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 <[email protected]> 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 <[email protected]> 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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
