############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data CluMSID ### ############################################################################## ############################################################################## * checking for file ‘CluMSID/DESCRIPTION’ ... OK * preparing ‘CluMSID’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘CluMSID_DI-MSMS.Rmd’ using rmarkdown 2024-07-04 16:47:18.296 R[58116:67294730] XType: Using static font registry. Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "CluMSID DI-MS/MS Tutorial", and the latter is "Clustering Spectra from High Resolution DI-MS/MS Data Using CluMSID". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check. --- finished re-building ‘CluMSID_DI-MSMS.Rmd’ --- re-building ‘CluMSID_GC-EI-MS.Rmd’ using rmarkdown Quitting from lines 127-130 [runCAMERA] (CluMSID_GC-EI-MS.Rmd) Error: processing vignette 'CluMSID_GC-EI-MS.Rmd' failed with diagnostics: wrong args for environment subassignment --- failed re-building ‘CluMSID_GC-EI-MS.Rmd’ --- re-building ‘CluMSID_MTBLS.Rmd’ using rmarkdown Quitting from lines 237-238 [dendro] (CluMSID_MTBLS.Rmd) Error: processing vignette 'CluMSID_MTBLS.Rmd' failed with diagnostics: QuartzBitmap_Output - unable to open file '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpSYtqSg/filee30455d2fb0e' --- failed re-building ‘CluMSID_MTBLS.Rmd’ --- re-building ‘CluMSID_lowres-LC-MSMS.Rmd’ using rmarkdown Quitting from lines 136-137 [MDS] (CluMSID_lowres-LC-MSMS.Rmd) Error: processing vignette 'CluMSID_lowres-LC-MSMS.Rmd' failed with diagnostics: QuartzBitmap_Output - unable to open file '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpSYtqSg/filee3046ee61590' --- failed re-building ‘CluMSID_lowres-LC-MSMS.Rmd’ --- re-building ‘CluMSID_tutorial.Rmd’ using rmarkdown Quitting from lines 504-505 [MDSplotplot_1] (CluMSID_tutorial.Rmd) Error: processing vignette 'CluMSID_tutorial.Rmd' failed with diagnostics: QuartzBitmap_Output - unable to open file '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpSYtqSg/filee30474e2c772' --- failed re-building ‘CluMSID_tutorial.Rmd’ SUMMARY: processing the following files failed: ‘CluMSID_GC-EI-MS.Rmd’ ‘CluMSID_MTBLS.Rmd’ ‘CluMSID_lowres-LC-MSMS.Rmd’ ‘CluMSID_tutorial.Rmd’ Error: Vignette re-building failed. Execution halted