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### Running command:
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###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RegionalST.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings RegionalST_1.5.5.tar.gz
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/RegionalST.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'RegionalST/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RegionalST' version '1.5.5'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'RegionalST' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'BiocStyle'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GetCellTypeSpecificDE_withProp: no visible binding for global variable
  'OneRegOut1'
GetCellTypeSpecificDE_withProp: no visible binding for global variable
  'twoCenter'
GetCellTypeSpecificDE_withProp: no visible binding for global variable
  'OneRegOut2'
Undefined global functions or variables:
  OneRegOut1 OneRegOut2 twoCenter
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'RegionalST-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RankCenterByEntropy
> ### Title: Automatically rank ROI centers based on entropy
> ### Aliases: RankCenterByEntropy
> 
> ### ** Examples
> 
> data("example_sce")
> example_sce <- mySpatialPreprocess(example_sce, platform="Visium")
> weight <- data.frame(celltype = c("Cancer Epithelial", "CAFs", "T-cells", "Endothelial",
+                                   "PVL", "Myeloid", "B-cells", "Normal Epithelial", "Plasmablasts"),
+                      weight = c(0.25,0.05,
+                                 0.25,0.05,
+                                 0.025,0.05,
+                                 0.25,0.05,0.025))
> example_sce <- RankCenterByEntropy(example_sce, weight, label = "celltype",
+                                   selectN = round(length(example_sce$spot)/10),
+                                   topN = 3, min_radius = 10,
+                                   radius_vec = c(10,15),
+                                   doPlot = TRUE)
Processing to Radius = 10


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Error in cor(sce$array_col, sce$pxl_col_in_fullres) : 
  supply both 'x' and 'y' or a matrix-like 'x'
Calls: RankCenterByEntropy ... eval -> <Anonymous> -> .make_vertices -> .flip_axis -> cor
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
GetCrossRegionalDE_raw       10.11   0.47   10.58
DoGSEA                        5.69   0.22   18.61
GetOneRadiusEntropy           5.76   0.07    5.83
GetCrossRegionalDE_withProp   5.27   0.29    5.58
GetOneRadiusEntropy_withProp  4.75   0.32    5.11
DrawDotplot                   4.33   0.14   16.96
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/RegionalST.Rcheck/00check.log'
for details.