Bug#940564: racon: FTBFS against libspoa3

2019-09-18 Thread Andreas Tille 
Control: tags -1 upstream
Control: forwarded -1 https://github.com/lbcb-sci/racon/issues/6

Bug#940564: racon: FTBFS against libspoa3

2019-09-17 Thread Andreas Tille 
Hi again,

On Tue, Sep 17, 2019 at 02:15:51PM +0200, Andreas Tille wrote:
> Latest upstream needs liblogger[1] which needs to be packaged new.
> I'm working on this (Python3 migration drained to many resources,
> sorry)
> 
> [1]  https://salsa.debian.org/med-team/liblogger

That's solved now but there is another incompatibility with spoa:

   https://github.com/lbcb-sci/racon/issues/6

Kind regards

  Andreas.

-- 
http://fam-tille.de

Bug#940564: racon: FTBFS against libspoa3

2019-09-17 Thread Andreas Tille 
Latest upstream needs liblogger[1] which needs to be packaged new.
I'm working on this (Python3 migration drained to many resources,
sorry)

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

-- 
http://fam-tille.de

Bug#940564: racon: FTBFS against libspoa3

2019-09-17 Thread Graham Inggs 

Source: racon
Version: 1.3.2-1
Severity: serious

Hi Maintainer

In a recent binNMU against libspoa3 [1], racon FTBFS with the errors below.

Regards
Graham


[1] 
https://buildd.debian.org/status/fetch.php?pkg=racon=amd64=1.3.2-1%2Bb2=1566980028=0



/usr/bin/c++   -I/<>/obj-x86_64-linux-gnu/config 
-I/<>/src  -g -O2 -fdebug-prefix-map=/<>=. 
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 
-D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic   -std=gnu++11 -o 
CMakeFiles/racon.dir/src/main.cpp.o -c /<>/src/main.cpp
/<>/src/polisher.cpp: In member function ‘void 
racon::Polisher::initialize()’:
/<>/src/polisher.cpp:169:15: error: ‘class 
bioparser::Parser’ has no member named ‘parse_objects’

  169 | tparser_->parse_objects(sequences_, -1);
  |   ^
/<>/src/polisher.cpp:196:33: error: ‘class 
bioparser::Parser’ has no member named ‘parse_objects’
  196 | auto status = sparser_->parse_objects(sequences_, 
kChunkSize);

  | ^
/<>/src/polisher.cpp:277:33: error: ‘class 
bioparser::Parser’ has no member named ‘parse_objects’
  277 | auto status = oparser_->parse_objects(overlaps, 
kChunkSize);

  | ^
...
/<>/src/window.cpp: In member function ‘bool 
racon::Window::generate_consensus(std::shared_ptr)’:
/<>/src/window.cpp:89:43: error: ‘using element_type = 
class spoa::AlignmentEngine’ {aka ‘class spoa::AlignmentEngine’} has no 
member named ‘align_sequence_with_graph’
   89 | alignment = 
alignment_engine->align_sequence_with_graph(

  |   ^
/<>/src/window.cpp:95:43: error: ‘using element_type = 
class spoa::AlignmentEngine’ {aka ‘class spoa::AlignmentEngine’} has no 
member named ‘align_sequence_with_graph’
   95 | alignment = 
alignment_engine->align_sequence_with_graph(

  |   ^
make[3]: *** [CMakeFiles/racon.dir/build.make:118: 
CMakeFiles/racon.dir/src/window.cpp.o] Error 1