I'm trying to setup a simple beakr service in Windows that implements the example at https://github.com/MazamaScience/beakr. I'm able to run the script from the command line successfully and I've been able to add the service in Windows using NSSM, but I am unable to start the service.
When I dig into the service error logs I see that Rscript.exe cannot be executed due to a non-specific permissions problem.
My Rscript.exe is running out of C:\Program Files\R<Version>\bin and my beakr.R script is running out of my User home directory.
If anyone has had success implementing a similar service (Web page based REST endpoint) using R in Windows, I would love to know how you did it.
This is what I did to run an R script as Service using latest pre-release version of NSSM on Windows 10:
Create a directory to store the files
In this example : C:\R\ServiceTest
Create in this directory a never ending script : ServiceTest.R
library(beepr)
# Test script : beeps every 10 seconds
while (T) {
beepr::beep(1)
if (interactive()) {
# Shows spin cursor to facilitate test in interactive mode
for (i in 1:10) {
if (i%%4==0) {cursor <- '/'}
if (i%%4==1) {cursor <- '-'}
if (i%%4==2) {cursor <- '\\'}
if (i%%4==3) {cursor <- '|'}
cat('\r',cursor)
flush.console()
Sys.sleep(1)
}
} else {
Sys.sleep(10)
}
}
I used to let this kind of script run in a console open on my desktop to check various alarms regularly.
Create a batch file to run the script : ServiceTest.bat
Rscript ServiceTest.R
Open an Admin console and make sure the batch file runs correctly:
C:\R\ServiceTest>ServiceTest.bat
C:\R\ServiceTest>Rscript ServiceTest.R
|
Cancel the batch (Ctrl+C)
Using the Admin console, install the batch file as service using NSSM :
nssm install
Set Service name : ServiceTest
Set Application path : C:\R\ServiceTest\ServiceTest.bat
Set Working directory : C:\R\ServiceTest\
Set Logon : Windows User + Password
Install Service
Open Windows Services Manager, find ServiceTest and start it : if everything went well, that's it!
If you get an error message, check Windows Event Log / Services : you can find there hints on the cause of the problem. Most common problems I encountered :
error on path
used local user instead of own user account / password to run the service
If you want to remove the service :
nssm remove ServiceTest
This replaced very nicely the many R consoles I left running in the background on my Desktop.
I see no reasons it wouldn't work with a REST endpoint.
Related
I'm using the gmailr package for sending emails from a r script.
Locally it's all working fine, but when I try to run this during a docker build step in google cloud I'm getting an error.
I implemented it in the following way described here.
So basically, locally the part of my code for sending emails looks like this:
gm_auth_configure(path = "credentials.json")
gm_auth(email = TRUE, cache = "secret")
gm_send_message(buy_email)
Please note, that I renamed the .secret folder to secret, because I want to deploy my script with docker in gcloud and didn't want to get any unexpected errors due to the dot in the folder name.
This is the code, which I'm now trying to run in the cloud:
setwd("/home/rstudio/")
gm_auth_configure(path = "credentials.json")
options(
gargle_oauth_cache = "secret",
gargle_oauth_email = "email.which.was.used.to.get.secret#gmail.com"
)
gm_auth(email = "email.which.was.used.to.get.secret#gmail.com")
When running this code in a docker build process, I'm receiving the following error:
Error in gmailr_POST(c("messages", "send"), user_id, class = "gmail_message", :
Gmail API error: 403
Request had insufficient authentication scopes.
Calls: gm_send_message -> gmailr_POST -> gmailr_query
I can reproduce the error locally, when I do not check the
following box.
Therefore my first assumption is, that the secret folder is not beeing pushed correctly in the docker build process and that the authentication tries to authenticate again, but in a non interactive-session the box can't be checked and the error is thrown.
This is the part of the Dockerfile.txt, where I'm pushing the files and running the script:
#2 ADD FILES TO LOCAL
COPY . /home/rstudio/
WORKDIR /home/rstudio
#3 RUN R SCRIPT
CMD Rscript /home/rstudio/run_script.R
and this is the folder, which contains all files / folders beeing pushed to the cloud.
My second assumption is, that I have to somehow specify the scope to use google platform for my docker image, but unfortunately I'm no sure where to do that.
I'd really appreciate any help! Thanks in advance!
For anyone experiencing the same problem, I was finally able to find a solution.
The problem is that GCE auth is set by the "gargle" package, instead of using the "normal user OAuth flow".
To temporarily disable GCE auth, I'm using the following piece of code now:
library(gargle)
cred_funs_clear()
cred_funs_add(credentials_user_oauth2 = credentials_user_oauth2)
gm_auth_configure(path = "credentials.json")
options(
gargle_oauth_cache = "secret",
gargle_oauth_email = "sp500tr.cloud#gmail.com"
)
gm_auth(email = "email.which.was.used.for.credentials.com")
cred_funs_set_default()
For further references see also here.
On the console.. I get the following -
Usage: java [-options] class [args...]
(to execute a class)
or java [-jar] [-options] jarfile [args...]
(to execute a jar file)
where options include:
-cp -classpath <directories and zip/jar files separated by ;>
set search path for application classes and resources
-D<name>=<value>
set a system property
-verbose[:class|gc|jni]
enable verbose output
-version print product version
-version:<value>
require the specified version to run
-showversion print product version and continue
-jre-restrict-search | -no-jre-restrict-search
include/exclude user private JREs in the version search
-agentlib:<libname>[=<options>]
load native agent library <libname>, e.g. -agentlib:hprof
see also, -agentlib:jdwp=help and -agentlib:hprof=help
-agentpath:<pathname>[=<options>]
load native agent library by full pathname
-javaagent:<jarpath>[=<options>]
load Java programming language agent, see java.lang.instrument
-? -help print this help message
-X print help on non-standard options
-splash:<imagepath> show splash screen with specified image
-ea[:<packagename>...|:<classname>]
-enableassertions[:<packagename>...|:<classname>]
enable assertions
-da[:<packagename>...|:<classname>]
-disableassertions[:<packagename>...|:<classname>]
disable assertions
-esa | -enablesystemassertions
enable system assertions
-dsa | -disablesystemassertions
disable system assertions
Eventually the server doesn't start and gets stopped after time-out. The Server was working fine. However, I wanted to restart it. I stopped the server completely and tried starting it. Since then I am facing this issue.
You can check the script that is getting executed when you right click and start the server.
Check if there are any unwanted entries in the java options which does not confirm to the java command line.
I need some Powershell advice.
I need to install an application's MSP update file on multiple Win08r2 servers. If I run these commands locally, within the target machine's PS window, it does exactly what I want it to:
$command = 'msiexec.exe /p "c:\test\My Application Update 01.msp" REBOOTPROMPT=S /qb!'
invoke-wmimethod -path win32_process -name create -argumentlist $command
The file being executed is located on the target machine
If I remotely connect to the machine, and execute the two commands, it opens two x64 msiexec.exe process, and one msiexec.exe *32 process, and just sits there.
If I restart the server, it doesn't show that the update was installed, so I don't think it's a timing thing.
I've tried creating and remotely executing a PS1 file with the two lines, but that seems to do the same thing.
If anyone has advice on getting my MSP update installed remotely, I'd be all ears.
I think I've included all the information I have, but if something is missing, please ask questions, and I'll fill in any blanks.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
My process for this is:
Read a CSV for server name and Administrator password
Create a credential with the password
Create a new session using the machine name and credential
Create a temporary folder to hold my update MSP file
Call a PS1 file that downloads the update file to the target server
>>> Creates a new System.Net.WebClient object
>>> Uses that web client object to download from the source to the location on the target server
Call another PS1 file that applies the patch that was just downloaded –>> This is where I’m having issues.
>>> Set the variable shown above
>>> Execute the file specified in the variable
Close the session to the target server
Move to the next server in the CSV…
If I open a PS window and manually set the variable, then execute it (as shown above in the two lines of code), it works fine. If I create a PS1 file on the target server, containing the same two lines of code, then right click > ‘Run With PowerShell’ it works as expected / desired. If I remotely execute my code in PowerGUI, it returns a block of text that looks like this, then just sits there. RDP’d into the server, the installer never launches. My understanding of the “Return Value” value is that “0″ means the command was successful.
PSComputerName : xx.xx.xx.xx
RunspaceId : bf6f4a39-2338-4996-b75b-bjf5ef01ecaa
PSShowComputerName : True
__GENUS : 2
__CLASS : __PARAMETERS
__SUPERCLASS :
__DYNASTY : __PARAMETERS
__RELPATH :
__PROPERTY_COUNT : 2
__DERIVATION : {}
__SERVER :
__NAMESPACE :
__PATH :
ProcessId : 4808
ReturnValue : 0
I even added a line of code between the variable and the execution that creates a text file on the desktop, just to verify I was getting into my ‘executeFile’ file, and that text file does get created. It seems that it’s just not remotely executing my MSP.
Thank you in advance for your assistance!
Catt11.
Here's the strategy I used to embed an msp into a powershell script. It works perfectly for me.
$file = "z:\software\AcrobatUpdate.msp"
$silentArgs = "/passive"
$additionalInstallArgs = ""
Write-Debug "Running msiexec.exe /update $file $silentArgs"
$msiArgs = "/update `"$file`""
$msiArgs = "$msiArgs $silentArgs $additionalInstallArgs"
Start-Process -FilePath msiexec -ArgumentList $msiArgs -Wait
You probably don't need to use the variables if you don't want to, you could hardcode the values. I have this set up as a function to which I pass those arguments, but if this is more of a one-shot deal, it might be easier to hard-code the values.
Hope that helps!
using Start-Process for MSP package is not a good practice because some update package lockdown powershell libs and so you must use WMI call
I've built a simple test app with clutter: A stage with two ClutterText actors to display two words. It works OK when I run it from within gnome but running it from the tty (not gnome-terminal or xterm) with xinit my_app_binary I get an error:
failed to create drawable
Unable to initialize Clutter: Unable to select the newly created GLX context
Window manager error: Unable to initialize Clutter
If I run xinit gnome-terminal from the same tty everything works, gnome-terminal shows up in a black screen. That's the same I want to do with my app.
Is there anything I can do to overcome this error?
All the above are tested in Linux Mint 12. After normal boot I switch to a tty (ALT-F1) and stop lightdm (sudo /etc/init.d/lightdm stop).
Thanks!
EDIT: running as root everything works, so the question is: how to run it as a regular user?
Be sure to set the DISPLAY-var - add it in front of your command
DISPLAY=:0.0 /path/to/myapp
Sometimes this is an access-rights problem - the app should be started with the user who started the X-server
su user-started-x -c 'DISPLAY=:0.0 /path/to/myapp'
I have written an R script that pulls some data from a database, performs several operations on it and post the output to a new database.
I would like this script to run every day at a specific time but I can not find any way to do this effectively.
Can anyone recommend a resource I could look at to solve this issue? I am running this script on a Windows machine.
Actually under Windows you do not even have to create a batch file first to use the Scheduler.
Open the scheduler: START -> All Programs -> Accesories -> System Tools -> Scheduler
Create a new Task
under tab Action, create a new action
choose Start Program
browse to Rscript.exe which should be placed e.g. here:
"C:\Program Files\R\R-3.0.2\bin\x64\Rscript.exe"
input the name of your file in the parameters field
input the path where the script is to be found in the Start in field
go to the Triggers tab
create new trigger
choose that task should be done each day, month, ... repeated several times, or whatever you like
Supposing your R script is mytest.r, located in D:\mydocuments\, you can create a batch file including the following command:
C:\R\R-2.10.1\bin\Rcmd.exe BATCH D:\mydocuments\mytest.r
Then add it, as a new task, to windows task scheduler, setting there the triggering conditions.
You could also omit the batch file. Set C:\R\R-2.10.1\bin\Rcmd.exe in the program/script textbox in task scheduler, and give as Arguments the rest of the initial command: BATCH D:\mydocuments\mytest.r
Scheduling R Tasks via Windows Task Scheduler (Posted on February 11, 2015)
taskscheduleR: R package to schedule R scripts with the Windows task manager (Posted on March 17, 2016)
EDIT
I recently adopted the use of batch files again, because I wanted the cmd window to be minimized (I couldn't find another way).
Specifically, I fill the windows task scheduler Actions tab as follows:
Program/script:
cmd.exe
Add arguments (optional):
/c start /min D:\mydocuments\mytest.bat ^& exit
Contents of mytest.bat:
C:\R\R-3.5.2\bin\x64\Rscript.exe D:\mydocuments\mytest.r params
Now there is built in option in RStudio to do this, to run scheduler first install below packages
install.packages('data.table')
install.packages('knitr')
install.packages('miniUI')
install.packages('shiny')
install.packages("taskscheduleR", repos = "http://www.datatailor.be/rcube", type =
"source")
After installing go to
**TOOLS -> ADDINS ->BROWSE ADDINS ->taskscheduleR -> Select it and execute it.**
Setting up the task scheduler
Step 1) Open the task scheduler (Start > search Task Scheduler)
Step 2) Click "Action" > "Create Task"
Step 3) Select "Run only when the user is logged on", uncheck "Run with highest priveledges", name your task,
configure for "Windows Vista/Windows Server 2008"
Step 4) Under the "Triggers" tab, set when you would like the script to run
Step 5) Under the "Actions" tab, put the full location of the Rscript.exe file, i.e.
"C:\Program Files\R\R-3.6.2\bin\Rscript.exe" (include the quotes)
Put the name of your script with with -e and source() in arguments wrapping it like this:
-e "source('C:/location_of_my_script/test.R')"
Troubleshooting a Rscript scheduled in the Task Scheduler
When you run a script using the Task Scheduler, it is difficult to troubleshoot any issues because you don't get any error messages.
This can be resolved by using the sink() function in R which will allow you to output all error messages to a file that you specify. Here is how you can do this:
# Set up error log ------------------------------------------------------------
error_log <- file("C:/location_of_my_script/error_log.Rout", open="wt")
sink(error_log, type="message")
try({
# insert your code here
})
The other thing that you will have to change to make your Rscript work is to specify the full file path of any file paths in your script.
This will not work in task scheduler:
source("./functions/import_function.R")
You will need to specify the full file path of any scripts you are sourcing within your Rscript:
source("C:/location_of_my_script/functions/import_function.R")
Additionally, I would remove any special characters from any file paths that you are referencing in your R script. For example:
df <- fread("C:/location_of_my_data/file#2342.csv")
may not run. Instead, try:
df <- fread("C:/location_of_my_data/file_2342.csv")
Changing windows passwords
Beware: Changing windows passwords will pause your task scheduler script(s). You will need to log back into the task scheduler and enter your password to get them started again.
I set up my tasks via the SCHTASKS program. For running scripts on startup, you would write something along the lines of
SCHTASKS /Create /SC ONSTART /TN MyProgram /TR "R CMD BATCH --vanilla d:\path\to\script.R"
See this website for more details on SCHTASKS. More details at Microsoft's website.
You can use Windows Task Scheduler.
After following any combination of these steps and you receive the "Argument Batch Ignored" error after R.exe runs, try this, it worked for me.
In Windows Task Scheduler:
Replace BATCH "C:\Users\desktop\yourscript.R"in the arguments field
with
CMD BATCH --vanilla --slave "C:\Users\desktop\yourscript.R"