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thierrygosselin / assigner

Population assignment analysis using R
http://thierrygosselin.github.io/assigner
GNU General Public License v3.0
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Error in checkForRemoteErrors(val) : 3 nodes produced errors #15

Closed gpasi closed 5 years ago

gpasi commented 5 years ago

Describe the bug When I tried to work through the first example on http://thierrygosselin.github.io/assigner/articles/get_started.html (Data 1: high structure), I always got the following error messages (see below).

To Reproduce Include the steps to reproduce the behavior:

Computation time, overall: 577 sec ########################## assignment_ngs completed ############################

warnings() Warnmeldungen: 1: In serialize(data, node$con) : 'package:stats' may not be available when loading 2: In serialize(data, node$con) : 'package:stats' may not be available when loading 3: In serialize(data, node$con) : 'package:stats' may not be available when loading 4: In serialize(data, node$con) : 'package:stats' may not be available when loading 5: In serialize(data, node$con) : 'package:stats' may not be available when loading 6: In serialize(data, node$con) : 'package:stats' may not be available when loading 7: In serialize(data, node$con) : 'package:stats' may not be available when loading 8: In serialize(data, node$con) : 'package:stats' may not be available when loading 9: In serialize(data, node$con) : 'package:stats' may not be available when loading 10: In serialize(data, node$con) : 'package:stats' may not be available when loading 11: In serialize(data, node$con) : 'package:stats' may not be available when loading 12: In serialize(data, node$con) : 'package:stats' may not be available when loading 13: In serialize(data, node$con) : 'package:stats' may not be available when loading 14: In serialize(data, node$con) : 'package:stats' may not be available when loading 15: In serialize(data, node$con) : 'package:stats' may not be available when loading 16: In serialize(data, node$con) : 'package:stats' may not be available when loading 17: In serialize(data, node$con) : 'package:stats' may not be available when loading 18: In serialize(data, node$con) : 'package:stats' may not be available when loading (truncated here)

[1] C:/Users/gp/Documents/R/win-library/3.6 [2] C:/Program Files/R/R-3.6.1/library

Screenshots grafik

thierrygosselin commented 5 years ago

I'm not able to reproduce the error on my Mac. It's definitely related to your PC and the parallelization process. What do you get when this is entered:

parallel::detectCores()
thierrygosselin commented 5 years ago

Also, try this to confirm my hypothesis above:

test1 <- assigner::assignment_ngs(
  data = data,
  assignment.analysis = "gsi_sim",
  markers.sampling = "ranked", 
  thl = 0.2,
  iteration.method = 5,
  parallel.core = 1
)
gpasi commented 5 years ago

Thanks for the quick reply.

Here is the output:

parallel::detectCores() [1] 4

Shall I still run the other code you sent?

Von: Thierry Gosselin [mailto:notifications@github.com] Gesendet: Donnerstag, 8. August 2019 17:43 An: thierrygosselin/assigner Cc: Pasinelli Gilberto; Author Betreff: Re: [thierrygosselin/assigner] Error in checkForRemoteErrors(val) : 3 nodes produced errors (#15)

I'm not able to reproduce the error on my Mac. It's definitely related to your PC and the parallelization process. What do you get when this is entered:

parallel::detectCores()

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/thierrygosselin/assigner/issues/15?email_source=notifications&email_token=AM3JREC2FIKCXUMRJR6QZSLQDQ5J3A5CNFSM4IKL3P4KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD34BDII#issuecomment-519573921, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AM3JREGAXHW7XHIML2GS2I3QDQ5J3ANCNFSM4IKL3P4A.

thierrygosselin commented 5 years ago

yes, do try this:

test1 <- assigner::assignment_ngs(
  data = data,
  assignment.analysis = "gsi_sim",
  markers.sampling = "ranked", 
  thl = 0.2,
  iteration.method = 5,
  parallel.core = 1
)
gpasi commented 5 years ago

I’ll try on Monday. Need to catch a train and are off tomorrow…

Thanks for your help so far! Gilberto

Von: Thierry Gosselin [mailto:notifications@github.com] Gesendet: Donnerstag, 8. August 2019 17:49 An: thierrygosselin/assigner Cc: Pasinelli Gilberto; Author Betreff: Re: [thierrygosselin/assigner] Error in checkForRemoteErrors(val) : 3 nodes produced errors (#15)

yes, do try this:

test1 <- assigner::assignment_ngs(

data = data,

assignment.analysis = "gsi_sim",

markers.sampling = "ranked",

thl = 0.2,

iteration.method = 5,

parallel.core = 1

)

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/thierrygosselin/assigner/issues/15?email_source=notifications&email_token=AM3JREAJRFS5TKZGDND2EXDQDQ6ARA5CNFSM4IKL3P4KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD34BXDI#issuecomment-519576461, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AM3JREHL3ATEDJYI6OLKV2TQDQ6ARANCNFSM4IKL3P4A.

thierrygosselin commented 5 years ago

Ok my guess is that you have a problem with your core + R.

open the issue if still an error

gpasi commented 5 years ago

Hi again

The problem does not seem to be resolved yet:

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[Workspace loaded from ~/.RData]

rm(list = ls())

library(assigner) Registered S3 method overwritten by 'spdep': method from plot.mst ape

data <- data_assigner_sim_01

test1 <- assigner::assignment_ngs(

  • data = data,
  • assignment.analysis = "gsi_sim",
  • markers.sampling = "ranked",
  • thl = 0.2,
  • iteration.method = 5,
  • parallel.core = 1
  • ) ################################################################################ ########################## assigner::assignment_ngs ############################ ################################################################################ Execution date/time: 20190812@1304 Assignment analysis with gsi_sim Folder created: assignment_analysis_method_ranked_20190812@1304 Calibrating REF/ALT alleles... Subsampling: not selected Conducting Assignment analysis using Training, Holdout, Leave-one-out Using training samples to rank markers based on Fst Holdout samples saved in your folder Starting parallel computations, for progress monitor activity in folder... Error in checkForRemoteErrors(val) : one node produced an error: 'assignment_data_iteration_1_markers_497.output.txt' does not exist in current working directory ('C:/Users/gp/Documents/assignment_analysis_method_ranked_20190812@1304/assignment_1'). In addition: There were 18 warnings (use warnings() to see them)

Computation time, overall: 110 sec ########################## assignment_ngs completed ############################

names(test1) Error: object 'test1' not found

Von: Thierry Gosselin [mailto:notifications@github.com] Gesendet: Donnerstag, 8. August 2019 18:13 An: thierrygosselin/assigner Cc: Pasinelli Gilberto; Author Betreff: Re: [thierrygosselin/assigner] Error in checkForRemoteErrors(val) : 3 nodes produced errors (#15)

Ok my guess is that you have a problem with your core + R.

open the issue if still an error

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/thierrygosselin/assigner/issues/15?email_source=notifications&email_token=AM3JRED6IQYUKLWPXPK3NO3QDRAYPA5CNFSM4IKL3P4KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD34D75Y#issuecomment-519585783, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AM3JREEY6HWA2LE3SIPKFE3QDRAYPANCNFSM4IKL3P4A.