##############################################################################
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###
### Running command:
###
###   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
###
##############################################################################
##############################################################################


* 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.

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL SpatialExperiment
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'SpatialExperiment' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SpatialExperiment)

R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library("testthat")
> library("SpatialExperiment")
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

> test_check("SpatialExperiment")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 247 ]

══ 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