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### Running command:
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###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SpatialExperiment.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings SpatialExperiment_1.9.3.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/SpatialExperiment.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'SpatialExperiment/DESCRIPTION' ... OK
* this is package 'SpatialExperiment' version '1.9.3'
* 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 'SpatialExperiment' 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 R 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
Unexported object imported by a ':::' call: 'S4Vectors:::disableValidity'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'SpatialExperiment-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SpatialExperiment-assays
> ### Title: Methods for named assays
> ### Aliases: SpatialExperiment-assays molecules molecules<-
> ###   molecules,SpatialExperiment-method
> ###   molecules<-,SpatialExperiment-method
> 
> ### ** Examples
> 
> example(SpatialExperiment)

SptlEx> #########################################################
SptlEx> # Example 1: Spot-based ST (10x Visium) using constructor
SptlEx> #########################################################
SptlEx> 
SptlEx> dir <- system.file(
SptlEx+     file.path("extdata", "10xVisium", "section1", "outs"),
SptlEx+     package = "SpatialExperiment")

SptlEx> # read in counts
SptlEx> fnm <- file.path(dir, "raw_feature_bc_matrix")

SptlEx> sce <- DropletUtils::read10xCounts(fnm)
as(<dgTMatrix>, "dgCMatrix") is deprecated since Matrix 1.5-0; do as(., "CsparseMatrix") instead

SptlEx> # read in image data
SptlEx> img <- readImgData(
SptlEx+     path = file.path(dir, "spatial"),
SptlEx+     sample_id="foo")

SptlEx> # read in spatial coordinates
SptlEx> fnm <- file.path(dir, "spatial", "tissue_positions_list.csv")

SptlEx> xyz <- read.csv(fnm, header = FALSE,
SptlEx+     col.names = c(
SptlEx+         "barcode", "in_tissue", "array_row", "array_col",
SptlEx+         "pxl_row_in_fullres", "pxl_col_in_fullres"))

SptlEx> # construct observation & feature metadata
SptlEx> rd <- S4Vectors::DataFrame(
SptlEx+     symbol = rowData(sce)$Symbol)

SptlEx> # construct 'SpatialExperiment'
SptlEx> (spe <- SpatialExperiment(
SptlEx+     assays = list(counts = assay(sce)),
SptlEx+     rowData = rd,
SptlEx+     colData = DataFrame(xyz),
SptlEx+     spatialCoordsNames = c("pxl_col_in_fullres", "pxl_row_in_fullres"),
SptlEx+     imgData = img,
SptlEx+     sample_id = "foo"))
class: SpatialExperiment 
dim: 50 50 
metadata(0):
assays(1): counts
rownames(50): ENSMUSG00000051951 ENSMUSG00000089699 ...
  ENSMUSG00000005886 ENSMUSG00000101476
rowData names(1): symbol
colnames: NULL
colData names(5): barcode in_tissue array_row array_col sample_id
reducedDimNames(0):
mainExpName: NULL
altExpNames(0):
spatialCoords names(2) : pxl_col_in_fullres pxl_row_in_fullres
imgData names(4): sample_id image_id data scaleFactor

SptlEx> #############################################################
SptlEx> # Example 2: Spot-based ST (10x Visium) using 'read10xVisium'
SptlEx> #############################################################
SptlEx> 
SptlEx> # see ?read10xVisium for details
SptlEx> example(read10xVisium)

rd10xV> dir <- system.file(
rd10xV+   file.path("extdata", "10xVisium"), 
rd10xV+   package = "SpatialExperiment")

rd10xV> sample_ids <- c("section1", "section2")

rd10xV> samples <- file.path(dir, sample_ids, "outs")

rd10xV> list.files(samples[1])
[1] "raw_feature_bc_matrix" "spatial"              

rd10xV> list.files(file.path(samples[1], "spatial"))
[1] "scalefactors_json.json"    "tissue_lowres_image.png"  
[3] "tissue_positions_list.csv"

rd10xV> file.path(samples[1], "raw_feature_bc_matrix")
[1] "F:/biocbuild/bbs-3.17-bioc/R/library/SpatialExperiment/extdata/10xVisium/section1/outs/raw_feature_bc_matrix"

rd10xV> (spe <- read10xVisium(samples, sample_ids, 
rd10xV+   type = "sparse", data = "raw", 
rd10xV+   images = "lowres", load = FALSE))
class: SpatialExperiment 
dim: 50 99 
metadata(0):
assays(1): counts
rownames(50): ENSMUSG00000051951 ENSMUSG00000089699 ...
  ENSMUSG00000005886 ENSMUSG00000101476
rowData names(1): symbol
colnames(99): AAACAACGAATAGTTC-1 AAACAAGTATCTCCCA-1 ...
  AAAGTCGACCCTCAGT-1 AAAGTGCCATCAATTA-1
colData names(4): in_tissue array_row array_col sample_id
reducedDimNames(0):
mainExpName: NULL
altExpNames(0):
spatialCoords names(2) : pxl_col_in_fullres pxl_row_in_fullres
imgData names(4): sample_id image_id data scaleFactor

rd10xV> # base directory 'outs/' from Space Ranger can also be omitted
rd10xV> samples2 <- file.path(dir, sample_ids)

rd10xV> (spe2 <- read10xVisium(samples2, sample_ids, 
rd10xV+   type = "sparse", data = "raw", 
rd10xV+   images = "lowres", load = FALSE))
class: SpatialExperiment 
dim: 50 99 
metadata(0):
assays(1): counts
rownames(50): ENSMUSG00000051951 ENSMUSG00000089699 ...
  ENSMUSG00000005886 ENSMUSG00000101476
rowData names(1): symbol
colnames(99): AAACAACGAATAGTTC-1 AAACAAGTATCTCCCA-1 ...
  AAAGTCGACCCTCAGT-1 AAAGTGCCATCAATTA-1
colData names(4): in_tissue array_row array_col sample_id
reducedDimNames(0):
mainExpName: NULL
altExpNames(0):
spatialCoords names(2) : pxl_col_in_fullres pxl_row_in_fullres
imgData names(4): sample_id image_id data scaleFactor

rd10xV> # tabulate number of spots mapped to tissue
rd10xV> cd <- colData(spe)

rd10xV> table(
rd10xV+   in_tissue = cd$in_tissue, 
rd10xV+   sample_id = cd$sample_id)
         sample_id
in_tissue section1 section2
    FALSE       28       27
    TRUE        22       22

rd10xV> # view available images
rd10xV> imgData(spe)
DataFrame with 2 rows and 4 columns
Error in magick_image_readpath(path, density, depth, strip, defines) : 
  Rterm.exe: UnableToOpenBlob `F:\biocbuild\bbs-3.17-bioc-rtools43\meat\SpatialExperiment.Rcheck\file:\F:\biocbuild\bbs-3.17-bioc\R\library\SpatialExperiment\extdata\10xVisium\section1\outs\spatial\tissue_lowres_image.png': Invalid argument @ error/blob.c/OpenBlob/2924
Calls: example ... NROW -> dim -> dim -> image_read -> magick_image_readpath
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_SpatialImage-methods.R:14'): dim,Stored-/LoadedSpatialImage is instant ──
  <Magick::ErrorBlob/C++Error/error/condition>
  Error in `magick_image_readpath(path, density, depth, strip, defines)`: Rterm.exe: UnableToOpenBlob `F:\biocbuild\bbs-3.17-bioc-rtools43\meat\SpatialExperiment.Rcheck\tests\testthat\file:\F:\biocbuild\bbs-3.17-bioc\R\library\SpatialExperiment\extdata\10xVisium\section1\outs\spatial\tissue_lowres_image.png': Invalid argument @ error/blob.c/OpenBlob/2924
  Backtrace:
      ▆
   1. ├─methods (local) dim(spi) at test_SpatialImage-methods.R:14:20
   2. └─SpatialExperiment (local) dim(spi)
   3.   └─magick::image_read(src)
   4.     └─magick:::magick_image_readpath(path, density, depth, strip, defines)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 247 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/SpatialExperiment.Rcheck/00check.log'
for details.