Release of Bio-Formats C++ 5.1.4

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 archived downloads 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 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
• 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 archived downloads.

For any problems or comments, please use the OME Forums or mailing lists.