How to add a search path to R?

Question

In this tutorial, there is a command pymol.dccm(cij, pdb, type="launch"). But I was told

> pymol.dccm(cij, pdb, type="launch")
Error in pymol.dccm(cij, pdb, type = "launch") : 
  Launching external program failed
  make sure 'C:/python27/PyMOL/pymol.exe' is in your search path
In addition: Warning message:
running command 'C:/python27/PyMOL/pymol.exe -cq' had status 127

I already have pymol installed on my PC. Can I ask how to add another search path to R?

Now I think pymol is a sub-package in bio3d. But I already installed bio3d and other commands can work (e.g. pdb <- read.pdb()). But why the pymol command could not work?

I tried

> .libPaths("path/to/pymol2/")

> .libPaths("path/to/pymol2/PyMOL")

> .libPaths("path/to/pymol2/PyMOL/PyMOLWin.exe")

> pymol.dccm(cij, pdb, type="launch")
Error in pymol.dccm(cij, pdb, type = "launch") : 
  Launching external program failed
  make sure 'C:/python27/PyMOL/pymol.exe' is in your search path
In addition: Warning message:
running command 'C:/python27/PyMOL/pymol.exe -cq' had status 127 

> PyMOLWin.dccm(cij, pdb, type="launch")
Error: could not find function "PyMOLWin.dccm"

So the .libPaths did not return error. But pymol.dccm and PyMOLWin.dccm did not work.

I also tried to install pymol package in R

> install.packages("pymol")
Warning in install.packages :
  package ‘pymol’ is not available (for R version 3.2.2)

`.libPaths` only influences where R looks for packages, not where it looks for executables. You'll want to set the PATH system variable. See this question for how to do that: https://stackoverflow.com/questions/24622725/how-to-set-path-on-windows-through-r-shell-command — MrFlick, Mar 15 '18 at 16:52
I have `PyMOLWin.exe` executable, but where is the `pymol` package? — lanselibai, Mar 15 '18 at 17:05

score 0 · Answer 1 · edited May 03 '20 at 07:23

0

There's a mistake in the tutorial command itself. The correct syntax for dccm is

pymol(cij, pdb, type="launch",exefile="C:/Program Files/pymol")

where exefile = file path to the ‘PYMOL’ program on your system (i.e. how is ‘PYMOL’ invoked). If NULL, use OS-dependent default path to the program.

edited May 03 '20 at 07:23

David Buck

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answered May 02 '20 at 18:17

Nidhi Gujar

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score 0 · Answer 2 · edited Nov 24 '21 at 06:27

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Try the following code, it worked perfectly for me:

pymol(cm, pdb.open, type="launch", exefile="%userprofile%/PyMOL/PyMOLWin.exe")

edited Nov 24 '21 at 06:27

Omkar T

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answered Nov 23 '21 at 18:00

Oche George

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Jordi · Answer 3 · 2018-03-15T16:57:40.670

-1

.libPaths("path/to/package/library") probably does what you need.

.libPaths gets/sets the library trees within which packages are looked for.

Set the path to the parent directory of the directory with the package name rather than the package directory itself.

edited Mar 15 '18 at 16:57

answered Mar 15 '18 at 16:29

Jordi

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I tried, but is there a specific `pymol` that `R` can recognise? Please see the updated question. – lanselibai Mar 15 '18 at 16:44
Did you try setting the path to the parent directory of that package folder you are trying to refer to? – Jordi Mar 15 '18 at 16:46
The essential part is just about how to set the path in R. That is why I only use link to refer. – lanselibai Mar 15 '18 at 16:55
Jordi, could you please tell me what is the exact path, "path/to/pymol2/", or "path/to/pymol2/PyMOL"? As @MrFlick mentioned, is there a difference between package and executable? – lanselibai Mar 15 '18 at 17:02
@lanselibai, if it is like any R package, you should find a DESCRIPTION file somewhere. This is the package directory. Set the path to the parent of that package directory. – Jordi Mar 15 '18 at 17:10

How to add a search path to R?

3 Answers3