@@ -1,7 +1,7 @@

 Package: CiteFuse

 Type: Package

 Title: CiteFuse: multi-modal analysis of CITE-seq data

-Version: 0.99.7

+Version: 0.99.8

 Authors@R: c(

     person("Yingxin", "Lin", email = "[email protected]", role = c("aut", "cre")

     ),

@@ -343,7 +343,7 @@ doWilcox <- function(exprsMat,

         keep <- meanPct[, 2] > exprs_pct

         test_res <- apply(exprsMat[keep,], 1, function(x)

-            stats::wilcox.test(x ~ tmp_celltype))

+            suppressWarnings(stats::wilcox.test(x ~ tmp_celltype)))

         test_res <- lapply(test_res, function(x) {

             stats <- x$statistic

@@ -168,6 +168,7 @@ preprocessing <- function(exprsMat = NULL,

 #'

 #' @examples

 #'

+#' \dontrun{

 #' tmpdir <- tempdir()

 #' tenXdata <- "http://cf.10xgenomics.com/samples/cell-exp/3.1.0/connect_5k_pbmc_NGSC3_ch1/"

 #' file <- "connect_5k_pbmc_NGSC3_ch1_filtered_feature_bc_matrix.tar.gz"

@@ -177,7 +178,7 @@ preprocessing <- function(exprsMat = NULL,

 #' sce_citeseq_10X <- readFrom10X(file.path(tmpdir,

 #' "filtered_feature_bc_matrix/"))

 #' sce_citeseq_10X

-#'

+#'}

 #'

 #' @export

 #'

@@ -30,6 +30,7 @@ A function to read the data from 10X

 }

 \examples{

+\dontrun{

 tmpdir <- tempdir()

 tenXdata <- "http://cf.10xgenomics.com/samples/cell-exp/3.1.0/connect_5k_pbmc_NGSC3_ch1/"

 file <- "connect_5k_pbmc_NGSC3_ch1_filtered_feature_bc_matrix.tar.gz"

@@ -39,6 +40,6 @@ untar(file.path(tmpdir,file),

 sce_citeseq_10X <- readFrom10X(file.path(tmpdir,

 "filtered_feature_bc_matrix/"))

 sce_citeseq_10X

-

+}

 }

@@ -572,7 +572,7 @@ de_res_filter

 Readers unfamiliar with the workflow of converting a count matrix into a `SingleCellExperiment` object may use the `readFrom10X` function to convert count matrix from a 10X experiment into an object that can be used for all functions in CiteFuse. 

-```{r}

+```{r eval = FALSE}

 tmpdir <- tempdir()

 download.file("http://cf.10xgenomics.com/samples/cell-exp/3.1.0/connect_5k_pbmc_NGSC3_ch1/connect_5k_pbmc_NGSC3_ch1_filtered_feature_bc_matrix.tar.gz", file.path(tmpdir, "/5k_pbmc_NGSC3_ch1_filtered_feature_bc_matrix.tar.gz"))

 untar(file.path(tmpdir, "5k_pbmc_NGSC3_ch1_filtered_feature_bc_matrix.tar.gz"),