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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,53 +1,32 @@ | ||
| #' Download PrecomputedData.db | ||
| #' | ||
| #' Downloads the PrecomputedData.db database that is needed for the | ||
| #' Download PrecomputedDataLight.db | ||
| #' | ||
| #' Downloads the PrecomputedDataLight.db database that is needed for the | ||
| #' computeGenericFeatures() function. This databased contains the values | ||
| #' of the Wilcoxon Rank tests and the CRUP correlations. | ||
| #' | ||
| #' | ||
| #' @param method Method to be used for downloading files. Check download.file() | ||
| #' manuals to see the current available methods | ||
| #' @return Integer code 0 if download was succesful and the file was saved in the | ||
| #' correct directory. In the case of failure errors will be raised. | ||
| #' manuals to see the current available methods | ||
| #' @param all Boolean value. When set to true, the PrecomputedDataAllTests.db | ||
| #' database will be downloaded too. This database holds all of the p-values | ||
| #' which are combined in "combined_tests" column. | ||
| #' @return Integer code 0 if download was succesful and the file was saved in | ||
| #' the correct directory. In the case of failure errors will be raised. | ||
| #' @examples | ||
| #' # methods accepts "internal", "wininet" (Windows only) ,"wget", "curl" etc. | ||
| #' # Assuming the user has wget available | ||
| #' downloadPrecomputedData(method="wget") | ||
| #' @export | ||
| #' @import utils | ||
|
|
||
| downloadPrecomputedData <- function(method) { | ||
| start_time <- Sys.time() | ||
| url <- "http://owww.molgen.mpg.de/~CENTRE_data/PrecomputedData.db" | ||
| cat("Downloading PrecomputedData.db\n") | ||
| exit <- download.file(url, | ||
| destfile=paste(system.file("extdata",package = "CENTRE") | ||
| , "PrecomputedData.db", | ||
| sep = "/") , | ||
| method = method) | ||
| if (exit != 0 ) { | ||
| stop("Download of PrecomputedData.db failed. Non-zero exit status.") | ||
| } | ||
|
|
||
| f <- system.file("extdata","PrecomputedData.db", package = "CENTRE") | ||
| if (!file.exists(f)){ | ||
| stop("Download of of PrecomputedData.db failed or file was saved in the wrong directory.") | ||
| } | ||
| ##Download sysdata.rda | ||
| url_sys <- "http://owww.molgen.mpg.de/~CENTRE_data/Annotation.db" | ||
| cat("Downloading sysdata.rda\n") | ||
| exit_sys <- download.file(url_sys, | ||
| destfile=paste(system.file("extdata", | ||
| package="CENTRE"), "Annotation.db", sep = "/"), | ||
| method = method) | ||
| if (exit_sys != 0 ) { | ||
| stop("Download Annotation.db failed. Non-zero exit status.") | ||
| } | ||
|
|
||
| fs <- system.file("extdata","PrecomputedData.db", package = "CENTRE") | ||
| if (!file.exists(fs)){ | ||
| stop("Download Annotation.db failed or file was saved in the wrong directory.") | ||
| } | ||
|
|
||
| cat(paste0('time: ', format(Sys.time() - start_time), "\n")) | ||
| return(0) | ||
| downloadPrecomputedData <- function(method, all = FALSE) { | ||
| start_time <- Sys.time() | ||
| #Download PrecomputedDataLight.db | ||
| downloader("PrecomputedDataLight.db", method) | ||
| #Download Annotation.db | ||
| downloader("Annotation.db", method) | ||
| if (all == TRUE) { | ||
| downloader("PrecomputedAllTests.db", method) | ||
| } | ||
| cat(paste0("time: ", format(Sys.time() - start_time), "\n")) | ||
| return(0) | ||
| } |
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