[med-svn] [Git][med-team/libssw][master] 3 commits: Drop symbol from symbols file that is not created by gcc-10

Andreas Tille gitlab at salsa.debian.org
Thu Jul 23 09:49:36 BST 2020 


Andreas Tille pushed to branch master at Debian Med / libssw


Commits:
61429a6e by Andreas Tille at 2020-07-23T09:09:49+02:00
Drop symbol from symbols file that is not created by gcc-10

- - - - -
4695c0ce by Andreas Tille at 2020-07-23T10:44:06+02:00
Restore build_all_libs.patch to build properly soversioned shared lib as well as static lib

- - - - -
c2c56864 by Andreas Tille at 2020-07-23T10:46:32+02:00
Upload to unstable

- - - - -


5 changed files:

- debian/changelog
- debian/libssw0.symbols
- debian/patches/build_all_libs.patch
- debian/patches/hardening.patch
- debian/patches/rename_tool.patch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,5 +1,8 @@
-libssw (1.1-10) UNRELEASED; urgency=medium
+libssw (1.1-10) unstable; urgency=medium
 
+  * Team upload
+
+  [ Michael R. Crusoe ]
   * Improve crossbuilding
   * Add "nojava" build profile
   * Add salsa-ci file (routine-update)
@@ -7,7 +10,11 @@ libssw (1.1-10) UNRELEASED; urgency=medium
   * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
     Repository-Browse.
 
- -- Michael R. Crusoe <michael.crusoe at gmail.com>  Sun, 16 Feb 2020 17:23:59 +0100
+  [ Andreas Tille ]
+  * Drop symbol from symbols file that is not created by gcc-10
+    Closes: #957481
+
+ -- Andreas Tille <tille at debian.org>  Thu, 23 Jul 2020 10:44:14 +0200
 
 libssw (1.1-9) unstable; urgency=medium
 


=====================================
debian/libssw0.symbols
=====================================
@@ -22,7 +22,6 @@ libssw.so.0 libssw0 #MINVER#
  _ZNK20StripedSmithWaterman7Aligner5AlignEPKcRKNS_6FilterEPNS_9AlignmentE at Base 1.1
  _ZNK20StripedSmithWaterman7Aligner5AlignEPKcS2_RKiRKNS_6FilterEPNS_9AlignmentE at Base 1.1
  _ZNSt6vectorIjSaIjEE17_M_realloc_insertIJRKjEEEvN9__gnu_cxx17__normal_iteratorIPjS1_EEDpOT_ at Base 1.1
- _ZNSt6vectorIjSaIjEEaSERKS1_ at Base 1.1
  _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED0Ev at Base 1.1
  _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED1Ev at Base 1.1
  _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED2Ev at Base 1.1


=====================================
debian/patches/build_all_libs.patch
=====================================
@@ -4,9 +4,17 @@ Description: build all libraries
  Not upstreamed as upstream intends their C source to be inlined with the
  code using the functions.
 Author: Sascha Steinbiss <sascha at steinbiss.name>
---- libssw.orig/src/Makefile
-+++ libssw/src/Makefile
-@@ -10,8 +10,8 @@
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -5,24 +5,29 @@ CXXFLAGS := $(CFLAGS)
+ LOBJS = ssw.o
+ LCPPOBJS = ssw_cpp.o
+ PROG = ssw_test
+-LIB = libssw.so
++SOVERS=.0
++LIB = libssw.so$(SOVERS)
++STATICLIB = libssw.a
+ EXAMPLE = example_c
  EXAMPLE_CPP = example_cpp
  JAVA_JAR = ssw.jar
  JAVA_LIB = libsswjni.so
@@ -17,7 +25,10 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
  
  .PHONY: all default java clean
  
-@@ -21,8 +21,8 @@
+-default: $(PROG) $(EXAMPLE) $(EXAMPLE_CPP) $(LIB) 
++default: $(PROG) $(EXAMPLE) $(EXAMPLE_CPP) $(LIB) $(STATICLIB)
+ 
+ all: default java
  
  java: $(JAVA_JAR) $(JAVA_LIB)
  
@@ -25,10 +36,13 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
 -	$(CC) $(CFLAGS) -fPIC -shared -rdynamic -o $@ $<
 +$(LIB): ssw.c ssw.h ssw_cpp.h ssw_cpp.cpp
 +	$(CXX) $(CPPFLAGS) $(CXXFLAGS) -fPIC -shared -rdynamic -Wl,-soname,$(LIB) -o $@ $^
++
++$(STATICLIB): $(LOBJS) $(LCPPOBJS)
++	ar rcs $@ $^
  
  $(PROG): main.c kseq.h
  
-@@ -38,10 +38,10 @@
+@@ -38,10 +43,10 @@ $(JAVA_LIB): sswjni.c ssw.c ssw.h
  	$(CC) $(CFLAGS) $(JAVA_INLCUDES) -fPIC -shared -rdynamic -o $@ $< ssw.c 
  
  $(JAVA_JAR): $(JAVA_OBJ)
@@ -41,7 +55,7 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
  	
  ssw.o: ssw.c ssw.h
  	$(CC) -c -o $@ $< $(CFLAGS)
-@@ -50,4 +50,4 @@
+@@ -50,4 +55,4 @@ ssw_cpp.o: ssw_cpp.cpp ssw_cpp.h ssw.h
  	$(CXX) -c -o $@ $< $(CXXFLAGS)
  
  clean:


=====================================
debian/patches/hardening.patch
=====================================
@@ -1,7 +1,7 @@
 Description: add hardening
 Author: Sascha Steinbiss <sascha at steinbiss.name>
---- libssw.orig/src/Makefile
-+++ libssw/src/Makefile
+--- a/src/Makefile
++++ b/src/Makefile
 @@ -1,7 +1,8 @@
 -CC = gcc
 -CXX = g++
@@ -15,20 +15,21 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
  LOBJS = ssw.o
  LCPPOBJS = ssw_cpp.o
  PROG = ssw_test
-@@ -22,20 +23,20 @@
+@@ -24,7 +25,7 @@ all: default java
  java: $(JAVA_JAR) $(JAVA_LIB)
  
  $(LIB): ssw.c ssw.h ssw_cpp.h ssw_cpp.cpp
 -	$(CXX) $(CPPFLAGS) $(CXXFLAGS) -fPIC -shared -rdynamic -Wl,-soname,$(LIB) -o $@ $^
 +	$(CXX) $(CPPFLAGS) $(CXXFLAGS) -fPIC -shared -rdynamic -Wl,-soname,$(LIB) -o $@ $^ $(LDFLAGS)
  
- $(PROG): main.c kseq.h
- 
+ $(STATICLIB): $(LOBJS) $(LCPPOBJS)
+ 	ar rcs $@ $^
+@@ -34,13 +35,13 @@ $(PROG): main.c kseq.h
  $(EXAMPLE): example.c
  
  $(PROG) $(EXAMPLE): $(LOBJS)
 -	$(CC) -o $@ $(filter-out %.h,$^) $(CFLAGS) -lm -lz
-+	$(CC) -o $@ $(filter-out %.h,$^) $(CPPFLAGS) $(CFLAGS) -lm -lz $(LDFLAGS)
++	$(CC) -o $@ $(filter-out %.h,$^) $(CFLAGS) $(CPPFLAGS) -lm -lz $(LDFLAGS)
  
  $(EXAMPLE_CPP): example.cpp $(LOBJS) $(LCPPOBJS)
 -	$(CXX) -o $@ $^ $(CXXFLAGS) -lm -lz
@@ -40,7 +41,7 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
  
  $(JAVA_JAR): $(JAVA_OBJ)
  	jar cvf $@ $^
-@@ -44,10 +45,10 @@
+@@ -49,10 +50,10 @@ $(JAVA_JAR): $(JAVA_OBJ)
  	javac -target 1.6 -source 1.6 $<
  	
  ssw.o: ssw.c ssw.h


=====================================
debian/patches/rename_tool.patch
=====================================
@@ -2,20 +2,20 @@ Description: build command line aligner
  This patch ensures that 'ssw_test' is called 'ssw-align' in Debian
  and also links against libssw.
 Author: Sascha Steinbiss <satta at debian.org>
---- libssw.orig/src/Makefile
-+++ libssw/src/Makefile
-@@ -5,7 +5,7 @@
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -5,7 +5,7 @@ AR ?= ar
  #CXXFLAGS := $(CFLAGS)
  LOBJS = ssw.o
  LCPPOBJS = ssw_cpp.o
 -PROG = ssw_test
 +PROG = ssw-align
- LIB = libssw.so
- EXAMPLE = example_c
- EXAMPLE_CPP = example_cpp
-@@ -25,11 +25,12 @@
- $(LIB): ssw.c ssw.h ssw_cpp.h ssw_cpp.cpp
- 	$(CXX) $(CPPFLAGS) $(CXXFLAGS) -fPIC -shared -rdynamic -Wl,-soname,$(LIB) -o $@ $^ $(LDFLAGS)
+ SOVERS=.0
+ LIB = libssw.so$(SOVERS)
+ STATICLIB = libssw.a
+@@ -30,11 +30,12 @@ $(LIB): ssw.c ssw.h ssw_cpp.h ssw_cpp.cp
+ $(STATICLIB): $(LOBJS) $(LCPPOBJS)
+ 	ar rcs $@ $^
  
 -$(PROG): main.c kseq.h
 +$(PROG): main.c kseq.h $(LIB)
@@ -25,12 +25,12 @@ Author: Sascha Steinbiss <satta at debian.org>
  
 -$(PROG) $(EXAMPLE): $(LOBJS)
 +$(EXAMPLE): $(LOBJS)
- 	$(CC) -o $@ $(filter-out %.h,$^) $(CPPFLAGS) $(CFLAGS) -lm -lz $(LDFLAGS)
+ 	$(CC) -o $@ $(filter-out %.h,$^) $(CFLAGS) $(CPPFLAGS) -lm -lz $(LDFLAGS)
  
  $(EXAMPLE_CPP): example.cpp $(LOBJS) $(LCPPOBJS)
---- libssw.orig/src/main.c
-+++ libssw/src/main.c
-@@ -297,7 +297,7 @@
+--- a/src/main.c
++++ b/src/main.c
+@@ -297,7 +297,7 @@ int main (int argc, char * const argv[])
  	}
  	if (optind + 2 > argc) {
  		fprintf(stderr, "\n");



View it on GitLab: https://salsa.debian.org/med-team/libssw/-/compare/a19c146931e078e0e56abc85684f5a3583165e63...c2c568647338036513f688cdd8171d551134a7ad

-- 
View it on GitLab: https://salsa.debian.org/med-team/libssw/-/compare/a19c146931e078e0e56abc85684f5a3583165e63...c2c568647338036513f688cdd8171d551134a7ad
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