Dplyr: Problems uploading to ubuntu

[pssguy]

Hi
Trying to install dplyr on an AWS instance. assertthat and BH unpack fine but with dplyr I get message that it has successfully unpacked and MD5 sums checked but then I get
** libs
g++ -I/usr/share/R/include -DNEDBUG etc.... and the system hangs

in the usr/local/lib/R/site-library there is now a file 00LOCK-dplyr

[pssguy]

actually it has now exited with
g++: internal compiler error:Killed(program cc1plus)

[romainfrancois]

We don't have much to go on. It might be due to low memory on the AWS machine. The compiler needs quite some memory to compile Rcpp client packages.

Were you able to compile Rcpp ?

[pssguy]

Sorry this is all new to me. How would I be able to tell if I had compiled it?

[romainfrancois]

What happens when you do install.packages( "Rcpp",type = "source" ) ?
How much memory do you have on the machine ?

[pssguy]

I already have Rcpp installed. Does it go in when I create a shiny server

Typing free I get this info
total 603168 free 488796

[pssguy]

Although I had Rcpp on the system already, I tried specifically installing it. Similar situation to dplyr
**libs
several messages then hangs on
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -03 -pipe -g -c attributes.cpp -o attributes.o

[kevinushey]

Don't use the -pipe argument. Having it on can increase memory usage.

[pssguy]

How do I avoid this. I entered
sudo su ­ - ­-c "R ­-e \"install.packages('Rcpp', repos='http://cran.rstudio.com/')\""

[kevinushey]

Try CXXFLAGS="-g -O3" sudo su - -c "R -e \"install.packages('Rcpp', repos='
http://cran.rstudio.com/')\""

On Fri, Feb 14, 2014 at 2:19 PM, pssguy [email protected] wrote:

How do I avoid this. I entered
sudo su - -c "R -e \"install.packages('Rcpp', repos='
http://cran.rstudio.com/')\""

Reply to this email directly or view it on GitHubhttps://github.com/hadley/dplyr/issues/262#issuecomment-35130680
.

[pssguy]

Thanks for suggestion. same result, unfortunately
Ended Warning:with end of file not at end of a line: new line inserted
Error: open CFI at the end of file; missing .cfi_endproc directive

Is that useful info?

[kevinushey]

That (AFAICS) still means you're running out of memory.

From http://hostingfu.com/article/compiling-with-gcc-on-low-memory-vps, you can also try

CXXFLAGS="-g -O2 --param ggc-min-expand=0  --param ggc-min-heapsize=8192" sudo su - -c "R -e \"install.packages('Rcpp', repos='http://cran.rstudio.com/')\""

It'll be slow as hell but it might work. (Can you confirm that the CXXFLAGS are, in fact, showing up in the compiler output? I'm not sure if they get passed through to the sudo su ... call.)

If that doesn't work, then, well, get more memory.

[anhqle]

Confirm that last comment by Kevin Ushey worked on my Ubuntu 12.04 LTS

[pssguy]

It did not work for me but prob due to the memory issue
After a few false steps, have just attached 4gig to my instance as swap memory and that seemed to do the trick. dplyr and the associated shiny app up and running

[paulrougieux]

kevinushey's answer above didn't work on my VPS. Matt Lacey posted How to compile dplyr on low memory VPS . He mannaged to install dplyr by adding a larger swap space. Unfortunately this operation is not permitted on my system: "swapon failed: Operation not permitted". But enlarging the swap size sounds like a way to install dplyr on low memory systems.

[rafaveguim]

I couldn't install dplyr into my DigitalOcean droplet with 512MB RAM. It failed even after upgrading it to 1GB RAM. What solved the problem for me was changing temporarily the default R compiler from g++ to clang. On my Fedora 24, the config file is located at /usr/lib64/R/etc/Makeconf.

Comment the following lines:

CC = gcc -m64
CXX = g++ -m64

And add the following:

CC = clang
CXX = clang++