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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 Banksy
###
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* checking for file ‘Banksy/DESCRIPTION’ ... OK
* preparing ‘Banksy’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘batch-correction.Rmd’ using rmarkdown
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing relative-counts-normalization

Quitting from batch-correction.Rmd:133-137 [unnamed-chunk-9]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 3/3 in VECTOR_ELT
---
Backtrace:
    ▆
 1. └─Banksy::computeBanksy(...)
 2.   └─base::lapply(...)
 3.     └─Banksy (local) FUN(X[[i]], ...)
 4.       └─Banksy:::computeNeighbors(...)
 5.         └─Banksy:::withKNNmedian(locs = locs, k_geom = k_geom, verbose = verbose)
 6.           ├─knnDF[, `:=`(weight, exp(-distance^2/median(distance)^2)), by = from]
 7.           └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'batch-correction.Rmd' failed with diagnostics:
attempt access index 3/3 in VECTOR_ELT
--- failed re-building ‘batch-correction.Rmd’

--- re-building ‘domain-segment.Rmd’ using rmarkdown
--- finished re-building ‘domain-segment.Rmd’

--- re-building ‘multi-sample.Rmd’ using rmarkdown
Performing relative-counts-normalization
Performing relative-counts-normalization
Performing relative-counts-normalization
Performing relative-counts-normalization
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

Quitting from multi-sample.Rmd:124-129 [unnamed-chunk-8]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 3/3 in VECTOR_ELT
---
Backtrace:
    ▆
 1. ├─BiocGenerics::lapply(...)
 2. └─base::lapply(...)
 3.   └─Banksy (local) FUN(X[[i]], ...)
 4.     └─base::lapply(...)
 5.       └─Banksy (local) FUN(X[[i]], ...)
 6.         └─Banksy:::computeNeighbors(...)
 7.           └─Banksy:::withKNNmedian(locs = locs, k_geom = k_geom, verbose = verbose)
 8.             ├─knnDF[, `:=`(weight, exp(-distance^2/median(distance)^2)), by = from]
 9.             └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'multi-sample.Rmd' failed with diagnostics:
attempt access index 3/3 in VECTOR_ELT
--- failed re-building ‘multi-sample.Rmd’

--- re-building ‘parameter-selection.Rmd’ using rmarkdown

Quitting from parameter-selection.Rmd:109-112 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 3/3 in VECTOR_ELT
---
Backtrace:
    ▆
 1. └─Banksy::computeBanksy(...)
 2.   └─base::lapply(...)
 3.     └─Banksy (local) FUN(X[[i]], ...)
 4.       └─Banksy:::computeNeighbors(...)
 5.         └─Banksy:::withKNNmedian(locs = locs, k_geom = k_geom, verbose = verbose)
 6.           ├─knnDF[, `:=`(weight, exp(-distance^2/median(distance)^2)), by = from]
 7.           └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'parameter-selection.Rmd' failed with diagnostics:
attempt access index 3/3 in VECTOR_ELT
--- failed re-building ‘parameter-selection.Rmd’

SUMMARY: processing the following files failed:
  ‘batch-correction.Rmd’ ‘multi-sample.Rmd’ ‘parameter-selection.Rmd’

Error: Vignette re-building failed.
Execution halted