* [PATCH] Fix jellyfish on non-x86_64
@ 2016-02-27 16:10 Ricardo Wurmus
2016-02-27 20:22 ` Efraim Flashner
2016-02-27 23:31 ` Andreas Enge
0 siblings, 2 replies; 7+ messages in thread
From: Ricardo Wurmus @ 2016-02-27 16:10 UTC (permalink / raw)
To: guix-devel
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This is an attempt to fix the building of Jellyfish on non-x86_64.
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
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From f86b1ecef4a3760cc7807f3cacdb0e820e8b4c1b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 27 Feb 2016 16:46:28 +0100
Subject: [PATCH] gnu: jellyfish: Disable SSE and intl128 when not on x86_64.
* gnu/packages/bioinformatics.scm (jellyfish)[arguments]: Append
"--with-sse=no" and "--with-int128=no" to configure flags unless the
system is x86_64.
---
gnu/packages/bioinformatics.scm | 6 +++++-
1 file changed, 5 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7b3838d..36bcfd4 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1984,7 +1984,11 @@ experiments and provide highly stable thresholds based on reproducibility.")
(list (string-append "--enable-ruby-binding="
(assoc-ref %outputs "ruby"))
(string-append "--enable-python-binding="
- (assoc-ref %outputs "python")))
+ (assoc-ref %outputs "python"))
+ ,@(let ((system (or (%current-target-system) (%current-system))))
+ (if (string-prefix? "x86_64" system)
+ '()
+ '("--with-sse=no" "--with-int128=no"))))
#:phases
(modify-phases %standard-phases
(add-before 'check 'set-SHELL-variable
--
2.6.3
^ permalink raw reply related [flat|nested] 7+ messages in thread
* Re: [PATCH] Fix jellyfish on non-x86_64
2016-02-27 16:10 [PATCH] Fix jellyfish on non-x86_64 Ricardo Wurmus
@ 2016-02-27 20:22 ` Efraim Flashner
2016-02-27 21:02 ` Ricardo Wurmus
2016-02-27 23:31 ` Andreas Enge
1 sibling, 1 reply; 7+ messages in thread
From: Efraim Flashner @ 2016-02-27 20:22 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: guix-devel
[-- Attachment #1: Type: text/plain, Size: 1602 bytes --]
On Sat, 27 Feb 2016 17:10:07 +0100
Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> wrote:
> * gnu/packages/bioinformatics.scm (jellyfish)[arguments]: Append
> "--with-sse=no" and "--with-int128=no" to configure flags unless the
> system is x86_64.
> ---
> gnu/packages/bioinformatics.scm | 6 +++++-
> 1 file changed, 5 insertions(+), 1 deletion(-)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index 7b3838d..36bcfd4 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -1984,7 +1984,11 @@ experiments and provide highly stable thresholds based on reproducibility.")
> (list (string-append "--enable-ruby-binding="
> (assoc-ref %outputs "ruby"))
> (string-append "--enable-python-binding="
> - (assoc-ref %outputs "python")))
> + (assoc-ref %outputs "python"))
> + ,@(let ((system (or (%current-target-system) (%current-system))))
> + (if (string-prefix? "x86_64" system)
> + '()
> + '("--with-sse=no" "--with-int128=no"))))
^^
this looks like it's spaced off by 1
> #:phases
> (modify-phases %standard-phases
> (add-before 'check 'set-SHELL-variable
--
Efraim Flashner <efraim@flashner.co.il> אפרים פלשנר
GPG key = A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351
Confidentiality cannot be guaranteed on emails sent or received unencrypted
[-- Attachment #2: OpenPGP digital signature --]
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^ permalink raw reply [flat|nested] 7+ messages in thread
* Re: [PATCH] Fix jellyfish on non-x86_64
2016-02-27 20:22 ` Efraim Flashner
@ 2016-02-27 21:02 ` Ricardo Wurmus
0 siblings, 0 replies; 7+ messages in thread
From: Ricardo Wurmus @ 2016-02-27 21:02 UTC (permalink / raw)
To: Efraim Flashner; +Cc: guix-devel
Efraim Flashner <efraim@flashner.co.il> writes:
> On Sat, 27 Feb 2016 17:10:07 +0100
> Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> wrote:
>
>> * gnu/packages/bioinformatics.scm (jellyfish)[arguments]: Append
>> "--with-sse=no" and "--with-int128=no" to configure flags unless the
>> system is x86_64.
>> ---
>> gnu/packages/bioinformatics.scm | 6 +++++-
>> 1 file changed, 5 insertions(+), 1 deletion(-)
>>
>> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
>> index 7b3838d..36bcfd4 100644
>> --- a/gnu/packages/bioinformatics.scm
>> +++ b/gnu/packages/bioinformatics.scm
>> @@ -1984,7 +1984,11 @@ experiments and provide highly stable thresholds based on reproducibility.")
>> (list (string-append "--enable-ruby-binding="
>> (assoc-ref %outputs "ruby"))
>> (string-append "--enable-python-binding="
>> - (assoc-ref %outputs "python")))
>> + (assoc-ref %outputs "python"))
>> + ,@(let ((system (or (%current-target-system) (%current-system))))
>> + (if (string-prefix? "x86_64" system)
>> + '()
>> + '("--with-sse=no" "--with-int128=no"))))
> ^^
> this looks like it's spaced off by 1
Oh, indeed. Fixed.
Is the general idea okay, though?
~~ Ricardo
^ permalink raw reply [flat|nested] 7+ messages in thread
* Re: [PATCH] Fix jellyfish on non-x86_64
2016-02-27 16:10 [PATCH] Fix jellyfish on non-x86_64 Ricardo Wurmus
2016-02-27 20:22 ` Efraim Flashner
@ 2016-02-27 23:31 ` Andreas Enge
2016-02-28 14:47 ` Ricardo Wurmus
1 sibling, 1 reply; 7+ messages in thread
From: Andreas Enge @ 2016-02-27 23:31 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: guix-devel
Hello,
on armhf, I get lots of errors such as these:
unit_tests/test_mer_dna.cc: In instantiation of ‘void {anonymous}::MerDNA_GetBits_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = {anonymous}::VTC<jellyfish::mer_dna_ns::mer_base_dynamic<long long unsigned int>, 1>]’:
unit_tests/test_mer_dna.cc:529:1: required from here
unit_tests/test_mer_dna.cc:464:96: error: no matching function for call to ‘min(long unsigned int, unsigned int)’
unit_tests/test_mer_dna.cc:464:96: note: candidates are:
In file included from /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_tree.h:61:0,
from /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/map:60,
from unit_tests/test_mer_dna.cc:20:
/gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algobase.h:194:5: note: template<class _Tp> const _Tp& std::min(const _Tp&, const _Tp&)
min(const _Tp& __a, const _Tp& __b)
^
/gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algobase.h:194:5: note: template argument deduction/substitution failed:
unit_tests/test_mer_dna.cc:464:96: note: deduced conflicting types for parameter ‘const _Tp’ (‘long unsigned int’ and ‘unsigned int’)
std::min(this->GetParam().size() - start, 8 * sizeof(typename TypeParam::Type::base_type));
^
In file included from /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_tree.h:61:0,
from /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/map:60,
from unit_tests/test_mer_dna.cc:20:
/gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algobase.h:240:5: note: template<class _Tp, class _Compare> const _Tp& std::min(const _Tp&, const _Tp&, _Compare)
min(const _Tp& __a, const _Tp& __b, _Compare __comp)
^
/gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algobase.h:240:5: note: template argument deduction/substitution failed:
unit_tests/test_mer_dna.cc:464:96: note: deduced conflicting types for parameter ‘const _Tp’ (‘long unsigned int’ and ‘unsigned int’)
std::min(this->GetParam().size() - start, 8 * sizeof(typename TypeParam::Type::base_type));
^
In file included from /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/algorithm:62:0,
from ./include/jellyfish/misc.hpp:34,
from ./include/jellyfish/mer_dna.hpp:33,
from unit_tests/test_mer_dna.cc:24:
/gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algo.h:3439:5: note: template<class _Tp> _Tp std::min(std::initializer_list<_Tp>)
min(initializer_list<_Tp> __l)
^
/gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algo.h:3439:5: note: template argument deduction/substitution failed:
unit_tests/test_mer_dna.cc:464:96: note: mismatched types ‘std::initializer_list<_Tp>’ and ‘long unsigned int’
std::min(this->GetParam().size() - start, 8 * sizeof(typename TypeParam::Type::base_type));
^
In file included from /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/algorithm:62:0,
from ./include/jellyfish/misc.hpp:34,
from ./include/jellyfish/mer_dna.hpp:33,
from unit_tests/test_mer_dna.cc:24:
/gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algo.h:3444:5: note: template<class _Tp, class _Compare> _Tp std::min(std::initializer_list<_Tp>, _Compare)
min(initializer_list<_Tp> __l, _Compare __comp)
^
/gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algo.h:3444:5: note: template argument deduction/substitution failed:
unit_tests/test_mer_dna.cc:464:96: note: mismatched types ‘std::initializer_list<_Tp>’ and ‘long unsigned int’
std::min(this->GetParam().size() - start, 8 * sizeof(typename TypeParam::Type::base_type));
^
unit_tests/test_mer_dna.cc: In instantiation of ‘void {anonymous}::MerDNA_GetBits_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = {anonymous}::VTC<jellyfish::mer_dna_ns::mer_base_dynamic<long long unsigned int>, 0>]’:
unit_tests/test_mer_dna.cc:529:1: required from here
unit_tests/test_mer_dna.cc:464:96: error: no matching function for call to ‘min(long unsigned int, unsigned int)’
unit_tests/test_mer_dna.cc:464:96: note: candidates are:
In file included from /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_tree.h:61:0,
from /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/map:60,
from unit_tests/test_mer_dna.cc:20:
/gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algobase.h:194:5: note: template<class _Tp> const _Tp& std::min(const _Tp&, const _Tp&)
min(const _Tp& __a, const _Tp& __b)
^
/gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algobase.h:194:5: note: template argument deduction/substitution failed:
unit_tests/test_mer_dna.cc:464:96: note: deduced conflicting types for parameter ‘const _Tp’ (‘long unsigned int’ and ‘unsigned int’)
std::min(this->GetParam().size() - start, 8 * sizeof(typename TypeParam::Type::base_type));
^
In file included from /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_tree.h:61:0,
from /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/map:60,
from unit_tests/test_mer_dna.cc:20:
/gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algobase.h:240:5: note: template<class _Tp, class _Compare> const _Tp& std::min(const _Tp&, const _Tp&, _Compare)
min(const _Tp& __a, const _Tp& __b, _Compare __comp)
^
/gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algobase.h:240:5: note: template argument deduction/substitution failed:
unit_tests/test_mer_dna.cc:464:96: note: deduced conflicting types for parameter ‘const _Tp’ (‘long unsigned int’ and ‘unsigned int’)
std::min(this->GetParam().size() - start, 8 * sizeof(typename TypeParam::Type::base_type));
^
In file included from /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/algorithm:62:0,
from ./include/jellyfish/misc.hpp:34,
from ./include/jellyfish/mer_dna.hpp:33,
from unit_tests/test_mer_dna.cc:24:
/gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algo.h:3439:5: note: template<class _Tp> _Tp std::min(std::initializer_list<_Tp>)
min(initializer_list<_Tp> __l)
^
/gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algo.h:3439:5: note: template argument deduction/substitution failed:
unit_tests/test_mer_dna.cc:464:96: note: mismatched types ‘std::initializer_list<_Tp>’ and ‘long unsigned int’
std::min(this->GetParam().size() - start, 8 * sizeof(typename TypeParam::Type::base_type));
^
In file included from /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/algorithm:62:0,
from ./include/jellyfish/misc.hpp:34,
from ./include/jellyfish/mer_dna.hpp:33,
from unit_tests/test_mer_dna.cc:24:
/gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algo.h:3444:5: note: template<class _Tp, class _Compare> _Tp std::min(std::initializer_list<_Tp>, _Compare)
min(initializer_list<_Tp> __l, _Compare __comp)
Is there maybe an assumption of 64bit?
Andreas
^ permalink raw reply [flat|nested] 7+ messages in thread
* Re: [PATCH] Fix jellyfish on non-x86_64
2016-02-27 23:31 ` Andreas Enge
@ 2016-02-28 14:47 ` Ricardo Wurmus
2016-02-28 14:52 ` Andreas Enge
0 siblings, 1 reply; 7+ messages in thread
From: Ricardo Wurmus @ 2016-02-28 14:47 UTC (permalink / raw)
To: Andreas Enge; +Cc: guix-devel
Andreas Enge <andreas@enge.fr> writes:
> Hello,
>
> on armhf, I get lots of errors such as these:
>
> unit_tests/test_mer_dna.cc: In instantiation of ‘void {anonymous}::MerDNA_GetBits_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = {anonymous}::VTC<jellyfish::mer_dna_ns::mer_base_dynamic<long long unsigned int>, 1>]’:
> unit_tests/test_mer_dna.cc:529:1: required from here
> unit_tests/test_mer_dna.cc:464:96: error: no matching function for call to ‘min(long unsigned int, unsigned int)’
> unit_tests/test_mer_dna.cc:464:96: note: candidates are:
> In file included from /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_tree.h:61:0,
> from /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/map:60,
> from unit_tests/test_mer_dna.cc:20:
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algobase.h:194:5: note: template<class _Tp> const _Tp& std::min(const _Tp&, const _Tp&)
> min(const _Tp& __a, const _Tp& __b)
> ^
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algobase.h:194:5: note: template argument deduction/substitution failed:
> unit_tests/test_mer_dna.cc:464:96: note: deduced conflicting types for parameter ‘const _Tp’ (‘long unsigned int’ and ‘unsigned int’)
> std::min(this->GetParam().size() - start, 8 * sizeof(typename TypeParam::Type::base_type));
> ^
> In file included from /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_tree.h:61:0,
> from /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/map:60,
> from unit_tests/test_mer_dna.cc:20:
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algobase.h:240:5: note: template<class _Tp, class _Compare> const _Tp& std::min(const _Tp&, const _Tp&, _Compare)
> min(const _Tp& __a, const _Tp& __b, _Compare __comp)
> ^
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algobase.h:240:5: note: template argument deduction/substitution failed:
> unit_tests/test_mer_dna.cc:464:96: note: deduced conflicting types for parameter ‘const _Tp’ (‘long unsigned int’ and ‘unsigned int’)
> std::min(this->GetParam().size() - start, 8 * sizeof(typename TypeParam::Type::base_type));
> ^
> In file included from /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/algorithm:62:0,
> from ./include/jellyfish/misc.hpp:34,
> from ./include/jellyfish/mer_dna.hpp:33,
> from unit_tests/test_mer_dna.cc:24:
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algo.h:3439:5: note: template<class _Tp> _Tp std::min(std::initializer_list<_Tp>)
> min(initializer_list<_Tp> __l)
> ^
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algo.h:3439:5: note: template argument deduction/substitution failed:
> unit_tests/test_mer_dna.cc:464:96: note: mismatched types ‘std::initializer_list<_Tp>’ and ‘long unsigned int’
> std::min(this->GetParam().size() - start, 8 * sizeof(typename TypeParam::Type::base_type));
> ^
> In file included from /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/algorithm:62:0,
> from ./include/jellyfish/misc.hpp:34,
> from ./include/jellyfish/mer_dna.hpp:33,
> from unit_tests/test_mer_dna.cc:24:
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algo.h:3444:5: note: template<class _Tp, class _Compare> _Tp std::min(std::initializer_list<_Tp>, _Compare)
> min(initializer_list<_Tp> __l, _Compare __comp)
> ^
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algo.h:3444:5: note: template argument deduction/substitution failed:
> unit_tests/test_mer_dna.cc:464:96: note: mismatched types ‘std::initializer_list<_Tp>’ and ‘long unsigned int’
> std::min(this->GetParam().size() - start, 8 * sizeof(typename TypeParam::Type::base_type));
> ^
> unit_tests/test_mer_dna.cc: In instantiation of ‘void {anonymous}::MerDNA_GetBits_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = {anonymous}::VTC<jellyfish::mer_dna_ns::mer_base_dynamic<long long unsigned int>, 0>]’:
> unit_tests/test_mer_dna.cc:529:1: required from here
> unit_tests/test_mer_dna.cc:464:96: error: no matching function for call to ‘min(long unsigned int, unsigned int)’
> unit_tests/test_mer_dna.cc:464:96: note: candidates are:
> In file included from /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_tree.h:61:0,
> from /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/map:60,
> from unit_tests/test_mer_dna.cc:20:
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algobase.h:194:5: note: template<class _Tp> const _Tp& std::min(const _Tp&, const _Tp&)
> min(const _Tp& __a, const _Tp& __b)
> ^
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algobase.h:194:5: note: template argument deduction/substitution failed:
> unit_tests/test_mer_dna.cc:464:96: note: deduced conflicting types for parameter ‘const _Tp’ (‘long unsigned int’ and ‘unsigned int’)
> std::min(this->GetParam().size() - start, 8 * sizeof(typename TypeParam::Type::base_type));
> ^
> In file included from /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_tree.h:61:0,
> from /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/map:60,
> from unit_tests/test_mer_dna.cc:20:
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algobase.h:240:5: note: template<class _Tp, class _Compare> const _Tp& std::min(const _Tp&, const _Tp&, _Compare)
> min(const _Tp& __a, const _Tp& __b, _Compare __comp)
> ^
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algobase.h:240:5: note: template argument deduction/substitution failed:
> unit_tests/test_mer_dna.cc:464:96: note: deduced conflicting types for parameter ‘const _Tp’ (‘long unsigned int’ and ‘unsigned int’)
> std::min(this->GetParam().size() - start, 8 * sizeof(typename TypeParam::Type::base_type));
> ^
> In file included from /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/algorithm:62:0,
> from ./include/jellyfish/misc.hpp:34,
> from ./include/jellyfish/mer_dna.hpp:33,
> from unit_tests/test_mer_dna.cc:24:
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algo.h:3439:5: note: template<class _Tp> _Tp std::min(std::initializer_list<_Tp>)
> min(initializer_list<_Tp> __l)
> ^
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algo.h:3439:5: note: template argument deduction/substitution failed:
> unit_tests/test_mer_dna.cc:464:96: note: mismatched types ‘std::initializer_list<_Tp>’ and ‘long unsigned int’
> std::min(this->GetParam().size() - start, 8 * sizeof(typename TypeParam::Type::base_type));
> ^
> In file included from /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/algorithm:62:0,
> from ./include/jellyfish/misc.hpp:34,
> from ./include/jellyfish/mer_dna.hpp:33,
> from unit_tests/test_mer_dna.cc:24:
> /gnu/store/i23hviqfy0pw7xjvqy263k55pz0zaf8m-gcc-4.9.3/include/c++/bits/stl_algo.h:3444:5: note: template<class _Tp, class _Compare> _Tp std::min(std::initializer_list<_Tp>, _Compare)
> min(initializer_list<_Tp> __l, _Compare __comp)
>
> Is there maybe an assumption of 64bit?
Possibly, but the author would like it to run on more than one architecture:
https://github.com/gmarcais/Jellyfish/issues/52#issuecomment-171319952
I don’t know if this fixes the build for i686 and mips. Do you think we
could apply it and check the build logs for errors then?
~~ Ricardo
^ permalink raw reply [flat|nested] 7+ messages in thread
* Re: [PATCH] Fix jellyfish on non-x86_64
2016-02-28 14:47 ` Ricardo Wurmus
@ 2016-02-28 14:52 ` Andreas Enge
2016-02-28 17:26 ` Ricardo Wurmus
0 siblings, 1 reply; 7+ messages in thread
From: Andreas Enge @ 2016-02-28 14:52 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: guix-devel
On Sun, Feb 28, 2016 at 03:47:16PM +0100, Ricardo Wurmus wrote:
> Possibly, but the author would like it to run on more than one architecture:
> https://github.com/gmarcais/Jellyfish/issues/52#issuecomment-171319952
> I don’t know if this fixes the build for i686 and mips. Do you think we
> could apply it and check the build logs for errors then?
Could you build the package for i686 (I think "--system=i686-linux" is the
magic option)? And maybe Mark could test it on one of the mips (mine is so
slow that I unplugged it; it would probably take a few days to get up to
par with master...). If it fixes no architecture, then there is not much
use in applying it (but also no harm; so as it will probably make
communication with the author easier if you can point to build logs,
why not apply it finally).
Andreas
^ permalink raw reply [flat|nested] 7+ messages in thread
* Re: [PATCH] Fix jellyfish on non-x86_64
2016-02-28 14:52 ` Andreas Enge
@ 2016-02-28 17:26 ` Ricardo Wurmus
0 siblings, 0 replies; 7+ messages in thread
From: Ricardo Wurmus @ 2016-02-28 17:26 UTC (permalink / raw)
To: Andreas Enge; +Cc: guix-devel
Andreas Enge <andreas@enge.fr> writes:
> On Sun, Feb 28, 2016 at 03:47:16PM +0100, Ricardo Wurmus wrote:
>> Possibly, but the author would like it to run on more than one architecture:
>> https://github.com/gmarcais/Jellyfish/issues/52#issuecomment-171319952
>> I don’t know if this fixes the build for i686 and mips. Do you think we
>> could apply it and check the build logs for errors then?
>
> Could you build the package for i686 (I think "--system=i686-linux" is the
> magic option)? And maybe Mark could test it on one of the mips (mine is so
> slow that I unplugged it; it would probably take a few days to get up to
> par with master...). If it fixes no architecture, then there is not much
> use in applying it (but also no harm; so as it will probably make
> communication with the author easier if you can point to build logs,
> why not apply it finally).
Yeah, it doesn’t fix the build on i686. I reported this to upstream.
Obviously, there’s no use in applying this patch.
~~ Ricardo
^ permalink raw reply [flat|nested] 7+ messages in thread
end of thread, other threads:[~2016-02-28 17:26 UTC | newest]
Thread overview: 7+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2016-02-27 16:10 [PATCH] Fix jellyfish on non-x86_64 Ricardo Wurmus
2016-02-27 20:22 ` Efraim Flashner
2016-02-27 21:02 ` Ricardo Wurmus
2016-02-27 23:31 ` Andreas Enge
2016-02-28 14:47 ` Ricardo Wurmus
2016-02-28 14:52 ` Andreas Enge
2016-02-28 17:26 ` Ricardo Wurmus
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