0

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.

I try doing it with this code and get the error below.

install.packages("devtools)
devtools::install_github("pbiecek/PISA2009lite")

Downloading GitHub repo pbiecek/PISA2009lite@master
from URL https://api.github.com/repos/pbiecek/PISA2009lite/zipball/master
Installing PISA2009lite
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL  \
  '/tmp/RtmpjQkC7c/devtools37a276ebf56a/pbiecek-PISA2009lite-de1b2af'  \
  --library='/home/cimentadaj/R/x86_64-pc-linux-gnu-library/3.4' --install-tests 

* installing *source* package ‘PISA2009lite’ ...
** 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

Any help is appreicated!

cimentadaj
  • 1,414
  • 10
  • 23
  • Have you tried installing the packages with RGui (i.e. not in RStudio)? – mikeck Aug 05 '17 at 15:53
  • @mikeck Yeah, same error. – cimentadaj Aug 05 '17 at 18:22
  • I would try downloading the package zips and installing rather than doing the download+install using `install_github`. It looks like maybe the install procedure is timing out? – mikeck Aug 05 '17 at 18:54
  • I just followed the answer from : https://stackoverflow.com/questions/30989027/how-to-install-a-package-from-a-download-zip-file and got the same error! Basically, I downloaded the .zip package, turned into a 'tarball' and installed that with install.packages() from Rgui. Got the same `killed` message. – cimentadaj Aug 05 '17 at 19:23
  • Same error with `R CMD INSTALL PISA2000lite_1.0.tar.gz` from command line. – cimentadaj Aug 05 '17 at 19:29
  • Hmmm I don't know then... I'd wonder about folder permissions except that the non-data parts of the package install ok. The only workaround I can think of is downloading the package zips and extracting to a folder, then loading with `devtools::load_all()`. – mikeck Aug 05 '17 at 19:42

0 Answers0