fix check

.Rbuildignore

@@ -2,3 +2,8 @@
 ^\.Rproj\.user$
 ^LICENSE\.md$
 ^\.github$
+^LICENSE\.md$
+^docker$
+^\.github$
+^\.idea$
+^\uploads$

DESCRIPTION

@@ -1,19 +1,24 @@
 Package: serovizr
-Title: R API for seroviz app
+Title: R API for SeroViz app
 Version: 0.0.0
 Authors@R: 
     person("Alex", "Hill", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0009-0003-8104-1890"))
-Description:
+Description: "R API for SeroViz app."
 License: GPL (>= 3)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
 Imports: 
     docopt,
-    porcelain,
+    jsonlite,
     logger,
-    Rook
+    mgcv,
+    plumber,
+    porcelain,
+    Rook,
+    stringr,
+    tibble
 Remotes:
     reside-ic/porcelain,
 Suggests:

R/api.R

@@ -8,7 +8,7 @@ target_get_version <- function() {
 
 target_post_dataset <- function(req, res) {
   parsed <- Rook::Multipart$parse(req)
-  file_body <- read.csv(parsed$file$tempfile)
+  file_body <- utils::read.csv(parsed$file$tempfile)
   filename <- parsed$file$filename
   filename <- stringr::str_remove_all(filename, paste0(".", tools::file_ext(filename)))
   path <- file.path("uploads", filename)
@@ -27,7 +27,7 @@ target_post_dataset <- function(req, res) {
     return(list(status = "failure", errors = list(error), data = NULL))
   }
 
-  write.csv(file_body, path, row.names = FALSE)
+  utils::write.csv(file_body, path, row.names = FALSE)
   return(filename)
 }
 
@@ -85,7 +85,7 @@ read_dataset <- function(name) {
     porcelain::porcelain_stop(paste("Did not find dataset with name ", name),
                               code = "BAD_REQUEST", status_code = 404L)
   }
-  dat <- read.csv(path)
+  dat <- utils::read.csv(path)
   dat$value <- as.numeric(dat$value)
   dat
 }
@@ -102,7 +102,7 @@ model_out <- function(dat) {
   }
   range <- range(dat$day, na.rm = TRUE)
   xseq <- range[1]:range[2]
-  list(x = xseq, y = predict(m, tibble::data_frame(day = xseq)))
+  list(x = xseq, y = stats::predict(m, tibble::data_frame(day = xseq)))
 }
 
 data_out <- function(dat) {

README.md

@@ -2,8 +2,7 @@
 
 <!-- badges: start -->
 [![Project Status: Concept – Minimal or no implementation has been done yet, or the repository is only intended to be a limited example, demo, or proof-of-concept.](https://www.repostatus.org/badges/latest/concept.svg)](https://www.repostatus.org/#concept)
-[![R build status](https://github.com/seroanalytics/serovizr/workflows/R-CMD-check/badge.svg)](https://github.com/seroanalytics/serovizr/actions)
-[![Codecov test coverage](https://codecov.io/gh/seroanalytics/serovizr/branch/master/graph/badge.svg)](https://codecov.io/gh/seroanalytics/serovizr?branch=master)
+[![R-CMD-check.yaml](https://github.com/seroanalytics/serovizr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/seroanalytics/serovizr/actions/workflows/R-CMD-check.yaml)[![Codecov test coverage](https://codecov.io/gh/seroanalytics/serovizr/branch/master/graph/badge.svg)](https://codecov.io/gh/seroanalytics/serovizr?branch=master)
 <!-- badges: end -->
 
 R API for the SeroViz app. Based on the [porcelain](https://github.com/reside-ic/porcelain) framework.

tests/testtthat.R

@@ -1,4 +1,4 @@
 library(testthat)
 library(serovizr)
 
-test_check("mintr")
+test_check("serovizr")