Develop Reference

Unable to locate a file in java project running in a executable jar

Both class.getResource(FILE_NAME) and class.getClass().getClassLoader().getResource(FILE_NAME) run perfectly inside my eclipse but the same code getting failed to locate the file which is inside the jar file, when run as an executable jar in windows machine.
I have gone through all related links available for this problem (well, not exactly the same issue but 90% in sync), asked for solution but no reply came from any of those posts, so I'm posting my issue as a separate question hoping for help on this.
In total, 4 cases I have ran to resolve but none worked so far and I'm out of ideas now.
class.getClass().getClassLoader().getResource("/resources/readme.txt");
class.getResource("/resources/readme.txt");
class.getClass().getClassLoader().getResource("resources/readme.txt");
class.getResource("resources/readme.txt");
Ouf of all the above 4 cases, only 2 cases ran successfully in eclipse which are as mentioned below.
class.getResource("/resources/readme.txt");
class.getClass().getClassLoader().getResource("resources/readme.txt");
The other 2 cases just throwing me Exception in thread "main" java.lang.NullPointerException
Coming to the executable jar, all 4 cases are throwing me the Exception in thread "main" java.lang.NullPointerException.
So I have created a folder named resources where my jar is residing and placed my files inside this folder and ran the jar. Now the jar is running without any issues referring to the files inside the resources folder I created. So wherever I run this jar (windows, linux etc.,) I need to create a resources folder and place my files under the folder. Now the question is, can it be possible to make my jar refer the resources folder which is inside the jar itself?
Any help on this is much appreciated!

To get your txt file:
File yourFileIsHere = new File("resources/readme.txt");
Where put your file?
In the same location of your jar, example:
myapp/yourjar.jar
myapp/resources/readme.txt
If you want read file inside of your "src" folder:
InputStream yourInputStream = new YourClass().getClass().getClassLoader().getResourceAsStream("readme.txt");

If you are using Spring:
org.springframework.util.ResourceUtils.getFile("classpath:readme.txt")
Otherwise:
import com.google.common.io.Resources
byte[] byteSource = Resources.asByteSource(Resources.getResource("readme.txt")).read()

method class.getClass().getClassLoader().getResource() may take 3 prefixes: url:, classpath: and file: each prefix tells what is your base of search. If you want to search inside your jar use classpath: prefix. That tells your classloader to search everywhere within your classpath. Here is one example how to deal with it with Spring tools. Look also at ResourceLoader class in Spring

Java with ImageJ

I am using ImageJ in java code for doing segmentation of objects in images using LevelSet.
I imported the jar file called "levelsets.ij.LevelSet". But I get an error as 'unidentified command' in the string field 'Level Sets' in the run command.
Can someone help me to identify the error in my program?
When executing the following code the string parameter "Level Sets" in line 3 is not identified as a command. Can you kindly help?
ImagePlus imp = new ImagePlus("image_plus", img);
imp.setRoi(new OvalRoi(54,51,11,7));
IJ.run(imp,"Level Sets", "method=[Active Contours] use_level_sets
grey_value_threshold=50 distance_threshold=0.50 advection=2.20
propagation=1 curvature=1 grayscale=20 convergence=0.0050
region=outside");
img = imp.getBufferedImage();

Manage your project dependencies using Maven. Add a dependency on the sc.fiji:level_sets artifact.
I identified this artifact by pressing L to bring up the Command Finder, typing in "level" and then looking at the File column to see which JAR file the levelsets.ij.LevelSet class came from.
See also the Development page of the ImageJ wiki.

R Shiny DesktopDeployR Stop Logging Error

I am trying to deploy R Shiny App as an Windows Desktop App. So far I have used the framework described at http://blog.analytixware.com/2014/03/packaging-your-shiny-app-as-windows.html and managed to make it work with the help of stackoverflow users (question name "R Shiny as Windows Desktop App Creates Text File With Warning").
An update to this framework has been developed and it has several advantages over the previous one, such as not relying on Google Chrome browser etc. and it is described here: http://oddhypothesis.blogspot.com/2016/04/desktop-deployr.html
All files can be found in the GitHub account of framework creator (link is presented in the description)
I have adjusted the following:
app.R
require(shinyjs,quietly = TRUE,warn.conflicts=FALSE)
require(markdown,quietly = TRUE,warn.conflicts=FALSE)
require(scales,quietly = TRUE,warn.conflicts=FALSE)
require(DT,quietly = TRUE,warn.conflicts=FALSE)
runApp("./app/shiny/", launch.browser=TRUE,quiet=TRUE)
packages.txt
Added the names of the packages I am using
# Primary package dependencies for the application that are loaded during
# startup.
#
# If not available, they will be installed into app/library. Custom source
# packages need to be installed manually.
# bare miniminum: configurations are stored in json format
jsonlite
# if deploying shiny based applications:
shiny
shinyjs
markdown
scales
DT
App does launch, it works. However a new folder is created called log with file error.log, which includes the following:
library paths:
... C:/Users/VoronecI/Desktop/New folder (2)/app/library
... C:/Users/VoronecI/Desktop/New folder (2)/dist/R-Portable/App/R-Portable/library
working path:
... C:/Users/VoronecI/Desktop/New folder (2)
Loading required package: methods
ensuring packages: jsonlite, shiny, shinyjs, markdown, scales, DT
Attaching package: 'shiny'
The following object is masked from 'package:jsonlite':
validate
Attaching package: 'shinyjs'
The following object is masked from 'package:shiny':
runExample
The following objects are masked from 'package:methods':
removeClass, show
Attaching package: 'DT'
The following objects are masked from 'package:shiny':
dataTableOutput, renderDataTable
Is there a way to prevent this logging of the unmeaningful error?
The reason why I want to get rid of it is because I further use Inno Setup Compiler to create .exe and this is not working when I have a log file updating each time I run the app.

As you can see in this file (line 66) https://github.com/wleepang/DesktopDeployR/blob/7c81e72c5beb29bf84ca65fd1d5bb5486caec51a/dist/script/wsf/js/run.js
The command is run as
var strCommand = [Rexe, Ropts, RScriptFile, "1>", Outfile, "2>&1"].join(" ");
which redirects command line outputs (that normally directly print to the screen) to the Outfile. You can change this line to
var strCommand = [Rexe, Ropts, RScriptFile].join(" ");
which will disable the logging. This might have other implications though (you might see a command window for example, I am not too sure but test it out).
Alternatively, you might be able to change this file https://github.com/wleepang/DesktopDeployR/blob/7c81e72c5beb29bf84ca65fd1d5bb5486caec51a/app/config.cfg (line 27) and set
- use_userprofile: true
(you need to uncomment this line, it is currently inside a block comment). This will make sure the log file goes into the user profile folder, and that might also solve your problem.

Ivona, I just finished developing the RInno package which also uses Inno Setup and the DesktopDeployR project to install local Shiny apps, and it will log errors without a problem.
To get started:
install.packages("RInno")
require(RInno)
RInno::install_inno()
Then you just need to call two functions to create an installation framework:
create_app(app_name = "myapp", app_dir = "path/to/myapp")
compile_iss()
If you are interested in other features, check out FI Labs - RInno. I'd be interested to know if turning off the error logging feature is something you would like to add ;)

NoClassDefFoundError when runnable jar

Hi Guys I have included the Webcam-Capture API in my project.
When I run it in Netbeans everything works fine. But when i compile everything to a runnable jar i get this message trying to run it by cmd line.
can anyone of you help me?
i already tried to unbound and rebound all jars and changing jdks but its not working

add -classpath flag in the command line ,pointing to the path where Webcam-Capture API exists in your file system, unless you want to create a single package executable.In your case It should be something like below
java -classpath YOURJAR.jar;folder_of_dependant_jar/*;. com.awesome.pagackage.Starter
Where YOURJAR.jar contains the com.awesome.pagackage.Starter.main(String args[])
You also mentioned that your jar is a runnable jar it also means that while exporting/building you can do one of the following way.( NOTE , this feature is in eclipse , but you would get the idea ).Each of the following options you see in the library handling does specific things.
The first option: Extracts the dependent jar into your target jar as java packaging.This means if your package is com.awesome.package and the dependent jar has package logic.package; , after the runnable jar is build you could find both these package exists in your jar file.
The second option: I think it is more on eclipse specific since eclipse adds few classes of its own , of runnable generation, so I am not explaining it here.
The third option : is the most interesting one. it creates folder stucture like below
ndon_lib\external.jar ( external jar file )
ndon.jar ( your jar file )
This time the manifest.mf file contains something like below.
Class-Path: . ndon_lib/external.jar
Main-Class: com.awesome.pagackage.Starter

You should set the classpath
java -cp "your.jar" "yourclass"

rJava Cannot add to classpath [duplicate]

I'm trying to use R to hook the Java code from the GSRad project. The GSRad Java code is available online and comes as a One-Jar project jar (I was not familiar with One-Jar until today). I can run the One-Jar file just dandy using the following command (after unzipping the file from the above link):
java -jar gsrad_sample.jar
When I pop open the gsrad_sample.jar file I see a jar titled clima_GSRAD-1.0.0.jar in the /lib/ directory which contains the class files I want to hook with R. I've pulled out the jar of my affection and tried the following, to no avail:
library(rJava)
.jinit()
.jaddClassPath( "/home/jal/Documents/DSSAT/gsrad/clima_GSRAD-1.0.0.jar" )
.jnew( "cra/clima/gsrad/GSRBristowCampbellStrategy" )
Any tips on how I might hook the classes inside the clima_GSRAD-1.0.0.jar? I'm flummoxed.
EDIT
The GSRad site requires registration which is annoying. The full zip file which contains the Doxygen documentation for the Java package as well as the One-Jar jar file is available here and if you pop that open the jar that has the classes I want to hook is this one.

Let me preface my answer by saying that I'm no expert in Java / rJava, so apologies if this isn't 100% correct. I hope it's a step in the right direction though.
Start by unzipping gsrad_sample.jar to C:/gsrad (or adjust your paths based on where you unzip it). Then add all the contents of C:/gsrad/lib to your class path:
library(rJava)
.jinit()
.jaddClassPath(dir( "C:/gsrad/lib", full.names=TRUE ))
.jclassPath()
.jnew( "cra/clima/gsrad/GSRBristowCampbellStrategy" )