I am trying to install EasyHrid-GTKDynamo package in Linux mint 20 but it failed. Kindly suggest me to install.
@Sergei V. Dolin, kindly finds the errors below. I am using python 2.7.18
Checking dependencies
gtk.........................OK
pygtk.......................OK
PyMOL.......................Fail
matplotlib..................Fail
Checking pDynamo
pBabel......................Fail
pCore.......................Fail
pMolecule...................Fail
pMoleculeScripts............Fail
Would like install PyMOL (Y/n):y
Reading package lists... Done
Building dependency tree
Reading state information... Done
pymol is already the newest version (2.3.0+dfsg-1build1).
0 upgraded, 0 newly installed, 0 to remove and 22 not upgraded.
Would like install matplotlib (Y/n):y
Reading package lists... Done
Building dependency tree
Reading state information... Done
Package python-matplotlib is not available, but is referred to by another package.
This may mean that the package is missing, has been obsoleted, or
is only available from another source
E: Package 'python-matplotlib' has no installation candidate
Would like to auto install pDynamo? (Y/n):y
(1)pDynamo-1.9.0
(2)pDynamo-1.8.0
(3)pDynamo-1.7.2
(4)other
Select a pDynamo version(1):1
Cython-0.19 PyYAML-3.10 pDynamo-1.9.0
Where would you like to install pDynamo? (/home/ranabir):/home/ranabir
--2021-04-24 13:49:43-- https://sites.google.com/site/pdynamomodeling/pDynamo-1.9.0.tgz
Resolving sites.google.com (sites.google.com)... 142.250.182.78, 2404:6800:4007:81b::200e
Connecting to sites.google.com (sites.google.com)|142.250.182.78|:443... connected.
HTTP request sent, awaiting response... 404 Not Found
2021-04-24 13:49:50 ERROR 404: Not Found.
tar (child): pDynamo-1.9.0.tgz: Cannot open: No such file or directory
tar (child): Error is not recoverable: exiting now
tar: Child returned status 2
tar: Error is not recoverable: exiting now
Reading package lists... Done
Building dependency tree
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:
The following packages have unmet dependencies:
python-dev : Depends: python (= 2.7.5-5ubuntu3)
E: Unable to correct problems, you have held broken packages.
Ranabir Majumder, From what I could find it is that pDynamo only works with version 3 of Python. Therefore, when you try to install the packages you need, the module management system refers to packages that support version 2 of Python. But unfortunately (or fortunately) version 2 is no longer supported. Try using version 3 of the language.
As is the case with python-matplotlib. (Package python-matplotlib is not available, but is referred to by another package. This may mean that the package is missing, has been obsoleted, or is only available from another source)
If the use of the second version of the Python language is essential, then I'm afraid you will have to manually search for the modules of previous versions you need.
P.S. Sorry if I couldn't help you.
Sergei V. Dolin Thanks for your reply.
I have also tried to install pDynamo with python3 separately but it is not working. I am getting the following:-
**************************************************************************
python3 Install.py
Traceback (most recent call last):
File "Install.py", line 6, in
from InstallUtilities import FindRootDirectory , \
File "/home/ranabir/Downloads/pDynamo-1.9.0/installation/InstallUtilities.py", line 60, in
from types import ListType, TupleType
ImportError: cannot import name 'ListType' from 'types' (/usr/lib/python3.8/types.py)
***************************************************************************
Even python2 is now not working and getting Error:-
####################################################
fatal error: Python.h: No such file or directory
4 | #include "Python.h"
| ^~~~~~~~~~
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
#####################################################
Also, python3 is not compatible with the EasyHydrid package.
******************************************************************************
python3 install.py
File "install.py", line 50
print text1
^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print(text1)?
******************************************************************************
Dear, Ranabir Majumder in this case:
python3 Install.py
Traceback (most recent call last):
File "Install.py", line 6, in
from InstallUtilities import FindRootDirectory , \
File "/home/ranabir/Downloads/pDynamo-1.9.0/installation/InstallUtilities.py", line 60, in
from types import ListType, TupleType
ImportError: cannot import name 'ListType' from 'types' (/usr/lib/python3.8/types.py)
check the import line, "from types import ListType, TupleType", perhaps in the "types" module, there are no such functions, or this module has a different name in language version 3
In this case:
fatal error: Python.h: No such file or directory
4 | #include "Python.h"
| ^~~~~~~~~~
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
What command did you use? There is a GCC compiler error, try updating packages and dependencies (sudo apt-get update && sudo apt-get upgrade -y)
And in the latter case:
python3 install.py
File "install.py", line 50
print text1
^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print(text1)?
You are using the syntax of the second version of the language, although you are running through the third version. They are quite different.
Sergei V. Dolin
For your kind information, I have used both versions of python (python2 & python3). In both cases I got errors.
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