Package: racon
Version: 1.4.21-1
Severity: serious
X-Debbugs-Cc: ni...@thykier.net
Hi,
A new version of libedlib (with a new ABI) has been uploaded to
unstable and that causes racon to fail to build from source.
Relevant parts of the amd64 log:
```
> /usr/bin/cmake -E cmake_link_script CMakeFiles/racon_test.dir/link.txt
> --verbose=1
> /usr/bin/c++ -g -O2 -ffile-prefix-map=/<>=.
> -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
> -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -Wl,-z,relro -Wl,-z,now -rdynamic
> CMakeFiles/racon_test.dir/test/racon_test.cpp.o
> CMakeFiles/racon_test.dir/src/logger.cpp.o
> CMakeFiles/racon_test.dir/src/polisher.cpp.o
> CMakeFiles/racon_test.dir/src/overlap.cpp.o
> CMakeFiles/racon_test.dir/src/sequence.cpp.o
> CMakeFiles/racon_test.dir/src/window.cpp.o -o bin/racon_test -lspoa -ledlib
> -lz /usr/lib/x86_64-linux-gnu/libgtest_main.a
> /usr/lib/x86_64-linux-gnu/libgtest.a -pthread
> /usr/bin/ld: CMakeFiles/racon_test.dir/test/racon_test.cpp.o: in function
> `calculateEditDistance(std::__cxx11::basic_string std::char_traits, std::allocator > const&,
> std::__cxx11::basic_string, std::allocator
> > const&)':
> ./obj-x86_64-linux-gnu/./test/racon_test.cpp:18: undefined reference to
> `edlibDefaultAlignConfig'
> /usr/bin/ld: ./obj-x86_64-linux-gnu/./test/racon_test.cpp:18: undefined
> reference to `edlibAlign'
> /usr/bin/ld: ./obj-x86_64-linux-gnu/./test/racon_test.cpp:22: undefined
> reference to `edlibFreeAlignResult'
> /usr/bin/ld: CMakeFiles/racon_test.dir/src/overlap.cpp.o: in function
> `racon::Overlap::align_overlaps(char const*, unsigned int, char const*,
> unsigned int)':
> ./obj-x86_64-linux-gnu/./src/overlap.cpp:208: undefined reference to
> `edlibNewAlignConfig'
> /usr/bin/ld: ./obj-x86_64-linux-gnu/./src/overlap.cpp:208: undefined
> reference to `edlibAlign'
> /usr/bin/ld: ./obj-x86_64-linux-gnu/./src/overlap.cpp:213: undefined
> reference to `edlibAlignmentToCigar'
> /usr/bin/ld: ./obj-x86_64-linux-gnu/./src/overlap.cpp:223: undefined
> reference to `edlibFreeAlignResult'
> collect2: error: ld returned 1 exit status
> make[3]: *** [CMakeFiles/racon_test.dir/build.make:182: bin/racon_test] Error
> 1
> make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu'
> make[2]: *** [CMakeFiles/Makefile2:88: CMakeFiles/racon_test.dir/all] Error 2
> make[2]: *** Waiting for unfinished jobs
> [100%] Linking CXX executable bin/racon
> /usr/bin/cmake -E cmake_link_script CMakeFiles/racon.dir/link.txt --verbose=1
> /usr/bin/c++ -g -O2 -ffile-prefix-map=/<>=.
> -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
> -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -Wl,-z,relro -Wl,-z,now -rdynamic
> -pthread CMakeFiles/racon.dir/src/main.cpp.o
> CMakeFiles/racon.dir/src/logger.cpp.o CMakeFiles/racon.dir/src/polisher.cpp.o
> CMakeFiles/racon.dir/src/overlap.cpp.o
> CMakeFiles/racon.dir/src/sequence.cpp.o CMakeFiles/racon.dir/src/window.cpp.o
> -o bin/racon -lspoa -ledlib -lz
> /usr/bin/ld: CMakeFiles/racon.dir/src/overlap.cpp.o: in function
> `racon::Overlap::align_overlaps(char const*, unsigned int, char const*,
> unsigned int)':
> ./obj-x86_64-linux-gnu/./src/overlap.cpp:208: undefined reference to
> `edlibNewAlignConfig'
> /usr/bin/ld: ./obj-x86_64-linux-gnu/./src/overlap.cpp:208: undefined
> reference to `edlibAlign'
> /usr/bin/ld: ./obj-x86_64-linux-gnu/./src/overlap.cpp:213: undefined
> reference to `edlibAlignmentToCigar'
> /usr/bin/ld: ./obj-x86_64-linux-gnu/./src/overlap.cpp:223: undefined
> reference to `edlibFreeAlignResult'
> collect2: error: ld returned 1 exit status
```
Thanks,
~Niels