Open Microscopy Environment

Dear All,

Today we have released the binary builds of Bio-Formats-C++ 5.1.4, together with the ome-cmake-superbuild package used for building Bio-Formats-C++ and its dependencies on Windows and other platforms. This is a new package split out from the Bio-Formats sources, which may be used to build the libraries required by Bio-Formats such as zlib, bzip2, icu, boost, libtiff and xerces-c.

The major goal of this release was porting Bio-Formats-C++ to Microsoft Windows, initially supporting Visual Studio 2013 (VS2013). This goal was realised, with Bio-Formats 5.1.4 (released on 07/09/15) being buildable with both VS2013 and also with VS2012. The CMake Super-Build released today works with VS2013 with the "Visual Studio 12 2013" (msbuild) generator; work has been done to support additional versions of Visual Studio and additional generators, which will be completed in subsequent releases.

See http://downloads.openmicroscopy.org/bio ... cpp/5.1.4/ for links to the source releases, documentation and API reference, and binary builds for a number of platforms which now include Windows with VS2013.

Bio-Formats Windows portability changes:

• Use pImpl in OME model objects to simplify future DLL exports
• Provide compatibility snprintf(3) for VS2013 and VS2012
• Use _putenv_s rather than setenv(3) with MSVC
• Added workaround for missing va_copy() in VS2012
• Made CMake use of shared or static libraries configurable; Windows currently uses static libraries until the libraries are updated to have the appropriate DLL exports
• Corrected use of boost::filesystem to use the correct native path type on all platforms; the TIFF code now uses native paths and the wide version of TIFFOpen on Windows
• Fixed a number of MSVC warnings, primarily unused variables in catch statements which GCC and clang don't warn about
• Do not reuse or compare iterators with different containers; MSVC doesn't like this and it's technically incorrect
• Updated unit tests to cope with minor floating point formatting differences on Windows
• Corrected static initialisation ordering issues on Windows (and with static libraries) in a number of places; these are primarily static mappings used during program initialisation. Previously we were making some assumptions which only held true with ELF/Mach-O linkers.
• Added missing directories to the include search path
• Added missing includes where missing on Windows but implicit elsewhere
• Reordered include order for lexical_cast to ensure usable MPL limits; added additional MPL tests with boost::variant to test the limits
• Search for both Debug and Release libraries on Windows, so the correct Debug and Release library dependencies will always be used

Additional Bio-Formats changes:

• Added additional functional checks for broken GCC <regex> implementation
• Corrected return in Timestamp ostream output operator
• Made CMake checks for xsd-fu failures stricter
• Removed CMake warnings about duplicate targets created by xsd-fu
• Default logging level set under all circumstances

CMake Super-Build components:

bioformats 5.1.4
boost 1.58
bzip2 1.0.6
icu 55.1
libpng 1.6.17
tiff 4.0.6
xerces-c 3.1.2
zlib 1.2.8

CMake Super-Build changes:

• CMake Super-Build logic moved out of the bioformats source tree into a separate source repository (see https://github.com/ome/ome-cmake-superbuild)
• Added ICU build
• Added VS2012 support to Xerces-C build
• Allowed use of generators other than Visual Studio's msbuild on Windows such as Ninja, to allow fast parallel building (not yet fully functional)
• Allowed verbose building with the Ninja generator
• Corrected libtiff symbol versioning
• Updated libtiff to 4.0.6; this provides BigTIFF support for Windows
• Allowed building from libtiff CVS HEAD

The software release is available at: http://downloads.openmicroscopy.org/bio ... -cpp/5.1.4

For any problems or comments, please use the OME forums or mailing lists: http://www.openmicroscopy.org/site/community

Roger Leigh
on behalf of the OME team