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.
Related
I am successfully compiling my Fortran subroutine with f2py. However, a folder is created as well as a pyd file.
If I do not put the created pyd file in the generated folder I get this error
ImportError: DLL load failed: The specified module could not be found.
If I put the generated .pyd file in the generated folder, my python script will run, and the import seems to work. However, if I run print(energy_f2py.__doc__) None is the output, and when I try to use the subroutine I get an error AttributeError: module 'energy_f2py' has no attribute 'potential_3'
potential_3 is the name of the subroutine inside energy_f2py.f90
I have also tried making energy_f2py.f90 a module containing the subroutine, with no difference in results.
This is the pyd file that is generated energy_f2py.cp36-win_amd64.pyd. I am using the commandline in Pycharm (windows 10 64 bit) to compile the Fortran file using
f2py -c -m energy_f2py energy_f2py.f90
python -m numpy.f2py -c -m energy_f2py energy_f2py.f90
The same thing happens.
It seems weird to me that both the pyd file is created as well as a folder, see the below image
I am stuck at this point... it seems like it is 95% of the way to working...
Lastly, this other post had a solution saying to name the Python and Fortran modules different names. I have tried this, and it did not make a difference either.
The best solution I found which worked was to partition my hardrive and install Linux. I chose to use Lubuntu, but you could use anything.
Everything works as it should on Linux.
Anther option to is to make it a static build, with the -static flag. This builds everything needed into a single file:
python -m numpy.f2py -c -m energy_f2py energy_f2py.f90 -static
You should then be able to use that .pyd file no matter what folder you've placed it in.
If you are using windows, I think adding --compiler=mingw32 may help. The defualt compiler is msvc on windows.
It occurs to me that the resulting .pyd module is looking for the DLL library in the same directory it itself resides in. Therefore, try moving the DLL from .libs directory to energy_f2py - it worked for me on Windows 10.
I am using Pycharm as my IDE (Python 3.7) and am trying to extract a password protected .rar file (I know the password) and have imported rarfile from unrar but am getting this error "LookupError: Couldn't find path to unrar library."
I also attempted changing my import statement to just say "import rarfile" but instead got the following error "rarfile.RarCannotExec: Unrar not installed?"
I also tried including this line of code, based on something I found in the rarfile documentation: rarfile.UNRAR_TOOL = "unrar" however I got the same errors.
Here is a snippet of my code:
from unrar import rarfile
def hacker(file_path):
passwords = open('pwds.txt', 'r')
with rarfile.RarFile(file_path) as file:
for line in passwords:
try:
file.pwd = line
file.extractall()
except RuntimeError:
pass
In addition to #tom answer for Windows 10 environment, the following steps should help:
Download the libfile via the link and install it.
For easy replication the following steps, choose the default path, C:\Program Files (x86)\UnrarDLL\
Go to Environment Variables window (link) and selected Advanced.
Click Environment Setting.
Under the User variables, select New.
In the New User Variables, rename the Variable name as UNRAR_LIB_PATH
To select the Variable Value, select Browse file. Depending on your system, 64bit enter C:\Program Files (x86)\UnrarDLL\x64\UnRAR64.dll, if your system is 32bit enter C:\Program Files (x86)\UnrarDLL\UnRAR.dll.
Save the environment path and rerun your Pycharm.
The graphical illustration is as below,
on different os need different solutions:
on Windows：
download the libfile, http://www.rarlab.com/rar/UnRARDLL.exe, install it;
you'd better choose the default path, C:\Program Files (x86)\UnrarDLL\
the most important is add the environment path, the varname enter UNRAR_LIB_PATH, pay attention, it must be!!!. then if your system is 64bit enter C:\Program Files (x86)\UnrarDLL\x64\UnRAR64.dll, if your system is 32bit enter C:\Program Files (x86)\UnrarDLL\UnRAR.dll.
after save the environment path, rerun your pycharm.
on Linux you need to make so file, which is a little difficult.
the same, download the libfile http://www.rarlab.com/rar/unrarsrc-5.4.5.tar.gz, you can choose the latest version.
after download extract the file get the file unrar, cd unrar ,then make lib, then make install-lib, we'll get file libunrar.so(in /usr/lib).
last, you also need to set the environment path, vim /etc/profile open file profile, add export UNRAR_LIB_PATH=/usr/lib/libunrar.so in the end of the file. then save the file, use source /etc/profile to make the environment successful.
rerun the .py file.
the resource website：https://blog.csdn.net/ysy950803/article/details/52939708
Additionally, after you do the things as mentioned by Tom.chen.kang and balandongiv, if you're using a 32bit DLL with 64bit Python, or vice-versa, then you'll probably get an error like this when you try to import unrar:-
OSError: [WinError 193] %1 is not a valid Win32 application
In that case do this:
For 32 Python & 32 bit DLL
Change your Environment variables for variable UNRAR_LIB_PATH to :
C:\Program Files (x86)\UnrarDLL\UnRAR.dll
For 64 bit Python & 64 bit DLL
Change your Environment variables for variable UNRAR_LIB_PATH to :
C:\Program Files (x86)\UnrarDLL\x64\UnRAR.dll
Restart your Pycharm or other Development Environment.
Creating a python executable in pycharm is harder than creating it in visual studio or creating a vb.net executable.
I thought I'd understand how to do this already but it looks like I have not.
I created a question regarding this in Dec of last year, here >> Create a simple python executable program and an icon to it - Hello World.
But I don't understand the answer or if it was answered completely. So I did my research again and found 2 helpful sites below that helped me create python executable without visual studio involved,
https://pythonhosted.org/PyInstaller/installation.html
https://pythonhosted.org/PyInstaller/usage.html#using-pyinstaller.
I followed the instructions exactly:
In command line, set path to C:\Python34\Scripts, then type pyinstaller "C:\Users\Desktop\PROGRAMs\TEST22.py".
This creates a TEST22.spec file in C:\Python34\Scripts and creates a folder TEST22 in C:\Python34\Scripts\dist and in there, are the TEST22.exe. I click on this executable to run the program, it runs completely fine. But when I copied the executable to the desktop, for example, it doesn't run. It seems like in the scripts folder there are files needed to run it and when it's a stand alone program there are no file to run it. Could someone let me know an easier way to create executable and please advise me on how I could fix it when the executable is copied to desktop or anywhere else and run it ?
Your answer lies in pyinstaller documentation. The dist folder itself is a standalone program directory. To get a single file exe with pyinstaller is not possible even thou pyinstaller has -F option for single exe since it dosnt contain data files.
I would suggest use py2exe and inno setup for creating installer
I have a script file that I was given to run in windows using Cygwin. When I try to use this file I get the following error
-bash: /sigdet/filename: cannot execute binary file: Exec format error.
sigdet is the folder within the Cygwin directory that I have the script. Rawdata is the name of the directory with the raw data files that the script is supposed to analyze.
To try and solve this, I have changed the file permissions, I have checked to make sure that it is on a 64 bit machine and the script appears to have compiled on a 64-bit machine. After these steps, I don't know what else the problem could be. Here are the commands I've entered:
I first changed the directory like so:
$ cd /sigdet/
Then I ran the script that is suppsed to work:
$ /sigdet/filename -i rawdata
Does the script file need to have an extension in windows? I've tried changing it to a .sh extension with no luck. I'm told that it just works on other windows machines just how it is.
Thanks to anyone that can help with this.
Your file is not an executable. It most probably contains ELF executable which is designed for Linux operating system, or it's corrupt.
If your file was a shell script, or in fact anything that contained plain text, you'd get different errors (such as, "expected command name" or "unknown command: XYZ" etc.)
Scripts are not supposed to have file extensions, like any executables. On the other hand, they should have shebangs: small text located in the first line that tells the system the path to the interpreter. For example, a Python executable script might be named whatever and have #!/usr/bin/python3 or similar in the first line. When you run it through ./whatever in the shell, it'll look for python3 in /usr/bin and run your file like this: /usr/bin/python3 ./whatever. (In fact, thanks to this you can also specify additional parameters that get passed to the interpreter.)
There is also a chance that your script is valid, but it contains a shebang pointing to bad interpreter. If that is the case, then most likely the path is correct, otherwise you'd get /whatever/interpreter: bad interpreter: no such file or directory error or similar. But then, all the other points apply to the interpreter (which is just another executable...)
If the script and/or interpreter was meant to be executed on Windows or Cygwin at least, it should either contain aforementioned shebang (#!/path in the first name) or it should be Windows executable (in which case the file data should begin with MZ letters, you can inspect it in notepad.) If it isn't, it means the files you were given can't run on Cygwin.
Had this same problem. Added the following at the top of makefile:
export ARCH = CYGNUS
What happened during the make process is that Linux and Windows versions of the executables were created. You just have to use ./.exe versions.
In my case, I got the error when I used a wrong command to compile my C program. When I used the right command:
gcc myprog.c -o myprog.exe
the error was resolved.
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.