[med-svn] [Git][med-team/mecat2][master] 2 commits: Update patches - no longer need DEXTRACTOR

Shayan Doust gitlab at salsa.debian.org
Mon Jun 29 20:50:55 BST 2020 


Shayan Doust pushed to branch master at Debian Med / mecat2


Commits:
24891165 by Shayan Doust at 2020-06-29T20:50:11+01:00
Update patches - no longer need DEXTRACTOR

- - - - -
5c72ccdb by Shayan Doust at 2020-06-29T20:50:30+01:00
Remove DEXTRACTOR/

- - - - -


4 changed files:

- debian/control
- debian/copyright
- debian/patches/use_system_packaged_libs.patch → debian/patches/modify_makefiles.patch
- debian/patches/series


Changes:

=====================================
debian/control
=====================================
@@ -4,7 +4,6 @@ Uploaders: Shayan Doust <hello at shayandoust.me>
 Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 13),
-               libhdf5-dev,
                zlib1g-dev
 Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/med-team/mecat2


=====================================
debian/copyright
=====================================
@@ -1,10 +1,12 @@
 Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: mecat2
 Source: https://github.com/xiaochuanle/MECAT2
-Files-Excluded: third_party/hdf5-1.10.4.tar.gz 
+Files-Excluded: third_party/hdf5-1.10.4.tar.gz
+                DEXTRACTOR/*
 Comment:
  The hdf5-1.10.4.tar.gz file in third_party/ was removed as this 
- already exists within the debian repository pre-packaged
+ already exists within the debian repository pre-packaged. DEXTRACTOR 
+ is packaged separately.
 
 Files: *
 Copyright: 20xx-20yy <upstream>


=====================================
debian/patches/use_system_packaged_libs.patch → debian/patches/modify_makefiles.patch
=====================================
@@ -1,20 +1,12 @@
-Description: use libraries that are already pre-packaged in Debian
- Modify the Makefiles so that we instead use libraries that are already within Debian as a package, and not one in some third_party/ directory to build (removed).
+Description: remove the need for using DEXTRACTOR
+ This is packaged separately.
 Author: Shayan Doust <hello at shayandoust.me> 
 Last-Update: 2020-06-29
 ---
 
 --- mecat2.orig/Makefile
 +++ mecat2/Makefile
-@@ -1,6 +1,7 @@
- PWD := $(shell pwd)
- OS_TYPE		:= $(shell echo `uname`)
- MACHINE_TYPE	:= $(shell echo `uname -m`)
-+MACHINE_TYPE_2 := $(shell echo `uname -m`)
- ifeq (${MACHINE_TYPE}, x86_64)
- 	MACHINE_TYPE = amd64
- endif
-@@ -8,13 +9,6 @@
+@@ -8,47 +8,13 @@
  
  BUILD_TOP_DIR := ${PWD}/${OS_TYPE}-${MACHINE_TYPE}
  
@@ -24,26 +16,33 @@ Last-Update: 2020-06-29
 -HDF5_INCLUDE = ${HDF5_INSTALL}/include
 -HDF5_LIB = ${HDF5_INSTALL}/lib/libhdf5.a
 -HDF5_TAR_GZ = ${BUILD_TOP_DIR}/hdf5-$(HDF5_VERSION).tar.gz
++.PHONY: all clean mecat
+ 
+-DEXTRACTOR_BIN_NAME = dexqv dexta dextract undexqv undexta
+-DEXTRACTOR_BIN = $(patsubst %, ${BUILD_DIR}/%, $(DEXTRACTOR_BIN_NAME))
+-
+-.PHONY: all clean mecat dextractor
 -
- DEXTRACTOR_BIN_NAME = dexqv dexta dextract undexqv undexta
- DEXTRACTOR_BIN = $(patsubst %, ${BUILD_DIR}/%, $(DEXTRACTOR_BIN_NAME))
+-all: mecat dextractor
++all: mecat
+ 
+ mecat:
+ 	cd src && make
  
-@@ -28,8 +22,6 @@
  clean:
  	cd src && make clean
- 	cd DEXTRACTOR && make -f ../dextract_makefile clean
+-	cd DEXTRACTOR && make -f ../dextract_makefile clean
 -	rm ${HDF5_INSTALL} -rf
 -	rm ${HDF5_SOURCE} -rf
- 	rm ${DEXTRACTOR_BIN} -f
- 
- dextractor: ${BUILD_TOP_DIR}/bin/dexqv ${BUILD_TOP_DIR}/bin/dexta ${BUILD_TOP_DIR}/bin/dextract ${BUILD_TOP_DIR}/bin/undexqv ${BUILD_TOP_DIR}/bin/undexta
-@@ -37,18 +29,5 @@
- 
- ${DEXTRACTOR_BIN}: ${HDF5_LIB}
- 	mkdir -p ${BUILD_DIR}		
+-	rm ${DEXTRACTOR_BIN} -f
+-
+-dextractor: ${BUILD_TOP_DIR}/bin/dexqv ${BUILD_TOP_DIR}/bin/dexta ${BUILD_TOP_DIR}/bin/dextract ${BUILD_TOP_DIR}/bin/undexqv ${BUILD_TOP_DIR}/bin/undexta
+-
+-
+-${DEXTRACTOR_BIN}: ${HDF5_LIB}
+-	mkdir -p ${BUILD_DIR}		
 -	cd DEXTRACTOR && make -f ../dextract_makefile HDF5_INCLUDE=${HDF5_INCLUDE} HDF5_LIB=${HDF5_LIB} 
-+	cd DEXTRACTOR && make -f ../dextract_makefile HDF5_INCLUDE=/usr/include/hdf5/serial/ HDF5_LIB=/usr/lib/${MACHINE_TYPE_2}-linux-gnu/hdf5/serial/ 
- 	cd DEXTRACTOR && cp ${DEXTRACTOR_BIN_NAME} ${BUILD_DIR}
+-	cd DEXTRACTOR && cp ${DEXTRACTOR_BIN_NAME} ${BUILD_DIR}
 -
 -${HDF5_LIB}: ${HDF5_TAR_GZ}
 -	tar -xzf ${BUILD_TOP_DIR}/hdf5-$(HDF5_VERSION).tar.gz -C ${BUILD_TOP_DIR} || exit 255
@@ -56,17 +55,35 @@ Last-Update: 2020-06-29
 -	version_major_minor=`echo "$(HDF5_VERSION)" | sed -E 's/\.[0-9]+$$//'`; \
 -	cp third_party/hdf5-1.10.4.tar.gz ${BUILD_TOP_DIR}/
 -	
--
+ 
 --- mecat2.orig/dextract_makefile
 +++ mecat2/dextract_makefile
-@@ -6,8 +6,8 @@
- all: dextract dexta undexta dexqv undexqv
- 
- dextract:
+@@ -1,28 +1 @@
+-CFLAG = -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing
+-CC = gcc
+-
+-HDF5_LIB ?= .libhdf5.a
+-
+-all: dextract dexta undexta dexqv undexqv
+-
+-dextract:
 -	#${CC} $(CFLAGS) -I$(HDF5_INCLUDE) -L$(HDF5_LIB) -o dextract dextract.c DB.c QV.c expr.c bax.c sam.c -lhdf5 -lz
 -	${CC} $(CFLAGS) -I$(HDF5_INCLUDE) -o dextract dextract.c DB.c QV.c expr.c bax.c sam.c ${HDF5_LIB} -lpthread  -lz -ldl -lm
-+	${CC} $(CFLAGS) -I$(HDF5_INCLUDE) -L$(HDF5_LIB) -o dextract dextract.c DB.c QV.c expr.c bax.c sam.c -lhdf5 -lz -lpthread -lm -ldl
-+	#${CC} $(CFLAGS) -I$(HDF5_INCLUDE) -o dextract dextract.c DB.c QV.c expr.c bax.c sam.c ${HDF5_LIB} -lpthread  -lz -ldl -lm
+-
+-dexta:
+-	${CC} ${CFLAGS} -o dexta dexta.c DB.c QV.c
+-
+-undexta:
+-	${CC} ${CFLAGS} -o undexta undexta.c DB.c QV.c
+-
+-dexqv:
+-	${CC} ${CFLAGS} -o dexqv dexqv.c DB.c QV.c
+-
+-undexqv:
+-	${CC} ${CFLAGS} -o undexqv undexqv.c DB.c QV.c
+-
+-.PHONY: clean
+-clean:
+-	rm -f dextract dexta undexta dexqv undexqv
+-
  
- dexta:
- 	${CC} ${CFLAGS} -o dexta dexta.c DB.c QV.c


=====================================
debian/patches/series
=====================================
@@ -1 +1 @@
-use_system_packaged_libs.patch
+modify_makefiles.patch



View it on GitLab: https://salsa.debian.org/med-team/mecat2/-/compare/8f0dfd5186810bf3d85ee5cccd4cd0a58f92415e...5c72ccdbaed16d950198394a762d03d6adf1e125

-- 
View it on GitLab: https://salsa.debian.org/med-team/mecat2/-/compare/8f0dfd5186810bf3d85ee5cccd4cd0a58f92415e...5c72ccdbaed16d950198394a762d03d6adf1e125
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20200629/f4a6e255/attachment-0001.html>

More information about the debian-med-commit mailing list