jklymak
commented
1 year ago Hi Ria
To run dbdreader you will need a c compiler. So you need to install Xcode on your Mac or a c compiler on your windows machine (I don't have one so can't really help with this step)
Note you do not need to use dbdreader. There is a less robust two-step method to translate the files all in Python if you prefer.
Hello everyone,
I would like to use pyglider to process Slocum glider data. When I installed pyglider today I ran into a couple of issues that I wanted to raise here. In the following I will list my steps to ensure that I have not done a mistake (I am very new to python and Slocum gliders):
1) I have installed the required packages and created a new environment as suggested on the website. conda create -n gliderwork conda activate gliderwork conda install -c conda-forge pyglider
2) I downloaded the example data manually, as import pyglider.example_data as pexamp pexamp.get_example_data('./') is not working.
3) Having the example data I wanted to run the example code to make sure that everything is working properly. The code is shown in the shown on the getting started : slocum (https://pyglider.readthedocs.io/en/latest/getting-started-slocum.html)
I wanted to run the first couple of lines to ensure the packages are imported properly. I received the following error message: Attribute Error: pyglider.slocum' has no attribute 'binary_to_timeseries
I sort of solved this issue by copying the code from pyglider.slocum from github and replacing the old code.
I then received another error message that dbdreader is not defined. I realized that dbdreader was not installed with the packages (I think its important to transform the binary code from for example *.dbd files?) I have tried to install dbdreader separately, but it failed miserably on both my MAC and my Windows Laptop.
I received the following error message: %%%%% Collecting dbdreader Using cached dbdreader-0.4.11.tar.gz (768 kB) Preparing metadata (setup.py) ... done Requirement already satisfied: numpy in ./opt/anaconda3/envs/gliderwork/lib/python3.11/site-packages (from dbdreader) (1.24.1) Building wheels for collected packages: dbdreader Building wheel for dbdreader (setup.py) ... error error: subprocess-exited-with-error
× python setup.py bdist_wheel did not run successfully. │ exit code: 1 ╰─> [15 lines of output] running bdist_wheel running build running build_py creating build creating build/lib.macosx-10.9-x86_64-cpython-311 creating build/lib.macosx-10.9-x86_64-cpython-311/dbdreader copying dbdreader/init.py -> build/lib.macosx-10.9-x86_64-cpython-311/dbdreader copying dbdreader/dbdreader.py -> build/lib.macosx-10.9-x86_64-cpython-311/dbdreader running build_ext building '_dbdreader' extension creating build/temp.macosx-10.9-x86_64-cpython-311 creating build/temp.macosx-10.9-x86_64-cpython-311/extension clang -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/riaoelerich/opt/anaconda3/envs/gliderwork/include -fPIC -O2 -isystem /Users/riaoelerich/opt/anaconda3/envs/gliderwork/include -Iextension/include -I/Users/riaoelerich/opt/anaconda3/envs/gliderwork/include/python3.11 -c extension/dbdreader.c -o build/temp.macosx-10.9-x86_64-cpython-311/extension/dbdreader.o xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun error: command '/usr/bin/clang' failed with exit code 1 [end of output]
note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for dbdreader Running setup.py clean for dbdreader Failed to build dbdreader Installing collected packages: dbdreader Running setup.py install for dbdreader ... error error: subprocess-exited-with-error
× Running setup.py install for dbdreader did not run successfully. │ exit code: 1 ╰─> [17 lines of output] running install /Users/riaoelerich/opt/anaconda3/envs/gliderwork/lib/python3.11/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py creating build creating build/lib.macosx-10.9-x86_64-cpython-311 creating build/lib.macosx-10.9-x86_64-cpython-311/dbdreader copying dbdreader/init.py -> build/lib.macosx-10.9-x86_64-cpython-311/dbdreader copying dbdreader/dbdreader.py -> build/lib.macosx-10.9-x86_64-cpython-311/dbdreader running build_ext building '_dbdreader' extension creating build/temp.macosx-10.9-x86_64-cpython-311 creating build/temp.macosx-10.9-x86_64-cpython-311/extension clang -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/riaoelerich/opt/anaconda3/envs/gliderwork/include -fPIC -O2 -isystem /Users/riaoelerich/opt/anaconda3/envs/gliderwork/include -Iextension/include -I/Users/riaoelerich/opt/anaconda3/envs/gliderwork/include/python3.11 -c extension/dbdreader.c -o build/temp.macosx-10.9-x86_64-cpython-311/extension/dbdreader.o xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun error: command '/usr/bin/clang' 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. ╰─> dbdreader
note: This is an issue with the package mentioned above, not pip. %%%%
Sorry for this rather lengthy issue. I wonder whether some of you have encountered this? Or whether I did something wrong?
Best wishes, Ria