Changes to fix warnings/ notes to satisfy CRAN checks

.gitignore

@@ -15,3 +15,4 @@ ensemblQueryR.Rproj
 /R/legacyCode.R
 .rprof.log
 rprof.log
+CRAN-SUBMISSION

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
 Version: 0.1.0
-Date: 2023-05-17 11:53:59 UTC
-SHA: 450efffe2986841750eb647321d214b58eaa0097
+Date: 2023-05-17 12:47:17 UTC
+SHA: 3e878f448b3431965ebf07207a4d2eb828af1c3f

DESCRIPTION

@@ -4,7 +4,7 @@ Title: Simple, Fast and Efficient Querying of the Ensembl API
 Version: 0.1.0
 Author: Aine Fairbrother-Browne
 Maintainer: The package maintainer <[email protected]>
-Description: Simple, Fast and Efficient Querying of the Ensembl API
+Description: Simple, Fast and Efficient Querying of the Ensembl API.
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
@@ -14,7 +14,9 @@ Imports:
     httr,
     jsonlite,
     magrittr,
+    parallel,
     purrr,
+    tibble,
     tidyr,
     vroom,
     xml2

NAMESPACE

@@ -10,10 +10,11 @@ export(ensemblQueryLDwithSNPwindowDataframe)
 export(pingEnsembl)
 import(dplyr)
 import(httr)
-import(jsonlite)
 import(parallel)
 import(purrr)
 import(tidyr)
 import(vroom)
 import(xml2)
+importFrom(jsonlite,fromJSON)
+importFrom(jsonlite,toJSON)
 importFrom(magrittr,"%>%")

R/ensemblQueryLDpairEndpoint.R

@@ -9,7 +9,7 @@
 #'
 #' @import httr
 #' @import xml2
-#' @import jsonlite
+#' @importFrom jsonlite fromJSON toJSON
 #' @import dplyr
 #' @import tidyr
 #' @import vroom
@@ -55,7 +55,7 @@ ensemblQueryLDwithSNPpair = function(rsid1, rsid2, pop="1000GENOMES:phase_3:EUR"
   server <- "https://rest.ensembl.org"
   ext <- paste0("/ld/human/pairwise/",rsid1,"/",rsid2,"?population_name=",pop)
 
-  r <- httr::GET(url=paste(server, ext, sep = ""), content_type("application/json"))
+  r <- httr::GET(url=paste(server, ext, sep = ""), httr::content_type("application/json"))
 
   # stop_for_status(r)
 
@@ -125,8 +125,10 @@ ensemblQueryLDwithSNPpair = function(rsid1, rsid2, pop="1000GENOMES:phase_3:EUR"
 #'
 #' @examples
 #'ensemblQueryLDwithSNPpairDataframe(
-#'  in.table=data.frame(rsid1=rep("rs6792369", 10), rsid2=rep("rs1042779", 10)),
-#'  pop="1000GENOMES:phase_3:EUR")
+#'  in.table=data.frame(rsid1=rep("rs6792369", 10),
+#'                      rsid2=rep("rs1042779", 10)),
+#'                      pop="1000GENOMES:phase_3:EUR"
+#')
 #'
 ensemblQueryLDwithSNPpairDataframe = function(in.table, pop="1000GENOMES:phase_3:EUR", cores=1){ #keep.original.table.row.n=FALSE
 

R/ensemblQueryLDregionEndpoint.R

@@ -9,7 +9,7 @@
 #'
 #' @import httr
 #' @import xml2
-#' @import jsonlite
+#' @importFrom jsonlite fromJSON toJSON
 #' @import dplyr
 #' @import tidyr
 #' @import vroom
@@ -57,7 +57,7 @@ ensemblQueryLDwithSNPregion = function(chr, start, end, pop="1000GENOMES:phase_3
   server <- "https://rest.ensembl.org"
   ext <- paste0("/ld/human/region/",chr,":",start,"..",end,"/",pop,"?")
 
-  r <- httr::GET(url=paste(server, ext, sep = ""), content_type("application/json"))
+  r <- httr::GET(url=paste(server, ext, sep = ""), httr::content_type("application/json"))
 
   # stop_for_status(r)
 

R/ensemblQueryLDwindowEndpoint.R

@@ -11,7 +11,7 @@
 #'
 #' @import httr
 #' @import xml2
-#' @import jsonlite
+#' @importFrom jsonlite fromJSON toJSON
 #' @import dplyr
 #' @import tidyr
 #' @import vroom
@@ -20,7 +20,8 @@
 #' @export
 #'
 #' @examples
-#' ensemblQueryLDwithSNPwindow(rsid="rs3851179", r2=0.8, d.prime=0.8, window.size=500, pop="1000GENOMES:phase_3:EUR")
+#' ensemblQueryLDwithSNPwindow(rsid="rs3851179", r2=0.8, d.prime=0.8,
+#'                             window.size=500, pop="1000GENOMES:phase_3:EUR")
 #'
 ensemblQueryLDwithSNPwindow = function(rsid, r2=0.8, d.prime=0.8, window.size=500, pop="1000GENOMES:phase_3:EUR"){
 
@@ -56,7 +57,7 @@ ensemblQueryLDwithSNPwindow = function(rsid, r2=0.8, d.prime=0.8, window.size=50
   server <- "https://rest.ensembl.org"
   ext <- paste0("/ld/human/",rsid,"/",pop,"?d_prime=",d.prime,";window_size=",window.size,";r2=",r2)
 
-  r <- httr::GET(url=paste(server, ext, sep = ""), content_type("application/json"))
+  r <- httr::GET(url=paste(server, ext, sep = ""), httr::content_type("application/json"))
 
   #-------------------- check output and write out ---------------------------
 
@@ -130,7 +131,9 @@ ensemblQueryLDwithSNPwindow = function(rsid, r2=0.8, d.prime=0.8, window.size=50
 #' @export
 #'
 #' @examples
-#' in.table = data.frame(rsid = rep(c("rs7153434","rs1963154","rs12672022","rs3852802","rs12324408","rs56346870"), 10))
+#' in.table = data.frame(rsid = rep(c("rs7153434","rs1963154","rs12672022",
+#'                                    "rs3852802","rs12324408","rs56346870"), 10))
+#'
 #' ensemblQueryLDwithSNPwindowDataframe(in.table=in.table,
 #'                                      r2=0.8,
 #'                                      d.prime=0.8,

R/ensemblQueryR-package.R

@@ -0,0 +1,9 @@
+#' @keywords internal
+"_PACKAGE"
+
+## usethis namespace: start
+#' @importFrom jsonlite fromJSON
+#' @importFrom jsonlite toJSON
+#' @importFrom magrittr %>%
+## usethis namespace: end
+NULL

R/helperFunctions.R

@@ -4,7 +4,7 @@
 #'
 #' @import httr
 #' @import xml2
-#' @import jsonlite
+#' @importFrom jsonlite fromJSON toJSON
 #' @importFrom magrittr %>%
 #'
 #' @export
@@ -33,7 +33,7 @@ ensemblQueryGetPops = function(){
 #'
 #' @import httr
 #' @import xml2
-#' @import jsonlite
+#' @importFrom jsonlite fromJSON toJSON
 #'
 #' @export
 #'
@@ -53,34 +53,3 @@ pingEnsembl = function(){
 
   return(response)
 }
-
-# estimateQueriesPerHour = function(cores, n.queries){
-#
-#   # based on a single-core run of 54000 queries (max ensembl API query rate per hour) to ensemblQueryLDwithSNPpairDataframe,
-#   # the time taken to run 54000 queries was estimated to be 1.937771.
-#   # Based on this, this function takes the cores and number of queries input by the user and will output the predicted queries per hour that your run will likely spawn
-#   # this assumes a linear effect of additional cores
-#   cores=20
-#   n.queries=1000
-#   api.limit.hourly = 54000
-#   time_to_run_54000_in_hours = (116.266269091765/60)
-#   per_hour_query_rate = 54000/time_to_run_54000_in_hours
-#   per_minute_query_rate = per_hour_query_rate/60
-#   per_second_query_rate = per_minute_query_rate/60
-#   time_for_one_query_seconds = (time_to_run_54000_in_hours/54000)*60*60
-#
-#
-#
-#   if(time_for_user_queries < 15){
-#     print(paste(
-#       "Warning: your query of size",n.queries,"using",cores,"cores may exceed the Ensembl REST API hourly query limit. Consider using fewer cores or splitting your query into smaller chunks."
-#     ))
-#   }
-#
-#
-#   predicted_requests_per_hour = n.queries/(time_to_run_54000_in_hours/cores)
-#
-#
-#
-# }
-

README.md

@@ -11,15 +11,21 @@ The goal of ensemblQueryR is to seemlessly integrate querying of Ensembl databas
 
 ## Installation
 
-You can install the development version of ensemblQueryR like so:
+You can install ensemblQueryR as below.
 
 ``` r
 # load remotes package
 library(remotes)
 
+# to install the development version
 remotes::install_github("ainefairbrother/ensemblQueryR")
+
+# to install the stable CRAN release
+install.packages("ensemblQueryR")
 ```
 
+Or from
+
 ## Setup 
 
 To check that the Ensembl server is up and running, the server can be pinged. 

benchmarking/ensemblQueryR_vs_LDlinkR.R

@@ -1,8 +1,8 @@
-# load libs
-devtools::load_all("/home/abrowne/projects/ensemblQueryR/")
-library(LDlinkR)
-library(magrittr)
-library(peakRAM)
+# # load libs
+# devtools::load_all("/home/abrowne/projects/ensemblQueryR/")
+# library(LDlinkR)
+# library(magrittr)
+# library(peakRAM)
 
 # -- 1. Run benchmarking for 100,1000,10000 queries --------------------------------------------