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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: Argument 1 must have names #16

Closed NadyaMamoozadeh closed 4 years ago

NadyaMamoozadeh commented 4 years ago

Hello! I am running the following code in R v3.5.1 using new installs of the radiator and assigner R packages (installed via devtools Sep 14, 2019) on my Mac:

test.tidy = radiator::tidy_genomic_data(data="test.gen", strata="subset_strata.txt")

assign1 <- assigner::assignment_ngs( data = test.tidy, assignment.analysis = "gsi_sim", markers.sampling = "ranked", thl = 0.2, iteration.method = 5 )

I get the following error:

##################### assigner::assignment_ngs ################ Execution date/time: 20190914@1348 Assignment analysis with gsi_sim Folder created: assignment_analysis_method_ranked_20190914@1348 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: Argument 1 must have names

Computation time, overall: 1 sec ###############assignment_ngs completed ############

I've attached my input files (subsets of my full dataset) so that you can recreate the issue. I am using 'test.gen' as input with the attached file, not 'test.txt' (will not let me upload with *.gen file extension). I see an earlier bug report from a user that was getting the same error but changing the file extension did not fix the problem. I've also attached the output from devtools::session_info(). I should also note that I get the same error when attempting to run the same code but using the test datasets provided in the assigner vignettes (data_assigner_sim_01, data_assigner_sim_02). Please let me know if any other information would be helpful! Thanks!

devtools_session_info.txt

subset_strata.txt

test.txt

thierrygosselin commented 4 years ago

Hi nrcombs, I’ll have a look today at the Thanks for reporting Cheers Thierry

NadyaMamoozadeh commented 4 years ago

Thanks Thierry for your response! After posting I realized that the issue must be with gsi_sim (perhaps either broken code within the gsi_sim algorithm itself, or its implementation of assigner). The dapc module works great. Will look forward to using the gsi_sim capabilities when available, thanks for this user-friendly program!

PeiwenLi commented 4 years ago

Hi nrcombs and Thierry, I ran into the same error following the script in https://thierrygosselin.github.io/assigner/articles/get_started.html under R v3.5.3 with radiator v1.0.0 and assinger v0.5.6. Would changing back to older version R be helpful? Thanks, Peiwen

thierrygosselin commented 4 years ago

This problem originate from another package it should now be fix.