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bpp-suite and deps: urls to GitHub (#30665)

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* bpp-core: moving url to github. Fixing compilation issue.

* bpp-phyl: moving url to github.

* bpp-seq: moving url to github

* bpp-popgen: new package

* bpp-suite: moving url to github, new version.

* bpp-popgen: removing unused cmake_args.
This commit is contained in:
snehring 2022-05-16 03:23:39 -05:00 committed by GitHub
parent 7803bc9e5f
commit e73b19024f
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GPG Key ID: 4AEE18F83AFDEB23
6 changed files with 62 additions and 8 deletions
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21
var/spack/repos/builtin/packages/bpp-core/global-graph-limits.patch Normal file
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@ -0,0 +1,21 @@
diff --git a/src/Bpp/Graph/GlobalGraph.cpp b/src/Bpp/Graph/GlobalGraph.cpp
index ca2d18f..d681314 100644
--- a/src/Bpp/Graph/GlobalGraph.cpp
+++ b/src/Bpp/Graph/GlobalGraph.cpp
@@ -42,6 +42,7 @@
#include <sstream>
#include <string>
#include <vector>
+#include <limits>
#include "../Exceptions.h"
#include "../Text/TextTools.h"
@@ -751,7 +752,7 @@ void GlobalGraph::orientate()
// if none, look for node wih minimum number of fathers
if (it == nextNodes.end())
{
- size_t nbF = numeric_limits<size_t>::infinity();
+ size_t nbF = std::numeric_limits<size_t>::infinity();
it = nextNodes.begin();
for ( ; it != nextNodes.end(); it++)

9
var/spack/repos/builtin/packages/bpp-core/package.py
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@ -10,10 +10,12 @@ class BppCore(CMakePackage):
"""Bio++ core library."""
homepage = "http://biopp.univ-montp2.fr/wiki/index.php/Installation"
url = "http://biopp.univ-montp2.fr/repos/sources/bpp-core-2.2.0.tar.gz"
url = "https://github.com/BioPP/bpp-core/archive/refs/tags/v2.4.1.tar.gz"
maintainers = ['snehring']
version('2.4.1', sha256='1150b8ced22cff23dd4770d7c23fad11239070b44007740e77407f0d746c0af6')
version('2.2.0', sha256='aacd4afddd1584ab6bfa1ff6931259408f1d39958a0bdc5f78bf1f9ee4e98b79')
version('2.2.0', sha256='aacd4afddd1584ab6bfa1ff6931259408f1d39958a0bdc5f78bf1f9ee4e98b79', deprecated=True)
depends_on('cmake@2.6:', type='build')
@ -21,5 +23,8 @@ class BppCore(CMakePackage):
# resolve ambiguous of 'isnan' function.
patch('clarify_isnan.patch', when='%fj')
# This is fixed in master, next release should be fine
patch('global-graph-limits.patch', when='@2.4.1')
def cmake_args(self):
return ['-DBUILD_TESTING=FALSE']

7
var/spack/repos/builtin/packages/bpp-phyl/package.py
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@ -10,9 +10,12 @@ class BppPhyl(CMakePackage):
"""Bio++ phylogeny library."""
homepage = "http://biopp.univ-montp2.fr/wiki/index.php/Installation"
url = "http://biopp.univ-montp2.fr/repos/sources/bpp-phyl-2.2.0.tar.gz"
url = "https://github.com/BioPP/bpp-phyl/archive/refs/tags/v2.4.1.tar.gz"
version('2.2.0', sha256='f346d87bbc7858924f3c99d7d74eb4a1f7a1b926746c68d8c28e07396c64237b')
maintainers = ['snehring']
version('2.4.1', sha256='e7bf7d4570f756b7773904ffa600ffcd77c965553ddb5cbc252092d1da962ff2')
version('2.2.0', sha256='f346d87bbc7858924f3c99d7d74eb4a1f7a1b926746c68d8c28e07396c64237b', deprecated=True)
depends_on('cmake@2.6:', type='build')
depends_on('bpp-core')

19
var/spack/repos/builtin/packages/bpp-popgen/package.py Normal file
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@ -0,0 +1,19 @@
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class BppPopgen(CMakePackage):
"""The Bio++ Population Genetics Library"""
homepage = "https://https://github.com/BioPP/bpp-popgen"
url = "https://github.com/BioPP/bpp-popgen/archive/refs/tags/v2.4.1.tar.gz"
maintainers = ['snehring']
version('2.4.1', sha256='03b57d71a63c8fa7f11c085e531d0d691fc1d40d4ea541070dabde0ab3baf413')
depends_on('bpp-seq')

6
var/spack/repos/builtin/packages/bpp-seq/package.py
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@ -10,10 +10,12 @@ class BppSeq(CMakePackage):
"""Bio++ seq library."""
homepage = "http://biopp.univ-montp2.fr/wiki/index.php/Installation"
url = "http://biopp.univ-montp2.fr/repos/sources/bpp-seq-2.2.0.tar.gz"
url = "https://github.com/BioPP/bpp-seq/archive/refs/tags/v2.4.1.tar.gz"
maintainers = ['snehring']
version('2.4.1', sha256='dbfcb04803e4b7f08f9f159da8a947c91906c3ca8b20683ac193f6dc524d4655')
version('2.2.0', sha256='0927d7fb0301c1b99a7353d5876deadb4a3040776cc74e8fe1c366fe920e7b6b')
version('2.2.0', sha256='0927d7fb0301c1b99a7353d5876deadb4a3040776cc74e8fe1c366fe920e7b6b', deprecated=True)
depends_on('cmake@2.6:', type='build')
depends_on('bpp-core')

8
var/spack/repos/builtin/packages/bpp-suite/package.py
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@ -11,15 +11,19 @@ class BppSuite(CMakePackage):
sequence analysis."""
homepage = "http://biopp.univ-montp2.fr/wiki/index.php/BppSuite"
url = "http://biopp.univ-montp2.fr/repos/sources/bppsuite/bppsuite-2.2.0.tar.gz"
url = "https://github.com/BioPP/bppsuite/archive/refs/tags/v2.4.1.tar.gz"
version('2.2.0', sha256='761fa5eec794af221d971ae70fd8c43171ad71a6bb5f20549263a1797b43f138')
maintainers = ['snehring']
version('2.4.1', sha256='0485adcc17e37439069d27e4fac144e5ae38036ba21f31e6d21f070ce4ea5199')
version('2.2.0', sha256='761fa5eec794af221d971ae70fd8c43171ad71a6bb5f20549263a1797b43f138', deprecated=True)
depends_on('cmake@2.6:', type='build')
depends_on('texinfo', type='build')
depends_on('bpp-core')
depends_on('bpp-seq')
depends_on('bpp-phyl')
depends_on('bpp-popgen', when='@2.4.1:')
# Clarify isinf's namespace, because Fujitsu compiler can't
# resolve ambiguous of 'isinf' function.