Build fails: undefined symbol: btllib::KmerBloomFilter::KmerBloomFilter

[yurivict]

c++  -o recipes/indexlr recipes/indexlr.p/_usr_ports_biology_btllib_work_btllib-1.6.0_recipes_indexlr.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,--start-group -ldl -lstdc++ -lm -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing subprojects/sdsl-lite/libsdsl.a libbtllib.a -Wl,--end-group -pthread -fopenmp -fopenmp
ld: error: undefined symbol: btllib::KmerBloomFilter::KmerBloomFilter(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&)
>>> referenced by indexlr.cpp
>>>               recipes/indexlr.p/_usr_ports_biology_btllib_work_btllib-1.6.0_recipes_indexlr.cpp.o:(main)
>>> referenced by indexlr.cpp
>>>               recipes/indexlr.p/_usr_ports_biology_btllib_work_btllib-1.6.0_recipes_indexlr.cpp.o:(main)

Version: 1.6.0 clang-15 FreeBSD 13.2

[vlad0x00]

Hi! How was btllib compiled? Using the compile script or manually using ninja commands?

[yurivict]

It is configured using meson, and then compiled using ninja. All in the FreeBSD ports framework.

[vlad0x00]

There was a similar problem on Arch Linux recently: https://github.com/bcgsc/abyss/issues/467 Try compiling btllib using the compile script at the root of the repo. Also look into whether your package build process has a way of disabling stripping symbols from the binaries, as that was the issue on Arch.

[yurivict]

The immediate reason of failure is because you don't check for errors after the commands. Particularly here the python3 executable doesn't exist but this script succeeds nevertheless.

You need to either check the exit status after every command, or use the STRICT mode for the shell scripts.

[vlad0x00]

Thank you for providing the information behind the error. We'll address it as soon as we can.

[vlad0x00]

The immediate reason of failure is because you don't check for errors after the commands. Particularly here the python3 executable doesn't exist but this script succeeds nevertheless.

You need to either check the exit status after every command, or use the STRICT mode for the shell scripts.

Hi @yurivict . We've merged a PR to address this: https://github.com/bcgsc/btllib/pull/103

I don't think this will address the problem raised in this issue, though. My guess is that the symbols are missing because they're stripped after install. btllib is a static library, and looking into FreeBSD docs (https://people.freebsd.org/~olivierd/porters-handbook/install.html), I found the following:

_"Do not use INSTALL_LIB to install static libraries, because stripping them renders them useless. Use INSTALLDATA instead."

If you're using INSTALL_LIB, that could be the cause of the issue. Alternatively, I think setting STRIP_CMD to an empty string might disable stripping.

[yurivict]

This was due to a missing python executable. btllib builds now.

Thanks for your help.