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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 EnrichedHeatmap
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* checking for file ‘EnrichedHeatmap/DESCRIPTION’ ... OK
* preparing ‘EnrichedHeatmap’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘EnrichedHeatmap.Rmd’ using knitr
The automatically generated colors map from the 1^st and 99^th of the values in the
matrix. There are outliers in the matrix whose patterns might be hidden by this color
mapping. You can manually set the color to `col` argument.

Use `suppressMessages()` to turn off this message.
All signal values are within [0, 1], so we assume it is methylation signal. Automatically
set limit [0, 1] to the smoothed values. If this is not the case, set argument `limit =
NA` in the function to remove the limits. Set `verbose = FALSE` to turn off this message.
All signal values are within [0, 1], so we assume it is methylation signal. Automatically
set limit [0, 1] to the smoothed values. If this is not the case, set argument `limit =
NA` in the function to remove the limits. Set `verbose = FALSE` to turn off this message.
All signal values are within [0, 1], so we assume it is methylation signal. Automatically
set limit [0, 1] to the smoothed values. If this is not the case, set argument `limit =
NA` in the function to remove the limits. Set `verbose = FALSE` to turn off this message.
All signal values are within [0, 1], so we assume it is methylation signal. Automatically
set limit [0, 1] to the smoothed values. If this is not the case, set argument `limit =
NA` in the function to remove the limits. Set `verbose = FALSE` to turn off this message.
All signal values are within [0, 1], so we assume it is methylation signal. Automatically
set limit [0, 1] to the smoothed values. If this is not the case, set argument `limit =
NA` in the function to remove the limits. Set `verbose = FALSE` to turn off this message.
`use_raster` is automatically set to TRUE for a matrix with more than 2000 rows. You can
control `use_raster` argument by explicitly setting TRUE/FALSE to it.

Set `ht_opt$message = FALSE` to turn off this message.
`use_raster` is automatically set to TRUE for a matrix with more than 2000 rows. You can
control `use_raster` argument by explicitly setting TRUE/FALSE to it.

Set `ht_opt$message = FALSE` to turn off this message.
--- finished re-building ‘EnrichedHeatmap.Rmd’

--- re-building ‘roadmap.Rmd’ using knitr
trying URL 'https://jokergoo.github.io/supplementary/EnrichedHeatmap-supplementary/roadmap_normalized_matrices.RData'
Content type 'application/octet-stream' length 26598186 bytes (25.4 MB)
==================================================
downloaded 25.4 MB

Quitting from lines 455-458 (roadmap.Rmd) 
Error: processing vignette 'roadmap.Rmd' failed with diagnostics:
there is no package called 'genefilter'
--- failed re-building ‘roadmap.Rmd’

--- re-building ‘row_odering.Rmd’ using knitr
`use_raster` is automatically set to TRUE for a matrix with more than 2000 rows. You can
control `use_raster` argument by explicitly setting TRUE/FALSE to it.

Set `ht_opt$message = FALSE` to turn off this message.
`use_raster` is automatically set to TRUE for a matrix with more than 2000 rows. You can
control `use_raster` argument by explicitly setting TRUE/FALSE to it.

Set `ht_opt$message = FALSE` to turn off this message.
`use_raster` is automatically set to TRUE for a matrix with more than 2000 rows. You can
control `use_raster` argument by explicitly setting TRUE/FALSE to it.

Set `ht_opt$message = FALSE` to turn off this message.
--- finished re-building ‘row_odering.Rmd’

--- re-building ‘visualize_categorical_signals_wrapper.Rmd’ using knitr
--- finished re-building ‘visualize_categorical_signals_wrapper.Rmd’

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

Error: Vignette re-building failed.
Execution halted