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abyss 2.1.4: fails to build with GCC 8 (#17614)

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* 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.
This commit is contained in:
t-nojiri 2020-08-05 02:11:52 +09:00 committed by GitHub
parent 9d2b60ac0c
commit 8977f7377a
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GPG Key ID: 4AEE18F83AFDEB23
2 changed files with 25 additions and 3 deletions
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11
var/spack/repos/builtin/packages/abyss/fix_BloomFilter.hpp.patch Normal file
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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';

17
var/spack/repos/builtin/packages/abyss/package.py
View File

@ -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')