Merge pull request #100 from Artur-man/main

updating windows compilers for TPS interpolation

R/annotation.R

@@ -297,6 +297,7 @@ annotateSpatialData <- function(object, label = "annotation", assay = NULL, use.
           } else {
             spatialpoints <- rownames(metadata)
           }
+
           new_label <- rep("undefined", length(spatialpoints))
           names(new_label) <- spatialpoints
           result_list <- list()
@@ -339,4 +340,3 @@ annotateSpatialData <- function(object, label = "annotation", assay = NULL, use.
     shiny::runApp(shiny::shinyApp(ui, server))
   }
 }
-

R/visualization.R

@@ -170,7 +170,10 @@ vrSpatialPlot <- function(object, group.by = "Sample", plot.segments = FALSE, gr
       return(gg[[1]] + theme(legend.position=legend.loc))
     }
   } else {
-    gg + theme(legend.position=legend.loc)
+    for(i in 1:length(assay_names)){
+      gg[[i]] <- gg[[i]] + theme(legend.position=legend.loc)
+    }
+    return(gg)
   }
 }
 
@@ -259,6 +262,7 @@ vrSpatialPlotSingle <- function(assay, metadata, group.by = "Sample", plot.segme
   } else {
     coords[[group.by]] <- metadata[,group.by]
   }
+
   if(!is.null(group.ids)){
     if(length(setdiff(group.ids,  coords[[group.by]])) > 0){
       # warning("Some groups defined in group.ids does not exist in group.by!")
@@ -358,6 +362,7 @@ vrSpatialPlotSingle <- function(assay, metadata, group.by = "Sample", plot.segme
 
         # add points
         if(n.tile == 0){
+
           g <- g +
             geom_point(mapping = aes_string(x = "x", y = "y", fill = group.by, color = group.by), coords, shape = cell.shape, size = rel(pt.size), alpha = alpha) +
             scale_fill_manual(values = colors, labels = names(colors), drop = FALSE, limits = names(colors)) +
@@ -591,7 +596,10 @@ vrSpatialFeaturePlot <- function(object, features, group.by = "label", plot.segm
       return(gg[[1]] + theme(legend.position=legend.loc))
     }
   } else {
-    return(gg + theme(legend.position=legend.loc))
+    for(i in 1:(length(features)*length(assay_names))){
+      gg[[i]] <- gg[[i]] + theme(legend.position=legend.loc)
+    }
+    return(gg)
   }
 }
 

cleanup

@@ -1,17 +1,6 @@
 #!/bin/sh
 rm -f src/Makevars configure.log autobrew
 rm -Rf .deps
-
-rm -Rf .deps
-rm -Rf .deps
-rm -Rf .deps
-rm -Rf .deps
-rm -Rf .deps
-rm -Rf .deps
-rm -Rf .deps
-rm -Rf .deps
-rm -Rf .deps
-rm -Rf .deps
 rm -Rf .deps
 rm -Rf .deps
 rm -Rf .deps

src/Makevars.win

@@ -1,20 +1,14 @@
-VERSION = 4.7.0
-RWINLIB = ../windows/opencv-$(VERSION)
+RWINLIB = ../windows/opencv
 PKG_CPPFLAGS = -I$(RWINLIB)/include/opencv4 -DHAVE_XFEATURES2D
-TARGET = lib$(subst gcc,,$(COMPILED_BY))$(R_ARCH)
+OLDLIBDIR = lib${subst gcc,,${COMPILED_BY}}${R_ARCH}
 
 PKG_LIBS = \
-  $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) \
-	-L$(RWINLIB)/$(TARGET) \
-	-L$(RWINLIB)/lib$(R_ARCH) \
-	-lopencv_ml470 -lopencv_objdetect470 -lopencv_photo470 -lopencv_stitching470 \
-	-lopencv_video470 -lopencv_calib3d470 -lopencv_xfeatures2d470 -lopencv_features2d470 -lopencv_highgui470 -lopencv_flann470 \
-	-lopencv_videoio470 -lopencv_imgcodecs470 -lopencv_imgproc470 -lopencv_core470 -llibopenjp2 -lquirc -ltbb \
-	-ljpeg -lwebp -lpng -lz -ltiff \
-	-lcomctl32 -lgdi32 -lole32 -lsetupapi -lws2_32 -lavifil32 -lavicap32 -lwinmm -lmsvfw32 \
-	-lopengl32 -lglu32 -lcomdlg32 -lOleAut32 -luuid
-
-CXX_STD=CXX11
+	-L$(RWINLIB)/$(OLDLIBDIR) \
+	-L$(RWINLIB)/lib \
+	-lopencv_ml481 -lopencv_objdetect481 -lopencv_photo481 -lopencv_stitching481 -lopencv_shape481 -lopencv_wechat_qrcode481 -lopencv_dnn481 \
+	-lopencv_video481 -lopencv_calib3d481 -lopencv_xfeatures2d481 -lopencv_features2d481 -lopencv_highgui481 -lopencv_flann481 \
+	-lopencv_videoio481 -lopencv_imgcodecs481 -lopencv_imgproc481 -lopencv_core481 -llibopenjp2 -lquirc \
+	-ljpeg -lwebp -lsharpyuv -lpng -lz -ltiff -lpthread -lgdi32 -lole32 -lopengl32 -lcomdlg32 -lOleAut32 -luuid
 
 all: clean winlibs
 
@@ -24,4 +18,4 @@ clean:
 winlibs:
 	"${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" "../tools/winlibs.R" ${VERSION}
 	mkdir -p ../inst
-	cp -r $(RWINLIB)/share ../inst/
+	cp -r $(RWINLIB)/share ../inst/

tools/winlibs.R

@@ -1,12 +1,18 @@
-# We need https
-if(getRversion() < "3.3.0") setInternet2()
-VERSION <- commandArgs(TRUE)
-
-# Downloads libssh2 + dependencies
-options(timeout = 400)
-if(!file.exists(sprintf("../windows/opencv-%s/include/opencv4/opencv2/opencv.hpp", VERSION))){
-  download.file(sprintf("https://github.com/rwinlib/opencv/archive/v%s.zip", VERSION), "lib.zip", quiet = TRUE)
+if(!file.exists("../windows/opencv/include/opencv4/opencv2/opencv.hpp")){
+  unlink("../windows", recursive = TRUE)
+  url <- if(grepl("aarch", R.version$platform)){
+    "https://github.com/r-windows/bundles/releases/download/opencv-4.8.1/opencv-4.8.1-clang-aarch64.tar.xz"
+  } else if(grepl("clang", Sys.getenv('R_COMPILED_BY'))){
+    "https://github.com/r-windows/bundles/releases/download/opencv-4.8.1/opencv-4.8.1-clang-x86_64.tar.xz"
+  } else if(getRversion() >= "4.3") {
+    "https://github.com/r-windows/bundles/releases/download/opencv-4.8.1/opencv-4.8.1-ucrt-x86_64.tar.xz"
+  } else {
+    "https://github.com/rwinlib/opencv/archive/refs/tags/v4.8.1.tar.gz"
+  }
+  download.file(url, basename(url), quiet = TRUE)
   dir.create("../windows", showWarnings = FALSE)
-  unzip("lib.zip", exdir = "../windows")
-  unlink("lib.zip")
-}
+  untar(basename(url), exdir = "../windows", tar = 'internal')
+  unlink(basename(url))
+  setwd("../windows")
+  file.rename(list.files(), 'opencv')
+}