I am completely new to all of this, but I was trying to install https://github.com/MrS0m30n3/youtube-dl-gui, which requires twodict.
Now, the manual simply says:
Install From Source
Download & extract source from here
Change directory into twodict-1.2/
Run sudo python setup.py install
Sorry for the idiotic question, but what is meant by "change directory into twodict-1.2/"?
I downloaded the source file, and when I extract it, where do I put it? If What is meant by the step 2? Which command would I have to run exactly? I don't get it.
Running MacOS.
Thanks!
Related
I'm trying to install wholebrain by Daniel Fürth, following the instructions on the macosX install page (available here). I am running MacOS Big Sur 11.5.2, R 4.1.2, and RStudio 2021.09.1.
Unfortunately, the program is not straight-forward to install and requires significant developer tools to work correctly. I'm not a programmer and have almost no experience with coding, so I've been mucking through the instructions for two days now trying to get the install to work correctly and I'm firmly stuck on the final step.
In RS, when I run, devtools::install_github("tractatus/wholebrain", INSTALL_opts=c("--no-multiarch")) I get the following error message:
/bin/sh: pkg-config: command not found filter.cpp:9:10: fatal error: 'fftw3.h' file not found #include "fftw3.h" ^~~~~~~~~ 1 error generated. make: *** [filter.o] Error 1 ERROR: compilation failed for package ‘wholebrain’
I have been trying to figure out what this means for quite awhile now and I think I've narrowed it down to R is not reading the location of the fftw header file from where it was installed by Homebrew. (I could be totally wrong, again- not a programmer)
From what I understand, Homebrew always installs under opt/homebrew/cellar. And, in fact, in there is the compiled fftw program with the needed "fftw3.h" file. But for some reason, RStudio is not able to find and read the file in that location.
From random googling and reading of other posted issues, I think that RStudio may expect the file to be under usr/local/include. Can I just copy and paste the header file into that folder? Or will I be screwing something up if I do that? I am totally intimidated by fftw's description of manual compilation so I don't really want to attempt that. Is there a way to change where R is looking for that header file? I already set my wd to "/" so shouldn't R be able to access any folder on my computer?
I want to post an answer here for anyone who comes after me with the same issue. It came down to RStudio not recognizing the programs Homebrew had installed because it wasn't reading the file location where Homebrew saves them. Homebrew always installs programs in /opt/homebrew/... Here is what I had to do:
In RStudio, open your Renviron file using this command: usethis::edit_r_environ()
In the file that opens (which for me was totally blank), type: PATH=/opt/homebrew/bin:${PATH}, or whatever your particular path you want prepended to the Renviron path is.
Quit RStudio and, when prompted, save. Re-open RStudio and run Sys.getenv("PATH") to check. Your new path (in the example above, '/opt/homebrew/bin') should now be prepended to the list of paths that RStudio will use when looking for programs/files. For me this now looks like /opt/homebrew/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/Library/Apple/usr/bin:/Applications/RStudio.app/Contents/MacOS/postback
Finally, I want to say thank you very much to Mark Setchell who really helped point me in the correct direction!
I've searched the web, and I'm still unclear on how to run R from the Mac terminal. I have Rstudio and the standalone R app installed. I thought I could just type "R" from the command line as I do with "python", but that doesn't work. Is it necessary to edit the PATH in my bash profile? If so, how do I give the correct location of R?
Thanks for any help
Edits after receiving comments
So, I'm running Sierra, and when I type "r" or "R" at the terminal, I get "-bash: R: command not found." If I type, "which R" in the terminal I do not get any output.
Here is the output from "echo $PATH": /usr/local/heroku/bin:/opt/local/bin:/opt/local/sbin:/Library/Frameworks/Python.framework/Versions/2.7/bin:/Users/samuelcolon/anaconda/bin:/Library/Frameworks/Python.framework/Versions/3.5/bin:/Users/samuelcolon/.rvm/gems/ruby-2.1.0/bin:/Users/samuelcolon/.rvm/gems/ruby-2.1.0#global/bin:/Users/samuelcolon/.rvm/rubies/ruby-2.1.0/bin:/Library/Frameworks/Python.framework/Versions/2.7/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Users/samuelcolon/.rvm/bin:/Users/samuelcolon/.rvm/bin
As for the installation, I believe I downloaded it directly from cran.r-project.org a while ago. I can locate the GUI in my applications and open it--
I have version 3.13. Is it possible, I only have R.app installed but not R? Perhaps that's the reason I'm getting the 'command not found' when typing "R" into the terminal?
Generally, I've been working in RStudio, but I'd still like to access R from the terminal and also to find where things are located. I'm fine with removing and re-installing R if it's easiest to start from square one. I hope the extra detail helps, and I appreciate the responses.
An answer for those not that familiar with Terminal and Bash.
I have done a fresh update install of R from the R.org cran site as part of seeking an answer to your question.
I found this latest install version 3.4.0 installs R for access in Terminal, and also installs R.app as part of the package.
To my understanding, reading support docs, if you have an older version of R it will update that. However it will not update an installation of R installed by the anaconda package.
Where are the R files stored?
I can only assume that with a fresh install of the latest R, R will work for you in Terminal.
To learn where the R files are that are being accessed - in Terminal after starting R, and in R.app, type:
>R.home()
In my case as example:
In R.app - the R version 3.4.0 is accessed in the top directory (not my user folder):
R.home()
[1] "/Library/Frameworks/R.framework/Resources"
In Terminal - the R version 3.3.2 is accessed in the Anaconda package, again in the top level directory.
R.home()
[1] "/anaconda/lib/R"
So I have two different versions of R, and Terminal accesses a different version to R.app.
How can I ensure I access the same version in Terminal as I do in the R.app?
For someone familiar with bash, and how the whole bash command system works I am sure there is a well constructed command. All the same here are some novice solutions.
-
• First Solution:
I could update the anaconda version, however, I would prefer not to as as other elements of the anaconda package my depend on this older version of R. For those not yet familiar with Terminal and bash, not such a novice solution.
-
• Second Solution:
This solution came from mko. It provides a single use solution. From the result above, and checking the directory structure a little further to find this R file.
Finding the significant R file enables me to edit an extension of the above path shown in the R.app. So add /bin/R to enter
/Library/Frameworks/R.framework/Resources/bin/R
Entering and pressing return will start R from this version.
Alternatively, one can find this file and icon in the GUI Finder, lead by the above result, and just double click on it, and it will open Terminal and a session with R running for you. Easy!
One could also make an alias of it and put it on your desktop for easy future starts.
-
• Third Solution:
My last solution I think may be best, adding to mko's solution. Make an alias.
Being in my home directory in Terminal I open .bash_profile using the nano text editor. (If you do not already know how to do this, then best not use this solution.)
I then add the line in this env file.
alias Rv340='/Library/Frameworks/R.framework/Resources/bin/R'
I then save the changes and exit this terminal session. I then open a new Terminal window. (This is so the changes to the env above are incorporated in the new terminal session).
Then when I enter the alias:
Rv340
The version of R I want opens.
You can choose a different alias name to "Rv340".
-
• Fourth Solution:
A second more permanent solution for opening the same version of R in Terminal is as follows.
Copy the path as showing in R.app in response to the R.home() command above, and add that path to PATH in your .bash_profile. (If you do not know already how to do this, then ignore this solution.) Do so as follows.
export PATH="/Library/Frameworks/R.framework/Resources:$PATH"
To my understanding, this ensures that bash looks here for R (and anything else), then moves on to the other paths in PATH. Since this adds this path to the beginning of $PATH, an env variable, bash looks here first where it finds the newer version first, and stops looking.
When it comes to understanding PATH in the env set up in .bash_profile the following two links were helpful.
About PATH.
How to correctly add a path to PATH.
This solution may muck with anaconda's invocation of R. I have yet to check this.
First of all, you have to start terminal application. You can use either built in Terminal.app, or you can use replacement. My favorite one is iTerm2
https://www.iterm2.com
Then, you simply open terminal window and run R. Just like shown below:
Have fun with R!
Just ran into the same issue when installing R-4.0.3.pkg on my MacBook (MacOS BigSur). Can open R.app to the clunky R GUI, but typing in 'R' in terminal doesn't work.
Turns out, an R executable lives here: /Library/Frameworks/R.framework/Versions/4.0/Resources/bin/R
So I added this alias to my newly created .zshrc script:
alias R '/Library/Frameworks/R.framework/Versions/4.0/Resources/bin/R'
Now when I type in R, it opens... I swear this all happened seamlessly in earlier versions.
There is currently a bug in CRAN's R installation package that results in it not correctly installing symbolic links to R and Rscript for commandline use. I've just verified this by inspecting the postflight script in their 4.0.5 installation package. This only impacts MacOS system releases of 20 and above (you can check with uname -r).
I've included more info here, along with what the "correct" fix should be: manually creating symbolic links to /usr/local/bin that point to the R and Rscript binaries themselves. If this is the current challenge, then this would be a far better solution to creating aliases or manipulating PATH in various ways, since it's what the installation package intended to do (and presumably will again soon).
R: command not found
In short, if this is the problem, then Ashkan Mirzaee's answer (https://stackoverflow.com/a/67202173/2093929) to create the symbolic links directly is correct in form, but might not have the right link command. The 4.0.5 package intends instead to use:
mkdir -p /usr/local/bin
cd /usr/local/bin
rm -f R Rscript
ln -s /Library/Frameworks/R.framework/Resources/bin/R .
ln -s /Library/Frameworks/R.framework/Resources/bin/Rscript .
You can create a symbolic link from R and Rscript binaries to /usr/local/bin to add them to the PATH:
sudo ln -s /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R /usr/local/bin
sudo ln -s /Library/Frameworks/R.framework/Versions/Current/Resources/bin/Rscript /usr/local/bin
Now which R should return /usr/local/bin/R and you can use R.
An easy way to open RStudio with admin privilege on macOS:
Go to Applications, then right click on RStudio
Select "Show Package Contents"
Go to Contents/MacOS
Now open terminal(in bash mode). Type sudo and drag the RStudio.exec into terminal and press on ENTER
Now RStudio will have admin access!
I am trying to install the pyperclip module for Python 3.6 on Windows (32 bit). I have looked at various documentations (Python documentation, pypi.python.org and online courses) and they all said the same thing.
1) Install and update pip
I downloaded get-pip.py from python.org and it ran immediately, so pip should be updated.
2) Use the command python -m pip install SomePackage
Okay here is where I'm having issues. Everywhere says to run this in the command line, or doesn't specify a place to run it.
I ran this in the command prompt: python -m pip install pyperclip. But I got the error message "'python' is not recognized as an internal or external command, operable program or batch file.
If I run it in Python 3.6, it says pip is an invalid syntax. Running it in IDLE gives me the same message.
I have no idea where else to run it. I have the pyperclip module in my python folder. It looks like a really simple problem, but I have been stuck on this for ages!
You need to add the location of the python.exe to your $PATH variable. This depends on your installation location. In my case it is C:\Anaconda3. The default is C:\Python as far as I know.
To edit your path variable you can do the following thing. Go to your Control Panel then search for system. You should see something like: "Edit the system environment variables". Click on this and then click on environment variables in the panel that opened. There you have a list of system variables. You should now look for the Path variable. Now click edit and add the Python path at the end. Make sure that you added a semicolon before adding the path to not mess with your previous configuration.
I downloaded the code of kibana 4.1.3 in GitHub.
I tried to run it, but I don't know how?
Here is the code I used,
sudo npm install
sudo bower install -allow-root
grunt
I am not exactly sure what you are looking at here.
I had a look here,
https://github.com/elastic/kibana
and it says this,
Download: http://www.elastic.co/downloads/kibana
Extract the files
Run bin/kibana on unix, or bin\kibana.bat on Windows.
Visit http://localhost:5601
When I downloaded something from here,
https://www.elastic.co/downloads/past-releases/kibana-4-1-3
The readme.txt file inside says this,
Installation
============
Download: http://www.elastic.co/downloads/kibana
Run bin/kibana on unix, or bin\kibana.bat on Windows.
Visit http://localhost:5601
Which is pretty much the same. In the bin folder there is a script, kibana, and I think that is what it is telling you to run.
Hopefully that helps, but I have no specific knowledge of what you are doing here. Please expand your question if you need further help.
I would like ask some help about my next problem:
I am working on a Symfony2 project. We installed Symfony2 via composer.
Now I would like to generate phpDocument used by phpDocumentor.
A did the following steps:
update composer: sudo php composer.phar self-update
add the following property to Symfony2/compose.json file:
"require-dev": {
"phpdocumentor/phpdocumentor": "2.*#dev"
},
Run composer command
sudo php composer.phar update
Result was success! The installed GraphViz version is: 1.0.2
When I try to generate phpDoc from source code finally I got a message:
Unable to find the dot command of the GraphViz package. Is GraphViz correctly installed and present in your path?
(Document generated as right...)
I tried to found a soulution about this problem but I couldn't.
Is anybody can help me to resolve this problem?
Environment is: Ubuntu release 12.04
Graphviz is a nice software that creates graphs, but PHP software can only provide wrappers that create Graphviz source files that then get parsed and morphed into pictures.
Phpdocumentor comes with it's own wrapper, but you still have to install the Graphviz software package.
On Ubuntu just run
sudo apt-get install graphviz
rerun phpdoc, at the end you will see the line
Execute transformation using writer "Graph"
that's all!
The error says that : GraphViz tool (needed for making charts and graphs in the documentation) is not installed, in that scenario you will have to download the suitable version and configure it ! And if you are sure that it is installed on your system, then you should check whether the command dot is available or not. On windows path environment variable needs to be set which makes the dot command execution to be available from any path. Fixing this may get your things working !
For Windows
Follow the steps below to resolve this error are:
download Windows Packages from https://graphviz.gitlab.io/_pages/Download/Download_windows.html
Just install it
add c:\Program Files\Graphviz*\dot.exe or c:\Program Files (x86)\Graphviz*\dot.exe to your environment variable PATH
run phpdoc
Re-start your machine & run phpdoc (if still shows the same error message)
For windows 7/10 just install https://graphviz.gitlab.io/download/ select the Stable install packages. Then add
C:\Program Files (x86)\Graphviz2.38\bin
to your system environment variables. Make sure to change the version to the one you downloaded.
To check if it works open a new instance of cmd or git bash and run dot. If it says dot is not a valid command then make sure the path to Graphviz bin folder is correct.