Comments (11)
enio23
commented on July 18, 2024
Hi Ansuman,
You having issues running the examples on the transcriptutorial or is it your own data? After installing CPLEX did you specify correctly the path where you have the cplex executable stored or you used the path which was set on the example? Can you please show us how you are using the runCARNIVAL function?
The memory issues with lpSolve are unfortunately to be expected since it relies on a matrix formulation of the ILP problems which can get quite large in size for real-case applications of CARNIVAL. We have only implemented lpSolve to run small test examples.
Cheers,
Enio
from carnival.
asumann
commented on July 18, 2024
Hi Enio,
I couldn't successfully install CPLEX. It looks like a common problem for OSx Catalina users. They suggest installing light mode but that is not available online to download right now..
I am testing the tutorial and for this I use the data given in the tutorial. Here is the CARNIVAL part:
> carnival_result = CARNIVAL::runCARNIVAL(inputObj= iniciators,
+ measObj = tfList$t,
+ netObj = sif,
+ weightObj = progenylist$score,
+ solverPath = "/var/folders/5h/nb97vjfj5w13g__ksqy9z0b40000gn/T/RtmpzOFfha/downloaded_packages/lpSolve/R/lpSolve",
+ solver = "lpSolve")
In lpSolve case, I give my path. But, it gives memory error so I assume path is not the problem. I installed CBC and got the same error I got from lpSolve. The problem is I cannot identify the error I got..
I tried online suggestions to successfully install CPLEX but it didn't work out. Here is the error I got after installing IBM CPLEX, maybe you can give some advice so that I can run CARNIVAL:
------Executable: cd "/Users/asu"; "/var/folders/5h/nb97vjfj5w13g__ksqy9z0b40000gn/T//IA759858543/IA759858543/jre/Contents/Home/jre/bin/java" -Xms16m -Xmx48m -cp "/Users/asu/cplex_studio2010-osx.app/Contents/Resources/Java/Execute.zip:/Users/asu/cplex_studio2010-osx.app/Contents/Resources/Java/IAClasses.zip:/Users/asu/cplex_studio2010-osx.app/Contents/Resources/Java/installscript.zip:/Users/asu/cplex_studio2010-osx.app/Contents/Resources/Java:/Users/asu/cplex_studio2010-osx.app/Contents/Resources/Java/linking.zip" -Dfile.encoding=UTF-8 -Djava.library.path=.:/Library/Java/Extensions:/Network/Library/Java/Extensions:/System/Library/Java/Extensions:/usr/lib/java:"/Users/asu":"/var/folders/5h/nb97vjfj5w13g__ksqy9z0b40000gn/T/IA759858543/IA759858543/jre/Contents/Home/jre/lib":"/Users/asu/cplex_studio2010-osx.app/Contents/Resources/Java":"/Users/asu/cplex_studio2010-osx.app/Contents/MacOS":"/Users/asu/cplex_studio2010-osx.app/Contents/Resources" -Xdock:name="CPLEX Optimization Studio 20.1" -Xdock:icon="/Users/asu/cplex_studio2010-osx.app/Contents/Resources/SelfExtractor.icns" com.zerog.lax.LAX "/var/folders/5h/nb97vjfj5w13g__ksqy9z0b40000gn/T/app.properties"-------
Invocation of this Java Application has caused an InvocationTargetException. This application will now exit. (LAX)
Stack Trace:
java.awt.IllegalComponentStateException: The frame is decorated
at java.awt.Frame.setBackground(Frame.java:986)
at Flexeraat7.setBackground(Unknown Source)
at com.zerog.ia.installer.AAMgr.initAAMgr(Unknown Source)
at com.zerog.ia.installer.LifeCycleManager.a5(Unknown Source)
at com.zerog.ia.installer.LifeCycleManager.executeApplication(Unknown Source)
at com.zerog.ia.installer.Main.main(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at com.zerog.lax.LAX.launch(Unknown Source)
at com.zerog.lax.LAX.main(Unknown Source)
This Application has Unexpectedly Quit: Invocation of this Java Application has caused an InvocationTargetException. This application will now exit. (LAX)
-Asuman
from carnival.
enio23
commented on July 18, 2024
Yes, it is best if you get CPLEx which you can get with no-cost here if you plan using it for academic purposes. You can just download it and find the cplex executable file and then store it anywhere on the computer.
For lpSolve it is not needed to set a path, however again lpSolve will not work for large/real case-studies.
Cheers,
Enio
from carnival.
asumann
commented on July 18, 2024
How about this error:
Error: vector memory exhausted (limit reached?)
In addition: Warning messages:
1: In controlNodeIdentifiers(netObj = netObj) :
Your network contains identifiers with '-' symbol and they will
be replaced with '_'
2: In controlNodeIdentifiers(netObj = netObj) :
Your network contains identifiers with '/' symbol and they will
be replaced with '_'
I am now having this with CPLEX. How can I solve it?
All the best,
Asuman
from carnival.
enio23
commented on July 18, 2024
I think you are still using lpSolve.
Did you set solver='cplex' and solverPath to the path where the cplex is?
from carnival.
asumann
commented on July 18, 2024
Yes, I did that.
from carnival.
enio23
commented on July 18, 2024
Can you please send me the part of the script where you are using the runCARNIVAL function? :) We usually did not face memory issues when using CPLEX.
from carnival.
asumann
commented on July 18, 2024
Just to make sure i also removed lpSolve package from library.
carnival_result = CARNIVAL::runCARNIVAL(inputObj= iniciators,
measObj = tfList$t,
netObj = sif,
weightObj = progenylist$score)
solverPath = "/Users/asu/cplex_studio2010-osx.app/Contents/MacOS/cplex_studio2010-osx",
solver = "cplex")
#timelimit=7200,
#mipGAP=0,
#poolrelGAP=0 )
Many thanks Enio!!
from carnival.
enio23
commented on July 18, 2024
Hmm ok. Not sure if the path you are setting does not actually point to the executable file. Does the cplex_studio2010-osx file you are pointing looks something like this. If yes, maybe can you also store this file somewhere else (i.e. Desktop, Documents, ..) and update the solverPath accordingly because not sure if using a dot character on the path string might mess up something when we read the solverPath parameter.
from carnival.
enio23
commented on July 18, 2024
Maybe I figured the possible error. Try running:
carnival_result = CARNIVAL::runCARNIVAL(inputObj= iniciators,
measObj = tfList$t,
netObj = sif,
weightObj = progenylist$score,
solverPath = "/Users/asu/cplex_studio2010-osx.app/Contents/MacOS/cplex_studio2010-osx",
solver = "cplex",
timelimit=7200,
mipGAP=0,
poolrelGAP=0 )from carnival.
asumann
commented on July 18, 2024
Hi Enio,
It is working now!! I want to explain how so it may help someone else save their time.
First of all, IBM CPLEX was not successfully installed to my OSx Catalina, thus runCARNIVAL was giving errors. Installation problem was solved after I disabled Dark Mode on my Mac. It was somehow interfering with the CPLEX installation. Unfortunately, I do not know about the bottom reasons.
After installing CPLEX successfully, RStudio session was aborted every time I run runCARNIVAL. I run the code in Terminal R console. Again interestingly, I had solverPath issue even though cplex exe path was correct as in:
> file.exists("/Applications/CPLEX_Studio201/cplex/bin/x86-64_osx/cplex")
[1] TRUE
I moved the .exe to another directory:
> file.exists("/Users/asu/cplex")
[1] TRUE
Finally, it run smoothly though it was computationally heavy. Next time, I will try to run on uni's HPC.
All the best,
Asuman
from carnival.
Related Issues (20)
- Feature Request: Omnipath network from original paper HOT 2
- Very different results with latest CARNIVAL release HOT 5
- Wrong column name inside the measurementsDf? HOT 1
- cbc error : 'data' must be of a vector type, was 'NULL' despite solution found HOT 1
- Reported 0 for perturbations activity HOT 1
- No DOT figure HOT 1
- Gurobi needs documentation
- How to use CARNIVAL to fit multiple conditions data HOT 2
- Some issues HOT 2
- Failing tests because local files were used HOT 1
- runCARNIVAL HOT 1
- Error in file(file, "rt"): cannot open the connection HOT 2
- progenyMembers.RData HOT 2
- Description about the output HOT 4
- error running Carnival with cbc solver HOT 1
- Carnival usage error HOT 2
- Transcription factors (TFs) absent from final carnival result HOT 12
- [BUG] Your bug or feature request HOT 3
- Using custom network for transcription factor input HOT 11
- General Recommendations for preprocessing RNA-Seq data HOT 2
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from carnival.