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assignment_ngs error: problem with 'mutate()' #23

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PeiwenLi opened this issue Mar 2, 2021 · 0 comments
Open

assignment_ngs error: problem with 'mutate()' #23

PeiwenLi opened this issue Mar 2, 2021 · 0 comments

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@PeiwenLi
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PeiwenLi commented Mar 2, 2021

I cannot help you if I cannot reproduce the problem.
Consequently, when reporting an issue, make sure to include:

Describe the bug
assigner::assignment_ngs does not work- suspecting it is a dplyr issue. I tried dplyr v1.0.0 and the latest v1.0.4

To Reproduce
Include the steps to reproduce the behavior:

  • the exact command (function, arguments, values) used
    Command I ran:
assigner::assignment_ngs(
  GENLIGHT391ind_3_realpop$genlight,
  assignment.analysis = "gsi_sim",
  markers.sampling = "ranked", 
  thl = 0.5,
  iteration.method = 30,
  adegenet.dapc.opt = "optim.a.score",
  marker.number = c(2, 4, 8, 16, 32, 64, 128, 200, 500, 1000, 2000, "all"),
  subsample = "min", 
  iteration.subsample = 3
)
  • the complete error message you're getting
Error: Problem with `mutate()` input `..1`.
x Can't subset columns that don't exist.
x Column `STRATA` doesn't exist.
ℹ Input `..1` is `(function (.cols = everything(), .fns = NULL, ..., .names = NULL) ...`.
Run `rlang::last_error()` to see where the error occurred.

Computation time, overall: 7 sec
  • the output of devtools::session_info()
    Strangely I have macOS11.2.2, but in the below session info it says 10.16?
─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 4.0.2 (2020-06-22)
 os       macOS  10.16                
 system   x86_64, darwin17.0          
 ui       RStudio                     
 language (EN)                        
 collate  en_CA.UTF-8                 
 ctype    en_CA.UTF-8                 
 tz       America/Toronto             
 date     2021-03-02                  

─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────
 package         * version  date       lib source                                   
 abind             1.4-5    2016-07-21 [1] CRAN (R 4.0.2)                           
 ade4            * 1.7-16   2020-10-28 [1] CRAN (R 4.0.2)                           
 adegenet        * 2.1.3    2020-05-10 [1] CRAN (R 4.0.2)                           
 adegraphics       1.0-15   2018-12-18 [1] CRAN (R 4.0.2)                           
 adephylo          1.1-11   2017-12-18 [1] CRAN (R 4.0.2)                           
 adespatial        0.3-10   2021-02-09 [1] CRAN (R 4.0.2)                           
 ape               5.4-1    2020-08-13 [1] CRAN (R 4.0.2)                           
 assertthat        0.2.1    2019-03-21 [1] CRAN (R 4.0.2)                           
 assigner        * 0.5.8    2021-02-26 [1] Github (thierrygosselin/assigner@d39a692)
 backports         1.2.1    2020-12-09 [1] CRAN (R 4.0.2)                           
 boot              1.3-25   2020-04-26 [1] CRAN (R 4.0.2)                           
 broom             0.7.3    2020-12-16 [1] CRAN (R 4.0.2)                           
 callr             3.5.1    2020-10-13 [1] CRAN (R 4.0.2)                           
 car               3.0-10   2020-09-29 [1] CRAN (R 4.0.2)                           
 carData           3.0-4    2020-05-22 [1] CRAN (R 4.0.2)                           
 cellranger        1.1.0    2016-07-27 [1] CRAN (R 4.0.2)                           
 class             7.3-17   2020-04-26 [1] CRAN (R 4.0.2)                           
 classInt          0.4-3    2020-04-07 [1] CRAN (R 4.0.2)                           
 cli               2.2.0    2020-11-20 [1] CRAN (R 4.0.2)                           
 cluster           2.1.0    2019-06-19 [1] CRAN (R 4.0.2)                           
 coda              0.19-4   2020-09-30 [1] CRAN (R 4.0.2)                           
 codetools         0.2-18   2020-11-04 [1] CRAN (R 4.0.2)                           
 colorspace        2.0-0    2020-11-11 [1] CRAN (R 4.0.2)                           
 cowplot           1.0.0    2019-07-11 [1] CRAN (R 4.0.2)                           
 crayon            1.3.4    2017-09-16 [1] CRAN (R 4.0.2)                           
 curl              4.3      2019-12-02 [1] CRAN (R 4.0.1)                           
 data.table        1.12.8   2019-12-09 [1] CRAN (R 4.0.1)                           
 data.tree         1.0.0    2020-08-03 [1] CRAN (R 4.0.2)                           
 DBI               1.1.0    2019-12-15 [1] CRAN (R 4.0.2)                           
 deldir            0.2-9    2021-01-16 [1] CRAN (R 4.0.2)                           
 desc              1.2.0    2018-05-01 [1] CRAN (R 4.0.2)                           
 devtools        * 2.3.2    2020-09-18 [1] CRAN (R 4.0.2)                           
 DiagrammeR        1.0.6.1  2020-05-08 [1] CRAN (R 4.0.2)                           
 digest            0.6.27   2020-10-24 [1] CRAN (R 4.0.2)                           
 dplyr           * 1.0.0    2020-05-29 [1] CRAN (R 4.0.2)                           
 e1071             1.7-3    2019-11-26 [1] CRAN (R 4.0.2)                           
 ellipsis          0.3.1    2020-05-15 [1] CRAN (R 4.0.2)                           
 expm              0.999-5  2020-07-20 [1] CRAN (R 4.0.2)                           
 fansi             0.4.1    2020-01-08 [1] CRAN (R 4.0.2)                           
 fastmap           1.0.1    2019-10-08 [1] CRAN (R 4.0.2)                           
 forcats           0.5.0    2020-03-01 [1] CRAN (R 4.0.2)                           
 foreign           0.8-80   2020-05-24 [1] CRAN (R 4.0.2)                           
 fs                1.4.2    2020-06-30 [1] CRAN (R 4.0.2)                           
 gdata             2.18.0   2017-06-06 [1] CRAN (R 4.0.2)                           
 generics          0.0.2    2018-11-29 [1] CRAN (R 4.0.2)                           
 ggplot2         * 3.3.2    2020-06-19 [1] CRAN (R 4.0.2)                           
 ggpubr            0.4.0    2020-06-27 [1] CRAN (R 4.0.2)                           
 ggsignif          0.6.0    2019-08-08 [1] CRAN (R 4.0.2)                           
 glue              1.4.1    2020-05-13 [1] CRAN (R 4.0.2)                           
 gmodels           2.18.1   2018-06-25 [1] CRAN (R 4.0.2)                           
 grur            * 0.1.4    2021-02-26 [1] Github (thierrygosselin/grur@d31c423)    
 gtable            0.3.0    2019-03-25 [1] CRAN (R 4.0.2)                           
 gtools            3.8.2    2020-03-31 [1] CRAN (R 4.0.2)                           
 haven             2.3.1    2020-06-01 [1] CRAN (R 4.0.2)                           
 hms               0.5.3    2020-01-08 [1] CRAN (R 4.0.2)                           
 htmltools         0.5.1.1  2021-01-22 [1] CRAN (R 4.0.2)                           
 htmlwidgets       1.5.1    2019-10-08 [1] CRAN (R 4.0.2)                           
 httpuv            1.5.4    2020-06-06 [1] CRAN (R 4.0.2)                           
 httr              1.4.2    2020-07-20 [1] CRAN (R 4.0.2)                           
 igraph            1.2.5    2020-03-19 [1] CRAN (R 4.0.2)                           
 jpeg              0.1-8.1  2019-10-24 [1] CRAN (R 4.0.2)                           
 jsonlite          1.7.2    2020-12-09 [1] CRAN (R 4.0.2)                           
 KernSmooth        2.23-17  2020-04-26 [1] CRAN (R 4.0.2)                           
 later             1.1.0.1  2020-06-05 [1] CRAN (R 4.0.2)                           
 lattice           0.20-41  2020-04-02 [1] CRAN (R 4.0.2)                           
 latticeExtra      0.6-29   2019-12-19 [1] CRAN (R 4.0.2)                           
 lazyeval          0.2.2    2019-03-15 [1] CRAN (R 4.0.2)                           
 LearnBayes        2.15.1   2018-03-18 [1] CRAN (R 4.0.2)                           
 lifecycle         0.2.0    2020-03-06 [1] CRAN (R 4.0.2)                           
 magrittr          1.5      2014-11-22 [1] CRAN (R 4.0.2)                           
 MASS              7.3-51.6 2020-04-26 [1] CRAN (R 4.0.2)                           
 Matrix            1.2-18   2019-11-27 [1] CRAN (R 4.0.2)                           
 memoise           1.1.0    2017-04-21 [1] CRAN (R 4.0.2)                           
 mgcv              1.8-31   2019-11-09 [1] CRAN (R 4.0.2)                           
 mime              0.9      2020-02-04 [1] CRAN (R 4.0.2)                           
 munsell           0.5.0    2018-06-12 [1] CRAN (R 4.0.2)                           
 nlme              3.1-148  2020-05-24 [1] CRAN (R 4.0.2)                           
 openxlsx          4.1.5    2020-05-06 [1] CRAN (R 4.0.2)                           
 permute           0.9-5    2019-03-12 [1] CRAN (R 4.0.2)                           
 phylobase         0.8.10   2020-03-01 [1] CRAN (R 4.0.2)                           
 pillar            1.4.6    2020-07-10 [1] CRAN (R 4.0.2)                           
 pinfsc50          1.2.0    2020-06-03 [1] CRAN (R 4.0.2)                           
 pkgbuild          1.1.0    2020-07-13 [1] CRAN (R 4.0.2)                           
 pkgconfig         2.0.3    2019-09-22 [1] CRAN (R 4.0.2)                           
 pkgload           1.1.0    2020-05-29 [1] CRAN (R 4.0.2)                           
 plyr            * 1.8.6    2020-03-03 [1] CRAN (R 4.0.2)                           
 png               0.1-7    2013-12-03 [1] CRAN (R 4.0.2)                           
 prettyunits       1.1.1    2020-01-24 [1] CRAN (R 4.0.2)                           
 processx          3.4.5    2020-11-30 [1] CRAN (R 4.0.2)                           
 progress          1.2.2    2019-05-16 [1] CRAN (R 4.0.2)                           
 promises          1.1.1    2020-06-09 [1] CRAN (R 4.0.2)                           
 ps                1.3.3    2020-05-08 [1] CRAN (R 4.0.2)                           
 purrr             0.3.4    2020-04-17 [1] CRAN (R 4.0.2)                           
 R6                2.4.1    2019-11-12 [1] CRAN (R 4.0.2)                           
 radiator        * 1.1.9    2021-01-21 [1] Github (thierrygosselin/radiator@5c6b865)
 randomForestSRC * 2.10.1   2021-02-10 [1] CRAN (R 4.0.2)                           
 raster            3.3-13   2020-07-17 [1] CRAN (R 4.0.2)                           
 RColorBrewer      1.1-2    2014-12-07 [1] CRAN (R 4.0.2)                           
 Rcpp              1.0.5    2020-07-06 [1] CRAN (R 4.0.2)                           
 readr             1.4.0    2020-10-05 [1] CRAN (R 4.0.2)                           
 readxl            1.3.1    2019-03-13 [1] CRAN (R 4.0.2)                           
 remotes           2.2.0    2020-07-21 [1] CRAN (R 4.0.2)                           
 reshape2          1.4.4    2020-04-09 [1] CRAN (R 4.0.2)                           
 rio               0.5.16   2018-11-26 [1] CRAN (R 4.0.2)                           
 rlang             0.4.10   2020-12-30 [1] CRAN (R 4.0.2)                           
 rncl              0.8.4    2020-02-10 [1] CRAN (R 4.0.2)                           
 RNeXML            2.4.5    2020-06-18 [1] CRAN (R 4.0.2)                           
 rprojroot         1.3-2    2018-01-03 [1] CRAN (R 4.0.2)                           
 rstatix           0.6.0    2020-06-18 [1] CRAN (R 4.0.2)                           
 rstudioapi        0.11     2020-02-07 [1] CRAN (R 4.0.2)                           
 scales            1.1.1    2020-05-11 [1] CRAN (R 4.0.2)                           
 seqinr            3.6-1    2019-09-07 [1] CRAN (R 4.0.2)                           
 sessioninfo       1.1.1    2018-11-05 [1] CRAN (R 4.0.2)                           
 sf                0.9-7    2021-01-06 [1] CRAN (R 4.0.2)                           
 shiny             1.6.0    2021-01-25 [1] CRAN (R 4.0.2)                           
 sp                1.4-5    2021-01-10 [1] CRAN (R 4.0.2)                           
 spData            0.3.8    2020-07-03 [1] CRAN (R 4.0.2)                           
 spdep             1.1-5    2020-06-29 [1] CRAN (R 4.0.2)                           
 stringi           1.4.6    2020-02-17 [1] CRAN (R 4.0.2)                           
 stringr           1.4.0    2019-02-10 [1] CRAN (R 4.0.2)                           
 testthat          2.3.2    2020-03-02 [1] CRAN (R 4.0.2)                           
 tibble            3.0.3    2020-07-10 [1] CRAN (R 4.0.2)                           
 tidyr             1.1.2    2020-08-27 [1] CRAN (R 4.0.2)                           
 tidyselect        1.1.0    2020-05-11 [1] CRAN (R 4.0.2)                           
 units             0.6-7    2020-06-13 [1] CRAN (R 4.0.2)                           
 usethis         * 2.0.0    2020-12-10 [1] CRAN (R 4.0.2)                           
 uuid              0.1-4    2020-02-26 [1] CRAN (R 4.0.2)                           
 vcfR            * 1.12.0   2020-07-28 [1] Github (knausb/vcfR@8a61e1c)             
 vctrs             0.3.6    2020-12-17 [1] CRAN (R 4.0.2)                           
 vegan             2.5-6    2019-09-01 [1] CRAN (R 4.0.2)                           
 viridisLite       0.3.0    2018-02-01 [1] CRAN (R 4.0.1)                           
 visNetwork        2.0.9    2019-12-06 [1] CRAN (R 4.0.2)                           
 withr             2.4.0    2021-01-16 [1] CRAN (R 4.0.2)                           
 XML               3.99-0.5 2020-07-23 [1] CRAN (R 4.0.2)                           
 xml2              1.3.2    2020-04-23 [1] CRAN (R 4.0.2)                           
 xtable            1.8-4    2019-04-21 [1] CRAN (R 4.0.2)                           
 yaml              2.2.1    2020-02-01 [1] CRAN (R 4.0.2)                           
 zip               2.1.1    2020-08-27 [1] CRAN (R 4.0.2)                           

[1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library
  • complete data required to reproduce the problem, a subset of it. The data remains confidential.

radiator_genlight391ind_3_realpop.RData.zip

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@PeiwenLi