliceCands.o : compileSpliceCands.c
- gcc -Wall -pedantic -ansi $(CPPFLAGS) -c compileSpliceCands.c
-+ gcc -Wall -pedantic -ansi $(CFLAGS) $(CPPFLAGS) -c compileSpliceCands.c
++ $(CC) -Wall -pedantic -ansi $(CFLAGS) $(CPPFLAGS) -c compileSpliceCands.c
all : compileSpliceCands
@@ -21,16 +21,20 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
# a strict signed-only usage strategy to avoid mistakes since we are not warned about this.
# - The order of object files in $(OBJS) IS IMPORTANT (see lldouble.hh)
-CFLAGS := -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 ${CFLAGS} # -DDEBUG -g -ggdb -pg
-+CPPFLAGS+=-Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread
++CPPFLAGS := -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread ${CPPCLAGS}
INCLS = -I../include
LIBS =
-@@ -39,7 +39,7 @@
- $(CC) -c $(CFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $@ $< $(INCLS)
+@@ -36,10 +36,10 @@
+ .SUFFIXES: .cc .o .so
+
+ .cc.o:
+- $(CC) -c $(CFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $@ $< $(INCLS)
++ $(CC) -c $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $@ $< $(INCLS)
homGeneMapping: main.cc $(OBJS)
- $(CC) $(CFLAGS) $(CPPFLAGS) -o $@ $^ $(INCLS) $(LIBS)
-+ $(CC) $(CFLAGS) $(CXXFLAGS) $(CPPFLAGS) -o $@ $^ $(INCLS) $(LIBS)
++ $(CC) $(CXXFLAGS) $(CPPFLAGS) -o $@ $^ $(INCLS) $(LIBS)
cp homGeneMapping ../../../bin/homGeneMapping
clean:
@@ -73,3 +77,93 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
clean:
rm -rf *o joingenes; rm -rf ../../bin/joingenes
+--- a/auxprogs/bam2hints/Makefile
++++ b/auxprogs/bam2hints/Makefile
+@@ -12,15 +12,15 @@
+ LIBS = -lbamtools -lz
+ SOURCES = bam2hints.cc
+ OBJECTS = $(SOURCES:.cc=.o)
+-CXXFLAGS += -Wall -O2 # -g -p -g -ggdb
++CXXFLAGS := -Wall -O2 $(CXXFLAGS) # -g -p -g -ggdb
+
+ LINK.cc = g++
+
+ # Recipe(s)
+-# $@: full target name of current target.
+-# $<: .c file of target.
+-bam2hints : $(OBJECTS)
+- $(LINK.cc) $(CXXFLAGS) $(LDFLAGS) -o $@ $(OBJECTS) $(LIBS)
++# $@: full target name of current target.
++# $<: .c file of target.
++bam2hints : $(OBJECTS)
++ $(LINK.cc) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(OBJECTS) $(LIBS)
+ cp bam2hints ../../bin
+
+ all:$(OBJECTS) # Compiles each foo.cc into foo.o
+--- a/auxprogs/bam2wig/Makefile
++++ b/auxprogs/bam2wig/Makefile
+@@ -9,22 +9,21 @@
+ PROGRAM = bam2wig
+ SOURCES = $(PROGRAM)
+ OBJECTS = $(SOURCES:.c=.o)
+-TOOLDIR=/home/mario/tools
++TOOLDIR=/usr/include
+ SAMTOOLS=$(TOOLDIR)/samtools/
+ HTSLIB=$(TOOLDIR)/htslib/
+-BCFTOOLS=$(TOOLDIR)/bcftools-1.2/
+ TABIX=$(TOOLDIR)/tabix/
+-INCLUDES=-I$(SAMTOOLS) -I. -I$(HTSLIB) -I$(BCFTOOLS) -I$(TABIX)
++INCLUDES=-I$(SAMTOOLS) -I. -I$(HTSLIB) -I$(TABIX)
+ VPATH=$(SAMTOOLS)
+-LIBS=$(SAMTOOLS)/libbam.a $(HTSLIB)/libhts.a -lcurses -lm -lz -lpthread
+-CFLAGS=-Wall -O2 $(INCLUDES)
+-CC=gcc
++LIBS=/usr/lib/libbam.a -lhts -lcurses -lm -lz -lpthread
++CFLAGS:=-Wall -O2 $(INCLUDES) $(CFLAGS)
++#CC=gcc
+
+ $(PROGRAM) : bam2wig.o
+- $(CC) $(CFLAGS) $^ -o $@ $(LIBS)
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) $^ -o $@ $(LIBS)
+
+ bam2wig.o : bam2wig.c
+- $(CC) $(CFLAGS) -c $^ -o $@ $(INCLUDES)
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -c $^ -o $@ $(INCLUDES)
+
+ clean:
+ rm -f $(OBJECTS) bam2wig.o
+--- a/auxprogs/checkTargetSortedness/Makefile
++++ b/auxprogs/checkTargetSortedness/Makefile
+@@ -18,7 +18,7 @@
+ INCLUDES = -I$(SAMTOOLS) -I.
+ # replace -lbam with the following in case you have your own samtools library: $(SAMTOOLS)/libbam.a
+ LIBS=-lbam -lcurses -lm -lz -lpthread
+-CC=gcc
++#CC=gcc
+
+ all:$(PROGRAM) $(OBJECTS)
+
+--- a/auxprogs/filterBam/src/Makefile
++++ b/auxprogs/filterBam/src/Makefile
+@@ -11,7 +11,7 @@
+ BAMTOOLS = /usr/include/bamtools
+ INCLUDES = -I$(BAMTOOLS) -Iheaders -I./bamtools
+ LIBS = -lbamtools -lz
+-CFLAGS = -std=c++0x
++CXXFLAGS := -std=c++0x ${CXXFLAGS}
+ VPATH = functions
+
+ all : $(PROGRAM) $(OBJECTS) CHECKBAM BIN
+@@ -28,10 +28,10 @@
+ fi
+
+ $(PROGRAM) : $(OBJECTS)
+- $(LINK.cc) $(CFLAGS) $(LDFLAGS) $^ -o $@ $(LIBS)
++ $(LINK.cc) $(CXXFLAGS) $(LDFLAGS) $^ -o $@ $(LIBS)
+
+ $(OBJECTS) : %.o:%.cc
+- $(LINK.cc) $(CFLAGS) $(CPPFLAGS) -c $^ -o $@ $(INCLUDES)
++ $(LINK.cc) $(CXXFLAGS) $(CPPFLAGS) -c $^ -o $@ $(INCLUDES)
+
+
+ clean:
diff --git a/debian/patches/search_config_path b/debian/patches/search_config_path
index 65b915a..d2e1452 100644
--- a/debian/patches/search_config_path
+++ b/debian/patches/search_config_path
@@ -5,7 +5,7 @@ Description: use Debian config path
Author: Sascha Steinbiss <sascha at steinbiss.name>
--- a/src/properties.cc
+++ b/src/properties.cc
-@@ -394,7 +394,8 @@
+@@ -407,7 +407,8 @@
if (dir){
configPath = string(dir);
} else { // third priority: relative to the path of the executable
diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch
index af16d04..e840105 100644
--- a/debian/patches/spelling.patch
+++ b/debian/patches/spelling.patch
@@ -112,7 +112,7 @@ Author: Sascha Steinbiss <satta at debian.org>
}
--- a/src/namgene.cc
+++ b/src/namgene.cc
-@@ -1389,7 +1389,7 @@
+@@ -1399,7 +1399,7 @@
istrm.close();
} else {
@@ -121,7 +121,7 @@ Author: Sascha Steinbiss <satta at debian.org>
}
}
-@@ -1439,7 +1439,7 @@
+@@ -1449,7 +1449,7 @@
istrm >> Constant::tail2tail_ovlp[i];
istrm.close();
} else {
diff --git a/debian/rules b/debian/rules
index 1a49b6f..508c374 100755
--- a/debian/rules
+++ b/debian/rules
@@ -9,15 +9,27 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
bin:
mkdir -p bin
+aln2wig: bin
+ $(MAKE) -C auxprogs/aln2wig
+
bam2hints: bin
$(MAKE) -C auxprogs/bam2hints
-homGeneMapping: bin
- $(MAKE) -C auxprogs/homGeneMapping/src
+bam2wig: bin
+ $(MAKE) -C auxprogs/bam2wig
checkTargetSortedness: bin
$(MAKE) -C auxprogs/checkTargetSortedness
+compileSpliceCands: bin
+ $(MAKE) -C auxprogs/compileSpliceCands
+
+filterBam: bin
+ $(MAKE) -C auxprogs/filterBam
+
+homGeneMapping: bin
+ $(MAKE) -C auxprogs/homGeneMapping/src
+
joingenes: bin
$(MAKE) -C auxprogs/joingenes
--
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