Closed gpasi closed 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()
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
)
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()
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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
)
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.
Ok my guess is that you have a problem with your core + R.
open the issue if still an error
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.
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:
the exact command (function, arguments, values) used: test1 <- assigner::assignment_ngs( data = data, assignment.analysis = "gsi_sim", markers.sampling = "ranked", thl = 0.2, iteration.method = 5 )
the complete error message you're getting Error in checkForRemoteErrors(val) : 3 nodes produced errors; first error: 'assignment_data_iteration_1_markers_497.output.txt' does not exist in current working directory ('C:/Users/gp/Documents/assignment_analysis_method_ranked_20190808@1453/assignment_1'). In addition: There were 18 warnings (use warnings() to see them)
Computation time, overall: 577 sec ########################## assignment_ngs completed ############################
the output of
devtools::session_info()
Session info -------------------------------------------------------------------------------------------------------------------------------- setting value
version R version 3.6.1 (2019-07-05) os Windows 7 x64 SP 1
system x86_64, mingw32
ui RStudio
language (EN)
collate German_Switzerland.1252
ctype German_Switzerland.1252
tz Europe/Berlin
date 2019-08-08
Packages ------------------------------------------------------------------------------------------------------------------------------------ package version date lib source
ade4 1.7-13 2018-08-31 [1] CRAN (R 3.6.1)
adegenet 2.1.1 2018-02-02 [1] CRAN (R 3.6.1)
ape 5.3 2019-03-17 [1] CRAN (R 3.6.1)
assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.1)
assigner 0.5.6 2019-08-08 [1] Github (thierrygosselin/assigner@b941111) backports 1.1.4 2019-04-10 [1] CRAN (R 3.6.0)
boot 1.3-22 2019-04-02 [2] CRAN (R 3.6.1)
callr 3.3.1 2019-07-18 [1] CRAN (R 3.6.1)
class 7.3-15 2019-01-01 [2] CRAN (R 3.6.1)
classInt 0.3-3 2019-04-26 [1] CRAN (R 3.6.1)
cli 1.1.0 2019-03-19 [1] CRAN (R 3.6.1)
cluster 2.1.0 2019-06-19 [2] CRAN (R 3.6.1)
coda 0.19-3 2019-07-05 [1] CRAN (R 3.6.1)
colorspace 1.4-1 2019-03-18 [1] CRAN (R 3.6.1)
crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.1)
curl 4.0 2019-07-22 [1] CRAN (R 3.6.1)
DBI 1.0.0 2018-05-02 [1] CRAN (R 3.6.1)
deldir 0.1-23 2019-07-31 [1] CRAN (R 3.6.1)
desc 1.2.0 2018-05-01 [1] CRAN (R 3.6.1)
devtools 2.1.0 2019-07-06 [1] CRAN (R 3.6.1)
digest 0.6.20 2019-07-04 [1] CRAN (R 3.6.1)
dplyr 0.8.3 2019-07-04 [1] CRAN (R 3.6.1)
e1071 1.7-2 2019-06-05 [1] CRAN (R 3.6.1)
expm 0.999-4 2019-03-21 [1] CRAN (R 3.6.1)
fs 1.3.1 2019-05-06 [1] CRAN (R 3.6.1)
gdata 2.18.0 2017-06-06 [1] CRAN (R 3.6.0)
ggplot2 3.2.0 2019-06-16 [1] CRAN (R 3.6.0)
glue 1.3.1 2019-03-12 [1] CRAN (R 3.6.1)
gmodels 2.18.1 2018-06-25 [1] CRAN (R 3.6.1)
gtable 0.3.0 2019-03-25 [1] CRAN (R 3.6.1)
gtools 3.8.1 2018-06-26 [1] CRAN (R 3.6.0)
hms 0.5.0 2019-07-09 [1] CRAN (R 3.6.1)
htmltools 0.3.6 2017-04-28 [1] CRAN (R 3.6.1)
httpuv 1.5.1 2019-04-05 [1] CRAN (R 3.6.1)
igraph 1.2.4.1 2019-04-22 [1] CRAN (R 3.6.1)
KernSmooth 2.23-15 2015-06-29 [2] CRAN (R 3.6.1)
later 0.8.0 2019-02-11 [1] CRAN (R 3.6.1)
lattice 0.20-38 2018-11-04 [2] CRAN (R 3.6.1)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 3.6.1)
LearnBayes 2.15.1 2018-03-18 [1] CRAN (R 3.6.0)
magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.1)
MASS 7.3-51.4 2019-03-31 [2] CRAN (R 3.6.1)
Matrix 1.2-17 2019-03-22 [2] CRAN (R 3.6.1)
memoise 1.1.0 2017-04-21 [1] CRAN (R 3.6.1)
mgcv 1.8-28 2019-03-21 [2] CRAN (R 3.6.1)
mime 0.7 2019-06-11 [1] CRAN (R 3.6.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 3.6.1)
nlme 3.1-140 2019-05-12 [2] CRAN (R 3.6.1)
pbmcapply 1.5.0 2019-07-10 [1] CRAN (R 3.6.1)
permute 0.9-5 2019-03-12 [1] CRAN (R 3.6.1)
pillar 1.4.2 2019-06-29 [1] CRAN (R 3.6.1)
pkgbuild 1.0.4 2019-08-05 [1] CRAN (R 3.6.1)
pkgconfig 2.0.2 2018-08-16 [1] CRAN (R 3.6.1)
pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.6.1)
plyr 1.8.4 2016-06-08 [1] CRAN (R 3.6.1)
prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.6.1)
processx 3.4.1 2019-07-18 [1] CRAN (R 3.6.1)
promises 1.0.1 2018-04-13 [1] CRAN (R 3.6.1)
ps 1.3.0 2018-12-21 [1] CRAN (R 3.6.1)
purrr 0.3.2 2019-03-15 [1] CRAN (R 3.6.1)
R6 2.4.0 2019-02-14 [1] CRAN (R 3.6.1)
radiator 1.1.1 2019-08-08 [1] Github (thierrygosselin/radiator@d79b062) Rcpp 1.0.2 2019-07-25 [1] CRAN (R 3.6.1)
readr 1.3.1 2018-12-21 [1] CRAN (R 3.6.1)
remotes 2.1.0 2019-06-24 [1] CRAN (R 3.6.1)
reshape2 1.4.3 2017-12-11 [1] CRAN (R 3.6.1)
rlang 0.4.0 2019-06-25 [1] CRAN (R 3.6.1)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.6.1)
rstudioapi 0.10 2019-03-19 [1] CRAN (R 3.6.1)
scales 1.0.0 2018-08-09 [1] CRAN (R 3.6.1)
seqinr 3.4-5 2017-08-01 [1] CRAN (R 3.6.1)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.6.1)
sf 0.7-7 2019-07-24 [1] CRAN (R 3.6.1)
shiny 1.3.2 2019-04-22 [1] CRAN (R 3.6.1)
sp 1.3-1 2018-06-05 [1] CRAN (R 3.6.1)
spData 0.3.0 2019-01-07 [1] CRAN (R 3.6.1)
spdep 1.1-2 2019-04-05 [1] CRAN (R 3.6.1)
stringi 1.4.3 2019-03-12 [1] CRAN (R 3.6.0)
stringr 1.4.0 2019-02-10 [1] CRAN (R 3.6.1)
testthat 2.2.1 2019-07-25 [1] CRAN (R 3.6.1)
tibble 2.1.3 2019-06-06 [1] CRAN (R 3.6.1)
tidyselect 0.2.5 2018-10-11 [1] CRAN (R 3.6.1)
units 0.6-3 2019-05-03 [1] CRAN (R 3.6.1)
usethis 1.5.1 2019-07-04 [1] CRAN (R 3.6.1)
vctrs 0.2.0 2019-07-05 [1] CRAN (R 3.6.1)
vegan 2.5-5 2019-05-12 [1] CRAN (R 3.6.1)
withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.1)
xtable 1.8-4 2019-04-21 [1] CRAN (R 3.6.1)
zeallot 0.1.0 2018-01-28 [1] CRAN (R 3.6.1)
[1] C:/Users/gp/Documents/R/win-library/3.6 [2] C:/Program Files/R/R-3.6.1/library
Screenshots![grafik](https://user-images.githubusercontent.com/53909648/62715409-bfac0980-ba00-11e9-94a8-8357fdfb091e.png)