No rule to make target '../external/bdsg//lib/libbdsg.so'

[hoppo]

Hi,

I have tried to build GFAse on linux (Rocky Linux release 8.8) and get the following error:- make[2]: *** No rule to make target '../external/bdsg//lib/libbdsg.so', needed by 'split_connected_components'. Stop.

I then searched under ..GFAse/external/bdsg and see that there are two lib directories created (lib and lib64). However, there is no libbdsg.so under the ../external/bdsg/lib/ directory, but it is under the ../external/bdsg/lib64 directory.

I then tried to download and build libbdsg (separately) and it built without a problem and only contained the lib directory.

As a workaround, I rename the ../external/bdsg/lib64 directory to ../external/bdsg/lib and this appeared to at least allow the build to finish and build the executables. I haven't extensively tested GFAse yet.

Is there something unique to my OS that builds GFAse incorrectly?

Thank you.

[rlorigro]

Hi @hoppo, yes unfortunately this lib vs lib64 is a common point of divergence among operating systems, we've seen the same thing occur with CentOS.

Obviously my first recommendation is to just use Ubuntu if possible, but as a more general alternative, it appears that it may be possible to to check explicitly for it based on this post using if("${CMAKE_INSTALL_LIBDIR}" STREQUAL "lib64") in our CMakeLists.txt..

[rlorigro]

If you wouldn't minding testing this on your OS as a positive example, you could try by adding the following line to your CMakeLists.txt:

message(STATUS "CMAKE_INSTALL_LIBDIR: " ${CMAKE_INSTALL_LIBDIR})

And see what it prints by running cmake. My Ubuntu OS returns lib.

[hoppo]

In my case, it is empty.. .... -- Detecting CXX compile features - done -- CMAKE_INSTALL_LIBDIR: -- CMAKE_CXX_COMPILER_ID: GNU ....

If I add the following:- include(GNUInstallDirs)

it returns lib64

And yes, we plan to move to ubuntu, but for the moment our cluster is still red hat linux.

[rlorigro]

OK, I made an untested commit to branch lib64, would you mind trying it out on your linux OS and see if it works? may need to remove the external dir

[hoppo]

Hi, Unfortunately, it doesn't seem to fix the issue. I still see two lib directories; lib and lib64

The contents of lib:- libgtest.so
libgtest_main.so
libsdsl.so -> libsdsl.so.3 libsdsl.so.2.3.0
libsdsl.so.3 -> libsdsl.so.2.3.0 pkgconfig

lib64:- libbdsg.so
libdivsufsort.so -> libdivsufsort.so.3 libdivsufsort.so.3 -> libdivsufsort.so.3.0.1 libdivsufsort.so.3.0.1
libdivsufsort64.so -> libdivsufsort64.so.3 libdivsufsort64.so.3 -> libdivsufsort64.so.3.0.1 libdivsufsort64.so.3.0.1
libhandlegraph.a
libhandlegraph.so
pkgconfig

Interestingly, when I build libbdsg independently, it only creates a lib directory. In the CMakeLists.txt, it has the following entry:- set(LIBRARY_OUTPUT_PATH ${CMAKE_CURRENT_SOURCE_DIR}/lib)

Thanks, Marie.