Merge pull request #199 from zhanghao-njmu/develop

Fix some bugs
zhanghao-njmu · Nov 2, 2023 · 063c3a5 · 063c3a5
2 parents 887a1bc + 6e53e8e
commit 063c3a5
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Showing 4 changed files with 9 additions and 4 deletions.
diff --git a/R/SCP-analysis.R b/R/SCP-analysis.R
@@ -4068,7 +4068,10 @@ RunMonocle2 <- function(srt, assay = NULL, slot = "counts", expressionFamily = "
                         root_state = NULL, seed = 11) {
   set.seed(seed)
   check_R(c("monocle", "DDRTree", "BiocGenerics", "Biobase", "VGAM"))
-  attachNamespace("DDRTree")
+
+  if (!"package:DDRTree" %in% search()) {
+    attachNamespace("DDRTree")
+  }
 
   assay <- assay %||% DefaultAssay(srt)
   expr_matrix <- as.sparse(GetAssayData(srt, assay = assay, slot = slot))

diff --git a/R/SCP-app.R b/R/SCP-app.R
@@ -591,7 +591,7 @@ RunSCExplorer <- function(base_dir = "SCExplorer",
                           style_script = require("styler", quietly = TRUE),
                           overwrite = FALSE,
                           return_app = TRUE) {
-  check_R(c("rhdf5", "HDF5Array", "shiny@1.6.0", "ggplot2", "ragg", "htmlwidgets", "plotly", "bslib", "future", "promises", "BiocParallel"))
+  check_R(c("rhdf5", "HDF5Array", "shiny", "ggplot2", "ragg", "htmlwidgets", "plotly", "bslib", "future", "promises", "BiocParallel"))
   DataFile_full <- paste0(base_dir, "/", DataFile)
   MetaFile_full <- paste0(base_dir, "/", MetaFile)
   if (!file.exists(DataFile_full) || !file.exists(MetaFile_full)) {

diff --git a/R/SCP-cellqc.R b/R/SCP-cellqc.R
@@ -344,7 +344,7 @@ RunCellQC <- function(srt, assay = "RNA", split.by = NULL,
   }
   status <- check_DataType(srt, slot = "counts", assay = assay)
   if (status != "raw_counts") {
-    stop("Data type is not raw counts!")
+    warning("Data type is not raw counts!")
   }
   if (!paste0("nCount_", assay) %in% colnames(srt@meta.data)) {
     srt@meta.data[[paste0("nCount_", assay)]] <- colSums(srt[[assay]]@counts)

diff --git a/R/Seurat-function.R b/R/Seurat-function.R
@@ -120,7 +120,9 @@ RunNMF.default <- function(object, assay = NULL, slot = "data", nbes = 50,
     check_R("zdebruine/RcppML")
     options("RcppML.verbose" = FALSE)
     options("RcppML.threads" = 0)
-    attachNamespace("Matrix")
+    if (!"package:Matrix" %in% search()) {
+      attachNamespace("Matrix")
+    }
     nmf.results <- RcppML::nmf(
       t(object),
       k = nbes, tol = tol, maxit = maxit,