Rfast takes too much RAM?

[Bernhardt]

Is it somehow possible to install the package Rfast on RStudio cloud? It seems like there is a problem with running out of memory. The compilation of the package stops at the function rint from the package.

[josh]

In a new project I was able to install Rfast without issue.
What had you done just prior to attempting to install?
Could you include the full error please?

[Bernhardt]

Prior to the installation I tested some code for speed with profvis. I checked for solutions online and tried to install Rfast. The first time it stopped the compilation at the function design_matrix. After a search online I was under the impression that there is an issue with the provided RAM. I cleaned up the workspace, detached most of the packages, und deleted unnecessary files. Then I tried again and it stopped at a later point, at function rint.

The message I get is:

Installing package into ‘/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.5’
(as ‘lib’ is unspecified)
trying URL 'http://package-proxy/src/contrib/Rfast_1.9.2.tar.gz'
Content type 'application/x-gzip' length 326022 bytes (318 KB)
==================================================
downloaded 318 KB

* installing *source* package ‘Rfast’ ...
** package ‘Rfast’ successfully unpacked and MD5 sums checked
** libs
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib/R/include" -DNDEBUG  -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.5/RcppArmadillo/include" -I/usr/local/include  -fopenmp -fpic  -g -O2 -c Diag.cpp -o Diag.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib/R/include" -DNDEBUG  -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.5/RcppArmadillo/include" -I/usr/local/include  -fopenmp -fpic  -g -O2 -c Norm.cpp -o Norm.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib/R/include" -DNDEBUG  -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.5/RcppArmadillo/include" -I/usr/local/include  -fopenmp -fpic  -g -O2 -c Rank.cpp -o Rank.o

... this goes on for a while until ...

g++ -std=gnu++11 -I"/opt/R/3.5.0/lib/R/include" -DNDEBUG  -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.5/RcppArmadillo/include" -I/usr/local/include  -fopenmp -fpic  -g -O2 -c rep.cpp -o rep.o
g++ -std=gnu++11 -I"/opt/R/3.5.0/lib/R/include" -DNDEBUG  -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.5/Rcpp/include" -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.5/RcppArmadillo/include" -I/usr/local/include  -fopenmp -fpic  -g -O2 -c rint.cpp -o rint.o
g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-5/README.Bugs> for instructions.
make: *** [rint.o] Error 4
/opt/R/3.5.0/lib/R/etc/Makeconf:168: recipe for target 'rint.o' failed
ERROR: compilation failed for package ‘Rfast’
* removing ‘/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.5/Rfast’
Warning in install.packages :
  installation of package ‘Rfast’ had non-zero exit status

The downloaded source packages are in
	‘/tmp/RtmpPfT2GT/downloaded_packages’

[josh]

@Bernhardt

g++: internal compiler error: Killed (program cc1plus)

This is what indicates out out memory.

It isn't clear to me why you get this in a new project while it succeeded for me, but we can add this to the cache of pre-built packages. Try again in about an hour.

[Bernhardt]

Thanks Josh! Still get the same error, however opening a new project and installing Rfast has worked. I switched the files to the new project with the installed Rfast.

[josh]

If you uninstall and reinstall Rfast in the original project, it ought to work as well.