* [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 [-- Attachment #1: Type: text/plain, Size: 68 bytes --] This is an attempt to fix the building of Jellyfish on non-x86_64. [-- Warning: decoded text below may be mangled, UTF-8 assumed --] [-- Attachment #2: 0001-gnu-jellyfish-Disable-SSE-and-intl128-when-not-on-x8.patch --] [-- Type: text/x-patch, Size: 1396 bytes --] 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 --] [-- Type: application/pgp-signature, Size: 819 bytes --] ^ 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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