##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:visiumStitched.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings visiumStitched_1.1.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/visiumStitched.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘visiumStitched/DESCRIPTION’ ... OK
* this is package ‘visiumStitched’ version ‘1.1.2’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘visiumStitched’ 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: ‘GenomeInfoDb’
  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
.fit_to_array_lsap: no visible binding for global variable ‘key’
.fit_to_array_lsap: no visible binding for global variable
  ‘capture_area’
.fit_to_array_lsap: no visible binding for global variable
  ‘pxl_row_in_fullres’
.fit_to_array_lsap: no visible binding for global variable
  ‘pxl_col_in_fullres’
.map_lsap: no visible binding for global variable ‘pxl_col_in_fullres’
.map_lsap: no visible binding for global variable ‘pxl_row_in_fullres’
.map_lsap: no visible binding for global variable
  ‘pxl_col_in_fullres_rounded’
.map_lsap: no visible binding for global variable
  ‘pxl_row_in_fullres_rounded’
Undefined global functions or variables:
  capture_area key pxl_col_in_fullres pxl_col_in_fullres_rounded
  pxl_row_in_fullres pxl_row_in_fullres_rounded
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
build_SpatialExperiment 70.173  4.706  75.270
add_array_coords        27.517  4.899  33.881
merge_overlapping       15.263  0.669  16.089
prep_fiji               12.539  3.189  15.718
as.Seurat               13.935  0.958  15.241
rescale_fiji_inputs     11.133  1.624  13.030
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/visiumStitched.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL visiumStitched
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘visiumStitched’ ...
** this is package ‘visiumStitched’ version ‘1.1.2’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (visiumStitched)

R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(visiumStitched)
Loading required package: 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
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Seqinfo
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("visiumStitched")
2025-10-23 01:06:08.098439 loading file /Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/a2355c2feaa3_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
2025-10-23 01:06:13.147617 loading file /Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/a2355c9fb0b5_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
2025-10-23 01:06:16.205703 loading file /Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/a2354866eeb6_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
2025-10-23 01:06:33.064961 loading file /Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/a2355c2feaa3_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
2025-10-23 01:06:37.661198 loading file /Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/d2a89b76dad_spatialDLPFC_spe_subset_example.rds%3Fdl%3D1
Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
2025-10-23 01:06:44.659026 loading file /Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/a2355c9fb0b5_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
2025-10-23 01:06:47.113698 loading file /Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/a2354866eeb6_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
Building SpatialExperiment using capture area as sample ID
2025-10-23 01:06:56.471591 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger
2025-10-23 01:07:00.728406 read10xVisiumAnalysis: reading analysis output from SpaceRanger
2025-10-23 01:07:01.173651 add10xVisiumAnalysis: adding analysis output from SpaceRanger
2025-10-23 01:07:01.485391 rtracklayer::import: reading the reference GTF file
2025-10-23 01:07:37.689999 adding gene information to the SPE object
2025-10-23 01:07:37.973114 adding information used by spatialLIBD
Overwriting imgData(spe) with merged images (one per group)
Adding array coordinates and overlap info
2025-10-23 01:07:41.231277 loading file /Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/a2355c2feaa3_visiumStitched_brain_spe.rds%3Frlkey%3Dnq6a82u23xuu9hohr86oodwdi%26dl%3D1
'sample_id's are duplicated across 'SpatialExperiment' objects to cbind; appending sample indices.
2025-10-23 01:07:55.259999 loading file /Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/a2355c9fb0b5_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
2025-10-23 01:07:57.53022 loading file /Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/a2354866eeb6_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
2025-10-23 01:08:07.362344 loading file /Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/a2355c9fb0b5_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 36 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 36 ]
> 
> proc.time()
   user  system elapsed 
128.641  13.323 142.717