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add patch to fix broken (hanging) Mash binaries #14511

Merged
merged 7 commits into from
Dec 7, 2021
Merged

add patch to fix broken (hanging) Mash binaries #14511

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bfb327b
use similar patches as for version 2.1
bedroge Dec 7, 2021
59f61a2
Update older patch for newer Mash versions
bedroge Dec 7, 2021
87349be
add checksums for patches
bedroge Dec 7, 2021
795f3a9
add sanity check command for Mash
bedroge Dec 7, 2021
21da879
replace 2.2 by version variable in patch fileame
bedroge Dec 7, 2021
0a25d7b
use Mash 2.1 patches for 2.0
bedroge Dec 7, 2021
311bab5
add checksums for patches
bedroge Dec 7, 2021
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12 changes: 11 additions & 1 deletion easybuild/easyconfigs/m/Mash/Mash-2.0-foss-2018a.eb
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,15 @@ toolchain = {'name': 'foss', 'version': '2018a'}

source_urls = ['https://github.com/marbl/Mash/archive/']
sources = ['v%(version)s.tar.gz']
checksums = ['7bea8cd3c266640bbd97f2e1c9d0168892915c1c14f7d03a9751bf7a3709dd01']
patches = [
'Mash-2.1_fix-hardcoding.patch',
'Mash-2.1_disable-memcpy-wrap.patch',
]
checksums = [
'7bea8cd3c266640bbd97f2e1c9d0168892915c1c14f7d03a9751bf7a3709dd01', # v2.0.tar.gz
'dc40511b25dab25e3fe88d4911ccf7bd793e60ba8f4b77a64488412d14796299', # Mash-2.1_fix-hardcoding.patch
'40990cf3d192b533736374bc67a54dbd839d90b0310a0a66f994891da1f85b6e', # Mash-2.1_disable-memcpy-wrap.patch
]

builddependencies = [('Autotools', '20170619')]
dependencies = [
Expand All @@ -27,4 +35,6 @@ sanity_check_paths = {
'dirs': ['include/mash'],
}

sanity_check_commands = ['mash --version']

moduleclass = 'bio'
2 changes: 2 additions & 0 deletions easybuild/easyconfigs/m/Mash/Mash-2.1-foss-2018b.eb
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Expand Up @@ -36,4 +36,6 @@ sanity_check_paths = {
'dirs': ['include/mash'],
}

sanity_check_commands = ['mash --version']

moduleclass = 'bio'
12 changes: 11 additions & 1 deletion easybuild/easyconfigs/m/Mash/Mash-2.2-GCC-9.3.0.eb
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Expand Up @@ -16,7 +16,15 @@ toolchainopts = {'cstd': 'c++17'}

source_urls = ['https://github.com/marbl/Mash/archive/']
sources = ['v%(version)s.tar.gz']
checksums = ['7ad006dbf0d6ffc3e164713ba955aab4cd24eaf85c864ac905f48cd8ba332691']
patches = [
'Mash-%(version)s_fix-hardcoding.patch',
'Mash-2.1_disable-memcpy-wrap.patch',
]
checksums = [
'7ad006dbf0d6ffc3e164713ba955aab4cd24eaf85c864ac905f48cd8ba332691', # v2.2.tar.gz
'0c7315af727a06f408ab3ca69da0860fc671aa870b448a41a509b1e6d7027db5', # Mash-2.2_fix-hardcoding.patch
'40990cf3d192b533736374bc67a54dbd839d90b0310a0a66f994891da1f85b6e', # Mash-2.1_disable-memcpy-wrap.patch
]

builddependencies = [('Autotools', '20180311')]
dependencies = [
Expand All @@ -33,4 +41,6 @@ sanity_check_paths = {
'dirs': ['include/mash'],
}

sanity_check_commands = ['mash --version']

moduleclass = 'bio'
20 changes: 20 additions & 0 deletions easybuild/easyconfigs/m/Mash/Mash-2.2_fix-hardcoding.patch
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Original file line number Diff line number Diff line change
@@ -0,0 +1,20 @@
don't hardcode -std=c++14, since -std=c++17 is required when building on top of CapnProto 0.8.0
--- Mash-2.2/configure.ac.orig 2021-12-07 10:56:35.099497741 +0100
+++ Mash-2.2/configure.ac 2021-12-07 10:57:09.343306342 +0100
@@ -33,7 +33,7 @@
AC_MSG_ERROR([Cap'n Proto compiler (capnp) not found.])
fi

-CPPFLAGS="-I$with_capnp/include -std=c++14"
+CPPFLAGS="-I$with_capnp/include $CXXFLAGS"

AC_CHECK_HEADER(capnp/common.h, [result=1], [result=0])

--- Mash-2.2/Makefile.in.orig 2021-12-07 10:57:13.619282453 +0100
+++ Mash-2.2/Makefile.in 2021-12-07 10:57:36.623153939 +0100
@@ -1,4 +1,4 @@
-CXXFLAGS += -O3 -std=c++14 -Isrc -I@capnp@/include -I@mathinc@
+CXXFLAGS += -Isrc -I@capnp@/include -I@mathinc@
CPPFLAGS += @amcppflags@

UNAME_S=$(shell uname -s)
12 changes: 11 additions & 1 deletion easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-10.3.0.eb
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,15 @@ toolchainopts = {'cstd': 'c++17'}

source_urls = ['https://github.com/marbl/Mash/archive/']
sources = ['v%(version)s.tar.gz']
checksums = ['f96cf7305e010012c3debed966ac83ceecac0351dbbfeaa6cd7ad7f068d87fe1']
patches = [
'Mash-2.2_fix-hardcoding.patch',
'Mash-2.1_disable-memcpy-wrap.patch',
]
checksums = [
'f96cf7305e010012c3debed966ac83ceecac0351dbbfeaa6cd7ad7f068d87fe1', # v2.3.tar.gz
'0c7315af727a06f408ab3ca69da0860fc671aa870b448a41a509b1e6d7027db5', # Mash-2.2_fix-hardcoding.patch
'40990cf3d192b533736374bc67a54dbd839d90b0310a0a66f994891da1f85b6e', # Mash-2.1_disable-memcpy-wrap.patch
]

builddependencies = [('Autotools', '20210128')]
dependencies = [
Expand All @@ -33,4 +41,6 @@ sanity_check_paths = {
'dirs': ['include/mash'],
}

sanity_check_commands = ['mash --version']

moduleclass = 'bio'