##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data SpatialDecon
###
##############################################################################
##############################################################################


* checking for file ‘SpatialDecon/DESCRIPTION’ ... OK
* preparing ‘SpatialDecon’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘SpatialDecon_vignette.Rmd’ using rmarkdown
2025-10-26 18:06:33.012 R[31141:551331962] XType: Using static font registry.

Quitting from SpatialDecon_vignette.Rmd:139-154 [downloadmatrix]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection to 'https://raw.github.com/Nanostring-Biostats/CellProfileLibrary/master/Mouse/Mouse_datasets_metadata.csv'
---
Backtrace:
    ▆
 1. └─SpatialDecon::download_profile_matrix(...)
 2.   └─utils::read.csv(...)
 3.     └─utils::read.table(...)
 4.       └─base::file(file, "rt")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'SpatialDecon_vignette.Rmd' failed with diagnostics:
cannot open the connection to 'https://raw.github.com/Nanostring-Biostats/CellProfileLibrary/master/Mouse/Mouse_datasets_metadata.csv'
--- failed re-building ‘SpatialDecon_vignette.Rmd’

--- re-building ‘SpatialDecon_vignette_NSCLC.Rmd’ using rmarkdown

Quitting from SpatialDecon_vignette_NSCLC.Rmd:132-147 [downloadmatrix]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection to 'https://raw.github.com/Nanostring-Biostats/CellProfileLibrary/master/Mouse/Mouse_datasets_metadata.csv'
---
Backtrace:
    ▆
 1. └─SpatialDecon::download_profile_matrix(...)
 2.   └─utils::read.csv(...)
 3.     └─utils::read.table(...)
 4.       └─base::file(file, "rt")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'SpatialDecon_vignette_NSCLC.Rmd' failed with diagnostics:
cannot open the connection to 'https://raw.github.com/Nanostring-Biostats/CellProfileLibrary/master/Mouse/Mouse_datasets_metadata.csv'
--- failed re-building ‘SpatialDecon_vignette_NSCLC.Rmd’

SUMMARY: processing the following files failed:
  ‘SpatialDecon_vignette.Rmd’ ‘SpatialDecon_vignette_NSCLC.Rmd’

Error: Vignette re-building failed.
Execution halted