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


* checking for file ‘maEndToEnd/DESCRIPTION’ ... OK
* preparing ‘maEndToEnd’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘MA-Workflow.Rmd’ using rmarkdown
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/183_II.CEL'
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/2255_I.CEL'
Content type 'unknown' length 11129107 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/2826_I.CEL'
Content type 'unknown' length 11172699 bytes (10.7 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/2978_I.CEL'
Content type 'unknown' length 11158567 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/2987_II.CEL'
Content type 'unknown' length 11161519 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/3258_II.CEL'
Content type 'unknown' length 11142571 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/3302_I.CEL'
Content type 'unknown' length 11145911 bytes (10.6 MB)
==================================================
trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/967/E-MTAB-2967/Files/3332_II.CEL'
Content type 'unknown' length 11187423 bytes (10.7 MB)
==================================================
trying URL 'https://www.ebi.ac.uk/biostudies/files/E-MTAB-2967/E-MTAB-2967.sdrf.txt'
Content type 'text/plain; charset=UTF-8' length 22516 bytes (21 KB)
==================================================
downloaded 21 KB

2025-09-23 13:06:11.780 R[23754:357042609] XType: com.apple.fonts is not accessible.
2025-09-23 13:06:11.780 R[23754:357042609] XType: XTFontStaticRegistry is enabled.

Quitting from MA-Workflow.Rmd:367-372 [importCelfiles]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! These do not exist:
	 /Users/biocbuild/Library/Caches/org.R-project.R/R/maEndToEnd/183_II.CEL
---
Backtrace:
    ▆
 1. └─oligo::read.celfiles(...)
 2.   └─oligo:::checkValidFilenames(filenames)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'MA-Workflow.Rmd' failed with diagnostics:
These do not exist:
	 /Users/biocbuild/Library/Caches/org.R-project.R/R/maEndToEnd/183_II.CEL
--- failed re-building ‘MA-Workflow.Rmd’

SUMMARY: processing the following file failed:
  ‘MA-Workflow.Rmd’

Error: Vignette re-building failed.
Execution halted