Fixing a thing

Prompt:

Fix one of the problems in one of our community packages at https://github.com/Stat585-at-ISU/lab-3-all-all-for-one-and-one-for-all, and write about it.

Instructions:

What we want to know is the exact warning or error message of the item you fixed, and a description of what you did, also as specific as possible.

Describe your experience below. Push this blog post to your blog-9 repo. Make sure the front matter check passes.

Which error or warning did you fix? … and how?

For this week’s blog, I decided to keep working on the Team2 package. The warning I identified dealt with us forgetting to include a library in the Imports section of the description, and using library within the functions. The error would be similar to the following message:

 checking dependencies in R code ... WARNING
  'library' or 'require' calls not declared from:
    'tabulizer' 'tidyverse'
  'library' or 'require' calls in package code:
    'tabulizer' 'tidyverse'
    Please use :: or requireNamespace() instead.
    See section 'Suggested packages' in the 'Writing R Extensions' manual.

The reason for this was that within the function pdf_to_table we were importing the library, like this:

pdf_to_tbl <- function(pdf, save_as = NULL) {

  library(tidyverse)       <--------- This command was problematic
  library(tabulizer)       <--------- This command was problematic
 
  plog <- tabulizer::extract_tables(file = pdf, method = "lattice")
  df <- lapply(plog, extract_data_frame_page)

  # identify the numeric columns, since some pages miss all "Report Number Assigned to Event"
  n <- length(df)
  numeric_columns <- df %>% lapply(., function(x)sapply(x, class)) %>%
    lapply(., function(x)which(x == "numeric")) %>%
    unlist %>% unique

  ## Combining the different pages
  df <- do.call(rbind, df)
  df[numeric_columns] <- suppressWarnings(lapply(df[numeric_columns], function(x)as.numeric(x)))

  if (!is.null(save_as) && dir.exists(dirname(save_as))){
    utils::write.csv(df, save_as, row.names = FALSE)
  }

  return(df)

}

I did three things to clear this warning: - Substitute the tidyverse call for the magrittr - Check if the name spaces “magrittr” and “tabulize” were available - In case they were, load the name space - Add magrittr and tabulizer to the Imports seciton of the description file

The updated function is as it follows:

pdf_to_tbl <- function(pdf, save_as = NULL) {

  
  if(!requireNamespace("tabulizer", quietly = TRUE)){
    warning("The tabulizer package is required for this function")
    return(NULL)
  }
  
  if(!requireNamespace("magrittr", quietly = TRUE)){
    warning("The magrittr package is required for this function")
    return(NULL)
  }
  
  
  loadNamespace('magrittr')
 
  
  
  plog <- tabulizer::extract_tables(file = pdf, method = "lattice")
  df <- lapply(plog, extract_data_frame_page)

  # identify the numeric columns, since some pages miss all "Report Number Assigned to Event"
  n <- length(df)
  numeric_columns <- df %>% lapply(., function(x)sapply(x, class)) %>%
    lapply(., function(x)which(x == "numeric")) %>%
    unlist %>% unique

  ## Combining the different pages
  df <- do.call(rbind, df)
  df[numeric_columns] <- suppressWarnings(lapply(df[numeric_columns], function(x)as.numeric(x)))

  if (!is.null(save_as) && dir.exists(dirname(save_as))){
    utils::write.csv(df, save_as, row.names = FALSE)
  }

  return(df)

}

The description file now also contains the updated Imports section

Package: Team2
Title: Get police presslogs
Version: 0.0.0.9000
Authors@R: c(
    person("Caio", "dos Santos", , "clsantos@iastate.edu", role = c("aut", "cre")),
    person("Alexandrea", "Arabio", , "aarabio@iastate.edu", role = "aut"),
    person("Maxwell", "Skinner", , "mskinn25@iastate.edu", role = "aut")
  )
Description: This package contains 3 functions to download, extract, and
    filter presslog data. Also, it contains a sample data set.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Imports: 
    lubridate,
    tabulizer,
    magrittr
Depends: 
    R (>= 2.10)
LazyData: true
LitrVersionUsed: 0.7.0
LitrId: afd1fe153acf34706b65fe5d2dcc1315