On 06/08/2017 2:57 PM, Duncan Murdoch wrote:
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.
Oops, I see below that you found it happens with plain R as well. Was
that tested on your server machine as well? It looks as though it has
some execution time limit (or disk or memory limit) and you're exceeding
it. So you should talk to your sysadmin.
Duncan Murdoch
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@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/>*
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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