Running with same environment, env variables, .libPaths().
In RStudio Server:
> source('https://gist.githubusercontent.com/abalter/a3e8fa6dec1103a59fea7d5cd32affc6/raw/4e61092389218141d4ff2d7267b0d4f198484695/test.R')
Error in file(filename, "r", encoding = encoding) :
internet routines cannot be loaded
We are working on two completely different systems. I would not expect the same behavior. I'm not saying it's a problem with the core source code of RStudio Server.
My output clearly shows what I see in RStudio Server and at the console.
It does seem to have something to do with the way RStudio loads my environment vs the console. That is what I need help tracking down.
Ok, but you are not giving too much information to work with, besides that test file.
Maybe if you share the content of your rstudio-server init file (e.g. /etc/init.d/rstudio-server on debian)
Also, do you install packages system wide or in your specific user library path? have you tried updating curl()package?
Looking at R's sources, I see that error message in places like the following:
and R is attempting to initialize internet routines here:
and it looks like it's attempting to dynamically load a module called internet.so. So you need to figure out where that module lives on your machine, and why R cannot find it (I suspect you have some custom environment / modifications to e.g. LD_LIBRARY_PATH affecting module lookup)
(deseq) balter@spectre3:~$ cat /etc/init.d/rstudio-server
#! /bin/bash
### BEGIN INIT INFO
# Provides: rstudio-server
# Required-Start: $remote_fs
# Required-Stop: $remote_fs
# Default-Start: 2 3 4 5
# Default-Stop: 0 1 6
# Short-Description: RStudio Server
# Description: RStudio Server provides a web interface to R
### END INIT INFO
# Author: RStudio <info@rstudio.com>
#
# Do NOT "set -e"
# PATH should only include /usr/* if it runs after the mountnfs.sh script
#PATH=/home/balter/conda/bin:/sbin:/usr/sbin:/bin:/usr/bin
PATH=/sbin:/usr/sbin:/bin:/usr/bin
DESC="RStudio Server"
NAME=rserver
DAEMON=/usr/lib/rstudio-server/bin/rserver
SCRIPTNAME=/etc/init.d/rstudio-server
source /home/balter/conda/etc/profile.d/conda.sh
conda activate
# Exit if the package is not installed
[ -x "$DAEMON" ] || exit 0
# Load the VERBOSE setting and other rcS variables
. /lib/init/vars.sh
# Define LSB log_* functions.
# Depend on lsb-base (>= 3.0-6) to ensure that this file is present.
. /lib/lsb/init-functions
#
# Function that starts the daemon/service
#
do_start()
{
# Return
# 0 if daemon has been started
# 1 if daemon was already running
# 2 if daemon could not be started
start-stop-daemon --start --quiet --exec $DAEMON --test > /dev/null \
|| return 1
start-stop-daemon --start --quiet --exec $DAEMON \
|| return 2
}
#
# Function that stops the daemon/service
#
do_stop()
{
# Return
# 0 if daemon has been stopped
# 1 if daemon was already stopped
# 2 if daemon could not be stopped
# other if a failure occurred
start-stop-daemon --stop --quiet --retry=TERM/30/KILL/5 --name $NAME
RETVAL="$?"
[ "$RETVAL" = 2 ] && return 2
return "$RETVAL"
}
case "$1" in
start)
[ "$VERBOSE" != no ] && log_daemon_msg "Starting $DESC" "$NAME"
do_start
case "$?" in
0|1) [ "$VERBOSE" != no ] && log_end_msg 0 ;;
2) [ "$VERBOSE" != no ] && log_end_msg 1 ;;
esac
;;
stop)
[ "$VERBOSE" != no ] && log_daemon_msg "Stopping $DESC" "$NAME"
do_stop
case "$?" in
0|1) [ "$VERBOSE" != no ] && log_end_msg 0 ;;
2) [ "$VERBOSE" != no ] && log_end_msg 1 ;;
esac
;;
restart|force-reload)
log_daemon_msg "Restarting $DESC" "$NAME"
do_stop
case "$?" in
0|1)
do_start
case "$?" in
0) log_end_msg 0 ;;
1) log_end_msg 1 ;; # Old process is still running
*) log_end_msg 1 ;; # Failed to start
esac
;;
*)
# Failed to stop
log_end_msg 1
;;
esac
;;
*)
echo "Usage: $SCRIPTNAME {start|stop|restart|force-reload}" >&2
exit 3
;;
esac
:
