Right, thanks, I overlooked that.
Does
example(cxxfunction, package = "inline", run.dontrun = TRUE)
run?
Nope!
If I run that call Ben I get:
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0'
And sure,
/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0
is what I have.
EDIT:
I added this to my .R/Makevars
FC = /usr/local/gfortran/bin/gfortran
FLIBS = -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
Yes, except for when using cores=4
, but that’s an RStudio
bug which there’s a workaround for :)
Daniel - I don’t know if you have solved this problem already, but since I came across your post when looking for a solution to exactly the same issue, I thought I’d share what worked for me: putting the following in your Makevars file. Hope it solves your problem.
CFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CCFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CXXFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CPPFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
bumping thread
bumping again
There’s a lot of results when googling which seem to deal with the OSX side of the issue. I don’t use OSX but the underlying issues is described at https://github.com/Andersbakken/rtags/issues/937#issuecomment-293459813 and https://github.com/cbcrg/tcoffee/issues/7#issuecomment-626081446 .
The issue is that somehow a math.h
is ending up in the compiler search path before the C++ math.h
. The solution will be to avoid this.
An example of how this can happen is if you include say, glibc before the c++ stdlib.
Hi,
I’ve installed R-4.0.0 and R-3.6.3 on Linux-Ubuntu 20.04 following the guide:
https://docs.rstudio.com/resources/install-r/
Where I changed the curl download from ubuntu-1604 to ubuntu-2004. I can start both within Rstudio and with R-4.0.0 in Rstudio I ran the advised code in OP but ended up installing some extra packages with the Terminal in order to get shinystan to work. Rstan works indeed, thank you!
Question: If i now start R-3.6.3 in Rstudio and run install.packages(‘rstan’, dependencies = TRUE) again, would you expect any complications? It is ok if Rstan just works in R4.0.0, but I could work more flexible if it works in multiple versions. However I am hesitant to just try it and risk breaking what is currently working.
On linux, you should be okay back to R 3.4.x and even previous versions if your C++ compiler supports the C++14 standard (although you may have to adjust the required version of R in the DESCRIPTION file).
That was wonderful Ben. Works like a charm, thank you for sharing!
Is this installation guide (install.txt) somewhere online? I found it very good and the official Rstan getting started does not seem to have this info about R 4.0.0 problems.
It’s not, no. It was just a document I sent to some students/faculty prior to a Stan seminar. I wouldn’t mind if the Stan team wanted to use it somewhere though.
I can update RStan’s getting started guide with this info. I’ll have a first run at adding this in and ping you for a quick review to see if I’ve missed anything (if that’s ok).
@bgoodri Any preference on whether this goes into the ‘RStan Getting Started’ page or gets added as separate ‘RStan & R4.0’ page?
I think I have a more updated one: install.txt (783.5 KB)
The main story though - Is the pre-R4.0 instructions should be fine on < 4.0 setups. After R 4.0, Rtools40 should be used on windows, and Xcode (only) should be used on osx. Any previous configurations should be stripped out (in .Rprofile, .Renviron, and R/Makevars{.win}). They can be recreated with optimization options only (and the Rstudio parallel fix for OSX); no need for paths.
@Stephen_Martin, would it be possible to provide some optimization options for default compilers in Win/Lin/OS X, so new people simply can cut and paste into their Makevars
?