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| author | Toyohisa Kameyama <kameyama@riken.jp> | 2019-10-03 02:54:50 +0900 |
|---|---|---|
| committer | Adam J. Stewart <ajstewart426@gmail.com> | 2019-10-02 12:54:50 -0500 |
| commit | b85ff04681ea1864ed5a66bcbe5e242ba54ecf6e (patch) | |
| tree | b1aa7d09e8fab96efb05a8bb7b2d43b9e0beec0d /var | |
| parent | 58c01792ef678cd9c2230812dd91c8a991d3cd65 (diff) | |
| download | spack-b85ff04681ea1864ed5a66bcbe5e242ba54ecf6e.tar.gz spack-b85ff04681ea1864ed5a66bcbe5e242ba54ecf6e.tar.bz2 spack-b85ff04681ea1864ed5a66bcbe5e242ba54ecf6e.tar.xz spack-b85ff04681ea1864ed5a66bcbe5e242ba54ecf6e.zip | |
denovogear: Add missing zlib depenbdency and fix open handling error. (#13017)
Diffstat (limited to 'var')
| -rw-r--r-- | var/spack/repos/builtin/packages/denovogear/package.py | 3 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/denovogear/stream-open.patch | 12 |
2 files changed, 15 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/denovogear/package.py b/var/spack/repos/builtin/packages/denovogear/package.py index f214d37ee3..61651ca492 100644 --- a/var/spack/repos/builtin/packages/denovogear/package.py +++ b/var/spack/repos/builtin/packages/denovogear/package.py @@ -22,3 +22,6 @@ class Denovogear(CMakePackage): depends_on('boost@1.47:1.60', type=('build')) depends_on('htslib@1.2:', type=('build')) depends_on('eigen', type=('build')) + depends_on('zlib', type=('link')) + + patch('stream-open.patch', when='@:1.1.1') diff --git a/var/spack/repos/builtin/packages/denovogear/stream-open.patch b/var/spack/repos/builtin/packages/denovogear/stream-open.patch new file mode 100644 index 0000000000..23d699cc7d --- /dev/null +++ b/var/spack/repos/builtin/packages/denovogear/stream-open.patch @@ -0,0 +1,12 @@ +diff -ru spack-src.org/src/dng-dnm.cc spack-src/src/dng-dnm.cc +--- spack-src.org/src/dng-dnm.cc 2015-04-21 09:16:59.000000000 +0900 ++++ spack-src/src/dng-dnm.cc 2019-10-02 15:08:28.892042247 +0900 +@@ -161,7 +161,7 @@ + int writeVCFHeader(std::ofstream& fo_vcf, string op_vcf_f, string bcf_file, string ped_file, string sample) + { + fo_vcf.open(op_vcf_f.c_str()); +- if(fo_vcf == NULL) { ++ if(fo_vcf.fail()) { + cerr<<"Unable to open vcf file for writing output. Exiting !"<<endl; + } + fo_vcf<<"##fileformat=VCFv4.1\n"; |