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

 Package: cBioPortalData

 Title: Exposes and makes available data from the cBioPortal web resources

-Version: 0.99.47

+Version: 0.99.48

 Authors@R: c(person("Levi", "Waldron", email = "[email protected]",

     role = "aut"),

     person("Marcel", "Ramos", email = "[email protected]",

@@ -8,14 +8,23 @@ Authors@R: c(person("Levi", "Waldron", email = "[email protected]",

 Description: The cBioPortalData package takes compressed resources

     from repositories such as cBioPortal and assembles a MultiAssayExperiment

     object with Bioconductor classes.

-Depends: R (>= 3.5.0)

+Depends: R (>= 3.5.0),

+    MultiAssayExperiment

 Imports:

     BiocFileCache (>= 1.5.3),

-    MultiAssayExperiment,

-    S4Vectors,

+    GenomeInfoDb,

+    GenomicRanges,

+    httr,

+    methods,

+    rappdirs,

     readr,

+    RaggedExperiment,

     RTCGAToolbox,

-    TCGAutils

+    S4Vectors,

+    SummarizedExperiment,

+    stats,

+    TCGAutils,

+    utils

 Suggests:

     BiocStyle,

     curl,

@@ -29,6 +38,7 @@ RoxygenNote: 6.1.0

 Collate: 

     'cBioPortalData-pkg.R'

     'cache.R'

+    'data.R'

     'utils.R'

     'loadStudy.R'

     'studyDownload.R'

@@ -14,6 +14,10 @@ importFrom(BiocFileCache,bfcneedsupdate)

 importFrom(BiocFileCache,bfcquery)

 importFrom(BiocFileCache,bfcremove)

 importFrom(BiocFileCache,bfcrpath)

+importFrom(BiocFileCache,bfcupdate)

+importFrom(GenomeInfoDb,"genome<-")

+importFrom(GenomeInfoDb,genome)

+importFrom(GenomicRanges,makeGRangesListFromDataFrame)

 importFrom(MultiAssayExperiment,ExperimentList)

 importFrom(MultiAssayExperiment,MultiAssayExperiment)

 importFrom(S4Vectors,"metadata<-")

@@ -22,8 +26,15 @@ importFrom(S4Vectors,SimpleList)

 importFrom(S4Vectors,isSingleString)

 importFrom(S4Vectors,metadata)

 importFrom(SummarizedExperiment,SummarizedExperiment)

+importFrom(SummarizedExperiment,rowData)

 importFrom(TCGAutils,TCGAbarcode)

 importFrom(TCGAutils,findGRangesCols)

 importFrom(TCGAutils,generateMap)

+importFrom(methods,as)

+importFrom(methods,is)

 importFrom(readr,read_tsv)

 importFrom(readr,type_convert)

+importFrom(stats,na.omit)

+importFrom(utils,data)

+importFrom(utils,download.file)

+importFrom(utils,untar)

@@ -1,9 +1,14 @@

 #' @importFrom S4Vectors isSingleString metadata metadata<- SimpleList DataFrame

-#' @importFrom SummarizedExperiment SummarizedExperiment

+#' @importFrom SummarizedExperiment SummarizedExperiment rowData

+#' @importFrom GenomicRanges makeGRangesListFromDataFrame

+#' @importFrom GenomeInfoDb genome genome<-

 #' @importFrom readr read_tsv type_convert

 #' @importFrom MultiAssayExperiment MultiAssayExperiment ExperimentList

 #' @importFrom TCGAutils generateMap TCGAbarcode findGRangesCols

 #' @import RTCGAToolbox

 #' @importFrom BiocFileCache BiocFileCache bfcquery bfcadd bfcneedsupdate

-#' bfcdownload bfcrpath bfcremove bfccache

+#' bfcdownload bfcrpath bfcremove bfccache bfcupdate

+#' @importFrom methods as is

+#' @importFrom stats na.omit

+#' @importFrom utils data download.file untar

 NULL

@@ -39,8 +39,10 @@ loadStudy <- function(cancer_study_id, use_cache = TRUE,

     cancer_file <- downloadStudy(cancer_study_id, use_cache)

-    filelist <- untar(cancer_file, list = TRUE,

-        extras = "--warning=no-unknown-keyword")

+    exarg <- if (rappdirs:::get_os() == "unix")

+        "--warning=no-unknown-keyword" else NULL

+

+    filelist <- untar(cancer_file, list = TRUE, extras = exarg)

     filelist <- gsub("^\\.\\/", "", filelist)

     filekeepind <- grep("^\\._", basename(filelist), invert = TRUE)

     filelist <- filelist[filekeepind]

@@ -169,8 +171,8 @@ cbioportal2se <- function(file, ...) {

   rowdat <- DataFrame(df[,!numeric.cols])

   ##  rownames(rowdat) <- make.names(rowdat[, 1], unique=TRUE)

   se <-

-    SummarizedExperiment(assays = as(df[, numeric.cols], "matrix"),

-                                               rowData = rowdat)

+    SummarizedExperiment::SummarizedExperiment(

+        assays = as(df[, numeric.cols], "matrix"), rowData = rowdat)

   if(!all(grep("TCGA", rowData(se)[, 1])))

       return(NULL)

   rownames(se) <- rowData(se)[, 1]

@@ -41,7 +41,7 @@ a cache if not already created. A specific directory can be used via

 Specify the directory location of the data cache. By default, it will

 got to the user's home/.cache and "appname" directory as specified by

-\link{user_cache_dir}. (default appname: MultiAssayExperimentData)

+\link{user_cache_dir}. (default appname: cBioPortalData)

 }

 \section{removeCache}{