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=/<<PKGBUILDDIR>>=. -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<long long unsigned int, std::pair<const long long
unsigned int,
std::shared_ptr<libmaus2::bambam::parallel::FragmentAlignmentBuffer> >,
std::_Select1st<std::pair<const long long unsigned int,
std::shared_ptr<libmaus2::bambam::parallel::FragmentAlignmentBuffer> > >,
std::less<long long unsigned int>, std::allocator<std::pair<const long long
unsigned int,
std::shared_ptr<libmaus2::bambam::parallel::FragmentAlignmentBuffer> > >
>::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const long long
unsigned int,
std::shared_ptr<libmaus2::bambam::parallel::FragmentAlignmentBuffer> > >’}
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<char>&, const
std::vector<libmaus2::bambam::parallel::GenericInputControlStreamInfo>&,
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<char>; libmaus2::bitio::BitVector =
libmaus2::bitio::BitVectorTemplate<long long unsigned int>; uint64_t = long
long unsigned int; std::__cxx11::string = std::__cxx11::basic_string<char>]’
| 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<char>]’
| 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<libmaus2::bambam::parallel::GenericInputControlMergeHeapEntryQueryName>::sam_allocate_encoder(libmaus2::bambam::parallel::BlockMergeControl<libmaus2::bambam::parallel::GenericInputControlMergeHeapEntryQueryName>*,
const char*&, int, <unresolved overloaded function type>)’
| 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 ‘<unresolved overloaded function type>’ 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<libmaus2::bambam::parallel::GenericInputControlMergeHeapEntryQueryName>::cram_allocate_encoder(libmaus2::bambam::parallel::BlockMergeControl<libmaus2::bambam::parallel::GenericInputControlMergeHeapEntryQueryName>*,
const char*&, int, <unresolved overloaded function type>)’
| cramsupport.context =
cram_allocate_encoder(this,ptext.first,ptext.second-ptext.first,sam_data_write_function);
| ./libmaus2/bambam/parallel/BlockMergeControl.hpp:428:12: note: candidate:
‘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]’
| void * cram_allocate_encoder(void *userdata, char const *header, size_t
const headerlength, cram_data_write_function_t writefunc)
| ^~~~~~~~~~~~~~~~~~~~~
| ./libmaus2/bambam/parallel/BlockMergeControl.hpp:428:12: note: no known
conversion for argument 4 from ‘<unresolved overloaded function type>’ 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: In instantiation of ‘void
libmaus2::bambam::parallel::BlockMergeControl<_heap_element_type>::enqueHeader()
[with _heap_element_type =
libmaus2::bambam::parallel::GenericInputControlMergeHeapEntryCoordinate]’:
| ./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<char>&, const
std::vector<libmaus2::bambam::parallel::GenericInputControlStreamInfo>&,
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::GenericInputControlMergeHeapEntryCoordinate;
std::ostream = std::basic_ostream<char>; libmaus2::bitio::BitVector =
libmaus2::bitio::BitVectorTemplate<long long unsigned int>; uint64_t = long
long unsigned int; std::__cxx11::string = std::__cxx11::basic_string<char>]’
| test/testparallelbamblocksort.cpp:223:68: required from ‘int
parallelbamblocksort(const libmaus2::util::ArgInfo&, bool, bool, const string&,
bool) [with order_type =
libmaus2::bambam::parallel::FragmentAlignmentBufferPosComparator;
heap_element_type =
libmaus2::bambam::parallel::GenericInputControlMergeHeapEntryCoordinate; bool
create_dup_mark_info = true; std::__cxx11::string =
std::__cxx11::basic_string<char>]’
| test/testparallelbamblocksort.cpp:283:4: required from here
| ./libmaus2/bambam/parallel/BlockMergeControl.hpp:346:49: error: no matching
function for call to
‘libmaus2::bambam::parallel::BlockMergeControl<libmaus2::bambam::parallel::GenericInputControlMergeHeapEntryCoordinate>::sam_allocate_encoder(libmaus2::bambam::parallel::BlockMergeControl<libmaus2::bambam::parallel::GenericInputControlMergeHeapEntryCoordinate>*,
const char*&, int, <unresolved overloaded function type>)’
| 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::GenericInputControlMergeHeapEntryCoordinate; 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 ‘<unresolved overloaded function type>’ 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<libmaus2::bambam::parallel::GenericInputControlMergeHeapEntryCoordinate>::cram_allocate_encoder(libmaus2::bambam::parallel::BlockMergeControl<libmaus2::bambam::parallel::GenericInputControlMergeHeapEntryCoordinate>*,
const char*&, int, <unresolved overloaded function type>)’
| cramsupport.context =
cram_allocate_encoder(this,ptext.first,ptext.second-ptext.first,sam_data_write_function);
| ./libmaus2/bambam/parallel/BlockMergeControl.hpp:428:12: note: candidate:
‘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::GenericInputControlMergeHeapEntryCoordinate; 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]’
| void * cram_allocate_encoder(void *userdata, char const *header, size_t
const headerlength, cram_data_write_function_t writefunc)
| ^~~~~~~~~~~~~~~~~~~~~
| ./libmaus2/bambam/parallel/BlockMergeControl.hpp:428:12: note: no known
conversion for argument 4 from ‘<unresolved overloaded function type>’ to
‘cram_data_write_function_t’ {aka ‘void (*)(void*, int, unsigned int, const
char*, unsigned int, _cram_data_write_block_type)’}
| /usr/include/c++/8/bits/stl_map.h: In member function ‘virtual void
libmaus2::bambam::parallel::RewriteControl::validateBlockFragmentFinished(libmaus2::bambam::parallel::ValidationFragment&,
bool)’:
| /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument
of type ‘std::_Rb_tree<long long unsigned int, std::pair<const long long
unsigned int, bool>, std::_Select1st<std::pair<const long long unsigned int,
bool> >, std::less<long long unsigned int>, std::allocator<std::pair<const long
long unsigned int, bool> > >::const_iterator’ {aka
‘std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, bool> >’}
changed in GCC 7.1
| __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument
of type ‘std::_Rb_tree<long long unsigned int, std::pair<const long long
unsigned int, bool>, std::_Select1st<std::pair<const long long unsigned int,
bool> >, std::less<long long unsigned int>, std::allocator<std::pair<const long
long unsigned int, bool> > >::const_iterator’ {aka
‘std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, bool> >’}
changed in GCC 7.1
| __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| In file included from /usr/include/c++/8/vector:69,
| from ./libmaus2/util/StackTrace.hpp:32,
| from ./libmaus2/exception/LibMausException.hpp:25,
| from ./libmaus2/bambam/DecoderBase.hpp:23,
| from ./libmaus2/bambam/CigarRunLengthDecoder.hpp:21,
| from ./libmaus2/bambam/CigarDecoder.hpp:21,
| from ./libmaus2/bambam/BamAlignmentDecoderBase.hpp:22,
| 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/vector.tcc: In member function ‘virtual void
libmaus2::bambam::parallel::RewriteControl::addWritePendingBgzfBlock(int64_t,
int64_t, libmaus2::lz::BgzfDeflateOutputBufferBase::shared_ptr_type, const
libmaus2::lz::BgzfDeflateZStreamBaseFlushInfo&)’:
| /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for
argument of type
‘__gnu_cxx::__normal_iterator<libmaus2::bambam::parallel::WritePendingObject*,
std::vector<libmaus2::bambam::parallel::WritePendingObject> >’ changed in GCC
7.1
| _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
| ./libmaus2/bambam/parallel/BlockMergeControl.hpp: In instantiation of ‘void
libmaus2::bambam::parallel::BlockMergeControl<_heap_element_type>::checkRewriteReorderQueue()
[with _heap_element_type =
libmaus2::bambam::parallel::GenericInputControlMergeHeapEntryCoordinate]’:
| ./libmaus2/bambam/parallel/BlockMergeControl.hpp:1597:7: required from
‘void
libmaus2::bambam::parallel::BlockMergeControl<_heap_element_type>::genericInputControlReorderWorkPackageFinished(libmaus2::bambam::parallel::AlignmentBuffer::shared_ptr_type,
libmaus2::bambam::parallel::FragmentAlignmentBuffer::shared_ptr_type) [with
_heap_element_type =
libmaus2::bambam::parallel::GenericInputControlMergeHeapEntryCoordinate;
libmaus2::bambam::parallel::AlignmentBuffer::shared_ptr_type =
std::shared_ptr<libmaus2::bambam::parallel::AlignmentBuffer>;
libmaus2::bambam::parallel::FragmentAlignmentBuffer::shared_ptr_type =
std::shared_ptr<libmaus2::bambam::parallel::FragmentAlignmentBuffer>]’
| ./libmaus2/bambam/parallel/BlockMergeControl.hpp:1573:10: required from here
| ./libmaus2/bambam/parallel/BlockMergeControl.hpp:1384:50: error: no matching
function for call to
‘libmaus2::bambam::parallel::BlockMergeControl<libmaus2::bambam::parallel::GenericInputControlMergeHeapEntryCoordinate>::sam_enque_compression_block(libmaus2::bambam::parallel::BlockMergeControl<libmaus2::bambam::parallel::GenericInputControlMergeHeapEntryCoordinate>*,
void*&, uint64_t&, const char**, unsigned int*, unsigned int*, size_t&, bool&,
<unresolved overloaded function type>, <unresolved overloaded function type>,
<unresolved overloaded function type>)’
| int const r = sam_enque_compression_block(this,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
| supportdata.context /* context */,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| passPointerObject->block->id,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| passPointerObject->D->begin(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| passPointerObject->S->begin(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| passPointerObject->L->begin(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| passPointerObject->numblocks,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| passPointerObject->block->final,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| sam_enque_compression_work_package_function,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| sam_data_write_function,
| ~~~~~~~~~~~~~~~~~~~~~~~~
| sam_compression_work_package_finished_function
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| );
| ~
| ./libmaus2/bambam/parallel/BlockMergeControl.hpp:1316:16: note: candidate:
‘static int
libmaus2::bambam::parallel::BlockMergeControl<_heap_element_type>::sam_enque_compression_block(void*,
void*, size_t, const char**, const size_t*, const size_t*, size_t, int,
cram_enque_compression_work_package_function_t, cram_data_write_function_t,
cram_compression_work_package_finished_t) [with _heap_element_type =
libmaus2::bambam::parallel::GenericInputControlMergeHeapEntryCoordinate; size_t
= unsigned int; cram_enque_compression_work_package_function_t = void
(*)(void*, void*); 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;
cram_compression_work_package_finished_t = void (*)(void*, unsigned int, int)]’
| static int sam_enque_compression_block(
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
| ./libmaus2/bambam/parallel/BlockMergeControl.hpp:1316:16: note: no known
conversion for argument 10 from ‘<unresolved overloaded function type>’ 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:1437:19: error: no matching
function for call to
‘libmaus2::bambam::parallel::BlockMergeControl<libmaus2::bambam::parallel::GenericInputControlMergeHeapEntryCoordinate>::cram_enque_compression_block(libmaus2::bambam::parallel::BlockMergeControl<libmaus2::bambam::parallel::GenericInputControlMergeHeapEntryCoordinate>*,
void*&, uint64_t&, const char**, unsigned int*, unsigned int*, size_t&, bool&,
<unresolved overloaded function type>, <unresolved overloaded function type>,
<unresolved overloaded function type>)’
| int const r = cram_enque_compression_block(
| ^
| ./libmaus2/bambam/parallel/BlockMergeControl.hpp:438:9: note: candidate: ‘int
libmaus2::bambam::parallel::BlockMergeControl<_heap_element_type>::cram_enque_compression_block(void*,
void*, size_t, const char**, const size_t*, const size_t*, size_t, int,
cram_enque_compression_work_package_function_t, cram_data_write_function_t,
cram_compression_work_package_finished_t) [with _heap_element_type =
libmaus2::bambam::parallel::GenericInputControlMergeHeapEntryCoordinate; size_t
= unsigned int; cram_enque_compression_work_package_function_t = void
(*)(void*, void*); 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;
cram_compression_work_package_finished_t = void (*)(void*, unsigned int, int)]’
| int cram_enque_compression_block(
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
| ./libmaus2/bambam/parallel/BlockMergeControl.hpp:438:9: note: no known
conversion for argument 10 from ‘<unresolved overloaded function type>’ 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: In instantiation of ‘void
libmaus2::bambam::parallel::BlockMergeControl<_heap_element_type>::checkRewriteReorderQueue()
[with _heap_element_type =
libmaus2::bambam::parallel::GenericInputControlMergeHeapEntryQueryName]’:
| ./libmaus2/bambam/parallel/BlockMergeControl.hpp:1597:7: required from
‘void
libmaus2::bambam::parallel::BlockMergeControl<_heap_element_type>::genericInputControlReorderWorkPackageFinished(libmaus2::bambam::parallel::AlignmentBuffer::shared_ptr_type,
libmaus2::bambam::parallel::FragmentAlignmentBuffer::shared_ptr_type) [with
_heap_element_type =
libmaus2::bambam::parallel::GenericInputControlMergeHeapEntryQueryName;
libmaus2::bambam::parallel::AlignmentBuffer::shared_ptr_type =
std::shared_ptr<libmaus2::bambam::parallel::AlignmentBuffer>;
libmaus2::bambam::parallel::FragmentAlignmentBuffer::shared_ptr_type =
std::shared_ptr<libmaus2::bambam::parallel::FragmentAlignmentBuffer>]’
| ./libmaus2/bambam/parallel/BlockMergeControl.hpp:1573:10: required from here
| ./libmaus2/bambam/parallel/BlockMergeControl.hpp:1384:50: error: no matching
function for call to
‘libmaus2::bambam::parallel::BlockMergeControl<libmaus2::bambam::parallel::GenericInputControlMergeHeapEntryQueryName>::sam_enque_compression_block(libmaus2::bambam::parallel::BlockMergeControl<libmaus2::bambam::parallel::GenericInputControlMergeHeapEntryQueryName>*,
void*&, uint64_t&, const char**, unsigned int*, unsigned int*, size_t&, bool&,
<unresolved overloaded function type>, <unresolved overloaded function type>,
<unresolved overloaded function type>)’
| int const r = sam_enque_compression_block(this,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
| supportdata.context /* context */,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| passPointerObject->block->id,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| passPointerObject->D->begin(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| passPointerObject->S->begin(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| passPointerObject->L->begin(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| passPointerObject->numblocks,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| passPointerObject->block->final,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| sam_enque_compression_work_package_function,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| sam_data_write_function,
| ~~~~~~~~~~~~~~~~~~~~~~~~
| sam_compression_work_package_finished_function
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| );
| ~
| ./libmaus2/bambam/parallel/BlockMergeControl.hpp:1316:16: note: candidate:
‘static int
libmaus2::bambam::parallel::BlockMergeControl<_heap_element_type>::sam_enque_compression_block(void*,
void*, size_t, const char**, const size_t*, const size_t*, size_t, int,
cram_enque_compression_work_package_function_t, cram_data_write_function_t,
cram_compression_work_package_finished_t) [with _heap_element_type =
libmaus2::bambam::parallel::GenericInputControlMergeHeapEntryQueryName; size_t
= unsigned int; cram_enque_compression_work_package_function_t = void
(*)(void*, void*); 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;
cram_compression_work_package_finished_t = void (*)(void*, unsigned int, int)]’
| static int sam_enque_compression_block(
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
| ./libmaus2/bambam/parallel/BlockMergeControl.hpp:1316:16: note: no known
conversion for argument 10 from ‘<unresolved overloaded function type>’ 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:1437:19: error: no matching
function for call to
‘libmaus2::bambam::parallel::BlockMergeControl<libmaus2::bambam::parallel::GenericInputControlMergeHeapEntryQueryName>::cram_enque_compression_block(libmaus2::bambam::parallel::BlockMergeControl<libmaus2::bambam::parallel::GenericInputControlMergeHeapEntryQueryName>*,
void*&, uint64_t&, const char**, unsigned int*, unsigned int*, size_t&, bool&,
<unresolved overloaded function type>, <unresolved overloaded function type>,
<unresolved overloaded function type>)’
| int const r = cram_enque_compression_block(
| ^
| ./libmaus2/bambam/parallel/BlockMergeControl.hpp:438:9: note: candidate: ‘int
libmaus2::bambam::parallel::BlockMergeControl<_heap_element_type>::cram_enque_compression_block(void*,
void*, size_t, const char**, const size_t*, const size_t*, size_t, int,
cram_enque_compression_work_package_function_t, cram_data_write_function_t,
cram_compression_work_package_finished_t) [with _heap_element_type =
libmaus2::bambam::parallel::GenericInputControlMergeHeapEntryQueryName; size_t
= unsigned int; cram_enque_compression_work_package_function_t = void
(*)(void*, void*); 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;
cram_compression_work_package_finished_t = void (*)(void*, unsigned int, int)]’
| int cram_enque_compression_block(
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
| ./libmaus2/bambam/parallel/BlockMergeControl.hpp:438:9: note: no known
conversion for argument 10 from ‘<unresolved overloaded function type>’ to
‘cram_data_write_function_t’ {aka ‘void (*)(void*, int, unsigned int, const
char*, unsigned int, _cram_data_write_block_type)’}
| 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::checkLargeBlockCompressionPending()’:
| /usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument
of type ‘std::_Rb_tree<long long unsigned int, std::pair<const long long
unsigned int,
std::shared_ptr<libmaus2::bambam::parallel::FragmentAlignmentBuffer> >,
std::_Select1st<std::pair<const long long unsigned int,
std::shared_ptr<libmaus2::bambam::parallel::FragmentAlignmentBuffer> > >,
std::less<long long unsigned int>, std::allocator<std::pair<const long long
unsigned int,
std::shared_ptr<libmaus2::bambam::parallel::FragmentAlignmentBuffer> > >
>::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const long long
unsigned int,
std::shared_ptr<libmaus2::bambam::parallel::FragmentAlignmentBuffer> > >’}
changed in GCC 7.1
| __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| In file included from /usr/include/c++/8/vector:69,
| from ./libmaus2/util/StackTrace.hpp:32,
| from ./libmaus2/exception/LibMausException.hpp:25,
| from ./libmaus2/bambam/DecoderBase.hpp:23,
| from ./libmaus2/bambam/CigarRunLengthDecoder.hpp:21,
| from ./libmaus2/bambam/CigarDecoder.hpp:21,
| from ./libmaus2/bambam/BamAlignmentDecoderBase.hpp:22,
| 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/vector.tcc:109:4: note: parameter passing for
argument of type
‘__gnu_cxx::__normal_iterator<libmaus2::bambam::parallel::SmallLinearBlockCompressionPendingObject*,
std::vector<libmaus2::bambam::parallel::SmallLinearBlockCompressionPendingObject>
>’ changed in GCC 7.1
| _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
libmaus2 previously built on e.g. armhf, so the correct severity is
serious.
Helmut
