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Building on Windows MSYS2

Update: Due to the rolling release nature of MSYS2, the MSYS2 build process is currently broken. The Boost 1.70+ library that is provided by MSYS2 is incompatible with OME libraries due to a change in CMake targets. Please use our guide for Cygwin to build MISA++ on Windows.

We tested building on Windows via the MSYS2 environment.

Please note that the Visual Studio compiler is not supported due to missing OpenMP 3.x capabilities.

We consider building on Windows experimental due to random crashes of compiled programs during starting. We were yet not able to find the cause of those crashes, although review using library inspection software hints at the inability to load dynamic libraries under certain circumstances.

Prerequisites

  1. Download and install MSYS2.
  2. Start MSYS2 (MinGW 64-bit) and update the packages by typing pacman -Syyu
  3. Let the process finish and close the terminal as instructed
  4. Restart MSYS2 (MinGW 64-bit)

Using the superbuild script

We provide fully automated scripts that installs MISA++ Core, the modules we provide, and all necessary dependencies.

  1. Download or clone the MISA++ Utils repository
  2. Open an MSYS2 (MinGW 64-bit) shell and navigate into the windows-builds/msys2/superbuild-win32 folder
  3. Run ./superbuild.sh and follow the instructions

To create a distributable package of the MISA++ applications, run following command:

./superbuild.sh
./package.py

To create a Fiji distribution that comes pre-installed with MISA++ for ImageJ and the MISA++ applications, run following command:

./superbuild.sh
./package.py
./package-fiji.sh
Warning

The OME libraries might be incompatible with the boost version provided by MSYS2 (Cannot find libraries). If this is the case four you, remove boost via pacman -R mingw-w64-x86_64-boost and remove the mingw-w64-$MSYS2_PLATFORM-boost \ line in superbuild.sh.

First make sure that patch is installed by running pacman -S patch.

Clone the MSYS2 package build script repository via git clone https://github.com/msys2/MINGW-packages.git and go back to the commit that contains the script to install Boost version 1.69 by navigating into the MINGW-packages repository and running git checkout fff2fc0d53aa95b85cee0c785e56159b0565ea72.

Navigate into the mingw-w64-boost folder and run makepkg -si. The command will compile the correct Boost version and install it.

Manually building

Install the necessary MSYS2 packages:

pacman -S --noconfirm --needed unzip mingw-w64-x86_64-cmake \
wget \
mingw-w64-x86_64-toolchain \
mingw-w64-x86_64-boost \
mingw-w64-x86_64-make \
libsqlite \
libsqlite-devel \
mingw-w64-x86_64-opencv \
mingw-w64-x86_64-libtiff \
mingw-w64-x86_64-xerces-c \
mingw-w64-x86_64-xalan-c \
mingw-w64-x86_64-libpng \
mingw-w64-x86_64-python2

Obtain the MISA++ sources and the sources of dependencies that are not in MSYS2. Build them like any CMake build:

cd $SOURCE_CODE
mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE=Release -DBUILD_SHARED_LIBS=OFF -DCMAKE_INSTALL_PREFIX=/mingw64/ -G "Unix Makefiles" ..
Warning
  • Building OME libraries dynamically caused segmentation faults during application runtime (Error 0xc0000005). Build the libraries statically to avoid the issue.
  • Dynamically built MISA++ libraries caused random (~ every 10th execution) 0xc0000005 errors. We again decided to only link statically.
  • OME Model requires OME_HOME to be set to /mingw64/ or any other folder that contains ./share/xml and ./share/xsl