Re: [Help needed] Racon
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
Reply to: