Question: minia 2.0.3 problem building from source - hdf5/hdf5.h missing?
0
gravatar for Torst
20 months ago by
Torst850
Australia
Torst850 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 • 600 views
ADD COMMENTlink modified 20 months ago by Rayan Chikhi1.2k • written 20 months ago by Torst850
0
gravatar for Rayan Chikhi
20 months 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 20 months ago • written 20 months ago by Rayan Chikhi1.2k
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