===============================
R CMD BUILD
===============================
* checking for file ‘scDesign3Workflow/DESCRIPTION’ ... OK
* preparing ‘scDesign3Workflow’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘scDesign3-CITEseq-vignette.Rmd’ using rmarkdown
--- finished re-building ‘scDesign3-CITEseq-vignette.Rmd’
--- re-building ‘scDesign3-DEanalysis-vignette.Rmd’ using rmarkdown
Quitting from lines 43-64 [unnamed-chunk-3] (scDesign3-DEanalysis-vignette.Rmd)
Error: processing vignette 'scDesign3-DEanalysis-vignette.Rmd' failed with diagnostics:
there is no package called 'monocle3'
--- failed re-building ‘scDesign3-DEanalysis-vignette.Rmd’
--- re-building ‘scDesign3-batchEffect-vignette.Rmd’ using rmarkdown
Quitting from lines 145-160 [unnamed-chunk-12] (scDesign3-batchEffect-vignette.Rmd)
Error: processing vignette 'scDesign3-batchEffect-vignette.Rmd' failed with diagnostics:
unused argument (filtered_gene = BATCH_data$filtered_gene)
--- failed re-building ‘scDesign3-batchEffect-vignette.Rmd’
--- re-building ‘scDesign3-clusterGOF-vignette.Rmd’ using rmarkdown
--- finished re-building ‘scDesign3-clusterGOF-vignette.Rmd’
--- re-building ‘scDesign3-conditionEffect-vignette.Rmd’ using rmarkdown
Quitting from lines 157-172 [unnamed-chunk-13] (scDesign3-conditionEffect-vignette.Rmd)
Error: processing vignette 'scDesign3-conditionEffect-vignette.Rmd' failed with diagnostics:
unused argument (filtered_gene = IFNB_data$filtered_gene)
--- failed re-building ‘scDesign3-conditionEffect-vignette.Rmd’
--- re-building ‘scDesign3-copulaCompare-vignette.Rmd’ using rmarkdown
Warning: ggrepel: 12 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: ggrepel: 6 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: ggrepel: 3 unlabeled data points (too many overlaps). Consider increasing max.overlaps
--- finished re-building ‘scDesign3-copulaCompare-vignette.Rmd’
--- re-building ‘scDesign3-introduction-vignette.Rmd’ using rmarkdown
Quitting from lines 166-181 [unnamed-chunk-11] (scDesign3-introduction-vignette.Rmd)
Error: processing vignette 'scDesign3-introduction-vignette.Rmd' failed with diagnostics:
unused argument (filtered_gene = PANCREAS_data$filtered_gene)
--- failed re-building ‘scDesign3-introduction-vignette.Rmd’
--- re-building ‘scDesign3-librarySize-vignette.Rmd’ using rmarkdown
--- finished re-building ‘scDesign3-librarySize-vignette.Rmd’
--- re-building ‘scDesign3-marginal-vignette.Rmd’ using rmarkdown
--- finished re-building ‘scDesign3-marginal-vignette.Rmd’
--- re-building ‘scDesign3-multiomics-vignette.Rmd’ using rmarkdown
Quitting from lines 158-187 [unnamed-chunk-10] (scDesign3-multiomics-vignette.Rmd)
Error: processing vignette 'scDesign3-multiomics-vignette.Rmd' failed with diagnostics:
unused argument (filtered_gene = RNA_data$filtered_gene)
--- failed re-building ‘scDesign3-multiomics-vignette.Rmd’
--- re-building ‘scDesign3-multipleLineages-vignette.Rmd’ using rmarkdown
--- finished re-building ‘scDesign3-multipleLineages-vignette.Rmd’
--- re-building ‘scDesign3-parallelization-vignette.Rmd’ using rmarkdown
--- finished re-building ‘scDesign3-parallelization-vignette.Rmd’
--- re-building ‘scDesign3-pseudotimeGOF-vignette.Rmd’ using rmarkdown
--- finished re-building ‘scDesign3-pseudotimeGOF-vignette.Rmd’
--- re-building ‘scDesign3-scATACseq-vignette.Rmd’ using rmarkdown
Quitting from lines 62-64 [unnamed-chunk-3] (scDesign3-scATACseq-vignette.Rmd)
Error: processing vignette 'scDesign3-scATACseq-vignette.Rmd' failed with diagnostics:
cannot read from connection
--- failed re-building ‘scDesign3-scATACseq-vignette.Rmd’
--- re-building ‘scDesign3-spatial-deconvolution.Rmd’ using rmarkdown
Quitting from lines 38-46 [unnamed-chunk-1] (scDesign3-spatial-deconvolution.Rmd)
Error: processing vignette 'scDesign3-spatial-deconvolution.Rmd' failed with diagnostics:
there is no package called 'IOBR'
--- failed re-building ‘scDesign3-spatial-deconvolution.Rmd’
--- re-building ‘scDesign3-spatial-vignette.Rmd’ using rmarkdown
--- finished re-building ‘scDesign3-spatial-vignette.Rmd’
--- re-building ‘scDesign3.Rmd’ using rmarkdown
--- finished re-building ‘scDesign3.Rmd’
SUMMARY: processing the following files failed:
‘scDesign3-DEanalysis-vignette.Rmd’
‘scDesign3-batchEffect-vignette.Rmd’
‘scDesign3-conditionEffect-vignette.Rmd’
‘scDesign3-introduction-vignette.Rmd’
‘scDesign3-multiomics-vignette.Rmd’
‘scDesign3-scATACseq-vignette.Rmd’
‘scDesign3-spatial-deconvolution.Rmd’
Error: Vignette re-building failed.
Execution halted
===============================
R CMD BUILD
===============================
* checking for file ‘scDesign3Workflow/DESCRIPTION’ ... OK
* preparing ‘scDesign3Workflow’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘scDesign3-CITEseq-vignette.Rmd’ using rmarkdown
Quitting from lines 78-99 [unnamed-chunk-6] (scDesign3-CITEseq-vignette.Rmd)
Quitting from lines 78-99 [unnamed-chunk-6] (scDesign3-CITEseq-vignette.Rmd)
Error: processing vignette 'scDesign3-CITEseq-vignette.Rmd' failed with diagnostics:
attempt to set an attribute on NULL
--- failed re-building ‘scDesign3-CITEseq-vignette.Rmd’
--- re-building ‘scDesign3-DEanalysis-vignette.Rmd’ using rmarkdown
Quitting from lines 43-64 [unnamed-chunk-3] (scDesign3-DEanalysis-vignette.Rmd)
Error: processing vignette 'scDesign3-DEanalysis-vignette.Rmd' failed with diagnostics:
there is no package called 'monocle3'
--- failed re-building ‘scDesign3-DEanalysis-vignette.Rmd’
--- re-building ‘scDesign3-batchEffect-vignette.Rmd’ using rmarkdown
Quitting from lines 145-160 [unnamed-chunk-12] (scDesign3-batchEffect-vignette.Rmd)
Error: processing vignette 'scDesign3-batchEffect-vignette.Rmd' failed with diagnostics:
unused argument (filtered_gene = BATCH_data$filtered_gene)
--- failed re-building ‘scDesign3-batchEffect-vignette.Rmd’
--- re-building ‘scDesign3-clusterGOF-vignette.Rmd’ using rmarkdown
--- finished re-building ‘scDesign3-clusterGOF-vignette.Rmd’
--- re-building ‘scDesign3-conditionEffect-vignette.Rmd’ using rmarkdown
Quitting from lines 157-172 [unnamed-chunk-13] (scDesign3-conditionEffect-vignette.Rmd)
Error: processing vignette 'scDesign3-conditionEffect-vignette.Rmd' failed with diagnostics:
unused argument (filtered_gene = IFNB_data$filtered_gene)
--- failed re-building ‘scDesign3-conditionEffect-vignette.Rmd’
--- re-building ‘scDesign3-copulaCompare-vignette.Rmd’ using rmarkdown
Warning: ggrepel: 6 unlabeled data points (too many overlaps). Consider increasing max.overlaps
--- finished re-building ‘scDesign3-copulaCompare-vignette.Rmd’
--- re-building ‘scDesign3-introduction-vignette.Rmd’ using rmarkdown
Quitting from lines 166-181 [unnamed-chunk-11] (scDesign3-introduction-vignette.Rmd)
Error: processing vignette 'scDesign3-introduction-vignette.Rmd' failed with diagnostics:
unused argument (filtered_gene = PANCREAS_data$filtered_gene)
--- failed re-building ‘scDesign3-introduction-vignette.Rmd’
--- re-building ‘scDesign3-librarySize-vignette.Rmd’ using rmarkdown
--- finished re-building ‘scDesign3-librarySize-vignette.Rmd’
--- re-building ‘scDesign3-marginal-vignette.Rmd’ using rmarkdown
--- finished re-building ‘scDesign3-marginal-vignette.Rmd’
--- re-building ‘scDesign3-multiomics-vignette.Rmd’ using rmarkdown
Quitting from lines 158-187 [unnamed-chunk-10] (scDesign3-multiomics-vignette.Rmd)
Error: processing vignette 'scDesign3-multiomics-vignette.Rmd' failed with diagnostics:
unused argument (filtered_gene = RNA_data$filtered_gene)
--- failed re-building ‘scDesign3-multiomics-vignette.Rmd’
--- re-building ‘scDesign3-multipleLineages-vignette.Rmd’ using rmarkdown
--- finished re-building ‘scDesign3-multipleLineages-vignette.Rmd’
--- re-building ‘scDesign3-parallelization-vignette.Rmd’ using rmarkdown
--- finished re-building ‘scDesign3-parallelization-vignette.Rmd’
--- re-building ‘scDesign3-pseudotimeGOF-vignette.Rmd’ using rmarkdown
--- finished re-building ‘scDesign3-pseudotimeGOF-vignette.Rmd’
--- re-building ‘scDesign3-scATACseq-vignette.Rmd’ using rmarkdown
--- finished re-building ‘scDesign3-scATACseq-vignette.Rmd’
--- re-building ‘scDesign3-spatial-deconvolution.Rmd’ using rmarkdown
Quitting from lines 38-46 [unnamed-chunk-1] (scDesign3-spatial-deconvolution.Rmd)
Error: processing vignette 'scDesign3-spatial-deconvolution.Rmd' failed with diagnostics:
there is no package called 'IOBR'
--- failed re-building ‘scDesign3-spatial-deconvolution.Rmd’
--- re-building ‘scDesign3-spatial-vignette.Rmd’ using rmarkdown
--- finished re-building ‘scDesign3-spatial-vignette.Rmd’
--- re-building ‘scDesign3.Rmd’ using rmarkdown
--- finished re-building ‘scDesign3.Rmd’
SUMMARY: processing the following files failed:
‘scDesign3-CITEseq-vignette.Rmd’ ‘scDesign3-DEanalysis-vignette.Rmd’
‘scDesign3-batchEffect-vignette.Rmd’
‘scDesign3-conditionEffect-vignette.Rmd’
‘scDesign3-introduction-vignette.Rmd’
‘scDesign3-multiomics-vignette.Rmd’
‘scDesign3-spatial-deconvolution.Rmd’
Error: Vignette re-building failed.
Execution halted