[med-svn] [cufflinks] 01/01: Revert the attempt to use the debian packaged liblemon
Andreas Tille
tille at debian.org
Tue Aug 16 11:39:13 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository cufflinks.
commit 94ac8af73745f128476e8445d1336e03a4dd8c94
Author: Andreas Tille <tille at debian.org>
Date: Tue Aug 16 13:38:27 2016 +0200
Revert the attempt to use the debian packaged liblemon
---
debian/changelog | 4 +-
debian/control | 3 +-
debian/copyright | 6 --
debian/patches/0003-fix_includes_path.patch | 37 +++++---
debian/patches/series | 1 -
debian/patches/use_debian_packaged_liblemon.patch | 100 ----------------------
debian/watch | 3 +-
7 files changed, 27 insertions(+), 127 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index f960b20..bd112b9 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,9 +1,7 @@
-cufflinks (2.2.1+dfsg-1) UNRELEASED; urgency=medium
+cufflinks (2.2.1-3) UNRELEASED; urgency=medium
* Use unversioned libboost. (Thanks for the hint to Gianfranco Costamagna)
TODO: Fix build with gcc-6
- Gianfranco Costamagna suggested to build against Debian packaged
- liblemon-dev - but this attempt failed. (see bug #833493)
-- Andreas Tille <tille at debian.org> Fri, 05 Aug 2016 08:56:59 +0200
diff --git a/debian/control b/debian/control
index 896d86b..6bf4e21 100644
--- a/debian/control
+++ b/debian/control
@@ -17,8 +17,7 @@ Build-Depends: debhelper (>= 9),
zlib1g-dev,
dh-autoreconf,
python,
- libeigen3-dev,
- liblemon-dev
+ libeigen3-dev
Standards-Version: 3.9.8
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/cufflinks.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/cufflinks.git
diff --git a/debian/copyright b/debian/copyright
index 75bd967..f5c98b3 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -22,12 +22,6 @@ Disclamer: This package is not part of the Debian operating system.
autobuilders to create binary packages.
.
The non-free component of Cufflinks is ‘locfit’ (see below).
-Files-Excluded: */src/lemon
- */build-aux
- */Makefile.in
- */aclocal.m4
- */config.h.in
- */configure
Files: *
Copyright: Copyright (C) 2003-2010 Cole Trapnell et al
diff --git a/debian/patches/0003-fix_includes_path.patch b/debian/patches/0003-fix_includes_path.patch
index 4451ef0..c6aa5f9 100644
--- a/debian/patches/0003-fix_includes_path.patch
+++ b/debian/patches/0003-fix_includes_path.patch
@@ -6,8 +6,8 @@ Subject: fix_includes_path.patch
src/hits.h | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
---- a/src/hits.h
-+++ b/src/hits.h
+--- cufflinks.orig/src/hits.h
++++ cufflinks/src/hits.h
@@ -18,7 +18,7 @@
#include <boost/shared_ptr.hpp>
@@ -17,9 +17,9 @@ Subject: fix_includes_path.patch
#include "common.h"
#include "multireads.h"
---- a/ax_check_eigen.m4
-+++ b/ax_check_eigen.m4
-@@ -66,7 +66,7 @@ export EIGEN_CPPFLAGS
+--- cufflinks.orig/ax_check_eigen.m4
++++ cufflinks/ax_check_eigen.m4
+@@ -66,7 +66,7 @@
AC_LANG_PUSH(C++)
AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
@@ -28,8 +28,19 @@ Subject: fix_includes_path.patch
]], [[
]])],[
AC_MSG_RESULT(yes)
---- a/src/abundances.cpp
-+++ b/src/abundances.cpp
+--- cufflinks.orig/configure
++++ cufflinks/configure
+@@ -6723,7 +6723,7 @@
+ cat >>conftest.$ac_ext <<_ACEOF
+ /* end confdefs.h. */
+
+-#include <Eigen/Dense>
++#include <eigen3/Eigen/Dense>
+
+ int
+ main ()
+--- cufflinks.orig/src/abundances.cpp
++++ cufflinks/src/abundances.cpp
@@ -50,7 +50,7 @@
#include "negative_binomial_distribution.h"
@@ -39,8 +50,8 @@ Subject: fix_includes_path.patch
//using Eigen::MatrixXd;
//#ifdef __USE_ISOC99
---- a/src/abundances.h
-+++ b/src/abundances.h
+--- cufflinks.orig/src/abundances.h
++++ cufflinks/src/abundances.h
@@ -18,7 +18,7 @@
#include <boost/numeric/ublas/matrix.hpp>
#include <boost/numeric/ublas/vector.hpp>
@@ -50,8 +61,8 @@ Subject: fix_includes_path.patch
#include "hits.h"
#include "scaffolds.h"
---- a/src/jensen_shannon.h
-+++ b/src/jensen_shannon.h
+--- cufflinks.orig/src/jensen_shannon.h
++++ cufflinks/src/jensen_shannon.h
@@ -14,7 +14,7 @@
#include <boost/numeric/ublas/io.hpp>
@@ -61,8 +72,8 @@ Subject: fix_includes_path.patch
namespace ublas = boost::numeric::ublas;
---- a/src/sampling.h
-+++ b/src/sampling.h
+--- cufflinks.orig/src/sampling.h
++++ cufflinks/src/sampling.h
@@ -35,7 +35,7 @@
#include <boost/random/variate_generator.hpp>
#include <boost/math/constants/constants.hpp>
diff --git a/debian/patches/series b/debian/patches/series
index 8a05716..7f0e077 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -5,4 +5,3 @@ gffread_show_usage.patch
0003-fix_includes_path.patch
format-security.patch
lib_eigen.patch
-use_debian_packaged_liblemon.patch
diff --git a/debian/patches/use_debian_packaged_liblemon.patch b/debian/patches/use_debian_packaged_liblemon.patch
deleted file mode 100644
index 7f23927..0000000
--- a/debian/patches/use_debian_packaged_liblemon.patch
+++ /dev/null
@@ -1,100 +0,0 @@
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -54,44 +54,6 @@ noinst_HEADERS = \
- graph_optimize.h \
- jensen_shannon.h \
- sampling.h \
-- lemon/maps.h \
-- lemon/bin_heap.h \
-- lemon/fib_heap.h \
-- lemon/bipartite_matching.h \
-- lemon/topology.h \
-- lemon/bucket_heap.h \
-- lemon/smart_graph.h \
-- lemon/list_graph.h \
-- lemon/error.h \
-- lemon/graph_utils.h \
-- lemon/bfs.h \
-- lemon/dfs.h \
-- lemon/math.h \
-- lemon/tolerance.h \
-- lemon/graph_adaptor.h \
-- lemon/concept_check.h \
-- lemon/bits/default_map.h \
-- lemon/bits/array_map.h \
-- lemon/bits/vector_map.h \
-- lemon/bits/debug_map.h \
-- lemon/bits/map_extender.h \
-- lemon/bits/base_extender.h \
-- lemon/bits/graph_adaptor_extender.h \
-- lemon/bits/graph_extender.h \
-- lemon/bits/invalid.h \
-- lemon/bits/path_dump.h \
-- lemon/bits/traits.h \
-- lemon/bits/utility.h \
-- lemon/bits/alteration_notifier.h \
-- lemon/bits/variant.h \
-- lemon/concepts/graph.h \
-- lemon/concepts/bpugraph.h \
-- lemon/concepts/graph_components.h \
-- lemon/concepts/ugraph.h \
-- lemon/concepts/heap.h \
-- lemon/concepts/maps.h \
-- lemon/concepts/path.h \
-- lemon/concepts/matrix_maps.h \
- locfit/design.h \
- locfit/lfcons.h \
- locfit/lfstruc.h \
-@@ -206,7 +168,7 @@ CLEANFILES = $(bin_SCRIPTS)
- # (echo '#!$(PYTHON)'; sed '/^#!/d' $<) > $@
-
- cufflinks_SOURCES = cufflinks.cpp
--cufflinks_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BOOST_SERIALIZATION_LIB) $(BAM_LIB)
-+cufflinks_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BOOST_SERIALIZATION_LIB) $(BAM_LIB) -llemon
- cufflinks_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) #$(ZLIB_LDFLAGS)
-
- cuffcompare_SOURCES = cuffcompare.cpp
---- a/src/graph_optimize.cpp
-+++ b/src/graph_optimize.cpp
-@@ -13,9 +13,10 @@
- #include "graph_optimize.h"
- // for graph optimization only
-
--#include <lemon/topology.h>
-+// #include <lemon/topology.h>
- #include <lemon/smart_graph.h>
--#include <lemon/bipartite_matching.h>
-+// #include <lemon/bipartite_matching.h>
-+#include <lemon/connectivity.h>
-
- #include "scaffold_graph.h"
- #include "scaffolds.h"
---- a/src/assemble.cpp
-+++ b/src/assemble.cpp
-@@ -16,10 +16,12 @@
- #include <vector>
- #include <iostream>
-
--#include <lemon/topology.h>
-+//#include <lemon/topology.h>
-
- //#include <lemon/graph_utils.h>
--#include <lemon/bipartite_matching.h>
-+//#include <lemon/bipartite_matching.h>
-+#include <lemon/connectivity.h>
-+#include <lemon/smart_graph.h>
-
- #include <boost/ref.hpp>
- // DON'T move this, or mystery compiler errors will result. Affects gcc >= 4.1
---- a/src/matching_merge.h
-+++ b/src/matching_merge.h
-@@ -14,7 +14,8 @@
-
- //#include <lemon/topology.h>
- #include <lemon/smart_graph.h>
--#include <lemon/bipartite_matching.h>
-+//#include <lemon/bipartite_matching.h>
-+#include <lemon/connectivity.h>
-
- #include "scaffold_graph.h"
- #include "scaffolds.h"
diff --git a/debian/watch b/debian/watch
index c05990d..30835ad 100644
--- a/debian/watch
+++ b/debian/watch
@@ -1,4 +1,3 @@
version=3
-opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
- https://github.com/cole-trapnell-lab/cufflinks/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
+https://github.com/cole-trapnell-lab/cufflinks/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cufflinks.git
More information about the debian-med-commit
mailing list