[med-svn] [jellyfish] 07/07: new upstream version
Michael Crusoe
misterc-guest at moszumanska.debian.org
Sat Mar 12 22:17:31 UTC 2016
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository jellyfish.
commit fc62b5499235fa94fbd19508bae6288ca01be6bd
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date: Sat Mar 12 08:09:57 2016 -0800
new upstream version
---
debian/README.todo | 5 +++++
debian/changelog | 5 +++--
debian/control | 6 +++---
debian/jellyfish-examples.lintian-overrides | 1 +
debian/libjellyfish-2.0-dev.install | 1 +
debian/patches/series | 1 +
debian/patches/spelling | 13 ++++++++++++
debian/rules | 31 ++++++++++++++++-------------
8 files changed, 44 insertions(+), 19 deletions(-)
diff --git a/debian/README.todo b/debian/README.todo
new file mode 100644
index 0000000..be7b9fc
--- /dev/null
+++ b/debian/README.todo
@@ -0,0 +1,5 @@
+docs/ directory is out of date but regenerating it produces errors
+
+ruby bindings break policy using upstream's install
+
+turning on the hardening options breaks the build
diff --git a/debian/changelog b/debian/changelog
index 05447a0..8e062e5 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-jellyfish (2.2.4-3) UNRELEASED; urgency=medium
+jellyfish (2.2.5-1) UNRELEASED; urgency=medium
[ Andreas Tille ]
* Enable Python and Perl bindings
@@ -12,6 +12,7 @@ jellyfish (2.2.4-3) UNRELEASED; urgency=medium
* Add call to setup.py in dh_autobuild override
[ Michael R. Crusoe ]
+ * New upstream version, fixes dataloss bug
* Upgrade Standards-Version to 3.9.7
* Mark python3- package as arch specifc, not indep; include shared library
dependencies
@@ -23,7 +24,7 @@ jellyfish (2.2.4-3) UNRELEASED; urgency=medium
* debian/rules: enable parallel builds & improve clean target
* debian/control: add myself as an uploader
- -- Michael R. Crusoe <crusoe at ucdavis.edu> Sat, 12 Mar 2016 07:49:18 -0800
+ -- Michael R. Crusoe <crusoe at ucdavis.edu> Sat, 12 Mar 2016 08:09:07 -0800
jellyfish (2.2.4-2) unstable; urgency=medium
diff --git a/debian/control b/debian/control
index 34c63a6..8f55e6a 100644
--- a/debian/control
+++ b/debian/control
@@ -17,7 +17,8 @@ Build-Depends: debhelper (>= 9),
swig,
python3-all-dev,
dh-python,
- perl
+ perl,
+ chrpath
Standards-Version: 3.9.7
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/jellyfish.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/jellyfish.git
@@ -69,8 +70,7 @@ Description: count k-mers in DNA sequences (dynamic library of jellyfish)
Package: libjellyfish-2.0-dev
Architecture: any-amd64
Section: libdevel
-Depends: ${shlibs:Depends},
- ${misc:Depends},
+Depends: ${misc:Depends},
libjellyfish-2.0-2 (= ${binary:Version})
Description: count k-mers in DNA sequences (development files of jellyfish)
JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
diff --git a/debian/jellyfish-examples.lintian-overrides b/debian/jellyfish-examples.lintian-overrides
new file mode 100644
index 0000000..240c2c2
--- /dev/null
+++ b/debian/jellyfish-examples.lintian-overrides
@@ -0,0 +1 @@
+jellyfish-examples: spelling-error-in-binary usr/lib/jellyfish/bin/test_all Usefull Useful
diff --git a/debian/libjellyfish-2.0-dev.install b/debian/libjellyfish-2.0-dev.install
new file mode 100644
index 0000000..97b3dd7
--- /dev/null
+++ b/debian/libjellyfish-2.0-dev.install
@@ -0,0 +1 @@
+debian/tmp/usr/lib/*/pkgconfig/jellyfish-2.0.pc
diff --git a/debian/patches/series b/debian/patches/series
index 144a51e..ea66f94 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -2,3 +2,4 @@ pkg-config-with-name
enable_c++11_error_deprecated-declarations.patch
drop-rpath
modern-g++
+spelling
diff --git a/debian/patches/spelling b/debian/patches/spelling
new file mode 100644
index 0000000..db6a3b8
--- /dev/null
+++ b/debian/patches/spelling
@@ -0,0 +1,13 @@
+Description: Spelling fixes
+Author: Michael R. Crusoe <crusoe at ucdavis.edu>
+--- jellyfish.orig/doc/jellyfish.tex
++++ jellyfish/doc/jellyfish.tex
+@@ -140,7 +140,7 @@
+ Important: the size of the couting field does NOT change the result,
+ it only impacts the amount of memory used. In particular, there is no
+ maximum value in the hash. Even if the counting field uses 5 bits, a
+-$k$-mer occuring 2 million times will have a value reported of 2
++$k$-mer occurring 2 million times will have a value reported of 2
+ million (i.e., it is not capped at $2^5$).
+
+ The \Opt{-c} specify the length (in bits) of the counting field. The
diff --git a/debian/rules b/debian/rules
index 080edec..790ad39 100755
--- a/debian/rules
+++ b/debian/rules
@@ -3,6 +3,11 @@
DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
build3vers := $(shell py3versions -sv)
+#export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+#DPKG_EXPORT_BUILDFLAGS = 1
+#include /usr/share/dpkg/buildflags.mk
+#breaks the build
+
export DH_OPTIONS
export PKG_CONFIG_LIBDIR=${CURDIR}
export PKG_CONFIG_ALLOW_SYSTEM_LIBS=true
@@ -10,23 +15,20 @@ export PKG_CONFIG_SYSROOT_DIR=${CURDIR}/debian/tmp/
export PERL_MM_OPT=INSTALLDIRS=vendor
%:
- dh $@ --with autoreconf,python3 --parallel
+ dh $@ --with autoreconf,python3 #--parallel
+
+override_dh_auto_install:
+ dh_auto_install -- install-data
override_dh_install:
# dh_install -X*.a -X*.la -Xpkgconfig
dh_install -ppython3-jellyfish
- set -e && for i in $(build3vers); do \
- cd swig/python ; \
- python$$i ./setup.py install \
- --install-layout=deb --root ../../debian/python3-jellyfish; \
- cd ../.. ; \
- done
+ pybuild -d swig/python --name jellyfish
dh_auto_configure --sourcedirectory=swig/perl5
- cd swig/perl5 ; \
- $(MAKE) OPTIMIZE="-O2 -g -Wall" ; \
- $(MAKE) install DESTDIR=$(CURDIR)/debian/tmp
-
+ dh_auto_build --sourcedirectory=swig/perl5
+ dh_auto_install --sourcedirectory=swig/perl5
+ chrpath --delete debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so
dh_install
d-shlibmove --commit \
--multiarch \
@@ -35,9 +37,8 @@ override_dh_install:
--movedev "debian/tmp/usr/include/$(DEBPKGNAME)*/$(DEBPKGNAME)/*.h" usr/include/$(DEBPKGNAME) \
debian/tmp/usr/lib/*/lib$(DEBPKGNAME)-*.so
-#override_dh_auto_configure:
-# # the doc says you need --enable-python-binding but we call setup.py manually
-# dh_auto_configure -- --enable-swig --enable-python-binding --enable-perl-binding
+override_dh_auto_configure:
+ dh_auto_configure -- --enable-swig --enable-perl-binding
override_dh_auto_clean:
set -e && for i in $(build3vers); do \
@@ -60,6 +61,8 @@ override_dh_auto_build:
mkdir -p debian/tmp_save_tests
cp -a tests/* debian/tmp_save_tests
dh_auto_build -- all bin/generate_sequence bin/test_all
+# cd doc ; RUBYLIB=$PWD PATH=$PATH:../bin make clean all ; cd ..
+# broken
# jellyfish contains a *really* big test which should *not* run on autobuilders
# if you have a *really* large machine you can try to activate this test by
--
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