diff options
| -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): |