simplifying - removing dependencies and vignettes

MRCIEU · Apr 21, 2024 · 88cc234 · 88cc234
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commit 88cc234
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Showing 9 changed files with 4 additions and 181 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -23,13 +23,10 @@ Imports:
     dplyr,
     httr,
     jsonlite,
-    magrittr,
-    rlang,
     stats
 Suggests: 
     knitr,
-    microbenchmark,
-    pander,
+    utils,
     rmarkdown,
     testthat
 VignetteBuilder: 

diff --git a/NAMESPACE b/NAMESPACE
@@ -2,7 +2,6 @@
 
 S3method(print,ApiStatus)
 S3method(print,GwasInfo)
-export("%>%")
 export(afl2_chrpos)
 export(afl2_list)
 export(afl2_rsid)
@@ -33,7 +32,5 @@ export(variants_chrpos)
 export(variants_gene)
 export(variants_rsid)
 export(variants_to_rsid)
-importFrom(magrittr,"%>%")
-importFrom(rlang,.data)
 importFrom(utils,read.table)
 importFrom(utils,write.table)
diff --git a/NEWS.md b/NEWS.md
@@ -6,6 +6,7 @@
 * Bug in tophits when result is empty
 * Removing version check at startup
 * Bug in querying when errors returned
+* Removing unnecessary dependancies and vignettes
 
 # ieugwasr 0.2.2
 * Reinstating https://api.opengwas.org/api/ as the API server address

diff --git a/R/globals.R b/R/globals.R
@@ -0,0 +1 @@
+utils::globalVariables(c(".", "%>%", ".data"))
diff --git a/R/utils-pipe.R b/R/utils-pipe.R
diff --git a/man/dot-data.Rd b/man/dot-data.Rd
diff --git a/man/pipe.Rd b/man/pipe.Rd
diff --git a/vignettes/guide.Rmd b/vignettes/guide.Rmd
@@ -26,7 +26,7 @@ From 1st May 2024, most queries to the OpenGWAS API will require user authentica
 
 To authenticate, you need to generate a token from the OpenGWAS website. The token behaves like a password, and it will be used to authorise the requests you make to the OpenGWAS API. Here are the steps to generate the token and then have `ieugwasr` automatically use it for your queries:
 
-1. Login to https://api.opengwas.io/profile
+1. Login to https://api.opengwas.io/profile/
 2. Generate a new token
 3. Add `OPENGWAS_JWT=<token>` to your `.Renviron` file. This file could be either in your home directory or in the working directory of your R session. You can check the location of your `.Renviron` file by running `Sys.getenv("R_ENVIRON_USER")` in R.
 4. Restart your R session

diff --git a/vignettes/timings.Rmd b/vignettes/timings.Rmd