missing data is still present after imputation in RF about radiator HOT 2 CLOSED

>   gc <- radiator::genomic_converter(data = miss.genlight,
+                                     output = "genlight",
+                                     imputation.method = "rf",
+                                     monomorphic.out = FALSE,
+                                 hierarchical.levels = "global",
+                                     verbose = TRUE)
#######################################################################
##################### radiator::genomic_converter #####################
#######################################################################
Function arguments and values:
Working directory: /mnt/ceph/stah3621/imputation
Input file: from global environment
Strata: no
Population levels: no
Population labels: no
Output format(s): tidy, genlight
Filename prefix: no
Filters:
Blacklist of individuals: no
Blacklist of genotypes: no
Whitelist of markers: no
monomorphic.out: FALSE
snp.ld: no
common.markers: TRUE
max.marker: no
pop.select: no
maf.thresholds: no

Imputations options:
imputation.method: rf
hierarchical.levels: global

parallel.core: 47

#######################################################################

Importing data

Number of markers missing in all individuals and removed: 1

Tidy genomic data:
    Number of markers: 500
    Number of chromosome/contig/scaffold: 1
    Number of individuals: 94

Preparing data for output

    Data is bi-allelic


#######################################################################
####################### grur::grur_imputations ########################
#######################################################################
Imputation method: rf
Hierarchical levels: global
On-the-fly-imputations options:
    number of trees to grow: 50
    minimum terminal node size: 1
    non-negative integer value used to specify random splitting: 10
    number of iterations: 10
Number of CPUs: 47
Note: If you have speed issues: follow radiator's vignette on parallel computing


Number of populations: 1
Number of individuals: 94
Number of markers: 500

Proportion of missing genotypes before imputations: 0.298319
On-the-fly-imputations using Random Forests algorithm
Imputations computed globally, take a break...
Adjusting REF/ALT alleles to account for imputations...
    generating REF/ALT dictionary
    integrating new genotype codings...

Proportion of missing genotypes after imputations: 0

Computation time: 8 sec
################## grur::grur_imputations completed ###################
Generating adegenet genlight object without imputation
Generating adegenet genlight object WITH imputations

Writing tidy data set:
[email protected]

Writing tidy data set:
[email protected]
############################### RESULTS ###############################
Data format of input: genlight
Biallelic data
Number of common markers: 500
Number of chromosome/contig/scaffold: 1
Number of individuals 94

Computation time: 12 sec
################ radiator::genomic_converter completed ################
Warning message:
In radiator::radiator_imputations_module(data = input, imputation.method = imputation.method,  :
  Missing data is still present in the dataset
    2 options:
    run the function again with hierarchical.levels = 'global'
    use common.markers = TRUE when using hierarchical.levels = 'strata'

> anyNA(as.matrix(gc$genlight.imputed))
[1] FALSE

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS  10.14.2

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/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  
[7] base     

other attached packages:
 [1] bindrcpp_0.2.2        psych_1.8.12          vegan_2.5-3          
 [4] lattice_0.20-38       permute_0.9-4         LEA_2.4.0            
 [7] tidyr_0.8.2           adegenet_2.1.1        ade4_1.7-13          
[10] randomForestSRC_2.8.0 radiator_0.0.21      

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS: /opt/modules/devel/R/3.5.1/lib64/R/lib/libRblas.so
LAPACK: /opt/modules/devel/R/3.5.1/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
 [1] dplyr_0.7.8           LEA_2.4.0             randomForestSRC_2.8.0
 [4] bindrcpp_0.2.2        psych_1.8.12          vegan_2.5-3
 [7] lattice_0.20-38       permute_0.9-4         tidyr_0.8.2
[10] radiator_0.0.21       adegenet_2.1.1        ade4_1.7-13