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=/<<PKGBUILDDIR>>=. -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<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::string = std::__cxx11::basic_string<char>]’
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<char>]’
test/testparallelbamblocksort.cpp:259:4: required from here
./libmaus2/bambam/parallel/BlockMergeControl.hpp:346:92: error: cannot convert
‘<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)’}
346 | samsupport.context =
sam_allocate_encoder(this,ptext.first,ptext.second-ptext.first,sam_data_write_function);
|
^~~~~~~~~~~~~~~~~~~~~~~
|
|
|
<unresolved overloaded function type>
./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
‘<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)’}
364 | cramsupport.context =
cram_allocate_encoder(this,ptext.first,ptext.second-ptext.first,sam_data_write_function);
|
^~~~~~~~~~~~~~~~~~~~~~~
|
|
|
<unresolved overloaded function type>
./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)
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
Any hint how to fix this would be very welcome.
Kind regards
Andreas.
On Mon, Aug 12, 2019 at 04:02:40PM +0200, Helmut Grohne wrote:
> 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
>
> _______________________________________________
> Debian-med-packaging mailing list
> [email protected]
> https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging
--
http://fam-tille.de
