[Seqan-dev] tophat with seqan 1.4.1 fails to build on mips/mipsel

[Alex Mestiashvili <alex@biotec.tu-dresden.de>]

Hi All,

there is another problem with seqan 1.4.1 and tophat - it fails to build 
on mips and mipsel architectures:

---
| make[3]: Entering directory '/«BUILDDIR»/tophat-2.0.12+dfsg/src'
| g++ -DHAVE_CONFIG_H -I. -I..   -D_FORTIFY_SOURCE=2  -Wall 
-Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized  -O3 -g -O2 -Wformat 
-Werror=format-security -DNDEBUG -pthread -I/usr/include  -c -o reads.o 
reads.cpp
| In file included from /usr/include/seqan/file.h:56:0,
|                  from /usr/include/seqan/score/score_matrix.h:40,
|                  from /usr/include/seqan/score.h:48,
|                  from /usr/include/seqan/find.h:45,
|                  from reads.cpp:21:
| /usr/include/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);        // "seqan-1.3.1/seqan/file/file_format_guess.h"(65)
|                                                                   ^
| In file included from /usr/include/seqan/file.h:84:0,
|                  from /usr/include/seqan/score/score_matrix.h:40,
|                  from /usr/include/seqan/score.h:48,
|                  from /usr/include/seqan/find.h:45,
|                  from reads.cpp:21:
| /usr/include/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>
|         ^
| /usr/include/seqan/file/file_format.h:154:2: note: 	virtual void* 
seqan::FileFormat<TFile, TData, TMeta, void>::formatID_() const
|   formatID_() const = 0;
|   ^
| /usr/include/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;
|   ^
| /usr/include/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;
|   ^
| /usr/include/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;
|   ^
| /usr/include/seqan/file/file_format.h:165:2: note: 	virtual void 
seqan::FileFormat<TFile, TData, TMeta, void>::goNext_(TFile&) const
|   goNext_(TFile & file) const = 0;
|   ^
| /usr/include/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;
|   ^
| /usr/include/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;
|   ^
| /usr/include/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;
|   ^
| make[3]: *** [reads.o] Error 1


help would be greatly appreciated.


Here are the full build logs:

https://buildd.debian.org/status/fetch.php?pkg=tophat&arch=mipsel&ver=2.0.12%2Bdfsg-1&stamp=1404743513


https://buildd.debian.org/status/fetch.php?pkg=tophat&arch=mips&ver=2.0.12%2Bdfsg-1&stamp=1404739146


Thank you,
Alex