Seqan knowledge needed (Was: Help needed in C++ / seqan issue)
Hello,
I intend to package mugsy which contains a copy (fork?) of some old
seqan version. In contrast to Gert's advise below I would prefer to
port this to the current (and future) seqan versions but I obviously
need some help. The full discussion between Gert and me starts here[2]
in the mailing list archive.
On Wed, Apr 15, 2015 at 12:21:07PM +0200, Gert Wollny wrote:
>
> > I guess the code copy of the old seqan will show several C++ problems as
> > well. So IMHO trying to work with this is similarly fruitless as trying
> > to port the code to new seqan.
> Usually solving these errors is quite straightforward, so if you think
> that for know it would make sense to include the old code, I could do
> the porting to the new C++ compiler, and then, when we have a test set
> we could focus on moving to the new seqan.
I wonder whether somebody might be able to give some hint on errors like
these:
...
g++ -I /usr/local/projects/angiuoli/boost/include/boost-1_38 -pedantic -ftemplate-depth-200 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O3 synchain-mugsy.cpp -c -o synchain-mugsy.o
In file included from /usr/include/c++/4.9/ext/hash_set:60:0,
from synchain-mugsy.cpp:83:
/usr/include/c++/4.9/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a futur
e date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this
warning use -Wno-deprecated. [-Wcpp]
#warning \
^
g++ -I /usr/local/projects/angiuoli/boost/include/boost-1_38 -pedantic -ftemplate-depth-200 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O3 -Wl,-z,relro synchain-mugsy.o -o /tmp/buildd/mugsy-
1r2.3+dfsg/chaining/synchain-mugsy; chmod 755 /tmp/buildd/mugsy-1r2.3+dfsg/chaining/synchain-mugsy
make[2]: Leaving directory '/tmp/buildd/mugsy-1r2.3+dfsg/chaining'
make -C mugsy-seqan/projects/library/apps
make[2]: Entering directory '/tmp/buildd/mugsy-1r2.3+dfsg/mugsy-seqan/projects/library/apps'
g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I.. -O9 -pedantic -W -Wall -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2 -Wl,-z,relro -lrt mugsy/mugs
y.cpp -o mugsy/mugsy
In file included from /usr/include/seqan/basic/basic_debug.h:58:0,
from /usr/include/seqan/basic.h:52,
from mugsy/mugsy.cpp:29:
mugsy/mugsy.cpp:79:1: error: '_proFloat' does not name a type
SEQAN_PROTIMESTART(__myProfileTime); // Profiling
^
mugsy/mugsy.cpp: In function 'void buildMatchesFromGraph(TGraph&, seqan::StringSet<TSequence, TSpec>&, TFragmentString&, TScoreValues&)':
mugsy/mugsy.cpp:2161:17: error: 'TFragment' has no member named 'reversed'
if(currfrag.reversed){
^
In file included from /usr/include/seqan/basic/basic_debug.h:58:0,
from /usr/include/seqan/basic.h:52,
from mugsy/mugsy.cpp:29:
mugsy/mugsy.cpp: In function 'void generateLCBs(seqan::Graph<seqan::Alignment<TStringSet, TCargo, TSpec> >&, TLCB&, TStringSet1&, TNames&, TGenomeNames&, TVertexOrientMap&, TIntervals&, const
seqan::MsaOptions<seqan::SimpleType<unsigned char, seqan::Dna5_>, TScore>&)':
mugsy/mugsy.cpp:3300:66: error: '__myProfileTime' was not declared in this scope
std::cerr << "Anchor conversion done: " << SEQAN_PROTIMEUPDATE(__myProfileTime) << " seconds" << std::endl;
^
mugsy/mugsy.cpp: In function 'std::vector<s_score> alignLCBs(TGraph&, TLCBs&, TStringSet1&, TStringSet2&, TNames&, TGenomeNames&, TVertexOrientMap&, TStream1&, std::map<TName, std::vector<TLo
c> >&, const seqan::MsaOptions<seqan::SimpleType<unsigned char, seqan::Dna5_>, TScore>&)':
mugsy/mugsy.cpp:3854:71: error: '__myProfileTime' was not declared in this scope
std::cerr << "Saving interval tree done: " << SEQAN_PROTIMEUPDATE(__myProfileTime) << " seconds" << std::endl;
^
mugsy/mugsy.cpp:4152:47: error: there are no arguments to 'MafFormat' that depend on a template parameter, so a declaration of 'MafFormat' must be available [-fpermissive]
write(strmmaf,currgOut,currnameSet,MafFormat(),curroffsets,currspanlens,currseqlens,currorients,lcblabel.str());
^
mugsy/mugsy.cpp:4152:47: note: (if you use '-fpermissive', G++ will accept your code, but allowing the use of an undeclared name is deprecated)
In file included from /usr/include/seqan/basic/basic_debug.h:58:0,
from /usr/include/seqan/basic.h:52,
from mugsy/mugsy.cpp:29:
mugsy/mugsy.cpp: In function 'void wholeGenomeAlignment(TGraph&, TStringSet&, TStringSet2&, TNames&, TGenomeNames&, const seqan::MsaOptions<seqan::SimpleType<unsigned char, seqan::Dna5_>, TSc
ore>&, TLCBs&, TVMap&, TStream&, TIMap&)':
...
Any help is welcome
Andreas.
[1] http://mugsy.sourceforge.net/
[2] https://lists.debian.org/debian-med/2015/04/msg00006.html
--
http://fam-tille.de
Reply to: