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CPernet / metaprivBIDS

assessing privacy of tabular metadata (with some BIDS bonuses like reading the json dictionary file)
https://metaprivbids.readthedocs.io/en/latest/
MIT License
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pygraph error #1

Closed CPernet closed 2 weeks ago

CPernet commented 2 weeks ago

I'm not sure where the error comes from at compilation -- miniconda or our baseline server ?? but then we use venv so should be the case ...

running from NRU server the install fails with this error gcc -pthread -B /usr/local/miniconda/20220815/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /usr/local/miniconda/20220815/include -fPIC -O2 -isystem /usr/local/miniconda/20220815/include -fPIC -DSWIG_PYTHON_STRICT_BYTE_CHAR -I/indirect/openneuropet/metapriv/include -I/usr/local/miniconda/20220815/include/python3.9 -c pygraphviz/graphviz_wrap.c -o build/temp.linux-x86_64-3.9/pygraphviz/graphviz_wrap.o pygraphviz/graphviz_wrap.c:3020:10: fatal error: graphviz/cgraph.h: No such file or directory

include "graphviz/cgraph.h"

            ^~~~~~~~~~~~~~~~~~~
  compilation terminated.
  error: command '/usr/bin/gcc' failed with exit code 1
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. error: legacy-install-failure

× Encountered error while trying to install package. ╰─> pygraphviz

note: This is an issue with the package mentioned above, not pip. hint: See above for output from the failure.

EmiKib commented 2 weeks ago

As I can see, it is a system-level dependencies so it also fails in a virtual environment. Maybe I can solve it by dockerizing the project. I am working on a solution.

does running:

sudo apt-get install graphviz graphviz-dev

work?

EmiKib commented 2 weeks ago

![Uploading Screenshot 2024-10-03 at 14.18.03.png…]()