===============================
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 45-54 [unnamed-chunk-3] (scDesign3-CITEseq-vignette.Rmd)
Error: processing vignette 'scDesign3-CITEseq-vignette.Rmd' failed with diagnostics:
package 'IRanges' required by 'GenomicRanges' could not be found
--- failed re-building ‘scDesign3-CITEseq-vignette.Rmd’
--- re-building ‘scDesign3-DEanalysis-vignette.Rmd’ using rmarkdown
Quitting from lines 43-61 [unnamed-chunk-3] (scDesign3-DEanalysis-vignette.Rmd)
Error: processing vignette 'scDesign3-DEanalysis-vignette.Rmd' failed with diagnostics:
package 'IRanges' required by 'GenomicRanges' could not be found
--- failed re-building ‘scDesign3-DEanalysis-vignette.Rmd’
--- re-building ‘scDesign3-batchEffect-vignette.Rmd’ using rmarkdown
Quitting from lines 42-46 [setup] (scDesign3-batchEffect-vignette.Rmd)
Error: processing vignette 'scDesign3-batchEffect-vignette.Rmd' failed with diagnostics:
package 'IRanges' required by 'GenomicRanges' could not be found
--- failed re-building ‘scDesign3-batchEffect-vignette.Rmd’
--- re-building ‘scDesign3-clusterGOF-vignette.Rmd’ using rmarkdown
Quitting from lines 45-52 [unnamed-chunk-3] (scDesign3-clusterGOF-vignette.Rmd)
Error: processing vignette 'scDesign3-clusterGOF-vignette.Rmd' failed with diagnostics:
package or namespace load failed for 'DuoClustering2018':
.onLoad failed in loadNamespace() for 'DuoClustering2018', details:
call: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
error: there is no package called 'IRanges'
--- failed re-building ‘scDesign3-clusterGOF-vignette.Rmd’
--- re-building ‘scDesign3-conditionEffect-vignette.Rmd’ using rmarkdown
Quitting from lines 43-47 [setup] (scDesign3-conditionEffect-vignette.Rmd)
Error: processing vignette 'scDesign3-conditionEffect-vignette.Rmd' failed with diagnostics:
package 'IRanges' required by 'GenomicRanges' could not be found
--- failed re-building ‘scDesign3-conditionEffect-vignette.Rmd’
--- re-building ‘scDesign3-copulaCompare-vignette.Rmd’ using rmarkdown
Quitting from lines 36-47 [setup] (scDesign3-copulaCompare-vignette.Rmd)
Error: processing vignette 'scDesign3-copulaCompare-vignette.Rmd' failed with diagnostics:
package or namespace load failed for 'DuoClustering2018':
.onLoad failed in loadNamespace() for 'DuoClustering2018', details:
call: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
error: there is no package called 'IRanges'
--- failed re-building ‘scDesign3-copulaCompare-vignette.Rmd’
--- re-building ‘scDesign3-introduction-vignette.Rmd’ using rmarkdown
Failed with error: 'package 'IRanges' required by 'GenomicRanges' could not be found'
Quitting from lines 47-49 [unnamed-chunk-2] (scDesign3-introduction-vignette.Rmd)
Error: processing vignette 'scDesign3-introduction-vignette.Rmd' failed with diagnostics:
unable to find required package 'SingleCellExperiment'
--- failed re-building ‘scDesign3-introduction-vignette.Rmd’
--- re-building ‘scDesign3-librarySize-vignette.Rmd’ using rmarkdown
Quitting from lines 44-51 [unnamed-chunk-2] (scDesign3-librarySize-vignette.Rmd)
Error: processing vignette 'scDesign3-librarySize-vignette.Rmd' failed with diagnostics:
package 'IRanges' required by 'GenomicRanges' could not be found
--- failed 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 35-42 [unnamed-chunk-2] (scDesign3-multiomics-vignette.Rmd)
Error: processing vignette 'scDesign3-multiomics-vignette.Rmd' failed with diagnostics:
package 'IRanges' required by 'GenomicRanges' could not be found
--- failed re-building ‘scDesign3-multiomics-vignette.Rmd’
--- re-building ‘scDesign3-multipleLineages-vignette.Rmd’ using rmarkdown
Quitting from lines 44-50 [setup] (scDesign3-multipleLineages-vignette.Rmd)
Error: processing vignette 'scDesign3-multipleLineages-vignette.Rmd' failed with diagnostics:
package 'IRanges' required by 'GenomicRanges' could not be found
--- failed re-building ‘scDesign3-multipleLineages-vignette.Rmd’
--- re-building ‘scDesign3-parallelization-vignette.Rmd’ using rmarkdown
Failed with error: 'package 'IRanges' required by 'GenomicRanges' could not be found'
Quitting from lines 62-64 [unnamed-chunk-3] (scDesign3-parallelization-vignette.Rmd)
Error: processing vignette 'scDesign3-parallelization-vignette.Rmd' failed with diagnostics:
unable to find required package 'SingleCellExperiment'
--- failed re-building ‘scDesign3-parallelization-vignette.Rmd’
--- re-building ‘scDesign3-pseudotimeGOF-vignette.Rmd’ using rmarkdown
Quitting from lines 45-51 [setup] (scDesign3-pseudotimeGOF-vignette.Rmd)
Error: processing vignette 'scDesign3-pseudotimeGOF-vignette.Rmd' failed with diagnostics:
package 'IRanges' required by 'GenomicRanges' could not be found
--- failed re-building ‘scDesign3-pseudotimeGOF-vignette.Rmd’
--- re-building ‘scDesign3-scATACseq-vignette.Rmd’ using rmarkdown
Quitting from lines 48-52 [unnamed-chunk-2] (scDesign3-scATACseq-vignette.Rmd)
Error: processing vignette 'scDesign3-scATACseq-vignette.Rmd' failed with diagnostics:
package 'IRanges' required by 'GenomicRanges' could not be found
--- 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:
package 'IRanges' required by 'GenomicRanges' could not be found
--- failed re-building ‘scDesign3-spatial-deconvolution.Rmd’
--- re-building ‘scDesign3-spatial-vignette.Rmd’ using rmarkdown
Quitting from lines 38-44 [unnamed-chunk-1] (scDesign3-spatial-vignette.Rmd)
Error: processing vignette 'scDesign3-spatial-vignette.Rmd' failed with diagnostics:
package 'IRanges' required by 'GenomicRanges' could not be found
--- failed re-building ‘scDesign3-spatial-vignette.Rmd’
--- re-building ‘scDesign3.Rmd’ using rmarkdown
Quitting from lines 44-48 [unnamed-chunk-2] (scDesign3.Rmd)
Error: processing vignette 'scDesign3.Rmd' failed with diagnostics:
package 'IRanges' required by 'GenomicRanges' could not be found
--- failed re-building ‘scDesign3.Rmd’
SUMMARY: processing the following files failed:
‘scDesign3-CITEseq-vignette.Rmd’ ‘scDesign3-DEanalysis-vignette.Rmd’
‘scDesign3-batchEffect-vignette.Rmd’
‘scDesign3-clusterGOF-vignette.Rmd’
‘scDesign3-conditionEffect-vignette.Rmd’
‘scDesign3-copulaCompare-vignette.Rmd’
‘scDesign3-introduction-vignette.Rmd’
‘scDesign3-librarySize-vignette.Rmd’
‘scDesign3-multiomics-vignette.Rmd’
‘scDesign3-multipleLineages-vignette.Rmd’
‘scDesign3-parallelization-vignette.Rmd’
‘scDesign3-pseudotimeGOF-vignette.Rmd’
‘scDesign3-scATACseq-vignette.Rmd’
‘scDesign3-spatial-deconvolution.Rmd’
‘scDesign3-spatial-vignette.Rmd’ ‘scDesign3.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 45-54 [unnamed-chunk-3] (scDesign3-CITEseq-vignette.Rmd)
Error: processing vignette 'scDesign3-CITEseq-vignette.Rmd' failed with diagnostics:
package 'SummarizedExperiment' could not be loaded
--- failed re-building ‘scDesign3-CITEseq-vignette.Rmd’
--- re-building ‘scDesign3-DEanalysis-vignette.Rmd’ using rmarkdown
Quitting from lines 43-61 [unnamed-chunk-3] (scDesign3-DEanalysis-vignette.Rmd)
Error: processing vignette 'scDesign3-DEanalysis-vignette.Rmd' failed with diagnostics:
package 'SummarizedExperiment' could not be loaded
--- failed re-building ‘scDesign3-DEanalysis-vignette.Rmd’
--- re-building ‘scDesign3-batchEffect-vignette.Rmd’ using rmarkdown
Quitting from lines 42-46 [setup] (scDesign3-batchEffect-vignette.Rmd)
Error: processing vignette 'scDesign3-batchEffect-vignette.Rmd' failed with diagnostics:
package 'SummarizedExperiment' could not be loaded
--- failed re-building ‘scDesign3-batchEffect-vignette.Rmd’
--- re-building ‘scDesign3-clusterGOF-vignette.Rmd’ using rmarkdown
Quitting from lines 45-52 [unnamed-chunk-3] (scDesign3-clusterGOF-vignette.Rmd)
Error: processing vignette 'scDesign3-clusterGOF-vignette.Rmd' failed with diagnostics:
package or namespace load failed for 'DuoClustering2018':
.onLoad failed in loadNamespace() for 'DuoClustering2018', details:
call: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
error: there is no package called 'Biostrings'
--- failed re-building ‘scDesign3-clusterGOF-vignette.Rmd’
--- re-building ‘scDesign3-conditionEffect-vignette.Rmd’ using rmarkdown
--- finished re-building ‘scDesign3-conditionEffect-vignette.Rmd’
--- re-building ‘scDesign3-copulaCompare-vignette.Rmd’ using rmarkdown
Quitting from lines 36-47 [setup] (scDesign3-copulaCompare-vignette.Rmd)
Error: processing vignette 'scDesign3-copulaCompare-vignette.Rmd' failed with diagnostics:
package 'scuttle' could not be loaded
--- failed re-building ‘scDesign3-copulaCompare-vignette.Rmd’
--- re-building ‘scDesign3-introduction-vignette.Rmd’ using rmarkdown
Quitting from lines 47-49 [unnamed-chunk-2] (scDesign3-introduction-vignette.Rmd)
Error: processing vignette 'scDesign3-introduction-vignette.Rmd' failed with diagnostics:
there is no package called 'SingleCellExperiment'
--- failed re-building ‘scDesign3-introduction-vignette.Rmd’
--- re-building ‘scDesign3-librarySize-vignette.Rmd’ using rmarkdown
Quitting from lines 44-51 [unnamed-chunk-2] (scDesign3-librarySize-vignette.Rmd)
Error: processing vignette 'scDesign3-librarySize-vignette.Rmd' failed with diagnostics:
package 'SingleCellExperiment' required by 'scran' could not be found
--- failed 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 57-61 [unnamed-chunk-4] (scDesign3-multiomics-vignette.Rmd)
Error: processing vignette 'scDesign3-multiomics-vignette.Rmd' failed with diagnostics:
there is no package called 'SingleCellExperiment'
--- failed re-building ‘scDesign3-multiomics-vignette.Rmd’
--- re-building ‘scDesign3-multipleLineages-vignette.Rmd’ using rmarkdown
Quitting from lines 60-62 [unnamed-chunk-3] (scDesign3-multipleLineages-vignette.Rmd)
Error: processing vignette 'scDesign3-multipleLineages-vignette.Rmd' failed with diagnostics:
there is no package called 'SingleCellExperiment'
--- failed 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-clusterGOF-vignette.Rmd’
‘scDesign3-copulaCompare-vignette.Rmd’
‘scDesign3-introduction-vignette.Rmd’
‘scDesign3-librarySize-vignette.Rmd’
‘scDesign3-multiomics-vignette.Rmd’
‘scDesign3-multipleLineages-vignette.Rmd’
‘scDesign3-spatial-deconvolution.Rmd’
Error: Vignette re-building failed.
Execution halted