minia 2.0.3 problem building from source - hdf5/hdf5.h missing?

Question

[Torst]

Is this some issue with assumption of hdf5 library being installed at system level instead of using bundled one?

cd /tmp/minia20151207-2659-lh8xo7/minia-2.0.3-Source/build/ext/gatb-core/src && /bio/linuxbrew/bin/g++-5 -Os -w -pipe -march=core2 -I/tmp/minia20151207-2659-lh8xo7/minia-2.0.3-Source/build/ext/gatb-core/include -I/tmp/minia20151207-2659-lh8xo7/minia-2.0.3-Source/thirdparty/gatb-core/src -I/tmp/minia20151207-2659-lh8xo7/minia-2.0.3-Source/thirdparty/gatb-core/thirdparty -O3 -DINT128_FOUND -DWITH_LAMBDA_EXPRESSION -std=c++0x -DWITH_MPHF -DDONT_USE_TR1 -Wno-invalid-offsetof -o CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Histogram.cpp.o -c /tmp/minia20151207-2659-lh8xo7/minia-2.0.3-Source/thirdparty/gatb-core/src/gatb/tools/misc/impl/Histogram.cpp In file included from /tmp/minia20151207-2659-lh8xo7/minia-2.0.3-Source/thirdparty/gatb-core/src/gatb/tools/math/NativeInt8.hpp:33:0, from /tmp/minia20151207-2659-lh8xo7/minia-2.0.3-Source/thirdparty/gatb-core/src/gatb/tools/storage/impl/StorageTools.hpp:34, from /tmp/minia20151207-2659-lh8xo7/minia-2.0.3-Source/thirdparty/gatb-core/src/gatb/tools/storage/impl/StorageTools.cpp:21: /tmp/minia20151207-2659-lh8xo7/minia-2.0.3-Source/thirdparty/gatb-core/src/gatb/tools/misc/api/Abundance.hpp:34:23: fatal error: hdf5/hdf5.h: No such file or directory compilation terminated.

Answer 1

[Rayan Chikhi]

Hmm, could you please give some more details on the system and the commands you typed to compile? Users do not need hdf5 to be preinstalled, it is packaged with minia sources.

I cannot reproduce the problem locally using these commands; minia builds correctly for me.

wget http://gatb-tools.gforge.inria.fr/versions/src/minia-2.0.3-Source.tar.gz

tar xf minia-2.0.3-Source.tar.gz

cd minia-2.0.3-Source

mkdir build

cd build

cmake .. && make -j 4