PyRx-0.9.2-linux-x86_64 on CentOS Stream 9

[Flavio Augusto Vicente Seixas]

Hi,
I had PyRx-0.9.2-linux-x86_64 on an octa-core PC running Linux CentOS-7. However, CentOS-7 is no longer supported and I needed to update to "CentOS Stream 9".
I tried to install the program as follows as root user:

first I install the dependencies:

yum install -y libpng12.x86_64 SDL2.x86_64 mesa-libGLU.x86_64

Then I install PyRx:

./PyRx-0.9.2-linux-x86_64.install

The installer runs well, without any error message, however, the program does not launch and the shortcut is not created.

I also tryed as root:
cd /usr/local/PyRx-0.9.2
./run.sh

However nothing happens, no error message and the programa does not launch.

OBS: I used SDL2.x86_64 since SDL.x86_64 is no loger available on CentOS Stream 9

Best regards,

Flavio

[Sarkis Dallakian]

Hi Flavio,

Thanks for the message. I had to remove &> /dev/null part from run.sh so it can show the error message. These are packages I installed to make it work:
sudo yum install https://rpmfind.net/linux/epel/9/Everything/x86_64/Packages/l/libpng12-1.2.57-18.el9.x86_64.rpm gtk2 sdl12-compat.x86_64 mesa-libGLU.x86_64

Let me know if it works for you.

Best regards,
Sarkis

[Flavio Augusto Vicente Seixas]

Dear Sargis,
Thank you very much for your reply.
The installation was successful now.
However, the version of PyRx I am using (-0.9.2) had a display problem that I mentioned in a previous post here:

https://sourceforge.net/p/pyrx/discussion/general/thread/752221a0/

Your recommendation that time, was to "Check for updates" to fix the problem.

Well, the problem appeared again after the installation of the original version, but when I checked for updates, I found the following error message:

Error in : <function checkforupdates="" at="" 0x9b886e0="">
Python 2.6.6 (r266:84292, Jan 22 2014, 09:42:36)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-4)] on linux2
Type "help", "copyright", "credits" or "license" for more information.</function>

noTK
Traceback (most recent call last):
File "/usr/local/PyRx-0.9.2/lib64/python2.6/site-packages/PyRx/wxMainFrame.py", line 338, in TryCommand
retObject = command(args, *kw)
File "/usr/local/PyRx-0.9.2/lib64/python2.6/site-packages/PyRx/update.py", line 45, in CheckForUpdates
txt = urllib.urlopen("http://pyrx.sourceforge.net/updates/check").readlines()
File "/usr/local/PyRx-0.9.2/lib64/python2.6/urllib.py", line 86, in urlopen
return opener.open(url)
File "/usr/local/PyRx-0.9.2/lib64/python2.6/urllib.py", line 207, in open
return getattr(self, name)(url)
File "/usr/local/PyRx-0.9.2/lib64/python2.6/urllib.py", line 362, in open_http
return self.http_error(url, fp, errcode, errmsg, headers)
File "/usr/local/PyRx-0.9.2/lib64/python2.6/urllib.py", line 375, in http_error
result = method(url, fp, errcode, errmsg, headers)
File "/usr/local/PyRx-0.9.2/lib64/python2.6/urllib.py", line 671, in http_error_301
return self.http_error_302(url, fp, errcode, errmsg, headers, data)
File "/usr/local/PyRx-0.9.2/lib64/python2.6/urllib.py", line 640, in http_error_302
data)
File "/usr/local/PyRx-0.9.2/lib64/python2.6/urllib.py", line 667, in redirect_internal
return self.open(newurl)
File "/usr/local/PyRx-0.9.2/lib64/python2.6/urllib.py", line 207, in open
return getattr(self, name)(url)
File "/usr/local/PyRx-0.9.2/lib64/python2.6/urllib.py", line 441, in open_https
h.endheaders()
File "/usr/local/PyRx-0.9.2/lib64/python2.6/httplib.py", line 908, in endheaders
self._send_output()
File "/usr/local/PyRx-0.9.2/lib64/python2.6/httplib.py", line 780, in _send_output
self.send(msg)
File "/usr/local/PyRx-0.9.2/lib64/python2.6/httplib.py", line 739, in send
self.connect()
File "/usr/local/PyRx-0.9.2/lib64/python2.6/httplib.py", line 1116, in connect
self.sock = ssl.wrap_socket(sock, self.key_file, self.cert_file)
File "/usr/local/PyRx-0.9.2/lib64/python2.6/ssl.py", line 338, in wrap_socket
suppress_ragged_eofs=suppress_ragged_eofs)
File "/usr/local/PyRx-0.9.2/lib64/python2.6/ssl.py", line 120, in init
self.do_handshake()
File "/usr/local/PyRx-0.9.2/lib64/python2.6/ssl.py", line 279, in do_handshake
self._sslobj.do_handshake()
IOError: [Errno socket error] [Errno 1] _ssl.c:490: error:14077410:SSL routines:SSL23_GET_SERVER_HELLO:sslv3 alert handshake failure

Could you help me?
Best regards,

Flavio

[Sarkis Dallakian]

Dear Flavio,

Yes, the Linux version has this issue. You can try updating using instructions from https://pyrx.sourceforge.io/blog/127-recent-changes-in-vina-web-services-and-mac-os-x-updates-

Best regards,
Sargis

[Flavio Augusto Vicente Seixas]

Dear Sarkis,

Thank you for the link.
But my PyRx-0.9.2 is installed at the following directory:

/usr/local/PyRx-0.9.2/

And inside the main directory of the above folder, there are not a folder named "PyRx" to replace by the new one downloaded (see picture attached).

How can I proceed??

Best regards,

Flavio

[Sarkis Dallakian]

Look inside lib64/python2.6/site-packages/PyRx

[Flavio Augusto Vicente Seixas]

Dear Sarkis,

I replaced the PyRx folder according to the instructions, but the program does not launch.

After replacing the PyRx folder, I go to the following directory:
/usr/local/PyRx-0.9.2

and used the command:

./run.sh

However, PyRx does not launch and no error message appears.

Could you help me?

Flavio

[Sarkis Dallakian]

Dear Flavio,

Sorry, no. The best option is to get the latest version for Windows. You can try using Download Snapshot on this version https://sourceforge.net/p/pyrx/code/472/tree/PyRxDev/PyRx/

[Flavio Augusto Vicente Seixas]

Dear Sarkis.
I really appreciate your help.
However, running PyRx in Windows is not an option for us, due to OS limitations.

So, I try to install Ubuntu 24.10 64-bit, Kernel Linux 6.11.0-14-generic x86_64 replacing CentOS9.

I successful install PyRx 0.9.2 in Ubuntu, but when I follow the instructions for update the version ( https://sourceforge.net/p/pyrx/code/HEAD/tree/PyRxDev/ ), I found the following error message:

root@perseus:/usr/local/PyRx-0.9.2# ./run.sh
root@perseus:/usr/local/PyRx-0.9.2# cannot import name OrderedDict
Traceback (most recent call last):
File "/usr/local/PyRx-0.9.2/runPyRx.py", line 98, in <module>
dlg = wx.lib.dialogs.ScrolledMessageDialog(None, msg, "Error starting PyRx")
File "/usr/local/PyRx-0.9.2/lib64/python2.6/site-packages/wx/lib/dialogs.py", line 32, in init
wx.Dialog.init(self, parent, -1, caption, pos, size, style)
File "/usr/local/PyRx-0.9.2/lib64/python2.6/site-packages/wx/windows.py", line 643, in __init__
_windows.Dialog_swiginit(self,windows.new_Dialog(args, *kwargs))
wx._core.PyNoAppError: The wx.App object must be created first!</module>

Could you help-me??

Best regards

[Sarkis Dallakian]

Dear Flavio,

Sorry, I don't have bandwidth for this currently. I have Ubuntu 20.04 vm and don't have time to get a newer vm.

Best regards