So far, I couldn't find out how to solve the following problem:
I have Python 3 installed under Windows 8.1. In addition to this Python installation, I have several other installations that came with programs such as QGIS and ArcGIS Pro. Those programs have their own Python installation with a Python exe shomewhere in their program folders.
Now I have a Python script that relies on some modules that are installed for QGIS Python. I want to run the script from the command line (or from within R). However, the script will be handled by my main Python installation that doesn't have the modules.
I tried to add some paths to the PATH and PYTHONPATH variables following instructions I found on the internet, but this only resulted in my Python IDE (Spyder) not starting anymore.
PATH:
C:\Users\Manuel\Python\Scripts\;C:\Users\Manuel\Python\;C:\Users\Manuel\AppData\Local\Programs\Python\Launcher\;C:\Users\Manuel\AppData\Roaming\TinyTeX\bin\win32;C:\Perl64\site\bin;C:\Perl64\bin;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0\;C:\Program Files (x86)\Windows Live\Shared;C:\Program Files\MiKTeX 2.9\miktex\bin\x64\;C:\Program Files (x86)\NVIDIA Corporation\PhysX\Common;C:\Program Files\IBM\SPSS\Statistics\24\JRE\bin;D:\x2go\PuTTY\;C:\Program Files (x86)\Common Files\Ulead Systems\MPEG;C:\Program Files;C:\Program Files\snap\bin;C:\Program Files\Inkscape\bin;D:\Program_Files\gdal\bin;C:\Users\Manuel\AppData\Local\GitHubDesktop\bin
PYTHONPATH:
C:\Program Files\Spyder\pkgs;C:\Users\Manuel;C:\Program Files\QGIS 3.14.16\apps\qgis\python\plugins;C:\Program Files\QGIS 3.14.16\apps\qgis\python;C:\Program Files\QGIS 3.14.16\apps\Python37
I also tried to replace "py" in the command prompt with C:\Programme\QGIS 3.14.16\bin\python3.exe, which also didn't work (Error: Access denied).
I tried this tutorial to import the modules within python, bit it gives
ImportError: DLL load failed while importing _core: Module not found
How can I tell the command prompt to use a specific Python installation in this single case (I want to use the other Python installation in every other case)?
I would do exact what you tried: "I also tried to replace "py" in the command prompt with the entire path to the QGIS Python exe, which also didn't work (Error: Access denied)."
But try to run it in a powershell with administrator privileges.
I've installed Python 3.8 on Win 10 machine. Path to Python is C:\Users\userid\AppData\Local\Programs\Python\Python38\
Path environment variable values are: C:\Users\userid\AppData\Local\Programs\Python\Python38\Scripts\;C:\Users\userid\AppData\Local\Programs\Python\Python38\python.exe
In order to test python, I created a simple script called "script.py" in directory C:\python_scripts.
Then I tried to run "script.py" from the directory where it is located, but got error:
C:\python_scripts> python script.py
C:\Users\userid\AppData\Local\Programs\Python\Python38\python.exe: can't open file 'script.py': [Errno 2] No such file or directory
What might be the cause of getting this error? i tried to run the script with both cmd and powershell, with the usual user rights and with elevated admin rights, still getting Errno 2.
No other versions of Python have been previously installed on this machine (which is a corporate one, if that might be significant)
Thank you
Thank you #OferSadan for your suggestion to use dir command, it helped me to solve the problem. The "script.py" had an additional .txt extension added to it for some reason, but the Windows explorer only showed .py extension by default. Now I deleted the trailing .txt suffix and the script runs
I am installing 7-ZIP using NSIS and then looking in the registry to see where it has been installed. Having detected the install location I am taking the path and creating a system variable named 7-ZIP using the NSIS command below.
${EnvVarUpdate} $0 "7-ZIP" "A" "HKLM" "<Install Path>"
I then append the 7-ZIP var to the PATH var.
After the install has finished I can see the new System var in the System Variables list.
The new 7-ZIP variable has also been amended to the PATH variable as the image below shows.
Now the issue I have is that when I start a cmd window and type 7z I would expext it to run the 7z.exe located in the C:\Program Files\7-Zip directory, but it does not and complains it cannot find it. If I then close the CMD window and edit the 7-ZIP variable, but don't actually chang anything. The same command then works when i try again with a new CMD window.
I just wonder whether anyone else has experienced this issue and if they found a work around?
I am using the IDE Netbeans to code a project c++ under Linux(red hat 7). As I need to use some math functions, I try to embed the julia language into my c++ project.
Here is what I have done:
Download the Julia from here (I choose this: Generic Linux binaries)
Set project properties: build-->C++ Complier-->Include Directories, add the include of Julia, something like this: ../myjulia/include/julia
Add the libraries: open a terminal and type the command line: sudo ln -s ../myjulia/lib/julia/libjulia.so /usr/lib/libjulia.so
Now if I run my project, I will get this error: System image file "../myproject/dist/Debug/GNU-Linux-x86/../lib/julia/sys.ji" not found
I hve checked this file: ../myjulia/lib/julia, in this file, there are all of the lib files (libjulia.so etc) and a file named "sys.ji".
I ran into this issue after installing Julia v0.3.10 on a Windows machine and thought I'd post it in case it can help someone else.
When I ran julia.exe it gave me the error message listed above.
Problem:
I had created a system environment variable called JULIA_HOME and pointed it to the directory where Julia was installed. Then, I added %JULIA_HOME%\bin to my PATH.
Solution:
I pointed JULIA_HOME to the \bin directory under the Julia install directory. Then, I added %JULIA_HOME% to my PATH
A "hello world" example from here
Now we know that we need to setup the julia context with this code:
jl_init(NULL);
In fact this code may not setup a good context because the project can't find the system image file "sys.ji". So what we need to do is using another function instead of jl_init: jl_init_with_image. This function accept two parameters: the first is the path of the image file, the second is the name of the image file. So we should use it like this: jl_init_with_image("/thePathOfSys.ji", "sys.ji"); One more thing: the path of sys.ji must be the absolute path.
I am running R on Windows, not as an administrator. When I install a package, the following command doesn't work:
> install.packages("zoo")
Installing package(s) into ‘C:/Program Files/R/R-2.15.2/library’
(as ‘lib’ is unspecified)
Warning in install.packages :
'lib = "C:/Program Files/R/R-2.15.2/library"' is not writable
To install a package, I have to specify a library location:
install.packages("zoo", lib="C:/software/Rpackages")
To load a package, I also have to specify the library location:
library("zoo", lib.loc="C:/software/Rpackages")
All of this is OK, but I wanted to see if I could add C:/software/Rpackages to the library path somehow and thus not have to type it each time.
As I searched online, I found that one way to do this is to edit the Rprofile.site file and to add the line
.libPaths("C:/software/Rpackages")
However, after doing this, and starting RStudio, this is the output that I get
> .libPaths()
[1] "C:/Program Files/R/R-2.15.2/library" "C:/Program Files/RStudio/R/library"
The .libPaths command that I added to the Rprofile.site doesn't seem to have had any effect! Why is this the case? Or more importantly, how can I fix the problem so that I can install and load packages without typing in the library location?
Note: if I start RStudio the .libPaths() command seems to work as it is supposed to
.libPaths("C:/software/Rpackages")
> .libPaths()
[1] "C:/software/Rpackages" "C:/Program Files/R/R-2.15.2/library"
Isn't that strange?
The proper solution is to set environment variable R_LIBS_USER to the value of the file path to your desired library folder as opposed to getting RStudio to recognize a Rprofile.site file.
To set environment variable R_LIBS_USER in Windows, go to the Control Panel (System Properties -> Advanced system properties -> Environment Variables -> User Variables) to a desired value (the path to your library folder), e.g.
Variable name: R_LIBS_USER
Variable value: C:/software/Rpackages
If for some reason you do not have access to the control panel, you can try running rundll32 sysdm.cpl,EditEnvironmentVariables from the command line on Windows and add the environment variable from there.
Setting R_LIBS_USER will ensure that the library shows up first in .libPaths() regardless of starting RStudio directly or by right-clicking an file and "Open With" to start RStudio.
The Rprofile solution can work if RStudio is always started by clicking the RStudio shortcut. In this case, setting the default working directory to the directory that houses your Rprofile will be sufficient. The Rprofile solution does not work when clicking on a file to start RStudio because that changes the working directory away from the default working directory.
I generally try to keep all of my packages in one library, but if you want to add a library why not append the new library (which must already exist in your filesystem) to the existing library path?
.libPaths( c( .libPaths(), "~/userLibrary") )
# obviously this would need to be a valid file directory in your OS
# min just happened to be on a Mac that day
Or (and this will make the userLibrary the first place to put new packages):
.libPaths( c( "~/userLibrary" , .libPaths() ) )
Then I get (at least back when I wrote this originally):
> .libPaths()
[1] "/Library/Frameworks/R.framework/Versions/2.15/Resources/library"
[2] "/Users/user_name/userLibrary"
The .libPaths function is a bit different than most other nongraphics functions. It works via side-effect. The functions Sys.getenv and Sys.setenv that report and alter the R environment variables have been split apart but .libPaths can either report or alter its target.
The information about the R startup process can be read at ?Startup help page and there is RStudio material at: https://support.rstudio.com/hc/en-us/articles/200549016-Customizing-RStudio
In your case it appears that RStudio is not respecting the Rprofile.site settings or perhaps is overriding them by reading an .Rprofile setting from one of the RStudio defaults. It should also be mentioned that the result from this operation also appends the contents of calls to .Library and .Library.site, which is further reason why an RStudio- (or any other IDE or network installed-) hosted R might exhibit different behavior.
Since Sys.getenv() returns the current system environment for the R process, you can see the library and other paths with:
Sys.getenv()[ grep("LIB|PATH", names(Sys.getenv())) ]
The two that matter for storing and accessing packages are (now different on a Linux box):
R_LIBS_SITE /usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library
R_LIBS_USER /home/david/R/x86_64-pc-linux-gnu-library/3.5.1/
I managed to solve the problem by placing the code in the .Rprofile file in the default working directory.
First, I found the location of the default working directory
> getwd()
[1] "C:/Users/me/Documents"
Then I used a text editor to write a simple .Rprofile file with the following line in it
.libPaths("C:/software/Rpackages")
Finally, when I start R and run .libPaths() I get the desired output:
> .libPaths()
[1] "C:/software/Rpackages" "C:/Program Files/R/R-2.15.2/library"
[3] "C:/Program Files/RStudio/R/library"
https://superuser.com/questions/749283/change-rstudio-library-path-at-home-directory
Edit ~/.Renviron
R_LIBS_USER=/some/path
I found what I think is a solution here (thank you Carl Schwarz at SFU) for adding a personal library that is permanently (you don't have to define it each session) recognized whether using R or Rstudio, and Rstudio treats it as the default on my Mac machine. I hadn't seen it laid out this explicitly on SO, so I summarized the steps they provided, for Windows and then for Mac.
For a Windows 7 OS:
Create a directory on the drive where you want to have your personal library, e.g. C:\User\Rlibs (or another that you have permissions to)
Search for/go to "Edit environment variable for your account" in the Windows search bar to edit control panel settings
Click "New..." in the middle of the "Environmental Variables" window
In the "New User Variable" window, type R_LIBS for the "Variable name", and the path to the personal library directory you created, e.g. C:\User\Rlibs
Click OK and you should see the Variable/Value pair in the User variables window
Click OK again
Now when you start R (or Rstudio) and type the command .libPaths() you should see the personal library you created as well as the R system library.
For Mac:
In your "Home" or "username" directory create a folder called Rlibs
Launch the Terminal application
Type: echo "R_LIBS=~/Rlibs" > .Renviron Make sure the spelling and case matches.
Type ls -a to see the full list of files in the directory, which should now include .Renvrion
Verify that the .Renviron file has been set properly: more .Renviron
Launch R/Rstudio and type .libPaths() and you should see the new path to your personal library.
If you do not have admin-rights, it can also be helpful to open the Rprofile.site-file located in \R-3.1.0\etc and add:
.First <- function(){
.libPaths("your path here")
}
This evaluates the .libPath() command directly at start
just change the default folder for your R libraries in a directory with no Administrator rights, e.g.
.libPaths("C:/R/libs")
On Ubuntu, the recommended way of changing the default library path for a user, is to set the R_LIBS_USER variable in the ~/.Renviron file.
touch ~/.Renviron
echo "R_LIBS_USER=/custom/path/in/absolute/form" >> ~/.Renviron
I've had real trouble understanding this. gorkypl gave the correct solution above when I last re-installed my OS & Rstudio but this time round, setting my environment variable didn't resolve.
Uninstallled both R and Rstudio, creating directories C:\R and C:\Rstudio then reinstalled both.
Define R_LIBS_USER user variable to your prefered directory (as per gorkypl's answer) and restart your machine for User variable to be loaded. Open Rstudio, errors should be gone.
You can also use Sys.setenv() to modify R_LIBS_USER to the path of your alternative library which is easier and does not need to restart your computer.
To see what R_LIBS_USER is set to:
?Sys.getenv()
Reading help(Startup) is useful.
If your default package library has been changed after installing a new version of R or by any other means, you can append both the libraries to use all the packages with the help of the commands below.
Get the existing library path :
.libPaths()
Now,set the existing and the old path :
.libPaths(c(.libPaths(), "~/yourOldPath"))
Hope it helps.
I read the readme. In that they mentioned use .libPaths() in command line to check which paths are there. I had 2 library paths earlier. When I used the command .libpath("C:/Program Files/R/R-3.2.4revised/library") where I wanted, it changed the library path. When I typed in .libPaths() at the command line again it showed me the correct path. Hope this helps
getwd()
# [1] "C:/Users/..../software/My R studio"
copy the above link with double inverted comma
.libPaths(new="C:/Users/..../software/My R studio")
Your default path will change for installing pakages
If you want to change your library path permanently (without calling .libPath() every time when entering in R, this works for me:
create .Rprofile under your home directory. (~/.Rprofile)
type
.libPaths(c( .libPaths(), "your new path" ))
in .Rprofile file, save.
open R (any directory) and check, just type .libPaths(), you can find your libaray path is updated!
Since most of the answers here are related to Windows & Mac OS, (and considering that I also struggled with this) I decided to post the process that helped me solve this problem on my Arch Linux setup.
Step 1:
Do a global search of your system (e.g. ANGRYSearch) for the term Renviron (which is the configuration file where the settings for the user libraries are set).
It should return only two results at the following directory paths:
/etc/R/
/usr/lib/R/etc/
NOTE: The Renviron config files stored at 1 & 2 (above) are hot-linked to each other (which means changes made to one file will automatically be applied [ in the same form / structure ] to the other file when the file being edited is saved - [ you also need sudo rights for saving the file post-edit ] ).
Step 2:
Navigate into the 1st directory path ( /etc/R/ ) and open the Renviron file with your favourite text editor.
Once inside the Renviron file search for the R_LIBS_USER tag and update the text in the curly braces section to your desired directory path.
EXAMPLE:
... Change From ( original entry ):
R_LIBS_USER=${R_LIBS_USER-'~/R/x86_64-pc-linux-gnu-library/4.0'}
... Change To ( your desired entry ):
R_LIBS_USER=${R_LIBS_USER-'~/Apps/R/rUserLibs'}
Step 3:
Save the Renviron file you've just edited ... DONE !!
I had the same problem and I run into this. If you want to create another location c("C:/Users/mynewlocation") should be working as well. As mentioned in here "You should be able to right-click on the Rstudio.exe icon, click Properties, and select an option to always run Rstudio as administrator. Be sure you use that same icon whenever you want to open Rstudio."
myPaths <- .libPaths() # get the paths
myPaths <- c(myPaths[2], myPaths[1]) # switch them
.libPaths(myPaths) # reassign them
I was looking into this because R was having issues installing into the default location and was instead just putting the packages into the temp folder. It turned out to be the latest update for Mcaffee Endpoint Security which apparently has issues with R. You can disable the threat protection while you install the packages and it will work properly.