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
