install.sh fails download remote files

[sverhoeven]

Describe the bug

http://servers.sparks-lab.org/downloads/dcomplex2.tar.gz gives 522 error

http://www.bioinf.org.uk/software/profit/235216/profit.tar.gz gives 503: Service Unavailable. error

To Reproduce
Steps to reproduce the behavior:

git clone --depth 1 -b main https://github.com/gdocking/gdock.git .
pip install matplotlib==3.8.4  # dont install 3.9.0rc2
python setup.py develop
bash install.sh /opt/gdock

Produces (click to see log)

 > [bartender builder 10/18] RUN bash install.sh /opt/gdock:
0.176 mkdir: cannot create directory ‘/opt/gdock/src’: File exists
0.179 --2024-10-04 09:19:45--  http://servers.sparks-lab.org/downloads/dcomplex2.tar.gz
0.179 Resolving servers.sparks-lab.org (servers.sparks-lab.org)... 172.67.130.213, 104.21.3.148, 2606:4700:3031::6815:394, ...
0.215 Connecting to servers.sparks-lab.org (servers.sparks-lab.org)|172.67.130.213|:80... connected.
0.218 HTTP request sent, awaiting response... 522 
21.58 2024-10-04 09:20:06 ERROR 522: (no description).
21.58 
21.60 tar (child): dcomplex2.tar.gz: Cannot open: No such file or directory
21.60 tar (child): Error is not recoverable: exiting now
21.60 tar: Child returned status 2
21.60 tar: Error is not recoverable: exiting now
21.60 rm: cannot remove 'dcomplex2.tar.gz': No such file or directory
21.60 install.sh: line 12: cd: dcomplex_single_file: No such file or directory
21.60 sed: can't read dcomplex.c: No such file or directory
21.62 /usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/Scrt1.o: in function `_start':
21.62 (.text+0x17): undefined reference to `main'
21.62 collect2: error: ld returned 1 exit status
21.86 Collecting git+https://github.com/joaorodrigues/fcc@fcc2
21.86   Cloning https://github.com/joaorodrigues/fcc (to revision fcc2) to /tmp/pip-req-build-2xvqr16g
21.86   Running command git clone --filter=blob:none --quiet https://github.com/joaorodrigues/fcc /tmp/pip-req-build-2xvqr16g
22.58   Running command git checkout -b fcc2 --track origin/fcc2
22.92   Switched to a new branch 'fcc2'
22.92   branch 'fcc2' set up to track 'origin/fcc2'.
22.92   Resolved https://github.com/joaorodrigues/fcc to commit 1a06cfa79816571deed33b16f7af037574d1e918
22.92   Preparing metadata (setup.py): started
23.02   Preparing metadata (setup.py): finished with status 'done'
23.24 Collecting numba
23.28   Downloading numba-0.60.0-cp39-cp39-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (3.7 MB)
23.64      ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.7/3.7 MB 10.2 MB/s eta 0:00:00
23.65 Requirement already satisfied: numpy in /venv/lib/python3.9/site-packages (from fccpy==0.1.0) (1.23.5)
23.71 Collecting h5py
23.72   Downloading h5py-3.12.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (5.4 MB)
24.03      ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.4/5.4 MB 17.5 MB/s eta 0:00:00
24.12 Collecting llvmlite<0.44,>=0.43.0dev0
24.13   Downloading llvmlite-0.43.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (43.9 MB)
27.76      ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 43.9/43.9 MB 12.7 MB/s eta 0:00:00
27.92 Installing collected packages: llvmlite, h5py, numba, fccpy
29.70   DEPRECATION: fccpy is being installed using the legacy 'setup.py install' method, because it does not have a 'pyproject.toml' and the 'wheel' package is not installed. pip 23.1 will enforce this behaviour change. A possible replacement is to enable the '--use-pep517' option. Discussion can be found at https://github.com/pypa/pip/issues/8559
29.70   Running setup.py install for fccpy: started
29.84   Running setup.py install for fccpy: finished with status 'done'
29.84 Successfully installed fccpy-0.1.0 h5py-3.12.1 llvmlite-0.43.0 numba-0.60.0
29.84 
29.84 [notice] A new release of pip is available: 23.0.1 -> 24.2
29.84 [notice] To update, run: pip install --upgrade pip
29.90 Cloning into 'haddock-tools'...
30.69 --2024-10-04 09:20:16--  http://www.bioinf.org.uk/software/profit/235216/profit.tar.gz
30.69 Resolving www.bioinf.org.uk (www.bioinf.org.uk)... 62.30.207.73
30.73 Connecting to www.bioinf.org.uk (www.bioinf.org.uk)|62.30.207.73|:80... connected.
30.75 HTTP request sent, awaiting response... 503 Service Unavailable
30.78 2024-10-04 09:20:16 ERROR 503: Service Unavailable.
30.78 
30.78 tar (child): profit.tar.gz: Cannot open: No such file or directory
30.78 tar (child): Error is not recoverable: exiting now
30.78 tar: Child returned status 2
30.78 tar: Error is not recoverable: exiting now
30.78 rm: cannot remove 'profit.tar.gz': No such file or directory
30.78 install.sh: line 36: cd: ProFit_V3.3/src: No such file or directory

Expected behavior
That package would install correctly.

Additional context
It worked 3 days ago, see Docker image at https://github.com/i-VRESSE/haddock3-webapp/pkgs/container/bartender/282969709?tag=v0.3.6
Similar to #42

[rvhonorato]

Yeah, unfortunately without dcomplex the whole project is dead 😔

I'm (very slowly) working on a rust re-write of gdock but this will still take a very longe time to be ready.