Dplyr: '.Random.seed' is not an integer vector but of type 'NULL', so ignored

[komalsrathi]

Hi,

I am getting this warning while using dplyr::filter. This happens the first time I run it but warning goes away the next time - not sure what is happening.

library(dplyr)
library(DT)

denovo <- read.delim('NLES10_733459.trio.phased.com.filtered.ad.de.nm.snpeff.anno.denovo.txt')

if(nrow(denovo) == 0)
{
  print("0 de novo variants found<br/>")
} else {
  dt <- plyr::count(denovo , 'impact_so')
  datatable(dat = data.frame(Description = dt$impact_so, 
                                 Variants = dt$freq, 
                                 Perc = prop.table(dt$freq)*100))
}

denovo %>% filter(recurrent_genes != "None") -> in_recurrent

Warning message:
In filter_impl(.data, dots) :
  '.Random.seed' is not an integer vector but of type 'NULL', so ignored

sessionInfo:

R version 3.3.0 (2016-05-03)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.6 (El Capitan)

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] DT_0.2               dplyr_0.5.0          BiocInstaller_1.23.9

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.7     digest_0.6.10   assertthat_0.1  R6_2.1.3        plyr_1.8.4     
 [6] jsonlite_1.0    DBI_0.5         magrittr_1.5    lazyeval_0.2.0  tools_3.3.0    
[11] htmlwidgets_0.7 yaml_2.1.13     rsconnect_0.4.3 htmltools_0.3.5 tibble_1.2   

The denovo data is here:
https://drive.google.com/open?id=0B-8gQV1WZcYdYm1BWmNZU1JzQ2s

[romainfrancois]

Can you reprexify this please, we don't have denovo

[komalsrathi]

Sorry about that. I have provided the exact code I am using and the google drive link for the data is at the end of the original post.

[romainfrancois]

Thanks. I can't reproduce the problem

> in_recurrent <- denovo %>% filter(recurrent_genes != "None")
> in_recurrent
 [1] variant_id         chrom              start              end
 [5] vcf_id             ref                alt                qual
 [9] filter             type               sub_type           call_rate
[13] num_hom_ref        num_het            num_hom_alt        aaf
[17] hwe                inbreeding_coef    pi                 gene
[21] transcript         is_exonic          is_coding          is_lof
[25] is_splicing        exon               codon_change       aa_change
[29] aa_length          biotype            impact             impact_so
[33] impact_severity    polyphen_pred      polyphen_score     sift_pred
[37] sift_score         an                 baseqranksum       clippingranksum
[41] db                 dp                 ds                 fs
[45] haplotypescore     inbreedingcoeff    lof                mq
[49] mqranksum          nmd                old_multiallelic   old_variant
[53] provean_prediction provean_score      qd                 readposranksum
[57] sift_prediction    sor                aminoacidchange    exac_af_all
[61] exac_an_all        functiongvs        literature_genes   polyphen
[65] recurrent_genes    rvis_genes         rvis_score         set
[69] gts                gt_types           gt_phases          gt_depths
[73] gt_ref_depths      gt_alt_depths      gt_quals           family_id
[77] family_members     family_genotypes   samples            family_count
<0 rows> (or 0-length row.names)

and filter does not use anything that needs .Randon.seed so this is likely not a dplyr issue.

[komalsrathi]

Alright I will close this then.

[jennybc]

I'm getting this warning from a call to purrr::map_df(). In an Rmd document and only when I render it, not when I run the code interactively. And only when I render that specific Rmd, not when I build the entire website it is part of. The whole project is available on GitHub but maybe it's better to see if a smaller reprex presents itself.

[stevekm]

Same as @jennybc , I am getting this error message when compiling an Rmd document to HTML and trying to use DT to print a datatable in the document. Is there a way to suppress this message? It does not seem to be affecting anything but I can't stop it from appearing in the document.

[jbintz]

Same as @jennybc but from call to readr::read_rds(), in Rmd document and only when I render it.

[jto888]

I understand this is closed, but I have been getting these mysterious warnings. Yes, I had imported plyr, and when I changed to a depend some warnings went away.

[pmcharrison]

I had this problem when running DT::datatable(...) and later plotly::plot_ly(...) in an Rmd document. A quick fix was to insert the following after DT::datatable(...):

rm(.Random.seed)
set.seed(1)

[jimhester]

This issue is ultimately caused by https://github.com/ramnathv/htmlwidgets/pull/265, which is fixed in the devel version of htmlwidgets, but not yet on CRAN.

[krlmlr]

Can we close this?

[lock[bot]]

This old issue has been automatically locked. If you believe you have found a related problem, please file a new issue (with reprex) and link to this issue. https://reprex.tidyverse.org/