kleinstein / scoper / issues / #13 - "spectralClones - vj" test fails

nima nouri

changed status to resolved

resolved by 168d24d

2020-05-12T22:14:21+00:00

Jason Vander Heiden reporter

changed status to open

2020-05-12T22:18:43+00:00

Jason Vander Heiden reporter

This isn’t fixed. And increasing the tolerance on the test condition isn’t a fix regardless.

> library(scoper)
>    db <- spectralClones(ExampleDb, method = "vj", 
+                          germline = "germline_alignment_d_mask",
+                          sequence = "sequence_alignment", 
+                          junction = "junction", v_call = "v_call", 
+                          j_call = "j_call", threshold=0.15,
+                          summarize_clones = FALSE)
>     clones <- as.integer(as.vector(tail(sort(table(db$clone_id)), 10)))
> 
> clones
 [1]  11  12  12  13  14  15  16  29  35 674

‌

2020-05-12T22:20:24+00:00

Jason Vander Heiden reporter

> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] scoper_1.0.0  ggplot2_3.3.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4.6       pillar_1.4.4       compiler_3.6.3     iterators_1.0.12   prettyunits_1.1.1  tools_3.6.3        progress_1.2.2    
 [8] lifecycle_0.2.0    tibble_3.0.1       gtable_0.3.0       nlme_3.1-147       lattice_0.20-41    pkgconfig_2.0.3    rlang_0.4.6       
[15] foreach_1.5.0      Matrix_1.2-18      igraph_1.2.5       cli_2.0.2          rstudioapi_0.11    parallel_3.6.3     withr_2.2.0       
[22] dplyr_0.8.5        vctrs_0.2.4        hms_0.5.3          diptest_0.75-7     ade4_1.7-15        grid_3.6.3         tidyselect_1.0.0  
[29] data.table_1.12.8  glue_1.4.0         R6_2.4.1           fansi_0.4.1        shazam_1.0.0       tidyr_1.0.2        seqinr_3.6-1      
[36] readr_1.3.1        purrr_0.3.4        magrittr_1.5       codetools_0.2-16   MASS_7.3-51.6      scales_1.1.0       ellipsis_0.3.0    
[43] kedd_1.0.3         assertthat_0.2.1   colorspace_1.4-1   ape_5.3            KernSmooth_2.23-17 stringi_1.4.6      doParallel_1.0.15 
[50] lazyeval_0.2.2     munsell_0.5.0      alakazam_1.0.1     crayon_1.3.4

‌

2020-05-12T22:26:46+00:00

Jason Vander Heiden reporter

See this for a potential fix (I don’t know if this is the problem, just a guess):

https://stackoverflow.com/questions/48626086/same-seed-different-os-different-random-numbers-in-r

2020-05-12T22:30:32+00:00

Jason Vander Heiden reporter

When setting the test requirements to identical both of the spectralClones tests fail locally and in Bitbucket pipelines:

[ OK: 2 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: Test spectralClones - novj (@test_clone.R#48) 
  2. Failure: Test spectralClones - vj (@test_clone.R#65)

‌