diff --git a/R/getEnrichrdb.R b/R/getEnrichrdb.R index 0cd0f03..551fb27 100644 --- a/R/getEnrichrdb.R +++ b/R/getEnrichrdb.R @@ -50,7 +50,7 @@ getEnrichrdb <- function(org = c('human','fly','yeast','worm','zebrafish'), res[[i]] = suppressWarnings(fst::read.fst(destfile)) } - res[['geneset_name']] <- NA + res[['geneset_name']] <- data.frame(term = character(0), name = character(0), stringsAsFactors = FALSE) #--- add org for other use ---# ensOrg_name <- ensOrg_name_data() diff --git a/R/getHgDisease.R b/R/getHgDisease.R index 6a4d24e..971e1f5 100644 --- a/R/getHgDisease.R +++ b/R/getHgDisease.R @@ -59,7 +59,7 @@ getHgDisease <- function(source = c('do','disgenet','ncg_v7','ncg_v6','covid19') data_dir, web_f_size, local_f_size) res[[i]] = suppressMessages(fst::read.fst(destfile)) }else{ - res[['geneset_name']] <- NA + res[['geneset_name']] <- data.frame(term = character(0), name = character(0), stringsAsFactors = FALSE) } #--- add org for other use ---# diff --git a/R/getKEGG.R b/R/getKEGG.R index 7096b81..c70a492 100644 --- a/R/getKEGG.R +++ b/R/getKEGG.R @@ -26,7 +26,7 @@ getKEGG <- function(org = 'hsa', # category <- tolower(category) if(category %in% c('disease','drug','network') & org != 'hsa'){ - stop(paste0('The categoty "',category, '" only support human...')) + stop(paste0('The category "',category, '" only supports human...')) } if(is.null(data_dir)){ @@ -41,7 +41,7 @@ getKEGG <- function(org = 'hsa', for(i in c("geneset","geneset_name")){ # i = 'geneset' url <- paste0(web.url(),sub_dir,category,'/',org,"_",i,".fst") - destfile <- paste0(data_dir, "/", org, "_",i,".fst") + destfile <- paste0(data_dir, "/", org, "_", category, "_", i, ".fst") web_f_size <- check_web_size(url) local_f_size <- file.size(destfile) if(is.na(local_f_size)) local_f_size = 0 diff --git a/R/getMsigdb.R b/R/getMsigdb.R index 256f276..7ccabb8 100644 --- a/R/getMsigdb.R +++ b/R/getMsigdb.R @@ -172,7 +172,7 @@ getMsigdb <- function(org = 'human', #------------------------------# res <- list() res[["geneset"]] <- geneset - res[["geneset_name"]] <- NA + res[["geneset_name"]] <- data.frame(term = character(0), name = character(0), stringsAsFactors = FALSE) # Add organism for other use, preserving the original output behavior. ensOrg_name <- ensOrg_name_data() diff --git a/R/utilities.R b/R/utilities.R index af4c24e..0829ce5 100644 --- a/R/utilities.R +++ b/R/utilities.R @@ -467,10 +467,11 @@ geneset_download <- function(url, destfile, data_dir, if (!ok) { if (!local_exists) { - message( - "No valid local cache is available.\n", + stop( + "Download failed and no local cache is available.\n", "Please download manually via: ", url, "\n", - "Then save to: ", destfile + "Then save to: ", destfile, + call. = FALSE ) } return(invisible(FALSE))