Writing cplex command file -> error thrown about carnival HOT 23 CLOSED

Thanks for reporting, I will try to fix it ASAP. In the meantime, I suggest you to use the previous release.
https://github.com/saezlab/CARNIVAL/releases/tag/v1.3

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Thanks all for commenting and reporting. The bug was fixed. If it is still persistent in your setup, please, share the code snippet with tiny data sample to reproduce. Thanks!

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@CosimoCristella Good point, thanks!

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Hi @laylagerami, unfortunately not. Honestly, I haven't looked into details at it. I'm waiting for devs to react and in the meantime using v1.3, as they suggested

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I am having the same problem. Works fine when using cbc solver, issue is only with cplex!

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Hey @ulrmu
Can you share your platform and R version? Also, can you run it with toy example?

Thanks

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Hi @ivanovaos ,
Thanks for looking into this.

I can run the toy example without any problem.

In case it's still relevant, this is my R version and platform:
R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS

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I tried v.1.3.0 but get the following error:
Solving LP problem...
sh: 1: /path/to/solver/: Permission denied

I also tried the latest update, but the same error as reported before is thrown.

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@ulrmu which solver do you use and what path did you provide for it? can you please post a code snippet?

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Hi,
I was experiencing the same issue in v.2.2.0 ( v.1.3.0 works fine) and manged to solve by specifying the full path for cplex solver and working/out directories, eg.:
cplexOpt = defaultCplexCarnivalOptions()
cplexOpt$solverPath = "/opt/ibm/ILOG/CPLEX_Studio1210/cplex/bin/x86-64_linux/cplex"
cplexOpt$outputFolder = '/path/to/outDir/'
cplexOpt$dirName = '/path/to/outDir/'
cplexOpt$workdir = '/path/to/workDir/'
However, I'm still having the issue described in #65

Hope it helps.

sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS

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@ivanovaos
I use the cplex solver with this command:
carnival_result = runCARNIVAL( #inputObj= iniciators,
measObj = tfList$t,
netObj = sif,
#weightObj = progenylist$score,
solverPath = "/path/to/solver/",
solver = "cplex",
timelimit=7200,
mipGAP=0,
poolrelGAP=0,
)

Please let me know if this is canonical or not.

@CosimoCristella
Thank you for your suggestion! Maybe it's obvious, but how should the cplex options be passed?

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@ulrmu
Sorry, I forgot to mention that the options were passed to runInverseCarnival:
runInverseCarnival(measurements = meas,
priorKnowledgeNetwork = sif,
weights = weights,
carnivalOptions = cplexOpt
)

Cheers!

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@CosimoCristella
Thank you! I get a weird error from the measurements input which I need to investigate further.
Did you manage to use the runCARNIVAL function?

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I think you get the input error when you try to pass a data.frame (as it was in v.1.3.0) rather than a named vector for arguments 'measurements' and 'weights'.
I don't think this workaround will work for runCARNIVAL as there's no argument in the function to specify the working directory.

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@CosimoCristella , that explains it, thank you!! I could finally run runInverseCarnival, running into the following error:

cplexOpt = defaultCplexCarnivalOptions()
cplexOpt$solverPath = "/path/to/solver/"
cplexOpt$outputFolder = '/path/to/dir/'
cplexOpt$dirName = '/path/to/dir/'
cplexOpt$workdir = '/path/to/dir/'

runInverseCarnival(measurements = meas_vec,
priorKnowledgeNetwork = sif,
#weights = weights,
carnivalOptions = cplexOpt
)

sh: 1: /path/to/solver/: Permission denied
Saving results...
Error in file(file, "rt") : cannot open the connection

You said you managed to get the above function to work using CARNIVAL_2.2.0, right? Did you encounter this problem as well?

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Hi Ulrmu,

I just re-tested runInverseCarnival() with the workaround I suggested above and can confirm it works for CARNIVAL v2.2.0 on my machine.
Are providing the full/correct path for the solver? Just follow the example I suggested above since the cplex solver should be located in your opt folder. Be sure to include the solver name 'cplex' and remove the '/' at the end of the path.

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@CosimoCristella Thank you, I fixed that and could run runInverseCarnival() \o/

However, using the newest CARNIVAL version, the problems with runCARNIVAL remain.

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@ulrmu Glad it helped! I think this new version still requires few adjustments and we should give devs some time to implement them.
In the meantime, if you have targets/inputs, why not going for runVanillaCarnival()?

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HI @CosimoCristella, did you manage to solve the issue in #65?

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Also having the same issue.
Error in file(file, ifelse(append, "a", "w")) :
cannot open the connection.
In file(file, ifelse(append, "a", "w")) :
cannot open file '/cplexCommand_t18_00_47d12_07_2021n26.txt': Read-only file system.
Tried changing the permissions on the files and directories and still come up with the same error.
I tried using CBC solver, but get no results from Carnival when using the transcript tutorial data (All the same code, just tried to use CBC).

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Thank you, @ivanovaos, for fixing the bug! It now works in my setup!

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Hi everyone, I got the same error in the 2.4.0 version.

R version 4.1.1 (2021-08-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

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