abyss 2.1.4: fails to build with GCC 8 (#17614)
* abyss 2.1.4: fails to build with GCC 8 * abyss 2.1.4: fails to build with GCC 8 * abyss 2.1.4: Revise the points indicated by the review.
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		| @@ -0,0 +1,11 @@ | ||||
| --- spack-src/lib/bloomfilter/BloomFilter.hpp.org	2018-10-17 07:04:45.000000000 +0900 | ||||
| +++ spack-src/lib/bloomfilter/BloomFilter.hpp	2020-07-16 15:41:03.607766127 +0900 | ||||
| @@ -230,7 +230,7 @@ | ||||
|   | ||||
|  	void writeHeader(std::ostream& out) const { | ||||
|  		FileHeader header; | ||||
| -		strncpy(header.magic, "BlOOMFXX", 8); | ||||
| +		memcpy(header.magic, "BlOOMFXX", 8); | ||||
|  		char magic[9]; | ||||
|  		strncpy(magic, header.magic, 8); | ||||
|  		magic[8] = '\0'; | ||||
| @@ -3,9 +3,19 @@ | ||||
| # | ||||
| # SPDX-License-Identifier: (Apache-2.0 OR MIT) | ||||
| 
 | ||||
| import numbers | ||||
| from spack import * | ||||
| 
 | ||||
| 
 | ||||
| def is_multiple_32(x): | ||||
|     """multiple of 32 """ | ||||
|     try: | ||||
|         return isinstance(int(x), numbers.Integral) and \ | ||||
|             not isinstance(x, bool) and int(x) % 32 == 0 | ||||
|     except ValueError: | ||||
|         return False | ||||
| 
 | ||||
| 
 | ||||
| class Abyss(AutotoolsPackage): | ||||
|     """ABySS is a de novo, parallel, paired-end sequence assembler | ||||
|        that is designed for short reads. The single-processor version | ||||
| @@ -18,9 +28,8 @@ class Abyss(AutotoolsPackage): | ||||
|     version('2.0.2', sha256='d87b76edeac3a6fb48f24a1d63f243d8278a324c9a5eb29027b640f7089422df') | ||||
|     version('1.5.2', sha256='8a52387f963afb7b63db4c9b81c053ed83956ea0a3981edcad554a895adf84b1') | ||||
| 
 | ||||
|     variant('maxk', values=int, default=0, | ||||
|             description='''set the maximum k-mer length. | ||||
|             This value must be a multiple of 32''') | ||||
|     variant('maxk', default=128, values=is_multiple_32, | ||||
|             description='set the maximum k-mer length.') | ||||
| 
 | ||||
|     depends_on('autoconf', type='build') | ||||
|     depends_on('automake', type='build') | ||||
| @@ -48,3 +57,5 @@ def configure_args(self): | ||||
|         if self.spec['mpi'].name == 'mpich': | ||||
|             args.append('--enable-mpich') | ||||
|         return args | ||||
| 
 | ||||
|     patch('fix_BloomFilter.hpp.patch', when='@2.0.0:2.1.4') | ||||
|   | ||||
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