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