Bug#934619: libmaus2 FTBFS (mostly 32bit): error: no matching function for call
Followup-For: Bug #934619 Control: severity -1 normal The outdated 32-bit binaries have been removed from the archive, so this is no longer a regression. Andreas
Bug#934619: libmaus2 FTBFS (mostly 32bit): error: no matching function for call
Control: tags -1 help
Control: tags -1 upstream
Control: forwarded -1 https://gitlab.com/german.tischler/libmaus2/issues/30
Hi,
I've tried to build the latest upstream version but it also has issues
for 32bit architectures:
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time
-D_FORTIFY_SOURCE=2 -W -Wall -Wnon-virtual-dtor -g -O2
-fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat
-Werror=format-security -O3 -std=gnu++0x -pthread -fopenmp -c -o
test/testmapperm-testmapperm.o `test -f 'test/testmapperm.cpp' || echo
'./'`test/testmapperm.cpp
In file included from test/testparallelbamblocksort.cpp:19:
./libmaus2/bambam/parallel/BlockMergeControl.hpp: In instantiation of ‘void
libmaus2::bambam::parallel::BlockMergeControl<_heap_element_type>::enqueHeader()
[with _heap_element_type =
libmaus2::bambam::parallel::GenericInputControlMergeHeapEntryQueryName]’:
./libmaus2/bambam/parallel/BlockMergeControl.hpp:571:6: required from
‘libmaus2::bambam::parallel::BlockMergeControl<_heap_element_type>::BlockMergeControl(libmaus2::parallel::SimpleThreadPool&,
std::ostream&, libmaus2::autoarray::AutoArray&, const
std::vector&,
libmaus2::bitio::BitVector*, int, uint64_t, uint64_t, uint64_t, uint64_t,
uint64_t, const string&, const string&, libmaus2::digest::DigestInterface*,
libmaus2::bambam::parallel::BlockMergeControlTypeBase::block_merge_output_format_t,
bool, bool, bool, uint64_t) [with _heap_element_type =
libmaus2::bambam::parallel::GenericInputControlMergeHeapEntryQueryName;
std::ostream = std::basic_ostream; libmaus2::bitio::BitVector =
libmaus2::bitio::BitVectorTemplate; uint64_t = long
long unsigned int; std::string = std::__cxx11::basic_string]’
test/testparallelbamblocksort.cpp:216:68: required from ‘int
parallelbamblocksort(const libmaus2::util::ArgInfo&, bool, bool, const string&,
bool) [with order_type =
libmaus2::bambam::parallel::FragmentAlignmentBufferQueryNameComparator;
heap_element_type =
libmaus2::bambam::parallel::GenericInputControlMergeHeapEntryQueryName; bool
create_dup_mark_info = false; std::string = std::__cxx11::basic_string]’
test/testparallelbamblocksort.cpp:259:4: required from here
./libmaus2/bambam/parallel/BlockMergeControl.hpp:346:92: error: cannot convert
‘’ to ‘cram_data_write_function_t’ {aka
‘void (*)(void*, int, unsigned int, const char*, unsigned int,
_cram_data_write_block_type)’}
346 |samsupport.context =
sam_allocate_encoder(this,ptext.first,ptext.second-ptext.first,sam_data_write_function);
|
^~~
|
|
|
./libmaus2/bambam/parallel/BlockMergeControl.hpp:1264:33: note: initializing
argument 4 of ‘static void*
libmaus2::bambam::parallel::BlockMergeControl<_heap_element_type>::sam_allocate_encoder(void*,
const char*, size_t, cram_data_write_function_t) [with _heap_element_type =
libmaus2::bambam::parallel::GenericInputControlMergeHeapEntryQueryName; size_t
= unsigned int; cram_data_write_function_t = void (*)(void*, int, unsigned int,
const char*, unsigned int, _cram_data_write_block_type); ssize_t = int;
cram_data_write_block_type = _cram_data_write_block_type]’
1264 | cram_data_write_function_t write_func
| ~~~^~
./libmaus2/bambam/parallel/BlockMergeControl.hpp:364:94: error: cannot convert
‘’ to ‘cram_data_write_function_t’ {aka
‘void (*)(void*, int, unsigned int, const char*, unsigned int,
_cram_data_write_block_type)’}
364 |cramsupport.context =
cram_allocate_encoder(this,ptext.first,ptext.second-ptext.first,sam_data_write_function);
|
^~~
|
|
|
./libmaus2/bambam/parallel/BlockMergeControl.hpp:428:124: note: initializing
argument 4 of ‘void*
libmaus2::bambam::parallel::BlockMergeControl<_heap_element_type>::cram_allocate_encoder(void*,
const char*, size_t, cram_data_write_function_t) [with _heap_element_type =
libmaus2::bambam::parallel::GenericInputControlMergeHeapEntryQueryName; size_t
= unsigned int; cram_data_write_function_t = void (*)(void*, int, unsigned int,
const char*, unsigned int, _cram_data_write_block_type); ssize_t = int;
cram_data_write_block_type = _cram_data_write_block_type]’
428 | void * cram_allocate_encoder(void *userdata, char const *header,
size_t const headerlength, cram_data_write_function_t writefunc)
|
Bug#934619: libmaus2 FTBFS (mostly 32bit): error: no matching function for call
Source: libmaus2
Version: 2.0.611-1
Severity: serious
Tags: ftbfs
libmaus2 fails to build from source on the buildds for most 32bit
architectures. For instance:
| g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time
-D_FORTIFY_SOURCE=2 -W -Wall -Wnon-virtual-dtor -g -O2
-fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat
-Werror=format-security -O3 -pthread -std=gnu++0x -pthread -fopenmp -c -o
test/testmapperm-testmapperm.o `test -f 'test/testmapperm.cpp' || echo
'./'`test/testmapperm.cpp
| In file included from /usr/include/c++/8/map:61,
| from ./libmaus2/serialize/Serialize.hpp:25,
| from ./libmaus2/autoarray/AutoArray.hpp:27,
| from ./libmaus2/bambam/BamAuxSortingBuffer.hpp:23,
| from ./libmaus2/bambam/BamAlignmentDecoderBase.hpp:23,
| from ./libmaus2/bambam/BamAlignment.hpp:24,
| from ./libmaus2/bambam/parallel/PushBackSpace.hpp:22,
| from ./libmaus2/bambam/parallel/AlignmentBuffer.hpp:22,
| from
./libmaus2/bambam/parallel/FragmentAlignmentBufferRewriteUpdateInterval.hpp:22,
| from test/testparallelbamrewrite.cpp:20:
| /usr/include/c++/8/bits/stl_map.h: In member function ‘void
libmaus2::bambam::parallel::RewriteControl::checkValidatedRewritePending()’:
| /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument
of type ‘std::_Rb_tree >,
std::_Select1st > >,
std::less, std::allocator > >
>::const_iterator’ {aka ‘std::_Rb_tree_const_iterator > >’}
changed in GCC 7.1
| __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| In file included from test/testparallelbamblocksort.cpp:19:
| ./libmaus2/bambam/parallel/BlockMergeControl.hpp: In instantiation of ‘void
libmaus2::bambam::parallel::BlockMergeControl<_heap_element_type>::enqueHeader()
[with _heap_element_type =
libmaus2::bambam::parallel::GenericInputControlMergeHeapEntryQueryName]’:
| ./libmaus2/bambam/parallel/BlockMergeControl.hpp:571:6: required from
‘libmaus2::bambam::parallel::BlockMergeControl<_heap_element_type>::BlockMergeControl(libmaus2::parallel::SimpleThreadPool&,
std::ostream&, libmaus2::autoarray::AutoArray&, const
std::vector&,
libmaus2::bitio::BitVector*, int, uint64_t, uint64_t, uint64_t, uint64_t,
uint64_t, const string&, const string&, libmaus2::digest::DigestInterface*,
libmaus2::bambam::parallel::BlockMergeControlTypeBase::block_merge_output_format_t,
bool, bool, bool, uint64_t) [with _heap_element_type =
libmaus2::bambam::parallel::GenericInputControlMergeHeapEntryQueryName;
std::ostream = std::basic_ostream; libmaus2::bitio::BitVector =
libmaus2::bitio::BitVectorTemplate; uint64_t = long
long unsigned int; std::__cxx11::string = std::__cxx11::basic_string]’
| test/testparallelbamblocksort.cpp:223:68: required from ‘int
parallelbamblocksort(const libmaus2::util::ArgInfo&, bool, bool, const string&,
bool) [with order_type =
libmaus2::bambam::parallel::FragmentAlignmentBufferQueryNameComparator;
heap_element_type =
libmaus2::bambam::parallel::GenericInputControlMergeHeapEntryQueryName; bool
create_dup_mark_info = false; std::__cxx11::string =
std::__cxx11::basic_string]’
| test/testparallelbamblocksort.cpp:273:4: required from here
| ./libmaus2/bambam/parallel/BlockMergeControl.hpp:346:49: error: no matching
function for call to
‘libmaus2::bambam::parallel::BlockMergeControl::sam_allocate_encoder(libmaus2::bambam::parallel::BlockMergeControl*,
const char*&, int, )’
| samsupport.context =
sam_allocate_encoder(this,ptext.first,ptext.second-ptext.first,sam_data_write_function);
|
^~~
| ./libmaus2/bambam/parallel/BlockMergeControl.hpp:1260:18: note: candidate:
‘static void*
libmaus2::bambam::parallel::BlockMergeControl<_heap_element_type>::sam_allocate_encoder(void*,
const char*, size_t, cram_data_write_function_t) [with _heap_element_type =
libmaus2::bambam::parallel::GenericInputControlMergeHeapEntryQueryName; size_t
= unsigned int; cram_data_write_function_t = void (*)(void*, int, unsigned int,
const char*, unsigned int, _cram_data_write_block_type); ssize_t = int;
cram_data_write_block_type = _cram_data_write_block_type]’
| static void *sam_allocate_encoder(
| ^~~~
| ./libmaus2/bambam/parallel/BlockMergeControl.hpp:1260:18: note: no known
conversion for argument 4 from ‘’ to
‘cram_data_write_function_t’ {aka ‘void (*)(void*, int, unsigned int, const
char*, unsigned int, _cram_data_write_block_type)’}
| ./libmaus2/bambam/parallel/BlockMergeControl.hpp:364:28: error: no matching
function for call to
‘libmaus2::bambam::parallel::BlockMergeControl::cram_allocate_encoder(libmaus2::bambam::parallel::BlockMergeControl*,
const char*&, int, )’
| cramsupport.context =
