vignettes/README.md

In Rhdf5lib: hdf5 library as an R package

Creating hdf5small_cxx.tar.gz

Instructions for creating the source tarball can now be found in downloadHDF5.Rmd.

Compiling on Windows

Compiling on Windows while using the Rtools toolchain took a number of attempts. This is a current 'best memory' of tħe required steps to build the versions of libhdf5.a and libhdf5_cpp.a shipped with the package. The instructions should be tested on a clean Windows machine and refined in the future.

Required software

Install both of these using the GUI installer provided. I'm going to assume they're in the default locations for all further steps.

• Rtools (https://cran.r-project.org/bin/windows/Rtools/)
• MSYS2 (http://www.msys2.org/)

CMAKE

I was unable to get ./configure to successfully build the libraries on Windows. It seems possible to complete the compilation, but the resulting libraries still don't work as exepcted. Hence we use cmake as suggested in the HDF5 documentation. The source zip file was obtained from https://www.hdfgroup.org/downloads/hdf5/source-code/#cmake

First, we make sure we have the required tools to build both 32 & 64-bit versions.

pacman -Syu ##upgrade msys, pacman & repos
pacman -S mingw-w64-x86_64-toolchain mingw64/mingw-w64-x86_64-cmake
pacman -S mingw-w64-i686-toolchain mingw32/mingw-w64-i686-cmake
#pacman -U http://repo.msys2.org/mingw/x86_64/mingw-w64-x86_64-rhash-1.3.6-2-any.pkg.tar.xz
#pacman -U http://repo.msys2.org/mingw/x86_64/mingw-w64-x86_64-cmake-3.12.1-1-any.pkg.tar.xz
#pacman -U http://repo.msys2.org/mingw/i686/mingw-w64-i686-rhash-1.3.6-2-any.pkg.tar.xz
#pacman -U http://repo.msys2.org/mingw/i686/mingw-w64-i686-cmake-3.12.1-1-any.pkg.tar.xz

Building 32-bit

export PATH=/c/Rtools/mingw_32/bin:/c/msys64/mingw32/bin:$PATH
export CPATH=/c/Rtools/mingw_32/i686-w64-mingw32/include:/c/Rtools/mingw_32/include:$CPATH
export LD_LIBRARY_PATH=/c/Rtools/mingw_32/i686-w64-mingw32/lib:/c/Rtools/mingw_32/lib:$LD_LiBRARY_PATH
mkdir /c/hdf5_build/CMake-hdf5-1.10.5/hdf5-1.10.5/build_32
cd /c/hdf5_build/CMake-hdf5-1.10.5/hdf5-1.10.5/build_32
rm -R *
cmake ../ -G "MSYS Makefiles" \
-DSITE_OS_BITS:STRING="32" \
-DCMAKE_C_STANDARD_LIBRARIES="-liberty" \
-DBUILD_SHARED_LIBS:BOOL=ON \
-DHDF5_BUILD_HL_LIB:BOOL=ON \
-DHDF5_ENABLE_Z_LIB_SUPPORT:BOOL=ON \
-DHDF5_ENABLE_SZIP_SUPPORT:BOOL=ON \
-DBUILD_TESTING:BOOL=OFF \
-DHDF5_BUILD_TOOLS:BOOL=OFF \
-DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING="TGZ" \
-DZLIB_TGZ_NAME:STRING="ZLib.tar.gz" \
-DSZIP_TGZ_NAME:STRING="SZip.tar.gz" \
-DTGZPATH:STRING="/c/hdf5_build/CMake-hdf5-1.10.5/" \
-DCMAKE_BUILD_TYPE:STRING="Release"
cmake --build . 2> stderr.txt

Building 64-bit

export PATH=/c/Rtools/mingw_64/bin:/c/msys64/mingw64/bin:$PATH
export CPATH=/c/Rtools/mingw_64/x86_64-w64-mingw32/include:/c/Rtools/mingw_64/include:$CPATH
export LD_LIBRARY_PATH=/c/Rtools/mingw_64/x86_64-w64-mingw32/lib:/c/Rtools/mingw_64/lib:$LD_LiBRARY_PATH
mkdir /c/hdf5_build/CMake-hdf5-1.10.5/hdf5-1.10.5/build_64
cd /c/hdf5_build/CMake-hdf5-1.10.5/hdf5-1.10.5/build_64
rm -R *
cmake ../ -G "MSYS Makefiles" \
-DSITE_OS_BITS:STRING="64" \
-DCMAKE_C_STANDARD_LIBRARIES="-liberty" \
-DBUILD_SHARED_LIBS:BOOL=ON \
-DHDF5_BUILD_HL_LIB:BOOL=ON \
-DHDF5_ENABLE_Z_LIB_SUPPORT:BOOL=ON \
-DHDF5_ENABLE_SZIP_SUPPORT:BOOL=ON \
-DBUILD_TESTING:BOOL=OFF \
-DHDF5_BUILD_TOOLS:BOOL=OFF \
-DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING="TGZ" \
-DZLIB_TGZ_NAME:STRING="ZLib.tar.gz" \
-DSZIP_TGZ_NAME:STRING="SZip.tar.gz" \
-DTGZPATH:STRING="/c/hdf5_build/CMake-hdf5-1.10.5/" \
-DCMAKE_BUILD_TYPE:STRING="Release"
cmake --build . 2> stderr.txt

In src/H5win32defs.h define H5open as #define HDopen(S,F,M) _open(S,F|_O_BINARY,M)

change line 291 H5Defl.h from

- if((fd = HDopen(full_name, O_RDONLY)) < 0)
+ if((fd = HDopen(full_name, O_RDONLY, 0)) < 0)

version=1.10.5
cd /c/hdf5_build/CMake-hdf5-${version}
mkdir /c/hdf5_build/CMake-hdf5-${version}/hdf5
mkdir /c/hdf5_build/CMake-hdf5-${version}/hdf5/c++
mkdir /c/hdf5_build/CMake-hdf5-${version}/hdf5/hl
cp /c/hdf5_build/CMake-hdf5-${version}/hdf5-${version}/src/*.h /c/hdf5_build/CMake-hdf5-${version}/hdf5/
cp /c/hdf5_build/CMake-hdf5-${version}/hdf5-${version}/c++/src/*.h /c/hdf5_build/CMake-hdf5-${version}/hdf5/c++/
cp /c/hdf5_build/CMake-hdf5-${version}/hdf5-${version}/hl/src/*.h /c/hdf5_build/CMake-hdf5-${version}/hdf5/hl/
cp /c/hdf5_build/CMake-hdf5-${version}/hdf5-${version}/hl/c++/src/*.h /c/hdf5_build/CMake-hdf5-${version}/hdf5/hl/
cp /c/hdf5_build/CMake-hdf5-${version}/hdf5-${version}/build_32/*.h /c/hdf5_build/CMake-hdf5-${version}/hdf5/
tar cf - hdf5 | gzip -6 > hdf5_headers_${version}.tar.gz

``` DIR32="${HOME}/Code/bioconductor/Rhdf5lib/src/winlib/i386/" cp /c/hdf5_build/CMake-hdf5-1.10.5/hdf5-1.10.5/build_32/bin/liblibhdf5.a "${DIR32}"libhdf5.a cp /c/hdf5_build/CMake-hdf5-1.10.5/hdf5-1.10.5/build_32/bin/liblibhdf5_cpp.a "${DIR32}"libhdf5_cpp.a cp /c/hdf5_build/CMake-hdf5-1.10.5/hdf5-1.10.5/build_32/bin/liblibhdf5_hl.a "${DIR32}"libhdf5_hl.a cp /c/hdf5_build/CMake-hdf5-1.10.5/hdf5-1.10.5/build_32/bin/liblibhdf5_hl_cpp.a "${DIR32}"libhdf5_hl_cpp.a

DIR64="${HOME}/Code/bioconductor/Rhdf5lib/src/winlib/x64/" cp /c/hdf5_build/CMake-hdf5-1.10.5/hdf5-1.10.5/build_64/bin/liblibhdf5.a "${DIR64}"libhdf5.a cp /c/hdf5_build/CMake-hdf5-1.10.5/hdf5-1.10.5/build_64/bin/liblibhdf5_cpp.a "${DIR64}"libhdf5_cpp.a cp /c/hdf5_build/CMake-hdf5-1.10.5/hdf5-1.10.5/build_64/bin/liblibhdf5_hl.a "${DIR64}"libhdf5_hl.a cp /c/hdf5_build/CMake-hdf5-1.10.5/hdf5-1.10.5/build_64/bin/liblibhdf5_hl_cpp.a "${DIR64}"libhdf5_hl_cpp.a

Rhdf5lib documentation built on Jan. 28, 2021, 2:02 a.m.