* using log directory 'd:/RCompile/CRANincoming/R-devel/spatialGE.Rcheck'
* using R version 4.5.0 alpha (2025-03-24 r88048 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'spatialGE/DESCRIPTION' ... OK
* this is package 'spatialGE' version '1.2.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Oscar Ospina <ospina.oe@gmail.com>'

New submission

Possibly misspelled words in DESCRIPTION:
  deconvolution (22:210)
  spatialGE (22:102)
  transcriptomics (22:63)

Found the following (possibly) invalid URLs:
  URL: https://kb.10xgenomics.com/hc/en-us/articles/360035487952-How-many-cells-are-captured-in-a-single-spot-
    From: inst/doc/basic_functions_vignette.html
    Status: 403
    Message: Forbidden
  URL: https://nanostring.com/products/cosmx-spatial-molecular-imager/nsclc-ffpe-dataset/ (moved to https://nanostring.com/products/cosmx-spatial-molecular-imager/ffpe-dataset/nsclc-ffpe-dataset/)
    From: inst/doc/spatial_enrichment_gradients_smi.html
    Status: 301
    Message: Moved Permanently
For content that is 'Moved Permanently', please change http to https,
add trailing slashes, or replace the old by the new URL.

Size of tarball: 5643434 bytes
* 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 serialization versions ... OK
* checking whether package 'spatialGE' can be installed ... OK
* used C++ compiler: 'g++.exe (GCC) 14.2.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 loading without being on the library search path ... OK
* checking use of S3 registration ... 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 ... [18s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'spatialGE-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: STclust
> ### Title: STclust: Detect clusters of spots/cells
> ### Aliases: STclust
> 
> ### ** Examples
> 
> 
> # Using included melanoma example (Thrane et al.)
> # Download example data set from spatialGE_Data
> thrane_tmp = tempdir()
> unlink(thrane_tmp, recursive=TRUE)
> dir.create(thrane_tmp)
> lk='https://github.com/FridleyLab/spatialGE_Data/raw/refs/heads/main/melanoma_thrane.zip?download='
> download.file(lk, destfile=paste0(thrane_tmp, '/', 'melanoma_thrane.zip'))
trying URL 'https://github.com/FridleyLab/spatialGE_Data/raw/refs/heads/main/melanoma_thrane.zip?download='
Content type 'application/zip' length 3400344 bytes (3.2 MB)
==================================================
downloaded 3.2 MB

> zip_tmp = list.files(thrane_tmp, pattern='melanoma_thrane.zip$', full.names=TRUE)
> unzip(zipfile=zip_tmp, exdir=thrane_tmp)
Warning in unzip(zipfile = zip_tmp, exdir = thrane_tmp) :
  error 1 in extracting from zip file
> # Generate the file paths to be passed to the STlist function
> count_files <- list.files(paste0(thrane_tmp, '/melanoma_thrane'),
+                           full.names=TRUE, pattern='counts')
> coord_files <- list.files(paste0(thrane_tmp, '/melanoma_thrane'),
+                          full.names=TRUE, pattern='mapping')
> clin_file <- list.files(paste0(thrane_tmp, '/melanoma_thrane'),
+                         full.names=TRUE, pattern='clinical')
> # Create STlist
> library('spatialGE')
> melanoma <- STlist(rnacounts=count_files[c(1,3)], spotcoords=coord_files[c(1,3)], samples=clin_file)
Error in detect_input(rnacounts = rnacounts, spotcoords = spotcoords,  : 
  Number of sample names do not match number of RNA counts tables.
Calls: STlist -> detect_input
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... ERROR
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # 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(spatialGE)
  > 
  > test_check("spatialGE")
  trying URL 'https://github.com/FridleyLab/spatialGE_Data/raw/refs/heads/main/melanoma_thrane.zip?download='
  Content type 'application/zip' length 3400344 bytes (3.2 MB)
  ==================================================
  downloaded 3.2 MB
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-tests.R:17:1'): (code run outside of `test_that()`) ────────────
  Error in `detect_input(rnacounts = rnacounts, spotcoords = spotcoords, 
      samples = samples)`: Number of sample names do not match number of RNA counts tables.
  Backtrace:
      ▆
   1. └─spatialGE::STlist(...) at test-tests.R:17:1
   2.   └─spatialGE:::detect_input(...)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [15s] ERROR
Error(s) in re-building vignettes:
--- re-building 'basic_functions_vignette.Rmd' using rmarkdown
trying URL 'https://bioconductor.statistik.tu-dortmund.de/cran/bin/windows/contrib/4.5/credentials_2.0.2.zip'
trying URL 'https://bioconductor.statistik.tu-dortmund.de/cran/bin/windows/contrib/4.5/zip_2.3.2.zip'
trying URL 'https://bioconductor.statistik.tu-dortmund.de/cran/bin/windows/contrib/4.5/gitcreds_0.1.2.zip'
trying URL 'https://bioconductor.statistik.tu-dortmund.de/cran/bin/windows/contrib/4.5/ini_0.3.1.zip'
trying URL 'https://bioconductor.statistik.tu-dortmund.de/cran/bin/windows/contrib/4.5/httpuv_1.6.15.zip'
trying URL 'https://bioconductor.statistik.tu-dortmund.de/cran/bin/windows/contrib/4.5/sourcetools_0.1.7-1.zip'
trying URL 'https://bioconductor.statistik.tu-dortmund.de/cran/bin/windows/contrib/4.5/later_1.4.1.zip'
trying URL 'https://bioconductor.statistik.tu-dortmund.de/cran/bin/windows/contrib/4.5/promises_1.3.2.zip'
trying URL 'https://bioconductor.statistik.tu-dortmund.de/cran/bin/windows/contrib/4.5/gert_2.1.5.zip'
trying URL 'https://bioconductor.statistik.tu-dortmund.de/cran/bin/windows/contrib/4.5/gh_1.4.1.zip'
trying URL 'https://bioconductor.statistik.tu-dortmund.de/cran/bin/windows/contrib/4.5/whisker_0.4.1.zip'
trying URL 'https://bioconductor.statistik.tu-dortmund.de/cran/bin/windows/contrib/4.5/shiny_1.10.0.zip'
trying URL 'https://bioconductor.statistik.tu-dortmund.de/cran/bin/windows/contrib/4.5/downlit_0.4.4.zip'
trying URL 'https://bioconductor.statistik.tu-dortmund.de/cran/bin/windows/contrib/4.5/httr2_1.1.1.zip'
trying URL 'https://bioconductor.statistik.tu-dortmund.de/cran/bin/windows/contrib/4.5/xopen_1.0.1.zip'
trying URL 'https://bioconductor.statistik.tu-dortmund.de/cran/bin/windows/contrib/4.5/brew_1.0-10.zip'
trying URL 'https://bioconductor.statistik.tu-dortmund.de/cran/bin/windows/contrib/4.5/commonmark_1.9.5.zip'
trying URL 'https://bioconductor.statistik.tu-dortmund.de/cran/bin/windows/contrib/4.5/usethis_3.1.0.zip'
trying URL 'https://bioconductor.statistik.tu-dortmund.de/cran/bin/windows/contrib/4.5/ellipsis_0.3.2.zip'
trying URL 'https://bioconductor.statistik.tu-dortmund.de/cran/bin/windows/contrib/4.5/miniUI_0.1.1.1.zip'
trying URL 'https://bioconductor.statistik.tu-dortmund.de/cran/bin/windows/contrib/4.5/pkgdown_2.1.1.zip'
trying URL 'https://bioconductor.statistik.tu-dortmund.de/cran/bin/windows/contrib/4.5/profvis_0.4.0.zip'
trying URL 'https://bioconductor.statistik.tu-dortmund.de/cran/bin/windows/contrib/4.5/rcmdcheck_1.4.0.zip'
trying URL 'https://bioconductor.statistik.tu-dortmund.de/cran/bin/windows/contrib/4.5/remotes_2.5.0.zip'
trying URL 'https://bioconductor.statistik.tu-dortmund.de/cran/bin/windows/contrib/4.5/roxygen2_7.3.2.zip'
trying URL 'https://bioconductor.statistik.tu-dortmund.de/cran/bin/windows/contrib/4.5/rversions_2.1.2.zip'
trying URL 'https://bioconductor.statistik.tu-dortmund.de/cran/bin/windows/contrib/4.5/sessioninfo_1.2.3.zip'
trying URL 'https://bioconductor.statistik.tu-dortmund.de/cran/bin/windows/contrib/4.5/urlchecker_1.0.1.zip'
trying URL 'https://bioconductor.statistik.tu-dortmund.de/cran/bin/windows/contrib/4.5/devtools_2.4.5.zip'
trying URL 'https://github.com/FridleyLab/spatialGE_Data/raw/refs/heads/main/tnbc_bassiouni.zip?download='
Content type 'application/zip' length 119463578 bytes (113.9 MB)
==================================================
downloaded 113.9 MB


Quitting from basic_functions_vignette.Rmd:112-114 [create_stlist]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `detect_input()`:
! If intended input is a Visium output, could not find directory path.
---
Backtrace:
    ▆
 1. └─spatialGE::STlist(...)
 2.   └─spatialGE:::detect_input(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'basic_functions_vignette.Rmd' failed with diagnostics:
If intended input is a Visium output, could not find directory path.
--- failed re-building 'basic_functions_vignette.Rmd'

--- re-building 'spatial_differential_expression.Rmd' using rmarkdown
trying URL 'https://github.com/FridleyLab/spatialGE_Data/raw/refs/heads/main/melanoma_thrane.zip?download='
Content type 'application/zip' length 3400344 bytes (3.2 MB)
==================================================
downloaded 3.2 MB


Quitting from spatial_differential_expression.Rmd:74-76 [create_stlist]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `detect_input()`:
! Could not open the RNA count file.
---
Backtrace:
    ▆
 1. └─spatialGE::STlist(...)
 2.   └─spatialGE:::detect_input(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'spatial_differential_expression.Rmd' failed with diagnostics:
Could not open the RNA count file.
--- failed re-building 'spatial_differential_expression.Rmd'

--- re-building 'spatial_enrichment_gradients_smi.Rmd' using rmarkdown
trying URL 'https://github.com/FridleyLab/spatialGE_Data/raw/refs/heads/main/nanostring_nsclc.zip?download='
Content type 'application/zip' length 53386446 bytes (50.9 MB)
==================================================
downloaded 50.9 MB


Quitting from spatial_enrichment_gradients_smi.Rmd:112-116 [create_stlist]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `detect_input()`:
! Could not open the RNA count file.
---
Backtrace:
    ▆
 1. └─spatialGE::STlist(...)
 2.   └─spatialGE:::detect_input(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'spatial_enrichment_gradients_smi.Rmd' failed with diagnostics:
Could not open the RNA count file.
--- failed re-building 'spatial_enrichment_gradients_smi.Rmd'

--- re-building 'troubleshooting.Rmd' using rmarkdown
--- finished re-building 'troubleshooting.Rmd'

SUMMARY: processing the following files failed:
  'basic_functions_vignette.Rmd' 'spatial_differential_expression.Rmd'
  'spatial_enrichment_gradients_smi.Rmd'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [13s] OK
* checking HTML version of manual ... OK
* DONE
Status: 3 ERRORs, 1 NOTE