Optimizing the interactions in the network produced an error

[adesalegn]

Hi Deeenes,

I was using your package for my study and all was cool but the code below was giving me an error. If you have some time I would really appreciate it your answer

optimization_results = lapply(1,mlrmbo_optimization, 
                              obj_fun = obj_fun_multi_topology_correction, 
         niter = 8, ncores = 6, nstart = 160, 
         additional_arguments = additional_arguments_topology_correction)

the error was here

Computing y column(s) for design. Not provided.
Mapping in parallel: mode = multicore; level = mlrMBO.feval; cpus = 12; elements = 160.
Error in stopWithJobErrorMessages(inds, vcapply(result.list[inds], as.character)) :
Errors occurred in 160 slave jobs, displaying at most 10 of them:

00001: Error in igraph::page_rank(G, algo = c("prpack"), vids = igraph::V(G), :
At prpack.cpp:55 : the sum of the elements in the reset vector must not be zero, Invalid value

00002: Error in igraph::page_rank(G, algo = c("prpack"), vids = igraph::V(G), :
At prpack.cpp:55 : the sum of the elements in the reset vector must not be zero, Invalid value

00003: Error in igraph::page_rank(G, algo = c("prpack"), vids = igraph::V(G), :
At prpack.cpp:55 : the sum of the elements in the reset vector must not be zero, Invalid value

00004: Error in igraph::page_rank(G, algo = c("prpack"), vids = igraph::V(G), :
At prpack.cpp:55 : the sum of the elements in the reset vector must not be zero, Invalid value

00005: Error in igraph::page_rank(G, algo = c("prpack"), vids = igraph::V(G), :
At prpack.cpp:55 : the sum of the elements in the reset vector must not be zero, Invalid value

00006: Error in igraph::page_rank(G, algo = c("prpack"), vids = igraph::V(G), :
At prpack.cpp:55 : the sum of the elements in the reset vector must not be zero, Invalid value

00007: Error in igraph::page_rank(G, algo = c("prpack"), vids = igraph::V(G), :
At prpack.cpp:55 : the sum of the elements in the reset vector must not be zero, Invalid value

00008: Error in igraph::page_rank(G, algo = c("prpack"), vids = igraph::V(G), :
At prpack.cpp:55 : the sum of the elements in the reset vector must not be zero, Invalid value

00009: Error in igraph::page_rank(G, algo = c("prpack"), vids = igraph::V(G), :
At prpack.cpp:55 : the sum of the elements in the reset vector must not be zero, Invalid value

00010: Error in igraph::page_rank(G, algo = c("prpack"), vids = igraph::V(G), :
At prpack.cpp:55 : the sum of the elements in the reset vector must not be zero, Invalid value](url)

Tracing back where it comes

traceback()
12: stop(obj)
11: stopf("Errors occurred in %i slave jobs, displaying at most 10 of them:\n\n%s\n%s",
n, collapse(msgs, sep = "\n"), extra.msg)
10: stopWithJobErrorMessages(inds, vcapply(result.list[inds], as.character))
9: checkResultsAndStopWithErrorsMessages(res)
8: parallelMap(wrapFun, xs.trafo, level = "mlrMBO.feval", impute.error = if (is.null(imputeY)) NULL else identity)
7: evalTargetFun.OptState(opt.state, xs, extras)
6: evalMBODesign.OptState(opt.state)
5: mboTemplate.OptProblem(opt.problem)
4: mboTemplate(opt.problem)
3: mbo(obj_fun, design = design, learner = surr.rf, control = ctrl,
show.info = TRUE, more.args = additional_arguments)
2: FUN(X[[i]], ...)
1: lapply(1, mlrmbo_optimization, obj_fun = obj_fun_multi_topology_correction,

Thank you!

[deeenes]

Hi @adesalegn,

Your top level call here is mlrmbo_optimization, which is a function from nichenetr. Have you tried to ask them? https://github.com/saeyslab/nichenetr/issues The error is deep in the nichenet code, which I have little knowledge about, in OmnipathR we only have a thin wrapper around it.

In general, I would check if the igraph, mlrMBO, mlr, parallelMap and nichenetr packages are all the latest versions. If you've run your code successfully before, I would check for recent updates, e.g. new igraph came out 2 months ago. Would be also interesting if you experience the error with any input or only for certain networks? I think in NicheNet errors are often related to particular network topologies, especially disconnected components.

Best,

Denes

[adesalegn]

Hi deeenes,

Thank you for the reply. However, is there any possibility to download the following files Results/Optimization_results.rds, Results/weighted_networksNonSourceWeights.rds, Results/ligand_target_matrixNoweights.rds, Results/ligand_target_matrixWithweights.rds, Results/weighted_networksWithSourceWeights.rds

Thank you! Best, AD

On Wed, Dec 22, 2021 at 12:03 PM deeenes @.***> wrote:

Hi @adesalegn https://github.com/adesalegn,

Your top level call here is mlrmbo_optimization, which is a function from nichenetr. Have you tried to ask them? https://github.com/saeyslab/nichenetr/issues The error is deep in the nichenet code, which I have little knowledge about, in OmnipathR we only have a thin wrapper around it.

In general, I would check if the igraph, mlrMBO, mlr, parallelMap and nichenetr packages are all the latest versions. If you've run your code successfully before, I would check for recent updates, e.g. new igraph came out 2 months ago. Would be also interesting if you experience the error with any input or only for certain networks? I think in NicheNet errors are often related to particular network topologies, especially disconnected components.

Best,

Denes

— Reply to this email directly, view it on GitHub https://github.com/saezlab/OmnipathR/issues/39#issuecomment-999485624, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANYNSRF56KIT2HSOJTYJZ5TUSGWA3ANCNFSM5KRNDSIA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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[deeenes]

Hi,

Is this about the case study in last years paper? This is the repository of the case study, where you can find the necessary information, or ask Alberto.

Best,

Denes

[alberto-valdeolivas]

Hello @adesalegn,

Sorry, I missed this message. In case you are still interested in these files, could you send me your email? I can deposit them in some location and share them with you. Some of the files are too big for github.

Best, Alberto.

[adesalegn]

Sure, here it is. @.*** Thanks!

On Mon, May 2, 2022, 10:24 Alberto Valdeolivas @.***> wrote:

Hello @adesalegn https://github.com/adesalegn,

Sorry, I missed this message. In case you are still interested in these files, could you send me your email? I can deposit them in some location and share them with you. Some of the files are too big for github.

Best, Alberto.

— Reply to this email directly, view it on GitHub https://github.com/saezlab/OmnipathR/issues/39#issuecomment-1114613621, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANYNSRCKYXHEZBNP2NFSWZ3VH6GLNANCNFSM5KRNDSIA . You are receiving this because you were mentioned.Message ID: @.***>

[alberto-valdeolivas]

Hello,

I generated a shareable link containing the files. Let me know if it works

https://1drv.ms/u/s!AsEej4TsWiVfgeAnQyVo40qn0Tcn8g?e=p94Ofb

Alberto