Hi Andreas, hi Nilesh, I notice that libedlib0 [1] exported the edlibAlign symbol, but not libedlib1, which is what is pulled in by libedlib-dev. Could that be the source of the problem?
Cheers, tony [1] https://salsa.debian.org/med-team/libedlib/-/blob/master/debian/libedlib0.symbols On Sun, Dec 19, 2021 at 08:00:35PM +0100, Andreas Tille wrote: > Hi, > > I've got the same in parallel and have no spontaneous idea how to > fix it. > > Kind regard > Andreas. > > Am Sun, Dec 19, 2021 at 11:50:33PM +0530 schrieb Nilesh Patra: > > Hi, > > > > The new version of racon got released, and I believe I made the adjustments > > in patches accordingly. > > However, the build chokes with the log given below. > > > > I have linked edlib as needed, and the dependency is also satisfied. The > > functions mentioned (edlibAlign, edlibAlignmentToCigar etc) > > are mentioned in /usr/include/edlib.h as well, so I am not sure what is > > triggering this. > > All my changes are in salsa. > > > > Any help is welcome. > > > > Regards, > > Nilesh > > > > > > [ 80%] Building CXX object CMakeFiles/racon_test.dir/test/racon_test.cpp.o > > /usr/bin/c++ -DTEST_DATA=\"/home/nilesh/packages/racon/racon/test/data/\" > > -I/home/nilesh/packages/racon/racon/src -g -O2 > > -ffile-prefix-map=/home/nilesh/packages/racon/racon=. > > -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include > > -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic > > -DGTEST_HAS_PTHREAD=1 -std=c++11 -MD -MT > > CMakeFiles/racon_test.dir/test/racon_test.cpp.o -MF > > CMakeFiles/racon_test.dir/test/racon_test.cpp.o.d -o > > CMakeFiles/racon_test.dir/test/racon_test.cpp.o -c > > /home/nilesh/packages/racon/racon/test/racon_test.cpp > > /usr/bin/c++ -DVERSION=\"1.5.0\" -I/home/nilesh/packages/racon/racon/src -g > > -O2 -ffile-prefix-map=/home/nilesh/packages/racon/racon=. > > -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include > > -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT > > CMakeFiles/racon_exe.dir/src/main.cpp.o -MF > > CMakeFiles/racon_exe.dir/src/main.cpp.o.d -o > > CMakeFiles/racon_exe.dir/src/main.cpp.o -c > > /home/nilesh/packages/racon/racon/src/main.cpp > > [ 90%] Linking CXX executable bin/racon > > /usr/bin/cmake -E cmake_link_script CMakeFiles/racon_exe.dir/link.txt > > --verbose=1 > > /usr/bin/c++ -g -O2 -ffile-prefix-map=/home/nilesh/packages/racon/racon=. > > -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include > > -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -Wl,-z,relro > > -Wl,-z,now CMakeFiles/racon_exe.dir/src/main.cpp.o -o bin/racon > > lib/libracon.a -lspoa -ledlib -lpthread -lz > > /usr/bin/ld: lib/libracon.a(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:210: undefined reference to > > `edlibNewAlignConfig' > > /usr/bin/ld: ./obj-x86_64-linux-gnu/./src/overlap.cpp:210: 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_exe.dir/build.make:101: bin/racon] Error 1 > > make[3]: Leaving directory > > '/home/nilesh/packages/racon/racon/obj-x86_64-linux-gnu' > > make[2]: *** [CMakeFiles/Makefile2:116: CMakeFiles/racon_exe.dir/all] Error > > 2
