Linking shared libraries in Micro-Manager for Linux

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Lately I have been working on a new Video4Linux2 device adapter for Micro-Manager. I encountered the following error after adding some functionality that introduced two Boost libraries as new dependencies in my project.

Traceback (most recent call last):
  File "RPiV4L2.py", line 17, in <module>
    mmc.loadDevice("camera", "RPiV4L2", "RPiV4L2")
  File "/home/micro-manager/app/lib/micro-manager/MMCorePy.py", line 3515, in loadDevice
    return _MMCorePy.CMMCore_loadDevice(self, label, moduleName, deviceName)
MMCorePy.CMMError: Failed to load device "RPiV4L2" from adapter module "RPiV4L2" [ Failed to load device adapter "RPiV4L2" [ Failed to load module "/home/micro-manager/app/lib/micro-manager/libmmgr_dal_RPiV4L2.so.0" [ /home/micro-manager/app/lib/micro-manager/libmmgr_dal_RPiV4L2.so.0: undefined symbol: _ZN5boost10filesystem6detail13dir_itr_closeERPvS3_ ] ] ]

I received this error when I tried to load the device in a Python script. At first I was puzzled because the code compiled without problems, but I soon found that the solution was simple.

The key part of the message is undefined symbol: _ZN5boost10filesystem6detail13dir_itr_closeERPvS3_. To troubleshoot this, I first demangled the symbol name by entering it at https://demangler.com/. I discovered that the symbol was referring to the function boost::filesystem::detail::dir_itr_close(void*&, void*&). I had added both the Boost filesystem and Boost regex libraries to this device adapter as dependencies, so it was not surprising that either of their names appeared in the error message.

Next, I used the ldd program to check which libraries my device adapter were linked against. (libmmgr_dal_RPiV4l2.so.0 is the name of the device adapter library file).

$ ldd libmmgr_dal_RPiV4L2.so.0
     linux-vdso.so.1 (0x7ec21000)
     libdl.so.2 => /lib/arm-linux-gnueabihf/libdl.so.2 (0x76e9c000)
     libstdc++.so.6 => /usr/lib/arm-linux-gnueabihf/libstdc++.so.6 (0x76d54000)
     libm.so.6 => /lib/arm-linux-gnueabihf/libm.so.6 (0x76cdc000)
     libc.so.6 => /lib/arm-linux-gnueabihf/libc.so.6 (0x76bee000)
     libgcc_s.so.1 => /lib/arm-linux-gnueabihf/libgcc_s.so.1 (0x76bc1000)
     libicudata.so.57 => /usr/lib/arm-linux-gnueabihf/libicudata.so.57 (0x75334000)
     libicui18n.so.57 => /usr/lib/arm-linux-gnueabihf/libicui18n.so.57 (0x75187000)
     libicuuc.so.57 => /usr/lib/arm-linux-gnueabihf/libicuuc.so.57 (0x7505e000)
     librt.so.1 => /lib/arm-linux-gnueabihf/librt.so.1 (0x75048000)
     libpthread.so.0 => /lib/arm-linux-gnueabihf/libpthread.so.0 (0x75024000)
     /lib/ld-linux-armhf.so.3 (0x76fb4000)

Neither libboost_filesystem nor libboost_regex are listed, so I knew that they were not linked with the device adapter.

There is a Makefile.am included in the directory of every device adapter in the Micro-Manager project. This file is used by Autotools define how the device adapter should be compiled and linked. Here is what my Makefile.am looked like:

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AM_CXXFLAGS = $(MMDEVAPI_CXXFLAGS)
deviceadapter_LTLIBRARIES = libmmgr_dal_RPiV4L2.la
libmmgr_dal_RPiV4L2_la_SOURCES = RPiV4L2.cpp RPiV4L2.h refactor.h ../../MMDevice/MMDevice.h ../../MMDevice/DeviceBase.h
libmmgr_dal_RPiV4L2_la_LIBADD = $(MMDEVAPI_LIBADD)
libmmgr_dal_RPiV4L2_la_LDFLAGS = $(MMDEVAPI_LDFLAGS)

After experimenting a bit, I discovered that I could instruct the linker to link against shared libraries by adding them to the libmmgr_dal_RPiV4L2_la_LDFLAGS variable with the -l flag. The resulting line now looks like:

libmmgr_dal_RPiV4L2_la_LDFLAGS = $(MMDEVAPI_LDFLAGS) -lboost_regex -lboost_filesystem

Finally, running ldd on the rebuilt device adapter now shows these two libraries:

$ ldd libmmgr_dal_RPiV4L2.so.0
     linux-vdso.so.1 (0x7ed74000)
     libboost_regex.so.1.62.0 => /usr/lib/arm-linux-gnueabihf/libboost_regex.so.1.62.0 (0x76e3c000)
     libboost_filesystem.so.1.62.0 => /usr/lib/arm-linux-gnueabihf/libboost_filesystem.so.1.62.0 (0x76e1b000)
     ...

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