> On Jan 22, 2020, at 11:56, Andreas Tille <andr...@an3as.eu> wrote:
>
> Control: tags -1 help
>
> I have fixed Python2->Python3 migration as well as the FTBFS with
> pbseqlib 5.3.3+dfsg-1 issue in Git[1]. Unfortunately there is another
> build issue in the C++ code which I have no idea how to fix:
>
>
> ...
> g++ -g -O2 -fdebug-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+ds=.
> -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14
> -Wall -Wuninitialized -pedantic -Wdate- time -D_FORTIFY_SOURCE=2 -MMD -MP
> -I/build/pbdagcon-0.3+git20180411.c14c422+ds/DAZZ_DB
> -I/build/pbdagcon-0.3+git20180411.c14c422+ds/DALIGNER
> -I/usr/include/pbseq/alignment -I/usr/include/ pbseq/pbdata
> -I/usr/include/pbseq/hdf -I/usr/include/pbseq -isystem.//third-party -c -o
> DazAlnProvider.o DazAlnProvider.cpp
> In file included from DazAlnProvider.cpp:10:
> DazAlnProvider.hpp:97:19: error: expected ')' before '&' token
> 97 | Target(DAZZ_DB& db, int tspace, int small);
> | ~ ^
> | )
> DazAlnProvider.hpp:122:5: error: 'DAZZ_DB' does not name a type
> 122 | DAZZ_DB db_;
> | ^~~~~~~
> DazAlnProvider.hpp:161:5: error: 'DAZZ_DB' does not name a type
> 161 | DAZZ_DB db_;
> | ^~~~~~~
> DazAlnProvider.cpp: In constructor 'DazAlnProvider::DazAlnProvider(const
> ProgramOpts&)':
> DazAlnProvider.cpp:34:33: error: 'db_' was not declared in this scope
> 34 | int status = Open_DB(path, &db_);
> | ^~~
> DazAlnProvider.cpp: In destructor 'virtual DazAlnProvider::~DazAlnProvider()':
> DazAlnProvider.cpp:74:15: error: 'db_' was not declared in this scope
> 74 | Close_DB(&db_);
> | ^~~
> DazAlnProvider.cpp: In member function 'virtual bool
> DazAlnProvider::nextTarget(std::string&, std::vector<dagcon::Alignment>&)':
> DazAlnProvider.cpp:125:25: error: 'db_' was not declared in this scope
> 125 | seq = Load_Subread(&db_, trg_->id, 0, trg_->length, targSeqBuf_,
> 0);
> | ^~~
> DazAlnProvider.cpp: At global scope:
> DazAlnProvider.cpp:225:15: error: expected constructor, destructor, or type
> conversion before '(' token
> 225 | Target::Target(DAZZ_DB& db, int tspace, int small) :
> | ^
> DazAlnProvider.cpp: In member function 'void Target::firstRecord(Record&,
> bool)':
> DazAlnProvider.cpp:246:14: error: 'db_' was not declared in this scope
> 246 | length = db_.reads[id].rlen;
> | ^~~
Just taking some educated guesses here, but the way this variable is used
indicates to me that the code expects it to be a HITS_DB, declared in
DAZZ_DB/DB.h. The DAZZ_DB subdirectory looks like a copy of upstream project
https://github.com/thegenemyers/DAZZ_DB
<https://github.com/thegenemyers/DAZZ_DB>. The latest revision of this calls
this type DAZZ_DB, not HITS_DB. So maybe the solution is to pull in the latest
revision of this?
