Our application is a RoR app, and currently uses JRuby version 1.7.22, and JRE 8_65. Our app is an on-prem solution, so we use JRuby to host our application on JVM at the target, Windows Server 2012 R2 system. We compile our ruby code, using
jruby -S jrubyc
This takes the .rb file and compiles it to a .class file. In the original .rb, it loads in the class file, like so.
load __FILE__.sub(/\.rb$/, ".class")
This all works with JRuby 1.7.22
Now, we want to update JRuby to 9.0.5.0, but are experiencing some problems when it comes to deploying our application. Basically, that line of code above inside of the .rb file is not working anymore, and we get the error when trying to run a rake db:setup
rake aborted!
LoadError: C:/appname/app/models/app_attribute.class is not compiled Ruby; use java_import to load normal classes
C:/appname/app/models/app_attribute.rb:1:in `<top>'
C:/appname/db/seeds.rb:10:in `<top>'
C:/appname/db/seeds.rb:9:in `block in (root)'
Tasks: TOP => db:setup => db:seed
(See full trace by running task with --trace)
Great. So I replace load with java_import
rake aborted!
ArgumentError: not a valid Java identifier: C:/appname/app/models/app_attribute.class
uri:classloader:/jruby/java/core_ext/object.rb:43:in `block in java_import'
uri:classloader:/jruby/java/core_ext/object.rb:34:in `java_import'
C:/appname/app/models/app_attribute.rb:1:in `<top>'
C:/appname/db/seeds.rb:10:in `<top>'
C:/appname/db/seeds.rb:9:in `block in (root)'
Tasks: TOP => db:setup => db:seed
(See full trace by running task with --trace)
Still not working, no matter what I try. I looked at this post: https://github.com/jruby/jruby/issues/3018
I tried to pass the parameter
jruby -Xaot.loadClasses=true
But I get a warning saying that aot.LoadClasses is not recognized. EVEN THOUGH I see it in the properties when I type
jruby -Xproperties
I have done A LOT of research on this, and have probably have looked at everything on the internet regarding this. Any input will be greatly appreciated. Is there something I missing? I am not fully adept in Java.
Thank you.
might be the same issue as https://github.com/jruby/jruby/issues/3651
which means you'll need to wait for 9.1 or use a snapshot http://ci.jruby.org/
since, the error is slightly different you should look into reproducing with snapshot and if it fails (might be Windows related) a step-by-step reproduction might speed-up getting the issue resolved.
jruby -Xaot.loadClasses=true
this is not needed with Warbler
But I get a warning saying that aot.LoadClasses is not recognized. EVEN THOUGH I see it in the properties when I type
hmm, could you reproduce this with an empty script and no JRUBY_OPTS ?
I have done A LOT of research on this, and have probably have looked at everything on the internet regarding this. Any input will be greatly appreciated.
you might want to try looking into the issue next time :) or considering getting some support
Is there something I missing? I am not fully adept in Java.
you shouldn't be missing anything - its not a Java issue ...
Related
I am running maxent from R, in the package biomod2 and the following error appeared. I do not come from a technical background and wasn't sure why is this error happening. Is it a memory problem or someone said the java path is not set. But I followed the instructions to set maxent to run in R and also downloaded Java Platform, Standard Edition Development Kit and set a path for it as explained in this pdf: http://modata.ceoe.udel.edu/dev/dhaulsee/class_rcode/r_pkgmanuals/MAXENT4R_directions.pdf
I would be really grateful if you could help me understand this problem and any solution to it.
Thanks a lot
Error in file(file, "rt") : cannot open the connection
In addition: Warning messages:
1: running command 'java' had status 1
2: running command 'java -mx512m -jar E:\bioclim_2.5min\model/maxent.jar environmentallayers
="rainfed/models/1432733200/m_47203134/Back_swd.csv"
samplesfile="rainfed/models/1432733200/m_47203134/Sp_swd.csv"
projectionlayers="rainfed/models/1432733200/m_47203134/Predictions/Pred_swd.csv"
outputdirectory="rainfed/models/1432733200/rainfed_PA1_Full_MAXENT_outputs"
outputformat=logistic redoifexists visible=FALSE linear=TRUE quadratic=TRUE
product=TRUE threshold=TRUE hinge=TRUE lq2lqptthreshold=80 l2lqthreshold=10
hingethreshold=15 beta_threshold=-1 beta_categorical=-1 beta_lqp=-1
beta_hinge=-1 defaultprevalence=0.5 autorun nowarnings notooltips
noaddsamplestobackground' had status 1
3: In file(file, "rt") :
cannot open file 'rainfed/models/1432733200/rainfed_PA1_Full_MAXENT_outputs/rainfed_PA1_
Full_Pred_swd.csv': No such file or directory
I've just manage to solve this problem - it is a problem with the file path specified. For me, I had a space in one of the folder names which was not accepted in the path to the maxent.jar file. From looking at your error, it looks like it might be the two backslashes.
E:\bioclim_2.5min\model/maxent.jar
should probably read
E:/bioclim_2.5min/model/maxent.jar
I have a program that uses Sqlite database. It works fine on Windows (exported jar or directly in Eclipse) but when I move it to linux server (plan is to use run it at certain intervals, cron job). I'm exporting it to jar from Eclipse and packing the sqlite-jdbc4-3.8.2-SNAPSHOT.jar with it. Error is this:
/$ /usr/bin/java -jar /home/username/Software.jar /home/username/
java.lang.UnsatisfiedLinkError: /tmp/sqlite-3.8.2-amd64-libsqlitejdbc.so: /tmp/sqlite-3.8.2-amd64-libsqlitejdbc.so: failed to map segment from shared object: Operation not permitted
Exception in thread "main" java.lang.UnsatisfiedLinkError: org.sqlite.core.NativeDB._open(Ljava/lang/String;I)V
at org.sqlite.core.NativeDB._open(Native Method)
at org.sqlite.core.DB.open(DB.java:161)
at org.sqlite.core.CoreConnection.open(CoreConnection.java:145)
at org.sqlite.core.CoreConnection.<init>(CoreConnection.java:66)
at org.sqlite.jdbc3.JDBC3Connection.<init>(JDBC3Connection.java:21)
at org.sqlite.jdbc4.JDBC4Connection.<init>(JDBC4Connection.java:23)
at org.sqlite.SQLiteConnection.<init>(SQLiteConnection.java:44)
at org.sqlite.JDBC.createConnection(JDBC.java:113)
at org.sqlite.JDBC.connect(JDBC.java:87)
at java.sql.DriverManager.getConnection(DriverManager.java:582)
at java.sql.DriverManager.getConnection(DriverManager.java:207)
....
So before you ask, I've made sure that sqlite-3.8.2-amd64-libsqlitejdbc.so in /tmp/ has all permissions (rwxrwxrwx). Still that native library is causing problems. It does get copied in /tmp/ folder though. That being said I totally suck in Linux... and for that reason I'm pretty much clueless what to try next.
What should I do? Switch connector?
EDIT:
Solved the problem by using System.setProperty("java.io.tmpdir", "/home/username/"); Apparently it for some reason couldn't execute the native library from tmp folder... Probably because it was created by root. Also I had to revert back to sqlite-jdbc-3.7.2.jar because the new one crashes on linux.
I had same problem, and I found the solution in this GitHub issue:
JAVA_OPTS=-Djava.io.tmpdir=/path/to/some/other/tmpdir bin/cerebro
Also look at this other SO answer.
I'm currently having real problems trying to get the gem Nokogiri to work in my applet. I have the jruby-complete-1.7.3 jar and have attempted to install gems using the normal install line:
java -jar jruby-compelete-1.7.3.jar -S gem install nokogiri
And also I have tried the Gem-In-A-Jar method. At first it works fine, and allows me to eval ruby code and store the data returned. My problem arises when I add in the line:
require 'nokogiri'
While that line works fine in the irb, when trying to access it from the applet I get the following error:
classpath:/META-INF/jruby.home/lib/ruby/shared/rubygems.rb:396 warning: can't
canonicalize loaded names due to security restrictions; disabling
Message: (LoadError) no such file to load -- nokogiri
Stacktrace:
org.jruby.exceptions.RaiseException: (LoadError) no such file to load -- nokogiri
at org.jruby.RubyKernel.require(org/jruby/RubyKernel.java:1027)
at RUBY.require(classpath:/META-INF/jruby.home/lib/ruby/shared/rubygems/custom_require.rb:36)
at RUBY.(root)(<script>:2)
I simply can't figure out why this exception is occuring. I've tried:
moving the gems manually into the "META-INF/jruby.home/lib/ruby/gems/shared" folder
I've added "require 'rubygems'" above the the nokogiri call.
Accessing the gems via the Gems-in-a-jar method: http://blog.nicksieger.com/articles/2009/01/10/jruby-1-1-6-gems-in-a-jar/
If anyone has an idea where I've gone wrong, or a solution to this issue, I'd greatly appreciate it.
I want to do something with the HypergraphDB in Java. I'm not very familiar with this language and IDE Netbeans.
I followed steps describing the HGDB installation:Link to tutorial
Now I want to write an example in Java (using NetbeansIDE).
So I created new project, added refferences to the downloaded libraries. OK, now I'm able to import packages with HGDB. The only thing I have in my main method is HyperGraph HG = new HyperGraph(dbLocation);. This code compiles. But get following runtime error:
run:
checkpoint kbytes:0
checkpoint minutes:0
java.lang.IllegalStateException: There is 1 existing transaction opened against the Environment.
Aborting open transactions ...
aborting <Transaction id="28">
at com.sleepycat.je.Environment.close(Environment.java:383)
at org.hypergraphdb.storage.bje.BJEStorageImplementation.shutdown(BJEStorageImplementation.java:178)
at org.hypergraphdb.HGStore.close(HGStore.java:355)
at org.hypergraphdb.HyperGraph.open(HyperGraph.java:392)
at org.hypergraphdb.HyperGraph.open(HyperGraph.java:213)
at org.hypergraphdb.HyperGraph.<init>(HyperGraph.java:200)
at hgdbtest.HgdbTest.main(HgdbTest.java:16)
Exception in thread "main" org.hypergraphdb.HGException: java.lang.NoSuchMethodError: org.hypergraphdb.storage.bje.LinkBinding.objectToEntry(Ljava/lang/Object;Lcom/sleepycat/je/DatabaseEntry;)V
at org.hypergraphdb.HyperGraph.open(HyperGraph.java:395)
at org.hypergraphdb.HyperGraph.open(HyperGraph.java:213)
at org.hypergraphdb.HyperGraph.<init>(HyperGraph.java:200)
at hgdbtest.HgdbTest.main(HgdbTest.java:16)
Caused by: java.lang.NoSuchMethodError: org.hypergraphdb.storage.bje.LinkBinding.objectToEntry(Ljava/lang/Object;Lcom/sleepycat/je/DatabaseEntry;)V
at org.hypergraphdb.storage.bje.BJEStorageImplementation.store(BJEStorageImplementation.java:234)
at org.hypergraphdb.HGStore.store(HGStore.java:119)
at org.hypergraphdb.HGTypeSystem.addPrimitiveTypeToStore(HGTypeSystem.java:185)
at org.hypergraphdb.HGTypeSystem.bootstrap(HGTypeSystem.java:234)
at org.hypergraphdb.HyperGraph.open(HyperGraph.java:355)
... 3 more
Java Result: 1
BUILD SUCCESSFUL (total time: 4 seconds)
I guess it's caused by the native API of the BerkeleyDB.
According to the tutorial, in project options I supply the -Djava.library.path=$HGDB_ROOT/lib/native/$PLATFORM argument on Run card as a VM Option. Instead of the system variables I use full-path to the libraries.
My OS in Windows7. I'm not sure about using slashes or backslashes or double-backslashes as a path-separator.?
So a simply question is: how have I to set up the IDE for using the HypergraphDB?
Thank you for advices!
Judging from the stack trace, you are using the latest version of HyperGraphDB. In that version, the native API is not used. Rather, it's Java only libraries. You have to include the BerkeleyDB Java Edition 5.0.34 jar in your runtime classpath. You can get it either from the Oracle http://www.oracle.com/technetwork/products/berkeleydb/downloads/index.html or from the HyperGraphDB Maven repository: http://hypergraphdb.org/maven/org/hypergraphdb/hgbdbje/1.2/hgbdbje-1.2.jar
I had the same issue. I fixed it (by accident) by fixing the order of the libraries on which you're HyperGraphDB application relies on. The library je-[version].jar has to be ABOVE (and hence to be referenced before) db-[version].jar
I'm trying to call a java program from python using command line. The code is as follows:
subprocess.check_output(["java", "pitt.search.semanticvectors.CompareTerms", "-queryvectorfile","termvectors.bin","term1","term2"])
I get the following error:
Error: Could not find or load main class pitt.search.semanticvectors.CompareTerms
This happens when I run the program from PyDev (version 2.5 in Eclipse 3.7.2). However, if I run the same code from the terminal, it works and I get the result I want.
I'm almost sure that the problem is related with some configuration of PyDev and how it handles the java CLASSPATH, which is:
/Users/feralvam/Programas/semanticvectors-3.4/semanticvectors-3.4.jar:/Users/feralvam/Programas/lucene-3.5.0/lucene-core-3.5.0.jar:/Users/feralvam/Programas/lucene-3.5.0/contrib/demo/lucene-demo-3.5.0.jar:
The class "pitt.search.semanticvectors.CompareTerms" is in "semanticvectors-3.4.jar".
Any help you could give me would be really appreciated.
Thanks!
The solution proposed by #eis worked. Now, the command is:
subprocess.check_output(["java", "-classpath", "/Users/feralvam/Programas/semanticvectors-3.4/semanticvectors-3.4.jar:/Users/feralvam/Programas/lucene-3.5.0/lucene-core-3.5.0.jar:/Users/feralvam/Programas/lucene-3.5.0/contrib/demo/lucene-demo-3.5.0.jar:", "pitt.search.semanticvectors.CompareTerms", "-queryvectorfile","/Users/feralvam/termvectors.bin","term1","term2"])