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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data beadarray
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* checking for file ‘beadarray/DESCRIPTION’ ... OK
* preparing ‘beadarray’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘ImageProcessing.Rmd’ using rmarkdown
--- finished re-building ‘ImageProcessing.Rmd’

--- re-building ‘beadarray.Rmd’ using rmarkdown
Usage: open [-e] [-t] [-f] [-W] [-R] [-n] [-g] [-h] [-s <partial SDK name>][-b <bundle identifier>] [-a <application>] [-u URL] [filenames] [--args arguments]
Help: Open opens files from a shell.
      By default, opens each file using the default application for that file.  
      If the file is in the form of a URL, the file will be opened as a URL.
Options: 
      -a                    Opens with the specified application.
      -b                    Opens with the specified application bundle identifier.
      -e                    Opens with TextEdit.
      -t                    Opens with default text editor.
      -f                    Reads input from standard input and opens with TextEdit.
      -F  --fresh           Launches the app fresh, that is, without restoring windows. Saved persistent state is lost, excluding Untitled documents.
      -R, --reveal          Selects in the Finder instead of opening.
      -W, --wait-apps       Blocks until the used applications are closed (even if they were already running).
          --args            All remaining arguments are passed in argv to the application's main() function instead of opened.
      -n, --new             Open a new instance of the application even if one is already running.
      -j, --hide            Launches the app hidden.
      -g, --background      Does not bring the application to the foreground.
      -h, --header          Searches header file locations for headers matching the given filenames, and opens them.
      -s                    For -h, the SDK to use; if supplied, only SDKs whose names contain the argument value are searched.
                            Otherwise the highest versioned SDK in each platform is used.
      -u, --url URL         Open this URL, even if it matches exactly a filepath
      -i, --stdin  PATH     Launches the application with stdin connected to PATH; defaults to /dev/null
      -o, --stdout PATH     Launches the application with /dev/stdout connected to PATH; 
          --stderr PATH     Launches the application with /dev/stderr connected to PATH to
          --env    VAR      Add an enviroment variable to the launched process, where VAR is formatted AAA=foo or just AAA for a null string value.
Usage: open [-e] [-t] [-f] [-W] [-R] [-n] [-g] [-h] [-s <partial SDK name>][-b <bundle identifier>] [-a <application>] [-u URL] [filenames] [--args arguments]
Help: Open opens files from a shell.
      By default, opens each file using the default application for that file.  
      If the file is in the form of a URL, the file will be opened as a URL.
Options: 
      -a                    Opens with the specified application.
      -b                    Opens with the specified application bundle identifier.
      -e                    Opens with TextEdit.
      -t                    Opens with default text editor.
      -f                    Reads input from standard input and opens with TextEdit.
      -F  --fresh           Launches the app fresh, that is, without restoring windows. Saved persistent state is lost, excluding Untitled documents.
      -R, --reveal          Selects in the Finder instead of opening.
      -W, --wait-apps       Blocks until the used applications are closed (even if they were already running).
          --args            All remaining arguments are passed in argv to the application's main() function instead of opened.
      -n, --new             Open a new instance of the application even if one is already running.
      -j, --hide            Launches the app hidden.
      -g, --background      Does not bring the application to the foreground.
      -h, --header          Searches header file locations for headers matching the given filenames, and opens them.
      -s                    For -h, the SDK to use; if supplied, only SDKs whose names contain the argument value are searched.
                            Otherwise the highest versioned SDK in each platform is used.
      -u, --url URL         Open this URL, even if it matches exactly a filepath
      -i, --stdin  PATH     Launches the application with stdin connected to PATH; defaults to /dev/null
      -o, --stdout PATH     Launches the application with /dev/stdout connected to PATH; 
          --stderr PATH     Launches the application with /dev/stderr connected to PATH to
          --env    VAR      Add an enviroment variable to the launched process, where VAR is formatted AAA=foo or just AAA for a null string value.
--- finished re-building ‘beadarray.Rmd’

--- re-building ‘beadlevel.Rmd’ using rmarkdown
2024-07-02 15:57:25.514 R[48197:246136882] XType: com.apple.fonts is not accessible.
2024-07-02 15:57:25.515 R[48197:246136882] XType: XTFontStaticRegistry is enabled.
--- finished re-building ‘beadlevel.Rmd’

--- re-building ‘beadsummary.Rmd’ using rmarkdown
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE33nnn/GSE33126/matrix/GSE33126_series_matrix.txt.gz'
Content type 'application/x-gzip' length 3658664 bytes (3.5 MB)
==================================================
downloaded 3.5 MB


Quitting from lines 524-532 [unnamed-chunk-37] (beadsummary.Rmd)
Error: processing vignette 'beadsummary.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘beadsummary.Rmd’

SUMMARY: processing the following file failed:
  ‘beadsummary.Rmd’

Error: Vignette re-building failed.
Execution halted