How to execute a R script file from java
0
I would like to call an R script from Java. I have done google searches on the topic, but almost all of the results I have seen would require me to add a dependency to some third party library. Can anyone show me a good way to accomplish the same thing without adding any dependencies to my code?
I'm setting up a new application which runs R script file from java using the following line
Runtime.getRuntime().exec("C:UsersThiruDesktop helloWorld.R");
but when I run the application I am getting following exception:
SEVERE: Servlet.service() for servlet [RenjinServlet] in context with
path
[/REngineCheck] threw exception
java.io.IOException: Cannot run program "C:UsersThiruDesktop":
CreateProcess error=5, Access is denied
at java.lang.ProcessBuilder.start(Unknown Source)
at java.lang.Runtime.exec(Unknown Source)
at java.lang.Runtime.exec(Unknown Source)
at java.lang.Runtime.exec(Unknown Source)
at org.r.Check.RenjinServlet.doGet(RenjinServlet.java:102)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:622)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter
(ApplicationFilterChain.java:291)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter
(ApplicationFilterChain.java:206)
at org.apache.tomcat.websocket.server.WsFilter.doFilter (WsFilter.java:52)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter
(ApplicationFilterChain.java:239)
at org.apache.catalina.core.ApplicationFilterChain.doFilter
(ApplicationFilterChain.java:206)
at org.apache.catalina.core.StandardWrapperValve.invoke
(StandardWrapperValve.java:217)
at org.apache.catalina.core.StandardContextValve.invoke
(StandardContextValve.java:106)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke
(AuthenticatorBase.java:502)
at org.apache.catalina.core.StandardHostValve.invoke
(StandardHostValve.java:142)
at org.apache.catalina.valves.ErrorReportValve.invoke
(ErrorReportValve.java:79)
at org.apache.catalina.valves.AbstractAccessLogValve.invoke
(AbstractAccessLogValve.java:616)
at org.apache.catalina.core.StandardEngineValve.invoke
(StandardEngineValve.java:88)
at org.apache.catalina.connector.CoyoteAdapter.service
(CoyoteAdapter.java:518)
at org.apache.coyote.http11.AbstractHttp11Processor.process
(AbstractHttp11Processor.java:1091)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process
(AbstractProtocol.java:673)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun
(NioEndpoint.java:1500)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run
(NioEndpoint.java:1456)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run
(TaskThread.java:61)
at java.lang.Thread.run(Unknown Source)
Caused by: java.io.IOException: CreateProcess error=5, Access is denied
at java.lang.ProcessImpl.create(Native Method)
at java.lang.ProcessImpl.<init>(Unknown Source)
at java.lang.ProcessImpl.start(Unknown Source)
... 28 more
java r rserve jri
edited Dec 29 '18 at 11:04
Joey Mallone
1,10121123
asked Dec 29 '18 at 10:51
Bharath PateruBharath Pateru
42112
add a comment |
0
I would like to call an R script from Java. I have done google searches on the topic, but almost all of the results I have seen would require me to add a dependency to some third party library. Can anyone show me a good way to accomplish the same thing without adding any dependencies to my code?
I'm setting up a new application which runs R script file from java using the following line
Runtime.getRuntime().exec("C:UsersThiruDesktop helloWorld.R");
but when I run the application I am getting following exception:
SEVERE: Servlet.service() for servlet [RenjinServlet] in context with
path
[/REngineCheck] threw exception
java.io.IOException: Cannot run program "C:UsersThiruDesktop":
CreateProcess error=5, Access is denied
at java.lang.ProcessBuilder.start(Unknown Source)
at java.lang.Runtime.exec(Unknown Source)
at java.lang.Runtime.exec(Unknown Source)
at java.lang.Runtime.exec(Unknown Source)
at org.r.Check.RenjinServlet.doGet(RenjinServlet.java:102)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:622)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter
(ApplicationFilterChain.java:291)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter
(ApplicationFilterChain.java:206)
at org.apache.tomcat.websocket.server.WsFilter.doFilter (WsFilter.java:52)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter
(ApplicationFilterChain.java:239)
at org.apache.catalina.core.ApplicationFilterChain.doFilter
(ApplicationFilterChain.java:206)
at org.apache.catalina.core.StandardWrapperValve.invoke
(StandardWrapperValve.java:217)
at org.apache.catalina.core.StandardContextValve.invoke
(StandardContextValve.java:106)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke
(AuthenticatorBase.java:502)
at org.apache.catalina.core.StandardHostValve.invoke
(StandardHostValve.java:142)
at org.apache.catalina.valves.ErrorReportValve.invoke
(ErrorReportValve.java:79)
at org.apache.catalina.valves.AbstractAccessLogValve.invoke
(AbstractAccessLogValve.java:616)
at org.apache.catalina.core.StandardEngineValve.invoke
(StandardEngineValve.java:88)
at org.apache.catalina.connector.CoyoteAdapter.service
(CoyoteAdapter.java:518)
at org.apache.coyote.http11.AbstractHttp11Processor.process
(AbstractHttp11Processor.java:1091)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process
(AbstractProtocol.java:673)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun
(NioEndpoint.java:1500)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run
(NioEndpoint.java:1456)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run
(TaskThread.java:61)
at java.lang.Thread.run(Unknown Source)
Caused by: java.io.IOException: CreateProcess error=5, Access is denied
at java.lang.ProcessImpl.create(Native Method)
at java.lang.ProcessImpl.<init>(Unknown Source)
at java.lang.ProcessImpl.start(Unknown Source)
... 28 more
java r rserve jri
edited Dec 29 '18 at 11:04
Joey Mallone
1,10121123
asked Dec 29 '18 at 10:51
Bharath PateruBharath Pateru
42112
If your windows is not configured to useRscriptto run files ending in.R, you may need to doRuntime.getRuntime().exec("C:pathtoRscript.exe C:UsersThiruDesktophellowWorld.R"). (I'm not familiar enough with java to know for sure if that should be a string with the cmd and all args, or if you need to pass a list with the cmd as the first, and your R script as the second element.)
– r2evans
Dec 29 '18 at 18:58
Dear @r2evans, It's not working I am getting file not found exception, but when I run like this in CMD I am getting the out put in cmd. E:E DriveSoftwaresR docsR-3.5.1binx64>Rscript C:UsersThiruDesktophelloWorld.R
– Bharath Pateru
Dec 31 '18 at 10:55
What happens if you tryRuntime.getRuntime().exec("E:E DriveSoftwaresR docsR-3.5.1binx64>Rscript C:UsersThiruDesktophelloWorld.R")?
– r2evans
Dec 31 '18 at 16:13
@r2evans, I am getting file not found exception when I run like this.
– Bharath Pateru
Jan 4 at 5:27
My guess (again, not a java guy) is that it had to do with including both the executable and its argument(s) in one string. Do you know how to useRuntime.getRuntime().exec? I do not.
– r2evans
Jan 5 at 13:39
add a comment |
0
0
0
I would like to call an R script from Java. I have done google searches on the topic, but almost all of the results I have seen would require me to add a dependency to some third party library. Can anyone show me a good way to accomplish the same thing without adding any dependencies to my code?
I'm setting up a new application which runs R script file from java using the following line
Runtime.getRuntime().exec("C:UsersThiruDesktop helloWorld.R");
but when I run the application I am getting following exception:
SEVERE: Servlet.service() for servlet [RenjinServlet] in context with
path
[/REngineCheck] threw exception
java.io.IOException: Cannot run program "C:UsersThiruDesktop":
CreateProcess error=5, Access is denied
at java.lang.ProcessBuilder.start(Unknown Source)
at java.lang.Runtime.exec(Unknown Source)
at java.lang.Runtime.exec(Unknown Source)
at java.lang.Runtime.exec(Unknown Source)
at org.r.Check.RenjinServlet.doGet(RenjinServlet.java:102)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:622)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter
(ApplicationFilterChain.java:291)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter
(ApplicationFilterChain.java:206)
at org.apache.tomcat.websocket.server.WsFilter.doFilter (WsFilter.java:52)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter
(ApplicationFilterChain.java:239)
at org.apache.catalina.core.ApplicationFilterChain.doFilter
(ApplicationFilterChain.java:206)
at org.apache.catalina.core.StandardWrapperValve.invoke
(StandardWrapperValve.java:217)
at org.apache.catalina.core.StandardContextValve.invoke
(StandardContextValve.java:106)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke
(AuthenticatorBase.java:502)
at org.apache.catalina.core.StandardHostValve.invoke
(StandardHostValve.java:142)
at org.apache.catalina.valves.ErrorReportValve.invoke
(ErrorReportValve.java:79)
at org.apache.catalina.valves.AbstractAccessLogValve.invoke
(AbstractAccessLogValve.java:616)
at org.apache.catalina.core.StandardEngineValve.invoke
(StandardEngineValve.java:88)
at org.apache.catalina.connector.CoyoteAdapter.service
(CoyoteAdapter.java:518)
at org.apache.coyote.http11.AbstractHttp11Processor.process
(AbstractHttp11Processor.java:1091)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process
(AbstractProtocol.java:673)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun
(NioEndpoint.java:1500)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run
(NioEndpoint.java:1456)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run
(TaskThread.java:61)
at java.lang.Thread.run(Unknown Source)
Caused by: java.io.IOException: CreateProcess error=5, Access is denied
at java.lang.ProcessImpl.create(Native Method)
at java.lang.ProcessImpl.<init>(Unknown Source)
at java.lang.ProcessImpl.start(Unknown Source)
... 28 more
java r rserve jri
edited Dec 29 '18 at 11:04
Joey Mallone
1,10121123
asked Dec 29 '18 at 10:51
Bharath PateruBharath Pateru
42112
I would like to call an R script from Java. I have done google searches on the topic, but almost all of the results I have seen would require me to add a dependency to some third party library. Can anyone show me a good way to accomplish the same thing without adding any dependencies to my code?
I'm setting up a new application which runs R script file from java using the following line
Runtime.getRuntime().exec("C:UsersThiruDesktop helloWorld.R");
but when I run the application I am getting following exception:
SEVERE: Servlet.service() for servlet [RenjinServlet] in context with
path
[/REngineCheck] threw exception
java.io.IOException: Cannot run program "C:UsersThiruDesktop":
CreateProcess error=5, Access is denied
at java.lang.ProcessBuilder.start(Unknown Source)
at java.lang.Runtime.exec(Unknown Source)
at java.lang.Runtime.exec(Unknown Source)
at java.lang.Runtime.exec(Unknown Source)
at org.r.Check.RenjinServlet.doGet(RenjinServlet.java:102)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:622)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter
(ApplicationFilterChain.java:291)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter
(ApplicationFilterChain.java:206)
at org.apache.tomcat.websocket.server.WsFilter.doFilter (WsFilter.java:52)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter
(ApplicationFilterChain.java:239)
at org.apache.catalina.core.ApplicationFilterChain.doFilter
(ApplicationFilterChain.java:206)
at org.apache.catalina.core.StandardWrapperValve.invoke
(StandardWrapperValve.java:217)
at org.apache.catalina.core.StandardContextValve.invoke
(StandardContextValve.java:106)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke
(AuthenticatorBase.java:502)
at org.apache.catalina.core.StandardHostValve.invoke
(StandardHostValve.java:142)
at org.apache.catalina.valves.ErrorReportValve.invoke
(ErrorReportValve.java:79)
at org.apache.catalina.valves.AbstractAccessLogValve.invoke
(AbstractAccessLogValve.java:616)
at org.apache.catalina.core.StandardEngineValve.invoke
(StandardEngineValve.java:88)
at org.apache.catalina.connector.CoyoteAdapter.service
(CoyoteAdapter.java:518)
at org.apache.coyote.http11.AbstractHttp11Processor.process
(AbstractHttp11Processor.java:1091)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process
(AbstractProtocol.java:673)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun
(NioEndpoint.java:1500)
at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run
(NioEndpoint.java:1456)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run
(TaskThread.java:61)
at java.lang.Thread.run(Unknown Source)
Caused by: java.io.IOException: CreateProcess error=5, Access is denied
at java.lang.ProcessImpl.create(Native Method)
at java.lang.ProcessImpl.<init>(Unknown Source)
at java.lang.ProcessImpl.start(Unknown Source)
... 28 more
java r rserve jri
java r rserve jri
edited Dec 29 '18 at 11:04
Joey Mallone
1,10121123
asked Dec 29 '18 at 10:51
Bharath PateruBharath Pateru
42112
edited Dec 29 '18 at 11:04
Joey Mallone
1,10121123
asked Dec 29 '18 at 10:51
Bharath PateruBharath Pateru
42112
edited Dec 29 '18 at 11:04
Joey Mallone
1,10121123
edited Dec 29 '18 at 11:04
Joey Mallone
1,10121123
edited Dec 29 '18 at 11:04
Joey Mallone
1,10121123
1,10121123
asked Dec 29 '18 at 10:51
Bharath PateruBharath Pateru
42112
asked Dec 29 '18 at 10:51
Bharath PateruBharath Pateru
42112
asked Dec 29 '18 at 10:51
Bharath PateruBharath Pateru
42112
42112
If your windows is not configured to useRscriptto run files ending in.R, you may need to doRuntime.getRuntime().exec("C:pathtoRscript.exe C:UsersThiruDesktophellowWorld.R"). (I'm not familiar enough with java to know for sure if that should be a string with the cmd and all args, or if you need to pass a list with the cmd as the first, and your R script as the second element.)
– r2evans
Dec 29 '18 at 18:58
Dear @r2evans, It's not working I am getting file not found exception, but when I run like this in CMD I am getting the out put in cmd. E:E DriveSoftwaresR docsR-3.5.1binx64>Rscript C:UsersThiruDesktophelloWorld.R
– Bharath Pateru
Dec 31 '18 at 10:55
What happens if you tryRuntime.getRuntime().exec("E:E DriveSoftwaresR docsR-3.5.1binx64>Rscript C:UsersThiruDesktophelloWorld.R")?
– r2evans
Dec 31 '18 at 16:13
@r2evans, I am getting file not found exception when I run like this.
– Bharath Pateru
Jan 4 at 5:27
My guess (again, not a java guy) is that it had to do with including both the executable and its argument(s) in one string. Do you know how to useRuntime.getRuntime().exec? I do not.
– r2evans
Jan 5 at 13:39
add a comment |
If your windows is not configured to useRscriptto run files ending in.R, you may need to doRuntime.getRuntime().exec("C:pathtoRscript.exe C:UsersThiruDesktophellowWorld.R"). (I'm not familiar enough with java to know for sure if that should be a string with the cmd and all args, or if you need to pass a list with the cmd as the first, and your R script as the second element.)
– r2evans
Dec 29 '18 at 18:58
Dear @r2evans, It's not working I am getting file not found exception, but when I run like this in CMD I am getting the out put in cmd. E:E DriveSoftwaresR docsR-3.5.1binx64>Rscript C:UsersThiruDesktophelloWorld.R
– Bharath Pateru
Dec 31 '18 at 10:55
What happens if you tryRuntime.getRuntime().exec("E:E DriveSoftwaresR docsR-3.5.1binx64>Rscript C:UsersThiruDesktophelloWorld.R")?
– r2evans
Dec 31 '18 at 16:13
@r2evans, I am getting file not found exception when I run like this.
– Bharath Pateru
Jan 4 at 5:27
My guess (again, not a java guy) is that it had to do with including both the executable and its argument(s) in one string. Do you know how to useRuntime.getRuntime().exec? I do not.
– r2evans
Jan 5 at 13:39
If your windows is not configured to use
Rscript to run files ending in .R, you may need to do Runtime.getRuntime().exec("C:pathtoRscript.exe C:UsersThiruDesktophellowWorld.R"). (I'm not familiar enough with java to know for sure if that should be a string with the cmd and all args, or if you need to pass a list with the cmd as the first, and your R script as the second element.)– r2evans
Dec 29 '18 at 18:58
If your windows is not configured to use
Rscript to run files ending in .R, you may need to do Runtime.getRuntime().exec("C:pathtoRscript.exe C:UsersThiruDesktophellowWorld.R"). (I'm not familiar enough with java to know for sure if that should be a string with the cmd and all args, or if you need to pass a list with the cmd as the first, and your R script as the second element.)– r2evans
Dec 29 '18 at 18:58
Dear @r2evans, It's not working I am getting file not found exception, but when I run like this in CMD I am getting the out put in cmd. E:E DriveSoftwaresR docsR-3.5.1binx64>Rscript C:UsersThiruDesktophelloWorld.R
– Bharath Pateru
Dec 31 '18 at 10:55
Dear @r2evans, It's not working I am getting file not found exception, but when I run like this in CMD I am getting the out put in cmd. E:E DriveSoftwaresR docsR-3.5.1binx64>Rscript C:UsersThiruDesktophelloWorld.R
– Bharath Pateru
Dec 31 '18 at 10:55
What happens if you try
Runtime.getRuntime().exec("E:E DriveSoftwaresR docsR-3.5.1binx64>Rscript C:UsersThiruDesktophelloWorld.R")?– r2evans
Dec 31 '18 at 16:13
What happens if you try
Runtime.getRuntime().exec("E:E DriveSoftwaresR docsR-3.5.1binx64>Rscript C:UsersThiruDesktophelloWorld.R")?– r2evans
Dec 31 '18 at 16:13
@r2evans, I am getting file not found exception when I run like this.
– Bharath Pateru
Jan 4 at 5:27
@r2evans, I am getting file not found exception when I run like this.
– Bharath Pateru
Jan 4 at 5:27
My guess (again, not a java guy) is that it had to do with including both the executable and its argument(s) in one string. Do you know how to use
Runtime.getRuntime().exec? I do not.– r2evans
Jan 5 at 13:39
My guess (again, not a java guy) is that it had to do with including both the executable and its argument(s) in one string. Do you know how to use
Runtime.getRuntime().exec? I do not.– r2evans
Jan 5 at 13:39
add a comment |
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If your windows is not configured to use
Rscriptto run files ending in.R, you may need to doRuntime.getRuntime().exec("C:pathtoRscript.exe C:UsersThiruDesktophellowWorld.R"). (I'm not familiar enough with java to know for sure if that should be a string with the cmd and all args, or if you need to pass a list with the cmd as the first, and your R script as the second element.)– r2evans
Dec 29 '18 at 18:58
Dear @r2evans, It's not working I am getting file not found exception, but when I run like this in CMD I am getting the out put in cmd. E:E DriveSoftwaresR docsR-3.5.1binx64>Rscript C:UsersThiruDesktophelloWorld.R
– Bharath Pateru
Dec 31 '18 at 10:55
What happens if you try
Runtime.getRuntime().exec("E:E DriveSoftwaresR docsR-3.5.1binx64>Rscript C:UsersThiruDesktophelloWorld.R")?– r2evans
Dec 31 '18 at 16:13
@r2evans, I am getting file not found exception when I run like this.
– Bharath Pateru
Jan 4 at 5:27
My guess (again, not a java guy) is that it had to do with including both the executable and its argument(s) in one string. Do you know how to use
Runtime.getRuntime().exec? I do not.– r2evans
Jan 5 at 13:39