@@ -1,6 +1,6 @@

 Package: BiocFileCache

 Title: Manage Files Across Sessions

-Version: 2.99.2

+Version: 2.99.3

 Authors@R: c(person("Lori", "Shepherd",

 email = "lori.shepherd@roswellpark.org",

 role = c("aut", "cre")),

@@ -323,7 +323,7 @@ setMethod("bfcadd", "missing",

 )

 {

 bfcadd(x=BiocFileCache(), rname=rname, fpath=fpath, rtype=rtype,

- action=action, proxy=proxy, download=download, config=config,

+ action=action, proxy=proxy, download=download, progress=progress, config=config,

 ext=ext, fname=fname,...)

 })

@@ -423,7 +423,7 @@ setMethod("bfcadd", "BiocFileCache",

 }

 )

 } else if (download) { # rtype == "web"

- .util_download(x, rid[i], proxy, config, progress, "bfcadd()", ...)

+ .util_download(x, rid[i], proxy, progress, config, "bfcadd()", ...)

 }

 }

@@ -626,7 +626,7 @@ setMethod("bfcupdate", "missing",

 #' @exportMethod bfcupdate

 setMethod("bfcupdate", "BiocFileCache",

 function(x, rids, ..., rname=NULL, rpath=NULL, fpath=NULL,

- proxy="", config=list(), progress=TRUE, ask=TRUE)

+ proxy="", progress=TRUE, config=list(), ask=TRUE)

 {

 stopifnot(!missing(rids), all(rids %in% bfcrid(x)))

 stopifnot(

@@ -691,7 +691,7 @@ setMethod("bfcupdate", "BiocFileCache",

 }

 if (doit) {

 .util_download_and_rename(

- x, rids[i], proxy, config, progress, "bfcupdate()", fpath[i], ...

+ x, rids[i], proxy, progress, config, "bfcupdate()", fpath[i], ...

 )

 .sql_set_fpath(x, rids[i], fpath[i])

 }

@@ -1057,7 +1057,7 @@ setMethod("bfcneedsupdate", "BiocFileCacheBase",

 #' @export

 setGeneric("bfcdownload",

- function(x, rid, proxy="", config=list(), ask=TRUE, FUN, ...)

+ function(x, rid, proxy="", progress=TRUE, config=list(), ask=TRUE, FUN, ...)

 standardGeneric("bfcdownload"),

 signature = "x"

 )

@@ -1069,7 +1069,7 @@ setGeneric("bfcdownload",

 setMethod("bfcdownload", "missing",

 function(x, rid, proxy="", config=list(), ask=TRUE, FUN, ...)

 {

- bfcdownload(x=BiocFileCache(), rid=rid, proxy=proxy, config=config, ask=ask,

+ bfcdownload(x=BiocFileCache(), rid=rid, proxy=proxy, progress=TRUE, config=config, ask=ask,

 FUN=FUN, ...)

 })

@@ -1088,7 +1088,7 @@ setMethod("bfcdownload", "missing",

 #' @aliases bfcdownload

 #' @exportMethod bfcdownload

 setMethod("bfcdownload", "BiocFileCache",

- function(x, rid, proxy="", config=list(), progress=TRUE, ask=TRUE, FUN, ...)

+ function(x, rid, proxy="", progress=TRUE, config=list(), ask=TRUE, FUN, ...)

 {

 stopifnot(

 !missing(rid), length(rid) > 0L,

@@ -1106,7 +1106,7 @@ setMethod("bfcdownload", "BiocFileCache",

 doit <- TRUE

 }

 if (doit)

- .util_download_and_rename(x, rid, proxy, config, progress, "bfcdownload()",

+ .util_download_and_rename(x, rid, proxy, progress, config, "bfcdownload()",

 FUN=FUN, ...)

 bfcrpath(x, rids=rid)

@@ -121,7 +121,7 @@

 #' @importFrom utils packageVersion

 .httr_download <-

- function(websource, localfile, proxy, config, progress, ...)

+ function(websource, localfile, proxy, progress, config, ...)

 {

 ## retrieve file from hub to cache

@@ -140,7 +140,7 @@

 if(missing(progress)){

 progress=TRUE

 }

- 

+

 if (!all(file.exists(dirname(localfile)))) dir.create(dirname(localfile), recursive=TRUE)

 # set up request using httr2

@@ -120,13 +120,13 @@

 }

 .util_download <-

- function(bfc, rid, proxy, config, progress, call, ...)

+ function(bfc, rid, proxy, progress, config, call, ...)

 {

 rpath <- .sql_get_rpath(bfc, rid)

 fpath <- .sql_get_fpath(bfc, rid)

 status <- Map(

 .httr_download, fpath, rpath,

- MoreArgs = list(proxy = proxy, config = config, progress = progress, ...)

+ MoreArgs = list(proxy = proxy, progress = progress, config = config, ...)

 )

 ok <- vapply(status, isTRUE, logical(1))

 if (!all(ok)) {

@@ -146,7 +146,7 @@

 }

 .util_download_and_rename <-

- function(bfc, rid, proxy, config, progress, call, fpath = .sql_get_fpath(bfc, rid),

+ function(bfc, rid, proxy, progress, config, call, fpath = .sql_get_fpath(bfc, rid),

 FUN, ...)

 {

 rpath <- .sql_get_rpath(bfc, rid)

@@ -164,7 +164,7 @@

 status <- Map(function(rpath, fpath) {

 temppath <- tempfile(tmpdir=bfccache(bfc))

- status <- .httr_download(fpath, temppath, proxy, config, progress, ...)

+ status <- .httr_download(fpath, temppath, proxy, progress, config, ...)

 if (!status)

 return("download failed")

@@ -181,8 +181,8 @@ bfcrid(x)

 rpath = NULL,

 fpath = NULL,

 proxy = "",

- config = list(),

 progress = TRUE,

+ config = list(),

 ask = TRUE

 )

@@ -220,14 +220,23 @@ bfcmeta(x, name, ...) <- value

 \S4method{bfcneedsupdate}{BiocFileCacheBase}(x, rids, ..., config = list())

-\S4method{bfcdownload}{missing}(x, rid, proxy = "", config = list(), ask = TRUE, FUN, ...)

+\S4method{bfcdownload}{missing}(

+ x,

+ rid,

+ proxy = "",

+ progress = TRUE,

+ config = list(),

+ ask = TRUE,

+ FUN,

+ ...

+)

 \S4method{bfcdownload}{BiocFileCache}(

 x,

 rid,

 proxy = "",

- config = list(),

 progress = TRUE,

+ config = list(),

 ask = TRUE,

 FUN,

 ...