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| author | George Hartzell <hartzell@alerce.com> | 2018-12-31 18:28:15 -0800 |
|---|---|---|
| committer | Adam J. Stewart <ajstewart426@gmail.com> | 2018-12-31 20:28:15 -0600 |
| commit | e6b2f0c1791e82beba548458b93564a0cd97b32b (patch) | |
| tree | 19bd7d2013a93245eec164714f21d4edbd0fcbc3 | |
| parent | fb52eb2a185f8675a2b9ce77902f9ba899977520 (diff) | |
| download | spack-e6b2f0c1791e82beba548458b93564a0cd97b32b.tar.gz spack-e6b2f0c1791e82beba548458b93564a0cd97b32b.tar.bz2 spack-e6b2f0c1791e82beba548458b93564a0cd97b32b.tar.xz spack-e6b2f0c1791e82beba548458b93564a0cd97b32b.zip | |
express: new version, use tags and fix gcc@6.0.0: (#10230)
* express: new version, use tags and fix gcc@6.0.0:
Express fails to build with gcc@6.0.0:.
The debian project [has a
fix](https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=811859) but
they don't seem to have pushed it upstream.
I've opened an issue and a PR in eXpress repo, but eXpress isn't
actively developed, so I'm fixing it here too.
Since the Spack package was created, the eXpress team tagged their
releases. I've updated the package to use the tags.
Version 1.5.1 used to be known as 2015-11-29 (same commit). 1.5.2 is
new(er).
* Make flake8 happ{y,ier}
| -rw-r--r-- | var/spack/repos/builtin/packages/express/gcc-6.patch | 21 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/express/package.py | 13 |
2 files changed, 30 insertions, 4 deletions
diff --git a/var/spack/repos/builtin/packages/express/gcc-6.patch b/var/spack/repos/builtin/packages/express/gcc-6.patch new file mode 100644 index 0000000000..ed1fb6b710 --- /dev/null +++ b/var/spack/repos/builtin/packages/express/gcc-6.patch @@ -0,0 +1,21 @@ +Description: Fix compilation with gcc-6 +Author: Gert Wollny <gw.fossdev@gmail.com> +Bug-Debian: https://bugs.debian.org/811859 + +--- a/src/targets.cpp ++++ b/src/targets.cpp +@@ -113,12 +113,12 @@ + + double ll = LOG_1; + double tot_mass = mass(with_pseudo); +- double tot_eff_len = cached_effective_length(lib.bias_table); ++ double tot_eff_len = cached_effective_length(static_cast<bool>(lib.bias_table)); + if (neighbors) { + foreach (const Target* neighbor, *neighbors) { + tot_mass = log_add(tot_mass, neighbor->mass(with_pseudo)); + tot_eff_len = log_add(tot_eff_len, +- neighbor->cached_effective_length(lib.bias_table)); ++ neighbor->cached_effective_length(static_cast<bool>(lib.bias_table))); + } + } + ll += tot_mass - tot_eff_len; diff --git a/var/spack/repos/builtin/packages/express/package.py b/var/spack/repos/builtin/packages/express/package.py index cfb262d313..df86e33233 100644 --- a/var/spack/repos/builtin/packages/express/package.py +++ b/var/spack/repos/builtin/packages/express/package.py @@ -13,15 +13,20 @@ class Express(CMakePackage): target sequences from sampled subsequences.""" homepage = "http://bio.math.berkeley.edu/eXpress/" - git = "https://github.com/adarob/eXpress.git" + url = "https://github.com/adarob/eXpress/archive/1.5.2.zip" - version('2015-11-29', commit='f845cab2c7f2d9247b35143e4aa05869cfb10e79') + # 1.5.1 used to be known as 2015-11-29 (same commit), but they've + # added tags, so lets use 'em + version('1.5.2', sha256='25a63cca3dac6bd0daf04d2f0b2275e47d2190c90522bd231b1d7a875a59a52e') + version('1.5.1', sha256='fa3522de9cc25f1ede22fa196928912a6da2a2038681911115ec3e4da3d61293') depends_on('boost') depends_on('bamtools') depends_on('zlib') - conflicts('%gcc@6.0.0:', when='@2015-11-29') + # patch from the debian package repo: + # https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=811859 + patch('gcc-6.patch', when='%gcc@6.0.0:') def patch(self): with working_dir('src'): @@ -32,7 +37,7 @@ class Express(CMakePackage): edit.filter('#include <api', '#include <%s' % self.spec[ 'bamtools'].prefix.include.bamtools.api) edit = FileFilter('CMakeLists.txt') - edit.filter('\${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/' + edit.filter(r'\${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/' 'libbamtools.a', '%s' % self.spec['bamtools'].libs) def setup_environment(self, spack_env, run_env): |