If someone could walk me through a particular problem, I'd really appreciate it... I think I know what's causing it, but I don't know how to fix it.
Problem-- Emacs ESS won't start up R.
Cause-- I've installed OpenFOAM, an open source fluids modeling kit that has it's own function called R, and executes with the letter "R". (I.e. type "R" in the command line and it tries to run an OpenFOAM function, not R). I think by installing OpenFoam, I have overwritten the previous "R" calling the language R, and so that messes with ESS trying to call R.
Environment-- I'm ssh'ing into a remote client running scientific linux where I don't have root access. I don't exactly understand what ESS is calling that is local to my account and what is not local.
Calling /usr/bin/./R from the command line starts an instance of R. How do I modify ESS such that it calls '/usr/bin/./R'?
This was the closest I could find, ESS to call different installations of R, but as far as I can tell, my system doesn't have R-1 or R-2 at all on its exec path, so I don't know how similar it is.
I had run into the same problem. Following the links and tips of Josh O'Brien, I put
;; Set default R version, (i.e. the one launched by typing M-x R <RET>)
(setq inferior-R-program-name "/usr/bin/R")
in my .emacs file. Now it works perfectly.
Related
I tried to run a Python script from R with:
system('python script.py arg1 arg2')
And got an error:
ImportError: No module named pandas
This was a bit of a surprise since the script was working from the terminal as expected. Having encountered this type of issue before (with knitr, whence the engine.path chunk option), I know to check:
Sys.which('python')
# python
# "/usr/bin/python"
And compare it to the command line:
$ which python
# /Users/michael.chirico/anaconda2/bin/python
(i.e., the error arises because I have pandas installed for the anaconda distribution, though TBH I don't know why I have a different distribution)
Hence I can fix my issue by running:
system('/Users/michael.chirico/anaconda2/bin/python script.py arg1 arg2')
My question is two-fold:
How does R's system/Sys.which find a different python than my terminal?
How can I fix this besides writing out the full binary path each time?
I read ?Sys.which for some hints, but to no avail. In particular, ?Sys.which suggests Sys.which is using which:
This is an interface to the system command which
This is clearly (?) untrue; to be sure, I checked Sys.which('which') and which which to confirm both are pointing to /usr/bin/which (goaded on by this tidbit):
On a Unix-alike the full path to which (usually /usr/bin/which) is found when R is installed.
To the latter, on a whim I tried Sys.setenv(python = '/Users/michael.chirico/anaconda2/bin/python') to no avail.
As some of the comments hint, this is a problem that arises because the PATH environment variable is different for programs launched by Finder (or the Dock) than it is in the Terminal. There are ways to set the PATH for Dock-launched applications, but they aren't pretty. Here's a place to start looking if you want to go that route:
https://apple.stackexchange.com/questions/51677/how-to-set-path-for-finder-launched-applications
The other thing you can do, which is probably more straightforward, is tell R to set the PATH variable when it starts up, using Sys.setenv to add the path to your desired Python instance. You can do that for just one project, for your whole user account, or for the whole system, by placing the command in a .Rprofile file in the corresponding location. More information on how to do this here:
https://stat.ethz.ch/R-manual/R-devel/library/base/html/Startup.html
I cannot run a R session from the command line by typing 'R', despite having
C:/Program Files/R
and
C:/Program Files/R/R-3.3.2/bin
in both 'Path' (System) and 'PATH' (User) environment variables (the latter directory is where the actual application is located, I was just trying everything by adding the former).
If I manually change the working directory to C:/Program Files/R/R-3.3.2/bin and type R, a session runs.
Any insight as to why this might be the case? Other programs such as Python 3 run fine, provided the the environment variable is set, why not with R?
This question is part of a larger problem where I am trying to get rpy2 working, but though successfully installed, none of it's basic functions are working, and I thought this maybe to do with a version of R being installed at C:/Users/Anaconda2/R (Because this dir was in Path). The R application installed here would not work when opened, but was the directory returned when I typed R RHOME into cmd - despite the fact this installation is not even functioning, and has apparently only existed since I installed rpy2 a couple of hours ago. I reasoned that rpy2 is trying to use the instance of R installed here rather than my normal one, thus causing the error when I call robjects.r. But this still doesn't explain why I can't run R from cmd. When using R.home(component = "home") from inside a an R session (in RStudio or out of it), it returns my normal, working R directory, at C:/PROGRA~1/R/R-33~1.2. By moving the R file tree installed in Anaconda's directory to a somewhere not in Path, I hoped Windows would find the correct installation via Path - but instead I just get Failed to create process.
My last guess was that Windows didn't like the space in "Program Files", but loads of variables in Path go through the same folder. Any ideas?
I am using:
Windows 10,
R 3.3.2,
Python 2.17.13
UPDATE, PERHAPS SOLVED:
On Josh O'Brien's recommendation (thanks!), I typed where R into cmd, returning:
C:\Users\charl\Anaconda2\Scripts\R.exe
C:\Program Files\R\R-3.3.2\bin\R.exe
The first path is marginally different from the C:\Users\charl\Anaconda2\R listed in my first post (both are in Path), and leads to a third R.exe. It's outside the R file tree located in Anaconda, unlike my standard R installation, but seems to be dependent on it nonetheless. If I remove this R.exe to another location (not in Path), Typing R in cmd will run R from the desired directory, thus fixing the problem. R.home() from inside that session confirms this.
My only remaining concern then; is whether this installation of R in Anaconda necessary for rpy2 or can I just delete it, fixing the original problem? It may just be my ignorance, but I was not conscious that installing rpy2 (I used the standard Windows installer rather than compiling manually) would install another instance of R - is it necessary for the package or just a default/option I failed to omit?
When I run a Julia Script that prints "Hello World" on HTCondor, I get the following error
fatal: error thrown and no exception handler available.
Base.InitError(mod=:Pkg, error=Base.KeyError(key="HOME"))
The code runs without a problem on my local Ubuntu machine. I can run
eval julia --version
in a bash script on condor and the output is
julia version 0.5.0
This problem has been discussed in two places on github: one, two.
ENV["HOME"] is used in a single file and the common recommendation is to modify that. However, I cannot change the julia installation on condor.
Is there a way to fix this on the fly before running a script without sudo?
As #sujeet suggested, it is possible to set environmental parameters in condor. The issue is resolved by adding the following line in the condor submit script
Environment = "HOME=""/tmp"""
, which sets the home directory to the tmp. Julia code runs fine then (as long one is careful not to write to home before resetting it in the script itself).
Hej,
When I try to call QIIME with a system call from R, i.e
system2("macqiime")
R stops responding. It's no problem with other command line programs though.
can certain programs not be called from R via system2() ?
MacQIIME version:
MacQIIME 1.8.0-20140103
Sourcing MacQIIME environment variables...
This is the same as a normal terminal shell, except your default
python is DIFFERENT (/macqiime/bin/python) and there are other new
QIIME-related things in your PATH.
(note that I am primarily interested to call QIIME from R Markdown with engine = "sh" which fails, too. But I strongly suspect the problems are related)
In my experience, when you call Qiime from unix command line, it usually creates a virtual shell of it`s own to run its commands which is different from regular system commands like ls or mv. I suspect you may not be able to run Qiime from within R unless you emulate that same shell or configuration Qiime requires. I tried to run it from a python script and was not successful.
I'm using Fedora 21 with GNU Emacs 24.5.1 and ESS version 15.03. In GUI mode I can use C-RET to pass code from an R script I'm editing to an inferior R process (it starts one up if I haven't yet), but that doesn't seem to work in console mode. Now C-RET just creates a new line in my R script. I've tried this using both emacs and emacs-nox installations.
I compiled ESS from source instead of using the outdated version in Fedora's package manager. Could that have anything to do with it?
The problem is that C-RET isn't a valid sequence in the terminal, so the C- is getting ignored and it's just interpreting the RET. See this answer for more explanation. Following some of the links there will take you to some workarounds, but they are not ideal. It doesn't look like there are any ways to completely change this behavior in the terminal (but I'd love to be told I'm wrong).