[med-svn] [Git][med-team/cdbfasta][master] 8 commits: New upstream version 1.00+git20230710.da8f5ba+dfsg
Andreas Tille (@tille)
gitlab at salsa.debian.org
Mon Nov 27 15:27:11 GMT 2023
Andreas Tille pushed to branch master at Debian Med / cdbfasta
Commits:
98a3343e by Andreas Tille at 2023-11-27T16:12:46+01:00
New upstream version 1.00+git20230710.da8f5ba+dfsg
- - - - -
cca8ace3 by Andreas Tille at 2023-11-27T16:12:46+01:00
routine-update: New upstream version
- - - - -
c6982f36 by Andreas Tille at 2023-11-27T16:12:46+01:00
Update upstream source from tag 'upstream/1.00+git20230710.da8f5ba+dfsg'
Update to upstream version '1.00+git20230710.da8f5ba+dfsg'
with Debian dir 8672146436384213d9f5fc24d505f34ae701bb9b
- - - - -
0576eb6b by Andreas Tille at 2023-11-27T16:12:46+01:00
routine-update: Standards-Version: 4.6.2
- - - - -
dbbff6e7 by Andreas Tille at 2023-11-27T16:13:02+01:00
Set upstream metadata fields: Repository-Browse.
Changes-By: lintian-brush
- - - - -
a3d7b0ac by Andreas Tille at 2023-11-27T16:24:44+01:00
Update and merge patches
- - - - -
fabcfbc3 by Andreas Tille at 2023-11-27T16:25:53+01:00
Upload to unstable
- - - - -
562be2de by Andreas Tille at 2023-11-27T16:26:31+01:00
Add Forwarded field
- - - - -
11 changed files:
- Makefile
- debian/changelog
- debian/control
- − debian/patches/cppflags.patch
- − debian/patches/cross.patch
- debian/patches/hardening.patch
- debian/patches/series
- debian/patches/use_debian_packaged_gclib.patch
- debian/patches/workaround-lintian-false-positive
- debian/upstream/metadata
- gcdbz.cpp
Changes:
=====================================
Makefile
=====================================
@@ -1,6 +1,8 @@
GCLDIR := ./gclib
SEARCHDIRS := -I${GCLDIR}
-CC := g++
+# Use the correct compiler (CXX, not CC) and respect the environment
+# by using ?=
+CXX ?= g++
BASEFLAGS = -Wall ${SEARCHDIRS} $(MARCH) -DENABLE_COMPRESSION=1 -D_FILE_OFFSET_BITS=64 \
-D_LARGEFILE_SOURCE -fno-exceptions -fno-rtti -fno-strict-aliasing \
@@ -9,39 +11,38 @@ BASEFLAGS = -Wall ${SEARCHDIRS} $(MARCH) -DENABLE_COMPRESSION=1 -D_FILE_OFFSET_
ifeq ($(findstring debug,$(MAKECMDGOALS)),)
DBGFLAGS = -O2 -g -DNDEBUG
- LDFLAGS =
else
DBGFLAGS = -g -DDEBUG -D_DEBUG
- LDFLAGS = -g
+ LDFLAGS += -g
endif
ifeq ($(findstring nommap,$(MAKECMDGOALS)),)
- CFLAGS = $(DBGFLAGS) $(BASEFLAGS)
+ CXXFLAGS += $(DBGFLAGS) $(BASEFLAGS)
else
- CFLAGS = $(DBGFLAGS) $(BASEFLAGS) -DNO_MMAP
+ CXXFLAGS += $(DBGFLAGS) $(BASEFLAGS) -DNO_MMAP
endif
%.o : %.c
- ${CC} ${CFLAGS} -c $< -o $@
+ ${CXX} ${CXXFLAGS} -c $< -o $@
%.o : %.cc
- ${CC} ${CFLAGS} -c $< -o $@
+ ${CXX} ${CXXFLAGS} -c $< -o $@
%.o : %.C
- ${CC} ${CFLAGS} -c $< -o $@
+ ${CXX} ${CXXFLAGS} -c $< -o $@
%.o : %.cpp
- ${CC} ${CFLAGS} -c $< -o $@
+ ${CXX} ${CXXFLAGS} -c $< -o $@
%.o : %.cxx
- ${CC} ${CFLAGS} -c $< -o $@
+ ${CXX} ${CXXFLAGS} -c $< -o $@
# C/C++ linker
-LINKER := g++
+LINKER := ${CXX}
#LDFLAGS =
#uncomment this when ENABLE_COMPRESSION
-LDFLAGS = -lz
+LDFLAGS += -lz
.PHONY : all
all: cdbfasta cdbyank
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+cdbfasta (1.00+git20230710.da8f5ba+dfsg-1) unstable; urgency=medium
+
+ * New upstream version
+ * Standards-Version: 4.6.2 (routine-update)
+ * Set upstream metadata fields: Repository-Browse.
+
+ -- Andreas Tille <tille at debian.org> Mon, 27 Nov 2023 16:25:27 +0100
+
cdbfasta (1.00+git20181005.014498c+dfsg-4) unstable; urgency=medium
* Mark Multi-Arch: foreign
=====================================
debian/control
=====================================
@@ -9,7 +9,7 @@ Build-Depends: debhelper-compat (= 13),
pkg-config,
libgclib-dev,
help2man
-Standards-Version: 4.6.0
+Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/cdbfasta
Vcs-Git: https://salsa.debian.org/med-team/cdbfasta.git
Homepage: https://github.com/gpertea/cdbfasta
=====================================
debian/patches/cppflags.patch deleted
=====================================
@@ -1,33 +0,0 @@
-Description: apply CPPFLAGS to enable functions fortification
-Author: Étienne Mollier <emollier at debian.org>
-Forwarded: not-needed
-Last-Update: 2021-10-17
----
-This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
---- cdbfasta.orig/Makefile
-+++ cdbfasta/Makefile
-@@ -23,19 +23,19 @@
- endif
-
- %.o : %.c
-- ${CC} ${CFLAGS} -c $< -o $@
-+ ${CC} $(CPPFLAGS) ${CFLAGS} -c $< -o $@
-
- %.o : %.cc
-- ${CC} ${CFLAGS} -c $< -o $@
-+ ${CC} $(CPPFLAGS) ${CFLAGS} -c $< -o $@
-
- %.o : %.C
-- ${CC} ${CFLAGS} -c $< -o $@
-+ ${CC} $(CPPFLAGS) ${CFLAGS} -c $< -o $@
-
- %.o : %.cpp
-- ${CC} ${CFLAGS} -c $< -o $@
-+ ${CC} $(CPPFLAGS) ${CFLAGS} -c $< -o $@
-
- %.o : %.cxx
-- ${CC} ${CFLAGS} -c $< -o $@
-+ ${CC} $(CPPFLAGS) ${CFLAGS} -c $< -o $@
-
- # C/C++ linker
-
=====================================
debian/patches/cross.patch deleted
=====================================
@@ -1,19 +0,0 @@
---- cdbfasta-1.00+git20181005.014498c+dfsg.orig/Makefile
-+++ cdbfasta-1.00+git20181005.014498c+dfsg/Makefile
-@@ -1,5 +1,6 @@
- GCLDIR := ./gclib
--SEARCHDIRS := `pkg-config --cflags libgclib`
-+PKG_CONFIG ?= pkg-config
-+SEARCHDIRS := `$(PKG_CONFIG) --cflags libgclib`
- CC := g++
-
- BASEFLAGS = -Wall ${SEARCHDIRS} $(MARCH) -DENABLE_COMPRESSION=1 -D_FILE_OFFSET_BITS=64 \
-@@ -42,7 +43,7 @@
- #LDFLAGS =
- #uncomment this when ENABLE_COMPRESSION
- LDFLAGS := -lz $(LDFLAGS)
--LIBS = `pkg-config --libs libgclib`
-+LIBS = `$(PKG_CONFIG) --libs libgclib`
-
- .PHONY : all
- all: cdbfasta cdbyank
=====================================
debian/patches/hardening.patch
=====================================
@@ -3,27 +3,28 @@ Description: Regard hardening CFLAGS setting
It was simply ignored. So I decided to override the LINKER variable in debian/rules.
Author: Andreas Tille <tille at debian.org>
Date: Tue, 18 Dec 2012 16:41:28 +0100
+Forwarded: not-needed
--- a/Makefile
+++ b/Makefile
-@@ -16,9 +16,9 @@ else
+@@ -17,9 +17,9 @@ else
endif
ifeq ($(findstring nommap,$(MAKECMDGOALS)),)
-- CFLAGS = $(DBGFLAGS) $(BASEFLAGS)
-+ CFLAGS := $(DBGFLAGS) $(BASEFLAGS) $(CFLAGS)
+- CXXFLAGS += $(DBGFLAGS) $(BASEFLAGS)
++ CXXFLAGS := $(DBGFLAGS) $(BASEFLAGS) $(CPPFLAGS) $(CFLAGS)
else
-- CFLAGS = $(DBGFLAGS) $(BASEFLAGS) -DNO_MMAP
-+ CFLAGS := $(DBGFLAGS) $(BASEFLAGS) -DNO_MMAP $(CFLAGS)
+- CXXFLAGS += $(DBGFLAGS) $(BASEFLAGS) -DNO_MMAP
++ CXXFLAGS := $(DBGFLAGS) $(BASEFLAGS) -DNO_MMAP $(CPPFLAGS) $(CFLAGS)
endif
%.o : %.c
-@@ -41,7 +41,7 @@ endif
- LINKER := g++
+@@ -42,7 +42,7 @@ endif
+ LINKER := ${CXX}
#LDFLAGS =
#uncomment this when ENABLE_COMPRESSION
--LDFLAGS = -lz
-+LDFLAGS := -lz $(LDFLAGS)
+-LDFLAGS += -lz
++LDFLAGS := -lz $(LDFLAGS)
.PHONY : all
all: cdbfasta cdbyank
=====================================
debian/patches/series
=====================================
@@ -1,5 +1,3 @@
workaround-lintian-false-positive
hardening.patch
use_debian_packaged_gclib.patch
-cross.patch
-cppflags.patch
=====================================
debian/patches/use_debian_packaged_gclib.patch
=====================================
@@ -1,25 +1,27 @@
Description: Use Debian packaged gclib
Author: Andreas Tille <tille at debian.org>
Last-Update: Sat, 13 Jun 2020 07:41:58 +0200
+Forwarded: not-needed
--- a/Makefile
+++ b/Makefile
-@@ -1,5 +1,5 @@
+@@ -1,5 +1,6 @@
GCLDIR := ./gclib
-SEARCHDIRS := -I${GCLDIR}
-+SEARCHDIRS := `pkg-config --cflags libgclib`
- CC := g++
-
- BASEFLAGS = -Wall ${SEARCHDIRS} $(MARCH) -DENABLE_COMPRESSION=1 -D_FILE_OFFSET_BITS=64 \
-@@ -42,6 +42,7 @@ LINKER := g++
++PKG_CONFIG ?= pkg-config
++SEARCHDIRS := `$(PKG_CONFIG) --cflags libgclib`
+ # Use the correct compiler (CXX, not CC) and respect the environment
+ # by using ?=
+ CXX ?= g++
+@@ -43,6 +44,7 @@ LINKER := ${CXX}
#LDFLAGS =
#uncomment this when ENABLE_COMPRESSION
- LDFLAGS := -lz $(LDFLAGS)
-+LIBS = `pkg-config --libs libgclib`
+ LDFLAGS := -lz $(LDFLAGS)
++LIBS = `$(PKG_CONFIG) --libs libgclib`
.PHONY : all
all: cdbfasta cdbyank
-@@ -49,11 +50,11 @@ debug: all
+@@ -50,11 +52,11 @@ debug: all
nommap: all
#when compression is enabled:
#cdbfasta: ./cdbfasta.o ./gcdbz.o ...
=====================================
debian/patches/workaround-lintian-false-positive
=====================================
@@ -3,6 +3,7 @@ Last-Update: 2011-04-12 08:39:38 +0000
Description: Lintian uses some string detection heuristics to spot statically linked Zlib
and this string triggers the warning. This change keeps Lintian happy and makes
the error message grammatically correct.
+Forwarded: not-needed
--- a/gcdbz.cpp
+++ b/gcdbz.cpp
=====================================
debian/upstream/metadata
=====================================
@@ -9,3 +9,4 @@ Registry:
Entry: SCR_016057
- Name: conda:bioconda
Entry: NA
+Repository-Browse: https://github.com/gpertea/cdbfasta
=====================================
gcdbz.cpp
=====================================
@@ -110,7 +110,6 @@ char* GCdbz::compress(GReadBuf *readbuf, char* delim) {
// (exactly as left after a previous call)
if (zf==NULL || uncompress)
GError("GCdbz Error: cannot use compress() method !\n");
- unsigned int total_out=0;
int c=0;
bool in_rec=true;
int delimlen=strlen(delim);
@@ -165,7 +164,6 @@ char* GCdbz::compress(GReadBuf *readbuf, char* delim) {
if (toWrite>0) {
if (fwrite(lbuf, 1, toWrite, zf)<toWrite)
GError("Error writing deflate chunk!\n");
- total_out+=toWrite;
zrecsize+=toWrite;
zpos+=toWrite;
}
View it on GitLab: https://salsa.debian.org/med-team/cdbfasta/-/compare/40ab2ecca48edd87bdb3e0ea48c687341f7c1a18...562be2de6c84efc8f5c2a3467ddc5f3c72ebc2ad
--
View it on GitLab: https://salsa.debian.org/med-team/cdbfasta/-/compare/40ab2ecca48edd87bdb3e0ea48c687341f7c1a18...562be2de6c84efc8f5c2a3467ddc5f3c72ebc2ad
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