[med-svn] [Git][med-team/emmax][master] 4 commits: DEP3

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / emmax


Commits:
f31edd57 by Andreas Tille at 2019-03-20T20:36:59Z
DEP3

- - - - -
da7cdba6 by Andreas Tille at 2019-03-20T20:37:12Z
spelling

- - - - -
57adf98f by Andreas Tille at 2019-03-20T20:49:53Z
Try to force hardening but no success to get rid of the lintian issue

- - - - -
deb4abd0 by Andreas Tille at 2019-03-20T20:51:07Z
Upload to new

- - - - -


10 changed files:

- debian/changelog
- debian/control
- debian/patches/aborts.patch
- debian/patches/clean.patch
- debian/patches/dynamic.patch
- + debian/patches/hardening.patch
- debian/patches/install.patch
- debian/patches/logfile.patch
- debian/patches/paths.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,5 +1,5 @@
-emmax (0~beta.20100307-1) UNRELEASED; urgency=low
+emmax (0~beta.20100307-1) unstable; urgency=low
 
-  * Initial release pending, not uploaded because of unknown license.
+  * Initial release (Closes: #925158)
 
- -- Andreas Tille <tille at debian.org>  Wed, 20 Mar 2019 13:55:07 +0100
+ -- Andreas Tille <tille at debian.org>  Wed, 20 Mar 2019 18:28:20 +0100


=====================================
debian/control
=====================================
@@ -25,6 +25,6 @@ Description: genetic mapping considering population structure
  association mapping accounting for the sample structure. In addition
  to the computational efficiency obtained by EMMA algorithm, EMMAX takes
  advantage of the fact that each locus explains only a small fraction of
- complex traits, which allows to avoid repetitive variance component
+ complex traits, which allows one to avoid repetitive variance component
  estimation procedure, resulting in a significant amount of increase in
  computational time of association mapping using mixed model.


=====================================
debian/patches/aborts.patch
=====================================
@@ -1,3 +1,7 @@
+Author: Steffen Moeller
+Last-Update: 2013-06-11 09:09:19 +0000
+Description: Clean exit when no options are given
+
 Index: emmax-0~beta.20100307/emmax-kin.c
 ===================================================================
 --- emmax-0~beta.20100307.orig/emmax-kin.c


=====================================
debian/patches/clean.patch
=====================================
@@ -1,3 +1,7 @@
+Author: Steffen Moeller
+Last-Update: 2013-06-11 09:09:19 +0000
+Description: Proper cleaning
+
 Index: emmax-0~beta.20100307/makefile
 ===================================================================
 --- emmax-0~beta.20100307.orig/makefile


=====================================
debian/patches/dynamic.patch
=====================================
@@ -1,3 +1,7 @@
+Author: Steffen Moeller
+Last-Update: 2013-06-11 09:09:19 +0000
+Description: Dynamic linking
+
 Index: emmax-0~beta.20100307/makefile
 ===================================================================
 --- emmax-0~beta.20100307.orig/makefile


=====================================
debian/patches/hardening.patch
=====================================
@@ -0,0 +1,18 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 20 Mar 2019 18:28:20 +0100
+Description: Propagate hardening options (unfortunately this does not help)
+
+--- a/makefile
++++ b/makefile
+@@ -5,9 +5,9 @@ PREFIX=/usr
+ INCFLAGS = 
+ LIBFLAGS = -Wall
+ 
+-COMPFLAGS = ${INCFLAGS} -O2 -Wall -g
++COMPFLAGS = ${INCFLAGS} -O2 -Wall -g $(CFLAGS)
+ CC = gcc
+-CLIBS = -L/usr/lib/atlas-base -L/usr/lib/lapack/ -llapack_atlas -llapack -lcblas -lblas -latlas -lcblas -lm -lz
++CLIBS = -L/usr/lib/atlas-base -L/usr/lib/lapack/ -llapack_atlas -llapack -lcblas -lblas -latlas -lcblas -lm -lz $(LDFLAGS)
+ 
+ all: emmax emmax-kin
+ 


=====================================
debian/patches/install.patch
=====================================
@@ -1,3 +1,7 @@
+Author: Steffen Moeller
+Last-Update: 2013-06-11 09:09:19 +0000
+Description: Proper install target
+
 Index: emmax-0~beta.20100307/makefile
 ===================================================================
 --- emmax-0~beta.20100307.orig/makefile


=====================================
debian/patches/logfile.patch
=====================================
@@ -1,3 +1,7 @@
+Author: Steffen Moeller
+Last-Update: 2013-06-11 09:09:19 +0000
+Description: Log only if file pointer exists
+
 Index: emmax-0~beta.20100307/emmax.c
 ===================================================================
 --- emmax-0~beta.20100307.orig/emmax.c


=====================================
debian/patches/paths.patch
=====================================
@@ -1,3 +1,7 @@
+Author: Steffen Moeller
+Last-Update: 2013-06-11 09:09:19 +0000
+Description: Fix header path of clapack.h
+
 Index: emmax-0~beta.20100307/emmax.c
 ===================================================================
 --- emmax-0~beta.20100307.orig/emmax.c


=====================================
debian/patches/series
=====================================
@@ -5,3 +5,4 @@ install.patch
 clean.patch
 logfile.patch
 atlas.patch
+hardening.patch



View it on GitLab: https://salsa.debian.org/med-team/emmax/compare/8a7d9d4b55379f3db0ca6282262457148784cf77...deb4abd0220c1014a903f22930dbc21dc80bc35a

-- 
View it on GitLab: https://salsa.debian.org/med-team/emmax/compare/8a7d9d4b55379f3db0ca6282262457148784cf77...deb4abd0220c1014a903f22930dbc21dc80bc35a
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