[R] Crash when installing heavy packages in remote server with R and Rstudio server

[Duncan Murdoch]

On 06/08/2017 9:17 AM, Jorge Cimentada wrote:
> Hi,
>
> I've been trying to install some very heavy packages from Github (~ 100MB -
> 300 MB) on my remote server using Rstudio server and I keep getting some
> crashes. These packages are pretty much datasets.

Based on your description, this is RStudio Server specific.  You'll need 
to write to their tech support for help.  This list is for R issues.

Duncan Murdoch

>
> I try doing it with this code and get the error below.
>
>> install.packages("devtools")
>
>> devtools::install_github("pbiecek/PISA2000lite")
> Downloading GitHub repo pbiecek/PISA2000lite at master
> from URL https://api.github.com/repos/pbiecek/PISA2000lite/zipball/master
> Installing PISA2000lite
> '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore
> --quiet CMD INSTALL  \
>   '/tmp/Rtmp1GoUVG/devtools76a72d179d7/pbiecek-PISA2000lite-54f4765'  \
>   --library='/home/cimentadaj/R/x86_64-pc-linux-gnu-library/3.4'
> --install-tests
>
> * installing *source* package ‘PISA2000lite’ ...
> ** data
> *** moving datasets to lazyload DB
> Killed
> Installation failed: Command failed (137)
>
>
>
> The package actually gets installed
> any(grepl("PISA2012lite", installed.packages()[, 1]))
>
> [1] TRUE
>
>
> But I once I load the library it's as if none of the datasets are
> available. I've used these packages for a long time on my local computer so
> I'm sure it's not the packages. The server has enough space to handle the
> packages, so it's not memory either. Below you can find the specs of the R
> session and the server
>
>
> R version 3.4.1 (2017-06-30)
>
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> Running under: Ubuntu 16.04.3 LTS
>
> Matrix products: default
>
> BLAS: /usr/lib/libblas/libblas.so.3.6.0
>
> LAPACK: /usr/lib/lapack/liblapack.so.3.6.0
>
>
> locale:
>
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> LC_TIME=en_US.UTF-8
>
>  [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8
>  LC_MESSAGES=en_US.UTF-8
>
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C
>
>
> [10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8
> LC_IDENTIFICATION=C
>
>
> attached base packages:
>
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
>
> loaded via a namespace (and not attached):
>
>  [1] httr_1.2.1      compiler_3.4.1  R6_2.2.2        tools_3.4.1
> withr_2.0.0     curl_2.8.1
>
>  [7] memoise_1.1.0   git2r_0.19.0    digest_0.6.12   devtools_1.13.3
>
>
> The disk info:
>
>
> Filesystem      Size  Used Avail Use% Mounted on
>
> udev            981M     0  981M   0% /dev
>
> tmpfs           201M   21M  180M  11% /run
>
> /dev/vda1        39G  9.1G   30G  24% /
>
> tmpfs          1001M  840K 1000M   1% /dev/shm
>
> tmpfs           5.0M     0  5.0M   0% /run/lock
>
> tmpfs          1001M     0 1001M   0% /sys/fs/cgroup
>
> /dev/vda15      105M  3.4M  102M   4% /boot/efi
>
> tmpfs           201M     0  201M   0% /run/user/1000
>
> And server specs from Digital Ocean:
> 2 GB Memory / 40 GB Disk / LON1 - Ubuntu 16.04.3 x64 from
>
> I posted the question in this
> <https://stackoverflow.com/questions/45522145/crash-when-installing-heavy-packages-in-remote-server-with-rstudio-server?noredirect=1#comment78011638_45522145>
> stackoverflow thread and actually found out that the problem is not from
> Rstudio server in itself because I get the exact same error with:
> R CMD INSTALL PISA2000lite_1.0.tar.gz
>
> Any idea why this might be occurring?
>
> -----------------------------------
>
> Jorge Cimentada
>
> *https://cimentadaj.github.io/ <https://cimentadaj.github.io/>*
>
> 	[[alternative HTML version deleted]]
>
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