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Published
20 hours ago •
thierrygosselin
thierrygosselin
assignment_ngs error: problem with 'mutate()'
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
Screenshots If applicable, add screenshots to help explain your problem.
