[med-svn] [Git][med-team/chip-seq][master] 2 commits: Only one patch for Makefile, propagate hardening flags, add autopkgtest

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / chip-seq


Commits:
f79f7d43 by Andreas Tille at 2020-03-24T21:21:02+01:00
Only one patch for Makefile, propagate hardening flags, add autopkgtest

- - - - -
c47742f8 by Andreas Tille at 2020-03-24T21:31:55+01:00
Add lintian override

- - - - -


8 changed files:

- + debian/examples
- + debian/lintian-overrides
- − debian/patches/fix_install.patch
- debian/patches/fix_linker.patch → debian/patches/fix_makefile.patch
- debian/patches/series
- + debian/tests/H3K4me3.sga
- + debian/tests/control
- + debian/tests/run-unit-test


Changes:

=====================================
debian/examples
=====================================
@@ -0,0 +1 @@
+debian/tests/*.sga


=====================================
debian/lintian-overrides
=====================================
@@ -0,0 +1,2 @@
+# see https://lists.debian.org/debian-med/2018/06/msg00043.html
+chip-seq: script-with-language-extension usr/bin/*.*


=====================================
debian/patches/fix_install.patch deleted
=====================================
@@ -1,15 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Mon, 23 Mar 2020 20:55:38 +0100
-Description: Fix install dir
-
---- a/Makefile
-+++ b/Makefile
-@@ -10,7 +10,7 @@ LDFLAGS += -O3 -std=gnu99 -fPIC -lm
- #binDir = $(PWD)/bin
- #manDir = /usr/share/man/man1/
- ifeq ($(prefix),)
--    prefix := $(DESTDIR).
-+    prefix := $(DESTDIR)
- endif
- binDir = $(prefix)/bin
- datDir = $(prefix)/share/chip-seq


=====================================
debian/patches/fix_linker.patch → debian/patches/fix_makefile.patch
=====================================
@@ -4,15 +4,25 @@ Description: Fix linker flags
 
 --- a/Makefile
 +++ b/Makefile
-@@ -3,7 +3,7 @@
+@@ -2,15 +2,15 @@
+ # Makefile for ChIP-Seq package
  #
  CC = gcc
- CFLAGS = -O3 -std=gnu99 -W -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
+-CFLAGS = -O3 -std=gnu99 -W -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
 -LDFLAGS = -O3 -std=gnu99 -fPIC -lm
++CFLAGS += -O3 -std=gnu99 -W -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
 +LDFLAGS += -O3 -std=gnu99 -fPIC -lm
  #CFLAGS = -O3 -std=gnu99 -W -pedantic
  #LDFLAGS = -O3 -std=gnu99 -fPIC -lm
  
+ #binDir = $(PWD)/bin
+ #manDir = /usr/share/man/man1/
+ ifeq ($(prefix),)
+-    prefix := $(DESTDIR).
++    prefix := $(DESTDIR)
+ endif
+ binDir = $(prefix)/bin
+ datDir = $(prefix)/share/chip-seq
 @@ -77,16 +77,16 @@ tools/filter_counts : $(FILTER_COUNTS_SR
  	$(CC) $(CFLAGS) -o tools/filter_counts $^
  


=====================================
debian/patches/series
=====================================
@@ -1,2 +1,2 @@
-fix_linker.patch
-fix_install.patch
+fix_makefile.patch
+# fix_install.patch


=====================================
debian/tests/H3K4me3.sga
=====================================
@@ -0,0 +1,11 @@
+NC_000001.9     H3K4me3 4794    +       1
+NC_000001.9     H3K4me3 6090    +       1
+NC_000001.9     H3K4me3 6099    +       1
+NC_000001.9     H3K4me3 6655    +       1
+NC_000001.9     H3K4me3 18453   -       1
+NC_000001.9     H3K4me3 19285   +       1
+NC_000001.9     H3K4me3 44529   +       1
+NC_000001.9     H3K4me3 46333   +       1
+NC_000001.9     H3K4me3 46349   -       1
+NC_000001.9     H3K4me3 52929   +       1
+NC_000001.9     H3K4me3 59412   +       1


=====================================
debian/tests/control
=====================================
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr


=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,19 @@
+#!/bin/bash
+set -e
+
+pkg=chip-seq
+
+export LC_ALL=C.UTF-8
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+  # Double quote below to expand the temporary directory variable now versus
+  # later is on purpose.
+  # shellcheck disable=SC2064
+  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+
+chipcor -A "H3K4me3 +" -B "H3K4me3 -" -b -1000 -e 1000 -w 1 -c 20 -n 1 H3K4me3.sga > H3K4me3_fc_n1.out



View it on GitLab: https://salsa.debian.org/med-team/chip-seq/-/compare/5934d18d1ef0c9298cc9e9d77caccbab0b9d9e2e...c47742f849c78495d01ec03c150af34aa100219a

-- 
View it on GitLab: https://salsa.debian.org/med-team/chip-seq/-/compare/5934d18d1ef0c9298cc9e9d77caccbab0b9d9e2e...c47742f849c78495d01ec03c150af34aa100219a
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