First of all, thanks for your answer.
Following your instructions, I blocked lines 186-195 in the "bin_extract_common.py" file.
The zip file shown in the image below is indeed generated.
(I'm not sure if this is right)
`gcc-5__Ou__gnunet__gnurl.zip    gcc-5__Ou__nettle__shadata.zip
gcc-5__Ou__nettle__aesdata.zip  gcc-5__Ou__nettle__twofishdata.zip
gcc-5__Ou__nettle__desdata.zip  gcc-5__Ou__pexec__pexec.zip
gcc-5__Ou__nettle__eccdata.zip  gcc-5__Ou__pspp__q2c.zip
gcc-5__Ou__nettle__gcmdata.zip
`

After that, the JSON file generated by this command is empty.
`python3 -u collect_and_filter.py --input-dir TRAIN_INDEXED --output-file=train.json`

I'm not sure if it's a version issue.

Finally, thank you very much for your warm and patient answer. You are a worthy scholar.