Merge branch 'devel'

.circleci/config.yml

@@ -17,9 +17,11 @@ jobs:
           command: |
             R -e "devtools::install_deps(dependencies = TRUE)"
             R -e "devtools::install_github('MangoTheCat/goodpractice')"
+          no_output_timeout: 30m
       - run:
           command: |
-            R -e "devtools::check()"
+            R -e "devtools::check(run_dont_test = TRUE)"
+          no_output_timeout: 30m
       - save_cache:
           key: deps1-{{ .Branch }}-{{ checksum "DESCRIPTION" }}-{{ checksum ".circleci/config.yml" }}
           paths:
@@ -31,6 +33,7 @@ jobs:
             R -e "goodpractice::gp(checks = grep('(rcmdcheck|covr)', goodpractice::all_checks(), invert=TRUE, value=TRUE))"
             R -e "cv <- covr::package_coverage(); print(cv); covr::report(x = cv, file = '/root/main/artifacts/gsodr-coverage.html', browse=FALSE)"
             R CMD Rd2pdf --force --output='/root/main/artifacts/gsodr-manual.pdf' .
+          no_output_timeout: 30m
       - store_artifacts:
           path: /root/main/artifacts/
           destination: artifacts

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: GSODR
 Type: Package
 Title: Global Surface Summary of the Day ('GSOD') Weather Data Client
-Version: 1.3.0
+Version: 1.3.1
 Authors@R: c(person("Adam", "Sparks", role = c("aut", "cre"),
     email = "[email protected]",
     comment = c(ORCID = "0000-0002-0061-8359")),

NEWS.md

@@ -1,3 +1,13 @@
+# GSODR 1.3.1
+
+## Bug fixes
+
+- Fix examples that did not run properly
+
+## Minor changes
+
+- Update internal database of station locations
+
 # GSODR 1.3.0
 
 ## New Functionality
@@ -10,10 +20,10 @@
 ## Bug fixes
 
 - Refactor internal functionality to be more clear and efficient in execution
-    
+
     - `country-list` is not loaded unless user has specified a country in
       `get_GSOD()`
-      
+
     - An instance where the FIPS code was determined twice was removed
 
 - Replace `\dontrun{}` with `\donttest{}` in documentation examples
@@ -28,19 +38,19 @@
 
 - Store internal database of station locations fields `BEGIN` and `END` as
   integer, not double
-  
+
 - Clarify code of conduct statement in README that it only applies to this,
   GSODR, project
-  
+
 - Prompt user for input with warning about reproducibility if using the
   `update_station_list()` function
 
 - Adds metadata header to the `tibble` returned by `get_inventory()`
 
 - Remove startup message to conform with rOpenSci guidelines
-  
+
 - Remove extra code, clean up code-chunks and use `hrbrthemes::theme_ipsum()`
-  for 
+  for
   [data-raw/fetch_isd-history.md](https://github.com/ropensci/GSODR/blob/master/data-raw/fetch_isd-history.md)
 
 --------------------------------------------------------------------------------

R/get_GSOD.R

@@ -11,7 +11,7 @@
 #'
 #' Parallel processing can be enabled using \code{\link[future]{plan}} to set
 #' up a parallel backend of your choice, e.g.,
-#' \code{future::plan(multisession)}. See examples for more.
+#' \code{future::plan("multisession")}. See examples for more.
 #'
 #' @details
 #' Stations reporting a latitude of < -90 or > 90 or longitude of < -180 or >
@@ -85,15 +85,15 @@
 #' AUS
 #'
 #' # Download agroclimatology data for 2015 using parallel processing
-#' future::plan(multisession)
+#' future::plan("multisession")
 #' ag <- get_GSOD(years = 2015, agroclimatology = TRUE)
 #'
 #' ag
 #'
 #' # Download global data for 2010 to 2015 with a maximum allowed 5 missing days
 #' # of data using parallel processing
 #'
-#' future::plan(multisession)
+#' future::plan("multisession")
 #' global <- get_GSOD(years = 2010:2015, max_missing = 5)
 #'
 #' global
@@ -194,16 +194,5 @@ get_GSOD <- function(years,
 
   GSOD_XY <- apply_process_gz(file_list, isd_history)
   return(GSOD_XY)
-  # Cleanup --------------------------------------------------------------------
-  files <-
-    list.files(
-      cache_dir,
-      ignore.case = TRUE,
-      include.dirs = TRUE,
-      full.names = TRUE,
-      recursive = TRUE,
-      pattern = ".gz$"
-    )
-  unlink(files, force = TRUE, recursive = TRUE)
-  rm(cache_dir)
 }
+

R/internal_functions.R

@@ -112,7 +112,7 @@
       tryCatch(
         Map(
           function(ftp, dest)
-            utils::download.file(
+            curl::curl_download(
               url = ftp,
               destfile = dest,
               mode = "wb"
@@ -190,7 +190,7 @@
               return()
           }
         }
-      
+
       pb <- dplyr::progress_estimated(length(years))
       purrr::walk(years, function(yr) {
         year_url <- sprintf(ftp_base, yr)
@@ -202,7 +202,7 @@
         purrr::map(station, ~ grep(., fils, value = TRUE)) %>%
           purrr::keep( ~ length(.) > 0) %>%
           purrr::flatten_chr() -> fils
-        
+
         if (length(fils) > 0) {
           # grab the station files
           purrr::walk(paste0(year_url, fils), retry_cfd)
@@ -247,7 +247,7 @@
            isd_history,
            cache_dir,
            years) {
-    
+
     station_list <-
       isd_history[isd_history$CTRY == country, ]$STNID
     station_list <- do.call(paste0,

R/reformat_GSOD.R

@@ -17,7 +17,7 @@
 #'
 #' Parallel processing can be enabled using \code{\link[future]{plan}} to set
 #' up a parallel backend of your choice, e.g.,
-#' \code{future::plan(multisession)}.  See examples for more.
+#' \code{future::plan("multisession")}.  See examples for more.
 #'
 #' @param dsn User supplied file path to location of data files on local disk
 #' for tidying.

codemeta.json

@@ -35,7 +35,7 @@
   "keywords": ["US-NCEI", "meteorological-data", "global-weather", "weather", "weather-data", "meteorology", "station-data", "surface-weather", "data-access", "US-NCDC", "r", "gsod", "ncdc", "weather-stations", "global-data", "ncei", "weather-information", "historical-weather", "historical-data", "daily-data", "daily-weather", "rstats", "r-package", "peer-reviewed"],
   "license": "https://spdx.org/licenses/MIT",
   "title": "GSODR",
-  "version": "1.3.0",
+  "version": "1.3.1",
   "name": "GSODR: Global Surface Summary of the Day ('GSOD') Weather Data Client",
   "issueTracker": "https://github.com/ropensci/GSODR/issues",
   "programmingLanguage": {
@@ -447,7 +447,7 @@
   "contIntegration": "https://travis-ci.org/ropensci/GSODR",
   "releaseNotes": "https://github.com/ropensci/GSODR/blob/master/NEWS.md",
   "readme": "https://github.com/ropensci/GSODR/blob/master/README.md",
-  "fileSize": "1237.803KB",
+  "fileSize": "1236.959KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",

cran-comments.md

@@ -2,9 +2,9 @@
 
   -  macOS, R version 3.5.1 (2018-07-02)
 
-  -  Debian Linux, R version 3.5.1 (2018-07-02)
+  -  Ubuntu Linux 18.04.1, R version 3.5.1 (2018-07-02)
 
-  -  win-builder, R Under development (unstable) (2018-09-20 r75339)
+  -  win-builder, R Under development (unstable) (2018-12-17 r75857)
 
   -  win-builder, R version 3.5.1 (2018-04-23)
 
@@ -13,10 +13,9 @@
 
 0 errors | 0 warnings | 1 note
 
-# New Minor Release
+# New Patch Release
 
-- This release adds functionality to support using the `future` package for
-  parallel processing
+- This release fixes examples that were incorrectly written and would not run
 
 # Reverse dependencies
 

data-raw/fetch_country-list.Rmd

@@ -21,7 +21,7 @@ codes are used when a user selects a single country for a data query.
 Read "country-list.txt" file from NCEI FTP server and merge with _countrycode_
 data.
 
-```{r download_merge_inspect, echo=TRUE, messages=FALSE}
+```{r download-merge-inspect, echo=TRUE, messages=FALSE}
 if (!require("countrycode"))
 {
   install.packages("countrycode",
@@ -32,7 +32,11 @@ if (!require("dplyr"))
   install.packages("dplyr",
                    repos = c(CRAN = "https://cran.rstudio.com"))
 }
+```
+
+```{r read-table, echo=TRUE, messages=FALSE}
 
+```{r download-and-merge, echo=TRUE, message=FALSE}
 countries <- readr::read_table(
   "ftp://ftp.ncdc.noaa.gov/pub/data/noaa/country-list.txt")[-1, c(1, 3)]
 names(countries)[2] <- "COUNTRY_NAME"
@@ -46,10 +50,12 @@ print(country_list)
 There are unnecessary data in several columns. _GSODR_ only requires FIPS, name,
 and ISO codes to function.
 
-```{r remove_uncessesary, echo=TRUE, messages=FALSE}
-
-country_list <- select(country_list, c("FIPS", "COUNTRY_NAME", "iso2c", "iso3c"))
 
+```{r remove-uncessesary, echo=TRUE, messages=FALSE}
+country_list <- dplyr::select(country_list, c("FIPS",
+                                              "COUNTRY_NAME",
+                                              "iso2c",
+                                              "iso3c"))
 country_list
 ```
 
@@ -65,9 +71,7 @@ save(country_list, file = "../inst/extdata/country_list.rda",
 
 Users of these data should take into account the following (from the 
 [NCEI website](http://www7.ncdc.noaa.gov/CDO/cdoselect.cmd?datasetabbv=GSOD&countryabbv=&georegionabbv=)): 
-
-> "The following data and products may have conditions placed on their
-> international commercial use. They can be used within the U.S. or for
+> "The following data and products may have conditions placed on their international commercial use. They can be used within the U.S. or for
 > non-commercial international activities without restriction. The non-U.S.
 > data cannot be redistributed for commercial purposes. Re-distribution of these
 > data by others must provide this same notification."