[med-svn] [plink1.9] 02/02: Refresh patches
Dylan Aïssi
bob.dybian-guest at moszumanska.debian.org
Thu Aug 25 05:52:02 UTC 2016
This is an automated email from the git hooks/post-receive script.
bob.dybian-guest pushed a commit to branch master
in repository plink1.9.
commit ce4c693c32a3aad712000bd0c4ef55b5e30c076b
Author: Dylan Aïssi <bob.dybian at gmail.com>
Date: Thu Aug 25 07:24:51 2016 +0200
Refresh patches
---
debian/changelog | 3 +-
debian/patches/01_Fix_use_dynamic_linking.patch | 61 ++++++++++++++++++++++++
debian/patches/01_Fix_use_internal_lib.patch | 63 -------------------------
debian/patches/02_Activate_Stable_Build.patch | 8 ++--
debian/patches/series | 2 +-
5 files changed, 68 insertions(+), 69 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index c74d034..ff0f328 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,5 +1,6 @@
-plink1.9 (1.90~b3.36-160416-2) UNRELEASED; urgency=medium
+plink1.9 (1.90~b3.40-160816-1) UNRELEASED; urgency=medium
+ * New upstream release.
* Set all hardening options.
* Update uscan options.
diff --git a/debian/patches/01_Fix_use_dynamic_linking.patch b/debian/patches/01_Fix_use_dynamic_linking.patch
new file mode 100644
index 0000000..0a63212
--- /dev/null
+++ b/debian/patches/01_Fix_use_dynamic_linking.patch
@@ -0,0 +1,61 @@
+Author: Dylan Aïssi <bob.dybian at gmail.com>
+Description: Fix use dynamic linking in Makefile.
+Last-Update: 2016-08-25
+Forwarded: No
+
+--- a/Makefile
++++ b/Makefile
+@@ -7,6 +7,7 @@
+ # (when enabled, "#define NOLAPACK" must be uncommented in plink_common.h)
+ NO_LAPACK =
+
++DYNAMIC_LINK = 1
+
+ # should autodetect system
+ SYS = UNIX
+@@ -20,9 +21,14 @@
+ endif
+
+ CFLAGS=-Wall -O2
+-BLASFLAGS=-L/usr/lib64/atlas -llapack -lcblas -latlas
+ LINKFLAGS=-lm -lpthread -ldl
+-ZLIB=zlib-1.2.8/libz.so.1.2.8
++ifdef DYNAMIC_LINK
++ BLASFLAGS=-llapack -lcblas -latlas
++ ZLIB=-lz -DDYNAMIC_ZLIB
++else
++ BLASFLAGS=-L/usr/lib64/atlas -llapack -lcblas -latlas
++ ZLIB=-L. zlib-1.2.8/libz.so.1.2.8
++endif
+
+ ifeq ($(SYS), MAC)
+ GCC_GTEQ_43 := $(shell expr `g++ -dumpversion | sed -e 's/\.\([0-9][0-9]\)/\1/g' -e 's/\.\([0-9]\)/0\1/g' -e 's/^[0-9]\{3,4\}$$/&00/'` \>= 40300)
+@@ -31,7 +37,7 @@
+ endif
+ BLASFLAGS=-framework Accelerate
+ LINKFLAGS=-ldl
+- ZLIB=zlib-1.2.8/libz.1.2.8.dylib
++ ZLIB=-L. zlib-1.2.8/libz.1.2.8.dylib
+ endif
+
+ ifeq ($(SYS), WIN)
+@@ -42,7 +48,7 @@
+ # NO_LAPACK.
+ BLASFLAGS=-L. lapack/liblapack.a -L. lapack/librefblas.a
+ LINKFLAGS=-lm -static-libgcc
+- ZLIB=zlib-1.2.8/libz.a
++ ZLIB=-L. zlib-1.2.8/libz.a
+ endif
+
+ ifdef NO_LAPACK
+@@ -57,8 +63,8 @@
+ # lead to minor problems when PLINK 2.0 is released.)
+
+ plink: $(SRC)
+- g++ $(CFLAGS) $(SRC) -o plink $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB)
++ g++ $(CFLAGS) $(SRC) -o plink $(BLASFLAGS) $(LINKFLAGS) $(ZLIB)
+
+ plinkw: $(SRC)
+ g++ $(CFLAGS) $(SRC) -c
+- gfortran -O2 $(OBJ) -o plink -Wl,-Bstatic $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB)
++ gfortran -O2 $(OBJ) -o plink -Wl,-Bstatic $(BLASFLAGS) $(LINKFLAGS) $(ZLIB)
diff --git a/debian/patches/01_Fix_use_internal_lib.patch b/debian/patches/01_Fix_use_internal_lib.patch
deleted file mode 100644
index 1076234..0000000
--- a/debian/patches/01_Fix_use_internal_lib.patch
+++ /dev/null
@@ -1,63 +0,0 @@
-Author: Dylan Aïssi <bob.dybian at gmail.com>
-Description: Fix the use of Debian internal libraries.
-Last-Update: 2015-01-23
-Forwarded: No
-
---- plink1.9.orig/Makefile
-+++ plink1.9/Makefile
-@@ -20,9 +20,9 @@
- endif
-
- CFLAGS=-Wall -O2
--BLASFLAGS=-L/usr/lib64/atlas -llapack -lcblas -latlas
--LINKFLAGS=-lm -lpthread -ldl
--ZLIB=zlib-1.2.8/libz.so.1.2.8
-+BLASFLAGS=-llapack -lcblas -latlas
-+LINKFLAGS=-lm -lpthread -ldl -lz
-+#ZLIB=zlib-1.2.8/libz.so.1.2.8
-
- ifeq ($(SYS), MAC)
- GCC_GTEQ_43 := $(shell expr `g++ -dumpversion | sed -e 's/\.\([0-9][0-9]\)/\1/g' -e 's/\.\([0-9]\)/0\1/g' -e 's/^[0-9]\{3,4\}$$/&00/'` \>= 40300)
-@@ -57,8 +57,9 @@
- # lead to minor problems when PLINK 2.0 is released.)
-
- plink: $(SRC)
-- g++ $(CFLAGS) $(SRC) -o plink $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB)
-+ g++ $(CFLAGS) $(SRC) -o plink $(BLASFLAGS) $(LINKFLAGS)
-
- plinkw: $(SRC)
- g++ $(CFLAGS) $(SRC) -c
-- gfortran -O2 $(OBJ) -o plink -Wl,-Bstatic $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB)
-+ gfortran -O2 $(OBJ) -o plink -Wl,-Bstatic $(BLASFLAGS) $(LINKFLAGS)
-+
---- plink1.9.orig/pigz.c
-+++ plink1.9/pigz.c
-@@ -297,7 +297,7 @@
- #include <stdio.h>
- #include <stdlib.h>
- #include <windows.h>
--#include "zlib-1.2.8/zlib.h"
-+#include <zlib.h>
-
- #include "pigz.h"
-
-@@ -519,7 +519,7 @@
- # include <sys/pstat.h>
- #endif
-
--#include "zlib-1.2.8/zlib.h" /* deflateInit2(), deflateReset(), deflate(), */
-+#include <zlib.h> /* deflateInit2(), deflateReset(), deflate(), */
- /* deflateEnd(), deflateSetDictionary(), crc32(),
- inflateBackInit(), inflateBack(), inflateBackEnd(),
- Z_DEFAULT_COMPRESSION, Z_DEFAULT_STRATEGY,
---- plink1.9.orig/plink_common.h
-+++ plink1.9/plink_common.h
-@@ -191,7 +191,7 @@
- #define VEC_BITS (VEC_BYTES * 8)
- #define VEC_BITS_M1 (VEC_BITS - 1)
-
--#include "zlib-1.2.8/zlib.h"
-+#include <zlib.h>
- #include "SFMT.h"
-
- // 64MB of non-workspace memory guaranteed for now.
diff --git a/debian/patches/02_Activate_Stable_Build.patch b/debian/patches/02_Activate_Stable_Build.patch
index 8998d0c..047a807 100644
--- a/debian/patches/02_Activate_Stable_Build.patch
+++ b/debian/patches/02_Activate_Stable_Build.patch
@@ -3,8 +3,8 @@ Description: Activate stable build.
Last-Update: 2015-01-23
Forwarded: No
---- plink1.9.orig/plink_common.h
-+++ plink1.9/plink_common.h
+--- a/plink_common.h
++++ b/plink_common.h
@@ -18,7 +18,7 @@
// Uncomment this to prevent all unstable features from being accessible from
@@ -12,5 +12,5 @@ Forwarded: No
-// #define STABLE_BUILD
+#define STABLE_BUILD
- #define PROG_NAME_STR "plink"
- #define PROG_NAME_CAPS "PLINK"
+ #define SPECIES_HUMAN 0
+ #define SPECIES_COW 1
diff --git a/debian/patches/series b/debian/patches/series
index c1895f8..e25033f 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,2 @@
-01_Fix_use_internal_lib.patch
+01_Fix_use_dynamic_linking.patch
02_Activate_Stable_Build.patch
--
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