Hi Jeroen,
On 1 December 2013 at 17:52, Jeroen Ooms wrote:
| Hi all :)
|
| I'm experiencing an issue with building Rcpp packages inside the OpenCPU
| sandbox. I think this issue was introduced with the upgrade to Rcpp 0.10.6.
The
I don't think this is us, and I don't think something changed. See below.
| problem is that g++ seems to ignore the TMPDIR environment variable, and
| instead always tries to use the default /tmp. When /tmp is not writable, this
| causes the compiling to fail.
|
| I am personally using RAppArmor to enforce these security policies, but an
| easier way to reproduce the problem is by temporarily disable write access to
/
| tmp. Something like this:
|
| #force custom TMP directory, replace jeroen with your username
| cd /tmp
| sudo mkdir test
| sudo chown jeroen test
| sudo chgrp jeroen test
| sudo chmod 755 /tmp
| TMPDIR=/tmp/test bash -c R
This should pass through to shells spawned.
First, straight bash:
edd@max:~$ FOOBAR=/bing bash
edd@max:~$ echo $FOOBAR
/bing
edd@max:~$ exit
Second, R
edd@max:~$ FOOBAR=/bing R -q -e 'system("echo $FOOBAR")'
R> system("echo $FOOBAR")
/bing
R>
R>
edd@max:~$
| #then in R do:
| tempdir() #check
| install.packages("RcppExamples") #or any other rcpp package
Note that install.packages() is a base R function, and not anything Rcpp adds.
We do have a few system() calls here or there for Rcpp Attributes and the like.
| The process fails with 'Fatal error: creating temporary file for '-e' failed
-L
| /usr/lib/R/lib -lR'. When using AppArmor, the error is actually more detailed
| and says that g++ tried to create a file /tmp/tmpfDbJ9KD.
|
| How can I make g++ use the same TMPDIR as the R process?
I think I'd start by setting TMPDIR. But here (in a virtual machine) I can't
even make g++ fail:
edd@billie:~/maxHome/tmp/jeroen$ cat hello.cpp
#include <iostream>
int main(void) {
std::cout << "Hello Jeroen\n";
return 0;
}
edd@billie:~/maxHome/tmp/jeroen$
edd@billie:~/maxHome/tmp/jeroen$ g++ -o hello hello.cpp && ./hello
Hello Jeroen
edd@billie:~/maxHome/tmp/jeroen$ mkdir /tmp/test; sudo chown edd:edd /tmp/test;
sudo chmod 0755 /tmp/test
edd@billie:~/maxHome/tmp/jeroen$ rm hello && TMPDIR=/tmp/test g++ -o hello
hello.cpp && ./hello
Hello Jeroen
edd@billie:~/maxHome/tmp/jeroen$
Dirk
--
Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com
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