[Debian-med-packaging] Bug#940564: racon: FTBFS against libspoa3

[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&arch=amd64&ver=1.3.2-1%2Bb2&stamp=1566980028&raw=0


/usr/bin/c++   -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/config 
-I/<<PKGBUILDDIR>>/src  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. 
-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 /<<PKGBUILDDIR>>/src/main.cpp
/<<PKGBUILDDIR>>/src/polisher.cpp: In member function ‘void 
racon::Polisher::initialize()’:
/<<PKGBUILDDIR>>/src/polisher.cpp:169:15: error: ‘class 
bioparser::Parser<racon::Sequence>’ has no member named ‘parse_objects’
   169 |     tparser_->parse_objects(sequences_, -1);
       |               ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/polisher.cpp:196:33: error: ‘class 
bioparser::Parser<racon::Sequence>’ has no member named ‘parse_objects’
   196 |         auto status = sparser_->parse_objects(sequences_, 
kChunkSize);
       |                                 ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/polisher.cpp:277:33: error: ‘class 
bioparser::Parser<racon::Overlap>’ has no member named ‘parse_objects’
   277 |         auto status = oparser_->parse_objects(overlaps, 
kChunkSize);
       |                                 ^~~~~~~~~~~~~
...
/<<PKGBUILDDIR>>/src/window.cpp: In member function ‘bool 
racon::Window::generate_consensus(std::shared_ptr<spoa::AlignmentEngine>)’:
/<<PKGBUILDDIR>>/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(
       |                                           ^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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