[med-svn] [plink1.9] 03/08: Update patch to fix makefile

[Dylan Aïssi]

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bob.dybian-guest pushed a commit to branch master
in repository plink1.9.

commit 45b96a6ebc9c59a06bbb20256f4db8176a30ed93
Author: Dylan Aïssi <bob.dybian at gmail.com>
Date:   Tue Sep 12 15:32:48 2017 +0200

    Update patch to fix makefile
---
 debian/changelog                     |  1 +
 debian/patches/01.Fix_Makefile.patch | 58 ++++++++++--------------------------
 debian/rules                         |  9 ++++--
 3 files changed, 23 insertions(+), 45 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 8d2ea59..f3031aa 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -2,6 +2,7 @@ plink1.9 (1.90~b4.7-170906-1) UNRELEASED; urgency=medium
 
   * New upstream release.
   * Add references to registries.
+  * Update 01.Fix_Makefile.patch.
 
  -- Dylan Aïssi <bob.dybian at gmail.com>  Wed, 19 Jul 2017 23:50:02 +0200
 
diff --git a/debian/patches/01.Fix_Makefile.patch b/debian/patches/01.Fix_Makefile.patch
index 317289c..6e7b9b8 100644
--- a/debian/patches/01.Fix_Makefile.patch
+++ b/debian/patches/01.Fix_Makefile.patch
@@ -1,45 +1,19 @@
 Author: Dylan Aïssi <bob.dybian at gmail.com>
-Description: Take into account the user-provided compiler flags.
-Last-Update: 2017-04-17
+Description: Take into account the user-provided CPPFLAGS compiler flags.
+Last-Update: 2017-09-12
 Forwarded: TODO
 
---- a/Makefile
-+++ b/Makefile
-@@ -5,11 +5,11 @@
- 
- # Leave blank after "=" to disable; put "= 1" to enable
- # (when enabled, "#define NOLAPACK" must be uncommented in plink_common.h)
--NO_LAPACK =
-+NO_LAPACK +=
- 
- # Variable that allows additional linker flags (e.g., "-L/path/to/libs") to be
- # passed into the linker; to use this, invoke 'make LINKFLAGS_EXTRA="<opts>"'.
--LINKFLAGS_EXTRA =
-+LINKFLAGS_EXTRA +=
- 
- .PHONY: clean
- 
-@@ -24,10 +24,10 @@
-   endif
- endif
- 
--CFLAGS=-Wall -O2
--BLASFLAGS=-L/usr/lib64/atlas -llapack -lcblas -latlas
--LINKFLAGS=-lm -lpthread -ldl
--ZLIB=../zlib-1.2.11/libz.so.1.2.11
-+CFLAGS+=-Wall -O2
-+BLASFLAGS+=-L/usr/lib64/atlas -llapack -lcblas -latlas
-+LINKFLAGS+=-lm -lpthread -ldl
-+ZLIB?=../zlib-1.2.11/libz.so.1.2.11
- 
- 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)
-@@ -51,7 +51,7 @@
- endif
- 
- ifdef NO_LAPACK
--  BLASFLAGS=
-+  BLASFLAGS+=
- endif
- 
- OBJS = plink.o plink_assoc.o plink_calc.o plink_cluster.o plink_cnv.o plink_common.o plink_data.o plink_dosage.o plink_family.o plink_filter.o plink_glm.o plink_help.o plink_homozyg.o plink_lasso.o plink_ld.o plink_matrix.o plink_misc.o plink_perm.o plink_rserve.o plink_set.o plink_stats.o SFMT.o dcdflib.o pigz.o yarn.o Rconnection.o hfile.o bgzf.o
+Index: plink1.9/Makefile
+===================================================================
+--- plink1.9.orig/Makefile
++++ plink1.9/Makefile
+@@ -96,7 +96,7 @@ clean:
+ # includes a C++ header and exposed functions will need to be declared with
+ # extern "C".
+ %.o: %.c
+-	$(CXX) -c $(CFLAGS) $< -o $@
++	$(CXX) -c $(CPPFLAGS) $(CFLAGS) $< -o $@
+ 
+ %.o: %.cc
+-	$(CXX) -x c++ -c $(CXXFLAGS) $< -o $@
++	$(CXX) -x c++ -c $(CPPFLAGS) $(CXXFLAGS) $< -o $@
diff --git a/debian/rules b/debian/rules
index 8948962..7e1ddf5 100755
--- a/debian/rules
+++ b/debian/rules
@@ -1,9 +1,10 @@
 #!/usr/bin/make -f
 
+export ZLIB = -lz
+export LDFLAGS = -lm -lpthread -ldl `dpkg-buildflags --get LDFLAGS`
+
 export DEB_BUILD_MAINT_OPTIONS = hardening=+all
-export DEB_CFLAGS_MAINT_APPEND = -DSTABLE_BUILD -DDYNAMIC_ZLIB `dpkg-buildflags --get CXXFLAGS` `dpkg-buildflags --get CPPFLAGS`
-export LINKFLAGS_EXTRA += `dpkg-buildflags --get LDFLAGS`
-export ZLIB += -lz
+export DEB_CPPFLAGS_MAINT_APPEND = -DSTABLE_BUILD -DDYNAMIC_ZLIB
 
 %:
 	dh $@
@@ -18,6 +19,8 @@ override_dh_auto_build:
 	mv plink plink1.9
 	help2man --no-discard-stderr --name="whole genome SNP analysis" ./plink1.9 > plink1.9.1
 
+override_dh_auto_install:
+
 override_dh_installman:
 	dh_installman plink1.9.1
 

-- 
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