error with README.md example

ghost commented 6 years ago

I am receiving an error running the README.md example that is due to not have parenthetical : Error in .::stats : unused argument (na.omit)

library(magrittr)
library(antigen.garnish)

  # download an example VCF
    dt <- "antigen.garnish_example.vcf" %T>%
    utils::download.file("http://get.rech.io/antigen.garnish_example.vcf", ., method = "libcurl") %>%

  # extract variants
    garnish_variants

full output:

trying URL 'http://get.rech.io/antigen.garnish_example.vcf'
Content type 'text/x-vcard; charset=utf-8' length 6690 bytes
==================================================
downloaded 6690 bytes

Loading VCFs
Scanning file to determine attributes.
File attributes:
  meta lines: 56
  header line: 57
  variant count: 3
  column count: 11
Meta line 56 read in.
All meta lines processed.
gt matrix initialized.
Character matrix gt created.
  Character matrix gt rows: 3
  Character matrix gt cols: 11
  skip: 0
  nrows: 3
  row_num: 0
Processed variant: 3
All variants processed
Error in .::stats : unused argument (na.omit)

It looks like it is failing during variant caller look-up

vcf@meta %>%
        unlist %>%
        stringr::str_extract(stringr::regex("(Strelka)|(Mutect)|(VarScan)|(samtools mpileup)|(somaticsniper)|(freebayes)|(virmid)",
          ignore_case = TRUE)) %>%
        stats::na.omit %>%
                 unlist %>%
data.table::first

Calling both stats::na.omit() and data.table::first() with parenthetical does returns [1] "strelka". Is this an environment issue with my install?

> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS

Matrix products: default
BLAS: /home/ubuntu/.anaconda2/lib/R/lib/libRblas.so
LAPACK: /home/ubuntu/.anaconda2/lib/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   base

other attached packages:
[1] data.table_1.10.4-3 magrittr_1.5        vcfR_1.7.0
[4] RevoUtils_10.0.8

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.16      lattice_0.20-35   ape_5.1           memuse_4.0-0
 [5] viridisLite_0.3.0 permute_0.9-4     MASS_7.3-48       grid_3.4.3
 [9] nlme_3.1-131      stringi_1.1.7     vegan_2.4-6       Matrix_1.2-12
[13] pinfsc50_1.1.0    tools_3.4.3       stringr_1.3.0     parallel_3.4.3
[17] compiler_3.4.3    cluster_2.0.6     mgcv_1.8-22