<div dir="ltr">Hi Allan,<div><br></div><div>Your command should have installed the hdf5 dependency among the other dependencies. The hdf5 dependency is required because there are functions for reading image data. Was there an error in compiling HDF5? There should be a log file in <cctbx installation directory>/base_tmp named HDF5_install_log. </div><div><br></div><div>Are you using a recent version of bootstrap.py? I just tested this on macOS 10.12.3 with conda 4.3.11 and the command-line tools for Xcode 8.2.1. The steps I followed (in a clean directory with just bootstrap.py) are,</div><div><br></div><div>1) conda create -n test python=2</div><div>2) source activate test</div><div>3) python bootstrap.py --with-python=`which python` --builder=cctbx --nproc=8</div><div>4) cd build; make</div><div><br></div><div>The `which python` command in step 3 just returns the path for the python in the "test" environment. Step 4 is just to make sure everything is compiled.</div><div><br></div><div>Let us know if you it still does not work. Thanks!</div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div>--</div><div><span style="font-size:12.8000001907349px">Billy K. Poon</span><br></div></div><div>Research Scientist, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory</div><div>1 Cyclotron Road, M/S 33R0345</div><div>Berkeley, CA 94720</div><div>Tel: (510) 486-5709</div><div>Fax: (510) 486-5909</div><div>Web: <a href="https://phenix-online.org" target="_blank">https://phenix-online.org</a></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Fri, Mar 17, 2017 at 7:27 AM, Allan Lyckegaard <span dir="ltr"><<a href="mailto:alyckegaard@xnovotech.com" target="_blank">alyckegaard@xnovotech.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi all,<br>
<br>
I am trying to install cctbx on my Mac (Sierra) using bootstrap.py with my Anaconda python.<br>
<br>
When executing 'python bootstrap.py --with-python=/Users/myuser/<wbr>miniconda2/envs/python2/bin/<wbr>python --builder=cctbx’ I get the following error:<br>
<br>
/usr/bin/c++ -o dxtbx/format/boost_python/<wbr>nexus_ext.o -c -DBOOST_HAS_INT128=1 -DBOOST_ALL_NO_LIB -DBOOST_PYTHON_MAX_BASES=2 -Wmost -Wno-unknown-pragmas -Wno-logical-op-parentheses -Wno-unused-local-typedefs -I/Users/myuser/Development/<wbr>cctbx/modules/boost -fPIC -fno-strict-aliasing -Wno-c++0x-extensions -Wno-array-bounds -DNDEBUG -O3 -ffast-math -I/Users/myuser/miniconda2/<wbr>envs/python2/include -I/Users/myuser/Development/<wbr>cctbx/base/include -I/Users/myuser/Development/<wbr>cctbx/build/include -I/Users/myuser/Development/<wbr>cctbx/modules/cctbx_project -I/Users/myuser/miniconda2/<wbr>envs/python2/include/python2.7 /Users/myuser/Development/<wbr>cctbx/modules/cctbx_project/<wbr>dxtbx/format/boost_python/<wbr>nexus_ext.cc<br>
warning: unknown warning option '-Wno-unused-local-typedefs' [-Wunknown-warning-option]<br>
1 warning generated.<br>
/usr/bin/c++ -o lib/dxtbx_format_nexus_ext.so -w -bundle -undefined dynamic_lookup dxtbx/format/boost_python/<wbr>nexus_ext.o -L/Users/myuser/Development/<wbr>cctbx/base/lib -lm -lhdf5<br>
ld: library not found for -lhdf5<br>
clang: error: linker command failed with exit code 1 (use -v to see invocation)<br>
scons: *** [lib/dxtbx_format_nexus_ext.<wbr>so] Error 1<br>
scons: building terminated because of errors.<br>
usr+sys time: 8.69 seconds<br>
wall clock time: 21.70 seconds<br>
Process failed with return code 2<br>
<br>
Any suggestions to how I solve this? I have not seen anywhere in the documentation that an hdf5 installation is a prerequisite.<br>
<br>
Cheers,<br>
/Allan<br>
<br>
<br>
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