Re: C++ help needed for new version of pbdagcon

[Andreas Tille]

On Sat, Aug 18, 2018 at 09:18:58AM +0800, Paul Wise wrote:
> On Fri, Aug 17, 2018 at 10:44 PM, Andrey Rahmatullin wrote:
> 
> > Looks like the project code was updated for s/HITS_DB/DAZZ_DB/ but the
> > DAZZ_DB submodule snapshot was not updated. Ask the upstream.
> 
> This sounds like an embedded code copy, you might want to talk to
> upstream to find out and get it removed.
> 
> https://wiki.debian.org/EmbeddedCodeCopies

Upstream has turned out to be not very responsive and regarding the
code copy you might like to read here:

https://lists.debian.org/debian-med/2018/07/msg00088.html

Kind regards

 Andreas. 

-- 
http://fam-tille.de

Re: C++ help needed for new version of pbdagcon

[Paul Wise]

On Fri, Aug 17, 2018 at 10:44 PM, Andrey Rahmatullin wrote:

> Looks like the project code was updated for s/HITS_DB/DAZZ_DB/ but the
> DAZZ_DB submodule snapshot was not updated. Ask the upstream.

This sounds like an embedded code copy, you might want to talk to
upstream to find out and get it removed.

https://wiki.debian.org/EmbeddedCodeCopies

-- 
bye,
pabs

https://wiki.debian.org/PaulWise

Re: C++ help needed for new version of pbdagcon

[Andrey Rahmatullin]

On Fri, Aug 17, 2018 at 01:16:25PM +0200, Andreas Tille wrote:
> DazAlnProvider.hpp:122:5: error: 'DAZZ_DB' does not name a type
>  DAZZ_DB db_;
>  ^~~
Looks like the project code was updated for s/HITS_DB/DAZZ_DB/ but the
DAZZ_DB submodule snapshot was not updated. Ask the upstream.

-- 
WBR, wRAR


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C++ help needed for new version of pbdagcon

[Andreas Tille]

Hi,

I've updated pbdagcon[1] to latest upstream commit.  Unfortunately the
build fails with:


...
g++ -g -O2 -fdebug-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+ds=. 
-fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -Wall 
-Wuninitialized -pedantic -Wdate-time -D_FORTIFY_SOURCE=
In file included from DazAlnProvider.cpp:10:
DazAlnProvider.hpp:97:19: error: expected ')' before '&' token
 Target(DAZZ_DB& db, int tspace, int small);
   ~   ^
   )
DazAlnProvider.hpp:122:5: error: 'DAZZ_DB' does not name a type
 DAZZ_DB db_;
 ^~~
DazAlnProvider.hpp:161:5: error: 'DAZZ_DB' does not name a type
 DAZZ_DB db_;
 ^~~
DazAlnProvider.cpp: In constructor 'DazAlnProvider::DazAlnProvider(const 
ProgramOpts&)':
DazAlnProvider.cpp:34:33: error: 'db_' was not declared in this scope
 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
 Close_DB(&db_);
   ^~~
DazAlnProvider.cpp: In member function 'virtual bool 
DazAlnProvider::nextTarget(std::__cxx11::string&, 
std::vector&)':
DazAlnProvider.cpp:125:25: error: 'db_' was not declared in this scope
 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
 Target::Target(DAZZ_DB& db, int tspace, int small) :
   ^
DazAlnProvider.cpp: In member function 'void Target::firstRecord(Record&, 
bool)':
...


Any hint how to fix this?


Kind regards

Andreas.


[1] https://salsa.debian.org/med-team/pbdagcon

-- 
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