[med-svn] [Git][med-team/qtltools][master] 7 commits: debian/patches/Makefile_config.patch: refresh

Michael R. Crusoe gitlab at salsa.debian.org
Sat Oct 10 17:29:04 BST 2020 


Michael R. Crusoe pushed to branch master at Debian Med / qtltools


Commits:
374470be by Michael R. Crusoe at 2020-10-10T17:58:44+02:00
debian/patches/Makefile_config.patch: refresh

- - - - -
514b3e41 by Michael R. Crusoe at 2020-10-10T18:01:05+02:00
Fix uses-deprecated-adttmp debian/tests/run-sample-analysis

- - - - -
204dad20 by Michael R. Crusoe at 2020-10-10T18:04:06+02:00
debian/upstream/metadata: added Repository{,-Browse} and Bug-{Database,Submit}.

- - - - -
62c83e69 by Michael R. Crusoe at 2020-10-10T18:04:49+02:00
routine-update: Add salsa-ci file

- - - - -
53818d2b by Michael R. Crusoe at 2020-10-10T18:04:49+02:00
routine-update: Rules-Requires-Root: no

- - - - -
73079f62 by Michael R. Crusoe at 2020-10-10T18:22:36+02:00
script/ is now scripts/

- - - - -
b25e46a3 by Michael R. Crusoe at 2020-10-10T18:27:46+02:00
routine-update: Ready to upload to unstable

- - - - -


7 changed files:

- debian/changelog
- debian/control
- debian/patches/Makefile_config.patch
- debian/qtltools-example.install
- + debian/salsa-ci.yml
- debian/tests/run-sample-analysis
- debian/upstream/metadata


Changes:

=====================================
debian/changelog
=====================================
@@ -1,7 +1,8 @@
-qtltools (1.3.1+dfsg-1) UNRELEASED; urgency=medium
+qtltools (1.3.1+dfsg-1) unstable; urgency=medium
 
-  [ Andreas Tille ]
   * Team upload.
+
+  [ Andreas Tille ]
   * Make really sure examples.tar.xz will not contain itself
   * debhelper-compat 12
   * Remove obsolete fields Contact, Name from debian/upstream/metadata
@@ -12,7 +13,16 @@ qtltools (1.3.1+dfsg-1) UNRELEASED; urgency=medium
   * Standards-Version: 4.5.0 (routine-update)
   * debhelper-compat 13 (routine-update)
 
- -- Dylan Aïssi <daissi at debian.org>  Sun, 06 Sep 2020 14:03:36 +0200
+  [ Michael R. Crusoe ]
+  * debian/patches/Makefile_config.patch: refresh
+  * Fix uses-deprecated-adttmp debian/tests/run-sample-analysis
+  * debian/upstream/metadata: added Repository{,-Browse} and
+    Bug-{Database,Submit}.
+  * Add salsa-ci file (routine-update)
+  * Rules-Requires-Root: no (routine-update)
+  * script/ is now scripts/
+
+ -- Michael R. Crusoe <crusoe at debian.org>  Sat, 10 Oct 2020 18:04:50 +0200
 
 qtltools (1.2+dfsg-2) unstable; urgency=medium
 


=====================================
debian/control
=====================================
@@ -17,6 +17,7 @@ Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/med-team/qtltools
 Vcs-Git: https://salsa.debian.org/med-team/qtltools.git
 Homepage: https://qtltools.github.io/qtltools/
+Rules-Requires-Root: no
 
 Package: qtltools
 Architecture: any


=====================================
debian/patches/Makefile_config.patch
=====================================
@@ -3,24 +3,22 @@ Description: Configure the makefile for Debian packaging.
 Last-Update: 2019-09-30
 Forwarded: not-needed
 
---- a/Makefile
-+++ b/Makefile
-@@ -28,11 +28,7 @@
- VPATH=$(shell for file in `find src -name *.cpp`; do echo $$(dirname $$file); done)
+--- qtltools.orig/Makefile
++++ qtltools/Makefile
+@@ -117,9 +117,7 @@
+ endif
  
  #DEFAULT VERSION (SET UP THE VARIABLES IN THE BEGINING OF THE MAKEFILE)
 -all: CXXFLAG=$(CXXFLAG_REL) $(CXXFLAG_WRN)
--all: IFLAG=-Ilib/OTools -Ilib -I$(RMATH_INC) -I$(HTSLD_INC) -I$(BOOST_INC)
--all: LIB_FILES=$(RMATH_LIB)/libRmath.a $(HTSLD_LIB)/libhts.a $(BOOST_LIB)/libboost_iostreams.a $(BOOST_LIB)/libboost_program_options.a
 -all: LDFLAG=$(CXXFLAG_REL)
 -all: $(BFILE)
 +all: debian
  
- #DEFAULT DEBUG VERSION (SET UP THE VARIABLES IN THE BEGINING OF THE MAKEFILE)
- all-dbg: CXXFLAG=$(CXXFLAG_DBG) $(CXXFLAG_WRN)
-@@ -129,6 +125,14 @@
- mac-dbg: LDFLAG=$(CXXFLAG_DBG) -L /opt/local/lib
- mac-dbg: $(BFILE)
+ #DEBUG VERSION (SET UP THE VARIABLES IN THE BEGINING OF THE MAKEFILE)
+ debug: CXXFLAG=$(CXXFLAG_DBG) $(CXXFLAG_WRN)
+@@ -199,6 +197,14 @@
+ 	rmdir --ignore-fail-on-non-empty -p $(DESTDIR)$(man1dir)
+ 	rmdir --ignore-fail-on-non-empty -p $(DESTDIR)$(autocompdir)
  
 +#DEBIAN PACKAGE VERSION
 +debian: CXXFLAG=$(CXXFLAG_REL) $(CXXFLAG_WRN) $(CXXFLAGS) $(CPPFLAGS)
@@ -33,3 +31,10 @@ Forwarded: not-needed
  #COMPILATION RULES
  $(BFILE): $(OFILE)
  	$(CXX) $^ $(LIB_FILES) -o $@ $(LIB_FLAGS) $(LDFLAG)
+@@ -308,4 +314,4 @@
+ clean-gwas:
+ 	rm -f obj/gwas_*.o $(BFILE)
+ 		
+-		
+\ No newline at end of file
++		


=====================================
debian/qtltools-example.install
=====================================
@@ -1,3 +1,3 @@
 debian/tests/run-sample-analysis /usr/share/doc/qtltools/examples/
 debian/upstream.example/examples.tar.xz /usr/share/doc/qtltools/examples/
-script/* /usr/share/doc/qtltools/examples/
+scripts/* /usr/share/doc/qtltools/examples/


=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml


=====================================
debian/tests/run-sample-analysis
=====================================
@@ -5,13 +5,13 @@
 # Last-Update: 2016-11-16
 
 pkg=qtltools
-if [ "$ADTTMP" = "" ] ; then
-  ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+  AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
 fi
-cd $ADTTMP
-cp -a /usr/share/doc/${pkg}/examples/* $ADTTMP
+cd $AUTOPKGTEST_TMP
+cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP
 
-tar Jxvf $ADTTMP/examples.tar.xz
+tar Jxvf $AUTOPKGTEST_TMP/examples.tar.xz
 
 # Mode PCA
 QTLtools pca \
@@ -54,4 +54,4 @@ QTLtools trans \
 	 --normal \
 	 --out trans.sample
 
-rm -f $ADTTMP/*
+rm -f $AUTOPKGTEST_TMP/*


=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,7 @@
+Repository-Browse: https://github.com/qtltools/qtltools
+Repository: https://github.com/qtltools/qtltools.git
+Bug-Database: https://github.com/qtltools/qtltools/issues
+Bug-Submit: https://github.com/qtltools/qtltools/issues/new
 Reference:
 - Author: >
     Olivier Delaneau and Halit Ongen and Andrew A. Brown and Alexandre



View it on GitLab: https://salsa.debian.org/med-team/qtltools/-/compare/67bb0ca999188342ed5f44c2a2ec6cf7c6d8fa07...b25e46a3d429aaa46f3e55ed1807c159e09fbe0d

-- 
View it on GitLab: https://salsa.debian.org/med-team/qtltools/-/compare/67bb0ca999188342ed5f44c2a2ec6cf7c6d8fa07...b25e46a3d429aaa46f3e55ed1807c159e09fbe0d
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