Removing devtools from requirements

QiStark · May 21, 2016 · a328323 · a328323
1 parent af2336a
commit a328323
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Showing 4 changed files with 8 additions and 7 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -58,7 +58,6 @@ Imports:
     GenomicFeatures,
     TxDb.Hsapiens.UCSC.hg19.knownGene,
     limma,
-    devtools,
     genefilter,
     ConsensusClusterPlus,
     RColorBrewer,
@@ -100,7 +99,8 @@ Suggests:
     testthat,
     png,
     BiocStyle,
-    rmarkdown
+    rmarkdown,
+    devtools
 VignetteBuilder: knitr
 LazyData: true
 URL: https://github.com/BioinformaticsFMRP/TCGAbiolinks

diff --git a/NAMESPACE b/NAMESPACE
@@ -104,8 +104,6 @@ importFrom(data.table,setDF)
 importFrom(data.table,setDT)
 importFrom(data.table,setcolorder)
 importFrom(data.table,setnames)
-importFrom(devtools,load_all)
-importFrom(devtools,use_data)
 importFrom(dnet,dCommSignif)
 importFrom(dnet,dNetInduce)
 importFrom(dnet,dNetPipeline)

diff --git a/R/TCGAupdate.R b/R/TCGAupdate.R
@@ -208,9 +208,11 @@ tcgaGetTable <- function(url, max = 0) {
 #'
 #' The package will be updated with lastest version of the table every week.
 #' @return platform/center/disease/data tables will be updated in the package
-#' @importFrom devtools use_data load_all
+# @importFrom devtools use_data load_all
 #' @keywords internal
 TCGAUpdate <- function(){
+    if (requireNamespace("devtools", quietly = TRUE)) {
+
     tcga.root <- "http://tcga-data.nci.nih.gov/tcgadccws/GetHTML?"
 
     # Get platform table
@@ -252,14 +254,15 @@ TCGAUpdate <- function(){
 
     gene.location <- get.GRCh.bioMart()
     #gene.location <- get("gene.location")
-    use_data(platform.table, disease.table, tcga.db, center.table,
+    devtools::use_data(platform.table, disease.table, tcga.db, center.table,
              DAVID_BP_matrix,DAVID_CC_matrix,DAVID_MF_matrix,
              EAGenes,gene.location,listEA_pathways, acc.subtype,
              lgg.gbm.subtype, luad.subtype,skcm.subtype,
              hnsc.subtype, kich.subtype, lusc.subtype, ucec.subtype,
              pancan.subtype, thca.subtype, prad.subtype, kirp.subtype, kirc.subtype,
              stad.subtype, brca.subtype, coad.subtype,
              internal = TRUE,overwrite = TRUE)
+    }
 }
 
 

diff --git a/vignettes/tcgaBiolinks.Rmd b/vignettes/tcgaBiolinks.Rmd
@@ -320,7 +320,7 @@ knitr::opts_chunk$set(cache=FALSE)
 ```
 
 ```{r, echo = FALSE,hide=TRUE, message=FALSE,warning=FALSE}
-devtools::load_all(".")
+library("TCGAbiolinks")
 ```
 
 ## Introduction