[med-svn] [phyml] 01/03: Upstream confirmed that beagle is not supported

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository phyml.

commit 692f450388872eb6c294f95b30b85ded94cf8e21
Author: Andreas Tille <tille at debian.org>
Date:   Tue Jun 27 13:19:53 2017 +0200

    Upstream confirmed that beagle is not supported
---
 debian/changelog |  7 +------
 debian/control   | 56 ++++++++++++++++++++++++++++----------------------------
 debian/rules     |  2 +-
 3 files changed, 30 insertions(+), 35 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index a0de87f..3aa3185 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,12 +1,7 @@
 phyml (3:3.3.20170530+dfsg-1) UNRELEASED; urgency=medium
 
   * New upstream version
-  * TODO past stretch release:
-    Since phyml-beagle is now a separate executable the Build-Depends
-    should be restricted to those architectures where it exist and
-    d/rules should be respect the build architecture and not build
-    phyml-beagle if libhmsbeagle does not exist on this arch.
-  * 
+  * Upstream confirmed that beagle is not supported
 
  -- Andreas Tille <tille at debian.org>  Sat, 24 Jun 2017 10:38:47 +0200
 
diff --git a/debian/control b/debian/control
index afac0c8..49aac21 100644
--- a/debian/control
+++ b/debian/control
@@ -9,7 +9,7 @@ Build-Depends: debhelper (>= 10),
                autotools-dev,
                dh-autoreconf,
                pkg-config,
-               libhmsbeagle-dev [any-amd64 any-i386 arm64 armhf],
+#               libhmsbeagle-dev [any-amd64 any-i386 arm64 armhf],
                libopenmpi-dev,
                chrpath
 Standards-Version: 3.9.8
@@ -45,30 +45,30 @@ Description: Phylogenetic estimation using Maximum Likelihood
  .
  This package also includes PhyTime.
 
-Package: phyml-beagle
-Architecture: any-amd64 any-i386 arm64 armhf
-Depends: ${shlibs:Depends},
-         ${misc:Depends},
-         openmpi-bin
-Description: Phylogenetic estimation using Maximum Likelihood
- PhyML is a software that estimates maximum likelihood phylogenies from
- alignments of nucleotide or amino acid sequences. It provides a wide
- range of options that were designed to facilitate standard phylogenetic
- analyses. The main strengths of PhyML lies in the large number of
- substitution models coupled to various options to search the space of
- phylogenetic tree topologies, going from very fast and efficient methods
- to slower but generally more accurate approaches. It also implements
- two methods to evaluate branch supports in a sound statistical framework
- (the non-parametric bootstrap and the approximate likelihood ratio test).
- .
- PhyML was designed to process moderate to large data sets. In theory,
- alignments with up to 4,000 sequences 2,000,000 character-long can
- be analyzed. In  practice however, the amount of memory required to process
- a data set is proportional of the product of the number of sequences by their
- length. Hence, a large number of sequences can only be processed provided
- that they are short. Also, PhyML can handle long sequences provided that
- they are not numerous. With most standard personal computers, the “comfort
- zone” for PhyML generally lies around 3 to 500 sequences less than 2,000
- character long.
- .
- This package contains the hmsbeagle optimisation.
+#Package: phyml-beagle
+#Architecture: any-amd64 any-i386 arm64 armhf
+#Depends: ${shlibs:Depends},
+#         ${misc:Depends},
+#         openmpi-bin
+#Description: Phylogenetic estimation using Maximum Likelihood
+# PhyML is a software that estimates maximum likelihood phylogenies from
+# alignments of nucleotide or amino acid sequences. It provides a wide
+# range of options that were designed to facilitate standard phylogenetic
+# analyses. The main strengths of PhyML lies in the large number of
+# substitution models coupled to various options to search the space of
+# phylogenetic tree topologies, going from very fast and efficient methods
+# to slower but generally more accurate approaches. It also implements
+# two methods to evaluate branch supports in a sound statistical framework
+# (the non-parametric bootstrap and the approximate likelihood ratio test).
+# .
+# PhyML was designed to process moderate to large data sets. In theory,
+# alignments with up to 4,000 sequences 2,000,000 character-long can
+# be analyzed. In  practice however, the amount of memory required to process
+# a data set is proportional of the product of the number of sequences by their
+# length. Hence, a large number of sequences can only be processed provided
+# that they are short. Also, PhyML can handle long sequences provided that
+# they are not numerous. With most standard personal computers, the “comfort
+# zone” for PhyML generally lies around 3 to 500 sequences less than 2,000
+# character long.
+# .
+# This package contains the hmsbeagle optimisation.
diff --git a/debian/rules b/debian/rules
index 39e99cc..d8dfeb0 100755
--- a/debian/rules
+++ b/debian/rules
@@ -26,7 +26,7 @@ override_dh_auto_build:
 	# move phyml binary to temporary dir inside debian/
 	mkdir -p $(CURDIR)/debian/bin
 	mv src/phyml $(CURDIR)/debian/bin/phyml
-ifeq ($(BUILDARCH),$(filter $(BUILDARCH), amd64 i386 arm64 armhf))
+ifeq ($(BUILDARCH),$(filter $(BUILDARCH), do_not_build_this)) # amd64 i386 arm64 armhf)) # upstream confirmed that beagle support is to weak
 	$(MAKE) distclean
 	dh_auto_configure -- --enable-beagle
 	dh_auto_build -- CFLAGS="$(CFLAGS) -I/usr/include/libhmsbeagle-1 -DBEAGLE" LDFLAGS="$(LDFLAGS)"

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/phyml.git