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RamRS/biostars-173494.txt Secret

Created December 24, 2019 22:12
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biostars-173494.txt
make all-recursive
make[1]: Entering directory '/home/pommy/inst/tophat-2.1.0'
Making all in src
make[2]: Entering directory '/home/pommy/inst/tophat-2.1.0/src'
Makefile:1598: warning: overriding recipe for target 'libbam.a'
Makefile:1129: warning: ignoring old recipe for target 'libbam.a'
g++ -DHAVE_CONFIG_H -I. -I.. -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -DNDEBUG -I./samtools-0.1.18 -pthread -I/home/pommy/include -I./SeqAn-1.3 -MT reads.o -MD -MP -MF .deps/reads.Tpo -c -o reads.o reads.cpp
In file included from ./SeqAn-1.3/seqan/basic.h:83:0,
from ./SeqAn-1.3/seqan/sequence.h:50,
from ./SeqAn-1.3/seqan/find.h:43,
from reads.cpp:22:
./SeqAn-1.3/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate>&)':
./SeqAn-1.3/seqan/basic/basic_holder.h:992:35: warning: typedef 'THolder' locally defined but not used [-Wunused-local-typedefs]
typedef Holder<TValue, Tristate> THolder;
^
./SeqAn-1.3/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate>&, const TSource&)':
./SeqAn-1.3/seqan/basic/basic_holder.h:1022:58: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
typedef typename Value<Holder<TValue, Tristate> >::Type THostValue;
^
./SeqAn-1.3/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
./SeqAn-1.3/seqan/basic/basic_holder.h:1520:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
^
./SeqAn-1.3/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
./SeqAn-1.3/seqan/basic/basic_holder.h:1545:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
^
./SeqAn-1.3/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
./SeqAn-1.3/seqan/basic/basic_holder.h:1569:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
^
In file included from ./SeqAn-1.3/seqan/basic.h:88:0,
from ./SeqAn-1.3/seqan/sequence.h:50,
from ./SeqAn-1.3/seqan/find.h:43,
from reads.cpp:22:
./SeqAn-1.3/seqan/basic/basic_allocator_chunkpool.h: In function 'void seqan::deallocate(seqan::Allocator<seqan::ChunkPool<SIZE, MAX_COUNT, TParentAllocator> >&, TValue*, TSize, seqan::Tag<TUsage>)':
./SeqAn-1.3/seqan/basic/basic_allocator_chunkpool.h:239:67: warning: typedef 'TAllocator' locally defined but not used [-Wunused-local-typedefs]
typedef Allocator<ChunkPool<SIZE, MAX_COUNT, TParentAllocator> > TAllocator;
^
In file included from ./SeqAn-1.3/seqan/sequence.h:73:0,
from ./SeqAn-1.3/seqan/find.h:43,
from reads.cpp:22:
./SeqAn-1.3/seqan/sequence/sequence_lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
./SeqAn-1.3/seqan/sequence/sequence_lexical.h:260:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
typedef typename Value<TLeft>::Type TLeftValue;
^
./SeqAn-1.3/seqan/sequence/sequence_lexical.h:261:39: warning: typedef 'TRightValue' locally defined but not used [-Wunused-local-typedefs]
typedef typename Value<TRight>::Type TRightValue;
^
In file included from ./SeqAn-1.3/seqan/sequence.h:87:0,
from ./SeqAn-1.3/seqan/find.h:43,
from reads.cpp:22:
./SeqAn-1.3/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
./SeqAn-1.3/seqan/sequence/string_base.h:919:47: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
./SeqAn-1.3/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
./SeqAn-1.3/seqan/sequence/string_base.h:929:47: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
./SeqAn-1.3/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
./SeqAn-1.3/seqan/sequence/string_base.h:942:47: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
./SeqAn-1.3/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
./SeqAn-1.3/seqan/sequence/string_base.h:952:47: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
./SeqAn-1.3/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
./SeqAn-1.3/seqan/sequence/string_base.h:1152:47: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
./SeqAn-1.3/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
./SeqAn-1.3/seqan/sequence/string_base.h:1164:47: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
./SeqAn-1.3/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
./SeqAn-1.3/seqan/sequence/string_base.h:1178:47: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
./SeqAn-1.3/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
./SeqAn-1.3/seqan/sequence/string_base.h:1190:47: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
./SeqAn-1.3/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, TPositionBegin, TPositionEnd, const TSource&, seqan::Tag<TUsage>)':
./SeqAn-1.3/seqan/sequence/string_base.h:1358:47: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
./SeqAn-1.3/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, TPositionBegin, TPositionEnd, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
./SeqAn-1.3/seqan/sequence/string_base.h:1372:47: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
./SeqAn-1.3/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, TPositionBegin, TPositionEnd, const TSourceValue*, seqan::Tag<TUsage>)':
./SeqAn-1.3/seqan/sequence/string_base.h:1388:47: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
./SeqAn-1.3/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, TPositionBegin, TPositionEnd, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
./SeqAn-1.3/seqan/sequence/string_base.h:1402:47: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
typedef String<TTargetValue, TTargetSpec> TTarget;
^
In file included from ./SeqAn-1.3/seqan/sequence.h:92:0,
from ./SeqAn-1.3/seqan/find.h:43,
from reads.cpp:22:
./SeqAn-1.3/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::ClearSpaceStringPacked_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
./SeqAn-1.3/seqan/sequence/string_packed.h:655:54: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
typedef typename Iterator<T, Standard>::Type TIterator;
^
In file included from ./SeqAn-1.3/seqan/sequence.h:102:0,
from ./SeqAn-1.3/seqan/find.h:43,
from reads.cpp:22:
./SeqAn-1.3/seqan/sequence/string_set_dependent_tight.h: In function 'typename seqan::Id<seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagInsist_> > > >::Type seqan::assignValueById(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagInsist_> > >&, TString&, TId1)':
./SeqAn-1.3/seqan/sequence/string_set_dependent_tight.h:232:45: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
typedef typename Size<TStringSet>::Type TSize;
^
In file included from ./SeqAn-1.3/seqan/modifier.h:54:0,
from ./SeqAn-1.3/seqan/find.h:44,
from reads.cpp:22:
./SeqAn-1.3/seqan/modifier/modifier_alphabet_expansion.h: In function 'void seqan::_initializeAlphabetConversionTable(seqan::ModifiedAlphabet<THost, seqan::ModExpand<CHAR, TSpec> >*, const TSource&)':
./SeqAn-1.3/seqan/modifier/modifier_alphabet_expansion.h:232:59: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
typedef ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > TTarget;
^
./SeqAn-1.3/seqan/modifier/modifier_alphabet_expansion.h: In function 'void seqan::_initializeAlphabetConversionTable(TTarget*, const seqan::ModifiedAlphabet<THost, seqan::ModExpand<CHAR, TSpec> >&)':
./SeqAn-1.3/seqan/modifier/modifier_alphabet_expansion.h:343:59: warning: typedef 'TSource' locally defined but not used [-Wunused-local-typedefs]
typedef ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > TSource;
^
./SeqAn-1.3/seqan/modifier/modifier_alphabet_expansion.h: In function 'void seqan::_initializeAlphabetOrdTable(TTarget*, const seqan::ModifiedAlphabet<THost, seqan::ModExpand<CHAR, TSpec> >&)':
./SeqAn-1.3/seqan/modifier/modifier_alphabet_expansion.h:364:59: warning: typedef 'TSource' locally defined but not used [-Wunused-local-typedefs]
typedef ModifiedAlphabet<THost, ModExpand<CHAR, TSpec> > TSource;
^
In file included from ./SeqAn-1.3/seqan/file.h:56:0,
from ./SeqAn-1.3/seqan/score/score_matrix.h:40,
from ./SeqAn-1.3/seqan/score.h:48,
from ./SeqAn-1.3/seqan/find.h:45,
from reads.cpp:22:
./SeqAn-1.3/seqan/file/file_generated_forwards.h: At global scope:
./SeqAn-1.3/seqan/file/file_generated_forwards.h:927:66: error: invalid abstract return type 'seqan::FileFormat<TFile, TData, TMeta, void>'
template <typename TFile, typename TData, typename TMeta> inline FileFormat<TFile, TData, TMeta, void> guessFileFormat(TFile & file, TData & data); // "projects/library/seqan/file/file_format_guess.h"(65)
^
In file included from ./SeqAn-1.3/seqan/file.h:84:0,
from ./SeqAn-1.3/seqan/score/score_matrix.h:40,
from ./SeqAn-1.3/seqan/score.h:48,
from ./SeqAn-1.3/seqan/find.h:45,
from reads.cpp:22:
./SeqAn-1.3/seqan/file/file_format.h:143:8: note: because the following virtual functions are pure within 'seqan::FileFormat<TFile, TData, TMeta, void>':
struct FileFormat<TFile, TData, TMeta, void>
^
./SeqAn-1.3/seqan/file/file_format.h:154:2: note: virtual void* seqan::FileFormat<TFile, TData, TMeta, void>::formatID_() const
formatID_() const = 0;
^
./SeqAn-1.3/seqan/file/file_format.h:157:2: note: virtual void seqan::FileFormat<TFile, TData, TMeta, void>::read_(TFile&, TData&) const
read_(TFile & file, TData & data) const = 0;
^
./SeqAn-1.3/seqan/file/file_format.h:159:2: note: virtual void seqan::FileFormat<TFile, TData, TMeta, void>::read_(TFile&, TData&, seqan::FileFormat<TFile, TData, TMeta, void>::TSize) const
read_(TFile & file, TData & data, TSize limit) const = 0;
^
./SeqAn-1.3/seqan/file/file_format.h:162:2: note: virtual void seqan::FileFormat<TFile, TData, TMeta, void>::readMeta_(TFile&, TMeta&) const
readMeta_(TFile & file, TMeta & meta) const = 0;
^
./SeqAn-1.3/seqan/file/file_format.h:165:2: note: virtual void seqan::FileFormat<TFile, TData, TMeta, void>::goNext_(TFile&) const
goNext_(TFile & file) const = 0;
^
./SeqAn-1.3/seqan/file/file_format.h:168:2: note: virtual seqan::FileFormat<TFile, TData, TMeta, void>::TSize seqan::FileFormat<TFile, TData, TMeta, void>::length_(TFile&) const
length_(TFile & file) const = 0;
^
./SeqAn-1.3/seqan/file/file_format.h:171:2: note: virtual void seqan::FileFormat<TFile, TData, TMeta, void>::write_(TFile&, TData&) const
write_(TFile & file, TData & data) const = 0;
^
./SeqAn-1.3/seqan/file/file_format.h:173:2: note: virtual void seqan::FileFormat<TFile, TData, TMeta, void>::write_(TFile&, TData&, TMeta&) const
write_(TFile & file, TData & data, TMeta & meta) const = 0;
^
Makefile:1347: recipe for target 'reads.o' failed
make[2]: *** [reads.o] Error 1
make[2]: Leaving directory '/home/pommy/inst/tophat-2.1.0/src'
Makefile:313: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/home/pommy/inst/tophat-2.1.0'
Makefile:253: recipe for target 'all' failed
make: *** [all] Error 2
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