Question: minia 2.0.3 problem building from source - hdf5/hdf5.h missing?
0
gravatar for Torst
2.0 years ago by
Torst860
Australia
Torst860 wrote:

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.

minia • 685 views
ADD COMMENTlink modified 2.0 years ago by Rayan Chikhi1.2k • written 2.0 years ago by Torst860
0
gravatar for Rayan Chikhi
2.0 years ago by
Rayan Chikhi1.2k
France, Lille, CNRS
Rayan Chikhi1.2k wrote:

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
ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by Rayan Chikhi1.2k
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