Issue in using molminer

[raviteja-python259]

Hey there, When i try to use molminer, i get the following error and Im not sure of it. I have a single pdf file which i wanted to run with ocsr to extract the molecular structure from the pdf.
can some one help me out.

**Cannot perform annotation in ChemSpider: 'chemspider_token' is empty.
Traceback (most recent call last):
File "/home/nx2236/anaconda3/envs/my_new_env/bin/molminer", line 11, in
load_entry_point('MolMiner==1.0.0', 'console_scripts', 'molminer')()
File "/home/nx2236/anaconda3/envs/my_new_env/lib/python3.5/site-packages/click/core.py", line 764, in call
return self.main(*args, **kwargs)
File "/home/nx2236/anaconda3/envs/my_new_env/lib/python3.5/site-packages/click/core.py", line 717, in main
rv = self.invoke(ctx)
File "/home/nx2236/anaconda3/envs/my_new_env/lib/python3.5/site-packages/click/core.py", line 1137, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/nx2236/anaconda3/envs/my_new_env/lib/python3.5/site-packages/click/core.py", line 956, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/nx2236/anaconda3/envs/my_new_env/lib/python3.5/site-packages/click/core.py", line 555, in invoke
return callback(*args, **kwargs)
File "/home/nx2236/anaconda3/envs/my_new_env/lib/python3.5/site-packages/molminer/cli.py", line 381, in ocsr
result = osra.process(output_formats=["smiles", "inchi", "inchikey"], process_kwargs)
File "/home/nx2236/anaconda3/envs/my_new_env/lib/python3.5/site-packages/molminer/OSRA.py", line 435, in process
stdout, stderr, exit_code = pdf_to_images(input_file, temp_dir, dpi=gm_dpi, trim=gm_trim)
File "/home/nx2236/anaconda3/envs/my_new_env/lib/python3.5/site-packages/molminer/utils.py", line 257, in pdf_to_images
raise RuntimeError("Error when converting PDF to PNG images. Stderr: {}".format(stderr))
RuntimeError: Error when converting PDF to PNG images. Stderr: /home/nx2236/anaconda3/envs/my_new_env/bin/gm.bin: /home/nx2236/anaconda3/envs/my_new_env/lib/molminer/../libtiff.so.5: no version information available (required by /home/nx2236/anaconda3/envs/my_new_env/lib/molminer/libGraphicsMagick.so.3)
/home/nx2236/anaconda3/envs/my_new_env/bin/gm: line 6: 4341 Illegal instruction (core dumped) LD_LIBRARY_PATH=realpath $DIR/../lib/molminer $DIR/gm.bin ${@:1}

[gorgitko]

Hello,

there is probably some problem with libtiff or GraphicsMagick.

Can you run in your molminer virtual environment: $ gm convert -density 300 <pdf_file.pdf> +adjoin -trim -quality 100 output-%d.png

Alternatively, if you want only OCSR, you can run OSRA directly from your molminer virtual environment.

[raviteja-python259]

Hey @gorgitko thanks for the response and that worked and i am looking only for OCSR, but when i do run OSRA directly from molminer virtual environment i get the following error. Can you help?

/anaconda3/envs/my_new_env/bin/osra.bin: /home/anaconda3/envs/my_new_env/lib/molminer/../libtiff.so.5: no version information available (required by /home/nx2236/anaconda3/envs/my_new_env/lib/molminer/libGraphicsMagick.so.3)
/home/anaconda3/envs/my_new_env/bin/osra.bin: /home/anaconda3/envs/my_new_env/lib/molminer/../libtiff.so.5: no version information available (required by /home/nx2236/anaconda3/envs/my_new_env/lib/molminer/liblept.so.5)
/home/anaconda3/envs/my_new_env/bin/osra: line 6: 13039 Illegal instruction (core dumped) LD_LIBRARY_PATH=realpath $DIR/../lib/molminer $DIR/osra.bin ${@:1}

[gorgitko]

OK, so there is probably a conflicting version of libtiff which is installed as a dependency of some package which molminer depends on. OSRA is compiled against libtiff which is packaged with molminer.

As a temporary solution, run this in your molminer venv: $ conda uninstall libtiff --force

It works for me and I hope it will also work for you. Unfortunately, molminer is not my priority anymore, but I hope I will find some time to fix this issue directly in the conda recipe.