I haven't been able to find the help I need on (on dummie level) for installing a new dictionary (danish) in emacs. To be honest I somewhat confused about ispell vs aspell. When typing "M-x ispell-buffer" a spelling control starts using english as default. I can change directory typing "M-x-ispell-change-dictionary" it suggest "dansk" but I get an error saying that the file /.../aspell/dict/danish" can not be opened for reading. I can deduct that the dictionary is not installed - but I cannot seem to finde a guide (step by step) on how to do this.
And then I have a bonus question. I have managed to install flyspell (or is that actually 'installing' as I have just addet the .el file to my emacs load path and loaded in my .emacs file?). This seem to work (wauw), and as I understand it flyspell is using the same dictionaries as ispell/aspell hence solving my probleme above would enable me to use flyspell in danish?
Any help is appreciated.
/Kira
If you are on Ubuntu or Debian system you can install the Danish aspell package from the commandline with
sudo apt-get install aspell-da
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 am trying to run the metal executable from my zsh terminal in order to meta-analyze GWAS data. I have the executable in the correct directory and have checked that it is not 0MB due to truncation.
Reproducible:
Download the Linux file from http://csg.sph.umich.edu/abecasis/metal/download/
In terminal:
PATH TO EXECUTABLE ./metal
zsh: exec format error: ./metal
You probably install wrong OS of go, for example, you might install go for MacOS in Linux
I solve this problem by installing go for correct OS
The executable has been pre-compiled on a certain distribution with libraries at a certain places at certain versions.
If you have a different distribution, libraries versions, it won't work and you better compile from the source.
Basically what you have to do is to download and extract the sources, go in the folder and execute make. (You will have probably to install make first.)
I think that's not your job at all so maybe you can find a geeky person to help you, because you may stumble upon problems, libraries to install, old versions not supported anymore, new versions not supported yet...
It happened to me when I emptied an executable by mistake.
~>true > a
~>wc -c a
0 a
~>./a
zsh: exec format error: ./a
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 downloaded GNAT ADA GPL 2014 and now trying to install on my Mac.
The directions below are the ones I am following, but I do not know where to look to find the file called doinstall. I might still need some help after finding it, but can anyone help me out here?
Navigate to the directory that contains a file called: doinstall
Enter: sudo mkdir /usr/local/gnat
Enter: sudo ./doinstall
Update your path as needed for your shell
You should have downloaded gnat-gpl-2014-x86_64-darwin-bin.tar.gz.
Go to some temporary directory (I use ~/tmp):
cd ~/tmp
Unpack the download, which creates a directory gnat-gpl-2014-x86_64-darwin-bin containing the binary distribution to be installed:
tar zxvf ~/Downloads/gnat-gpl-2014-x86_64-darwin-bin.tar.gz
Enter that directory, which contains (amongst others) doinstall:
cd gnat-gpl-2014-x86_64-darwin-bin
Execute doinstall to enter the installation dialog:
sudo ./doinstall
Remove the unpacked download:
cd ..
rm -rf gnat-gpl-2014-x86_64-darwin-bin
Now you can update PATH as needed for your shell.
What Simon Wright said is correct, but if you're running on Yosemite there's an extra problem: for some obscure reason, Adacore GNAT is broken on Yosemite. You have to make it think it's compiling for Mavericks:
export MACOSX_DEPLOYMENT_TARGET=10.9 # Yosemite workaround
That can go in a few different places, but I put it near the top of the /usr/local/gnat/bin/gps script so it doesn't interfere with the xcodebuild environment.
Also, I found GTKAda to be nearly impossible to install from source; if you download the XNAdaLib-GPL package from http://sourceforge.net/projects/gnuada/ you can install that and get everything you need without having to wade through Adacore's mess. (You may want to use the Adacore version of Glade for GUI design though; for some reason the Sourceforge package's version is localized in French and I'm not sure if it can be switched to English.)
Finally, since this is a bit duct-tape-and-baling-wire, I would recommend not shipping any production mission-critical code with this environment; either roll back to Mavericks or wait for GNAT 2015.
I've installed Aspell where I get a desktop icon-as in I can drag and drop text files in it and the spell check works as expected. However, when I try using the aspell function in Rstudio, I get this as a message: No suitable spell-checker program found. I am unsure of the steps I need to take to remedy this so R picks up on the fact I've installed Aspell. Any help would be greatly appreciated.
I am now getting this as my error
Error in aspell(visit1total) : Running aspell failed with diagnostics:
Error: No word lists can be found for the language "en_US".
Again, I would appreciate any help anyone can offer. I am using Windows 7. Thank you for your time.
To elaborate the first answer from:
https://superuser.com/questions/601928/how-do-i-add-missing-dictionaries-for-aspell
Download and untar the latest english dictionary (http://ftp.gnu.org/gnu/aspell/dict/en/ - currently v7.1.0):
wget ftp://ftp.gnu.org/gnu/aspell/dict/en/aspell6-en-7.1-0.tar.bz2
tar xvjf aspell6-en-7.1-0.tar.bz2
Then follow the README to install as follows:
cd aspell6-en-7.1-0/
./configure
make
make install
This is a problem with not having fully configured Aspell for use on Windows. Consider reviewing my post on performing a full installation of aspell on Windows