UMMS-Biocore/debrowser

Posit Cloud
#1


I would like to run the above mentioned project in RStudio Cloud. I can run it on my machine, but not on the cloud. I think the error has to do with running out of memory compiling some packages(RCppEigen being 1). Can someone help me figure this out? Here are the directions I am following from the website.

# Installation instructions:
# 1. Install DEBrowser and its dependencies by running the lines below
# in R or RStudio.

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("debrowser")

# 2. Load the library

library(debrowser)

# 3. Start DEBrowser

startDEBrowser()
#2

Hi @mknafl!

For packages hosted on CRAN, we provide a package cache mechanism for rstudio.cloud to help out with packages that require a lot of memory when building from source (keeping in mind that during this phase of our product we limit sessions to 1GB memory). Unfortunately, we do not have such a feature for bioconductor packages.

If the problem is related only to RcppEigen failing to build, it now appears to be cached for R 3.6.0 so please try to install again. If there is a bioconductor package that is failing on out-of-memory-like conditions, there isn't much help we can offer at this time. Perhaps you could try installing all of the dependent packages first, restart your session (to clear the memory utilization) and then install just the single bioconductor package that is problematic?

Good Luck!

1 Like
#3

I am new to RStudioCloud so I am not sure I am doing exactly what you suggested. I did try to install RcppEigen on its own using the below commands and response. I did this by going to Tools->InstallPackages Is there a different way to do this that gets the cached copy? Also, what do you mean by restart my session, logout and then back in?

install.packages("RcppEigen")
Installing package into ‘/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
also installing the dependency ‘Rcpp’

trying URL 'http://package-proxy/src/contrib/Rcpp_1.0.1.tar.gz'
Content type 'application/x-gzip' length 3663937 bytes (3.5 MB)

downloaded 3.5 MB

trying URL 'http://package-proxy/src/contrib/RcppEigen_0.3.3.5.0.tar.gz'
Content type 'application/x-gzip' length 1636334 bytes (1.6 MB)

downloaded 1.6 MB

  • installing source package ‘Rcpp’ ...
    ** package ‘Rcpp’ successfully unpacked and MD5 sums checked
    ** using staged installation
    ** libs
    g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c Date.cpp -o Date.o
    g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c Module.cpp -o Module.o
    g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c Rcpp_init.cpp -o Rcpp_init.o
    g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c api.cpp -o api.o
    g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c attributes.cpp -o attributes.o
    g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c barrier.cpp -o barrier.o
    g++ -std=gnu++11 -shared -L/opt/R/3.6.0/lib/R/lib -L/usr/local/lib -o Rcpp.so Date.o Module.o Rcpp_init.o api.o attributes.o barrier.o -L/opt/R/3.6.0/lib/R/lib -lR
    installing to /home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-Rcpp/00new/Rcpp/libs
    ** R
    ** inst
    ** byte-compile and prepare package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** installing vignettes
    ** testing if installed package can be loaded from temporary location
    ** checking absolute paths in shared objects and dynamic libraries
    ** testing if installed package can be loaded from final location
    ** testing if installed package keeps a record of temporary installation path
  • DONE (Rcpp)
  • installing source package ‘RcppEigen’ ...
    ** package ‘RcppEigen’ successfully unpacked and MD5 sums checked
    ** using staged installation
    ** libs
    g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include" -I/usr/local/include -I../inst/include -fpic -g -O2 -c RcppEigen.cpp -o RcppEigen.o
    g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include" -I/usr/local/include -I../inst/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
    g++ -std=gnu++11 -I"/opt/R/3.6.0/lib/R/include" -DNDEBUG -I"/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/include" -I/usr/local/include -I../inst/include -fpic -g -O2 -c fastLm.cpp -o fastLm.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: *** [fastLm.o] Error 4
    /opt/R/3.6.0/lib/R/etc/Makeconf:176: recipe for target 'fastLm.o' failed
    ERROR: compilation failed for package ‘RcppEigen’
  • removing ‘/home/rstudio-user/R/x86_64-pc-linux-gnu-library/3.6/RcppEigen’
    Warning in install.packages :
    installation of package ‘RcppEigen’ had non-zero exit status

The downloaded source packages are in
‘/tmp/Rtmpauno2H/downloaded_packages’

#4

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