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### Running command:
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###   /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_0.99.15.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/visiumStitched.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘visiumStitched/DESCRIPTION’ ... OK
* this is package ‘visiumStitched’ version ‘0.99.15’
* 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 ... OK
* 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 ‘visiumStitched-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: build_SpatialExperiment
> ### Title: Build stitched 'SpatialExperiment'
> ### Aliases: build_SpatialExperiment
> 
> ### ** Examples
> 
> ########################################################################
> #   Prepare sample_info
> ########################################################################
> 
> sample_info <- dplyr::tibble(
+     group = "Br2719",
+     capture_area = c("V13B23-283_A1", "V13B23-283_C1", "V13B23-283_D1")
+ )
> #   Add 'spaceranger_dir' column
> sr_dir <- tempdir()
> temp <- unzip(
+     spatialLIBD::fetch_data("visiumStitched_brain_spaceranger"),
+     exdir = sr_dir
+ )
2025-02-12 22:03:43.253673 loading file /Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/df066998fe9c_visiumStitched_brain_spaceranger.zip%3Frlkey%3Dbdgjc6mgy1ierdad6h6v5g29c%26dl%3D1
> sample_info$spaceranger_dir <- file.path(
+     sr_dir, sample_info$capture_area, "outs", "spatial"
+ )
> 
> #   Add Fiji-output-related columns
> fiji_dir <- tempdir()
> temp <- unzip(
+     spatialLIBD::fetch_data("visiumStitched_brain_Fiji_out"),
+     exdir = fiji_dir
+ )
2025-02-12 22:03:44.794096 loading file /Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/df063b73e9ed_visiumStitched_brain_fiji_out.zip%3Frlkey%3Dptwal8f5zxakzejwd0oqw0lhj%26dl%3D1
> sample_info$fiji_xml_path <- temp[grep("xml$", temp)]
> sample_info$fiji_image_path <- temp[grep("png$", temp)]
> 
> ## Re-size images and add more information to the sample_info
> sample_info <- rescale_fiji_inputs(sample_info, out_dir = tempdir())
> 
> ## Preparing Fiji coordinates and images for build_SpatialExperiment()
> spe_input_dir <- tempdir()
> prep_fiji_coords(sample_info, out_dir = spe_input_dir)
[1] "/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpAnQQ34/Br2719/tissue_positions.csv"
> prep_fiji_image(sample_info, out_dir = spe_input_dir)
[1] "/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpAnQQ34/Br2719/tissue_lowres_image.png"
[2] "/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpAnQQ34/Br2719/scalefactors_json.json" 
> 
> ########################################################################
> #   Build the SpatialExperiment
> ########################################################################
> 
> #    Since we don't have access to the original GTF used to run SpaceRanger,
> #    we must explicitly supply our own GTF to build_SpatialExperiment(). We use
> #    GENCODE release 32, intended to be quite close to the actual GTF used,
> #    which is available from:
> #    https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38-2024-A.tar.gz
> bfc <- BiocFileCache::BiocFileCache()
> gtf_cache <- BiocFileCache::bfcrpath(
+     bfc,
+     paste0(
+         "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/",
+         "release_32/gencode.v32.annotation.gtf.gz"
+     )
+ )
adding rname 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_32/gencode.v32.annotation.gtf.gz'
Warning: download failed
  web resource path: ‘ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_32/gencode.v32.annotation.gtf.gz’
  local file path: ‘/Users/biocbuild/Library/Caches/org.R-project.R/R/BiocFileCache/df061f0ee886_gencode.v32.annotation.gtf.gz’
  reason: Failure when receiving data from the peer [ftp.ebi.ac.uk]: Recv failure: Connection reset by peer
Warning: bfcadd() failed; resource removed
  rid: BFC3103
  fpath: ‘ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_32/gencode.v32.annotation.gtf.gz’
  reason: download failed
Warning in value[[3L]](cond) : 
trying to add rname 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_32/gencode.v32.annotation.gtf.gz' produced error:
  bfcadd() failed; see warnings()
Error in BiocFileCache::bfcrpath(bfc, paste0("ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/",  : 
  not all 'rnames' found or unique.
Calls: <Anonymous> -> <Anonymous>
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
add_array_coords 11.581  2.393  48.529
as.Seurat         5.753  0.666  22.279
* 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
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/visiumStitched.Rcheck/00check.log’
for details.