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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 Chicago
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* checking for file ‘Chicago/DESCRIPTION’ ... OK
* preparing ‘Chicago’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Chicago.Rmd’ using rmarkdown
Loading required package: data.table

Welcome to CHiCAGO - version 1.25.0
If you are new to CHiCAGO, please consider reading the vignette through the command: vignette("Chicago").
NOTE: Default values of tlb.minProxOEPerBin and tlb.minProxB2BPerBin changed as of Version 1.1.5. No action is required unless you specified non-default values, or wish to re-run the pipeline on old chicagoData objects. See news(package="Chicago")
Reading custom experimental settings from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/PCHiCdata/extdata/sGM12878Settings/sGM12878.settingsFile...
Read 4 items
Locating <baitmapfile>.baitmap in /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/PCHiCdata/extdata/hg19TestDesign...
Found h19_chr20and21.baitmap
Locating <rmapfile>.rmap in /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/PCHiCdata/extdata/hg19TestDesign...
Found h19_chr20and21.rmap
Locating <nperbinfile>.npb in /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/PCHiCdata/extdata/hg19TestDesign...
Found h19_chr20and21.npb
Locating <nbaitsperbinfile>.nbpb in /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/PCHiCdata/extdata/hg19TestDesign...
Found h19_chr20and21.nbpb
Locating <proxOEfile>.poe in /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/PCHiCdata/extdata/hg19TestDesign...
Found h19_chr20and21.poe
Checking the design files...
Reading the settings from NPB file header...
Checking the integrity of the NPB file...
Reading NPerBin file...
Checking the integrity of the NBPB file...
Reading NBaitsPerBin file...
Reading /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/PCHiCdata/extdata/GMchinputFiles/GM_rep1.chinput
Processing input...
minFragLen = 150 maxFragLen = 40000
Filtered out 2593 interactions involving other ends < minFragLen or > maxFragLen.
minNPerBait = 250
Filtered out 251 baits with < minNPerBait reads.

Removed interactions with fragments adjacent to baits.
Filtered out 0 baits without proximal non-Bait2bait interactions

Reading /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/PCHiCdata/extdata/GMchinputFiles/GM_rep2.chinput
Processing input...
minFragLen = 150 maxFragLen = 40000
Filtered out 13520 interactions involving other ends < minFragLen or > maxFragLen.
minNPerBait = 250
Filtered out 7 baits with < minNPerBait reads.

Removed interactions with fragments adjacent to baits.
Filtered out 0 baits without proximal non-Bait2bait interactions

Reading /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/PCHiCdata/extdata/GMchinputFiles/GM_rep3.chinput
Processing input...
minFragLen = 150 maxFragLen = 40000
Filtered out 8941 interactions involving other ends < minFragLen or > maxFragLen.
minNPerBait = 250
Filtered out 25 baits with < minNPerBait reads.

Removed interactions with fragments adjacent to baits.
Filtered out 0 baits without proximal non-Bait2bait interactions

Merging samples...
Computing merged scores...

Computing sample scaling factors...

Reading NPerBin file...
Computing normalisation scores...

*** Running normaliseBaits...

Normalising baits...
Reading NPerBin file...
Computing binwise means...

*** Running normaliseOtherEnds...

Preprocessing input...
Computing trans-counts...
Filtering out 3 other ends with top 0.01% number of trans-interactions
Binning...
Computing total bait counts...
Reading NBaitsPerBin file...
Computing scaling factors...
Computing binwise means...
Computing normalised counts...
Post-processing...

*** Running estimateTechnicalNoise...

Estimating technical noise based on trans-counts...
Binning baits based on observed trans-counts...
Defining interaction pools and gathering the observed numbers of trans-counts per pool...
Computing the total number of possible interactions per pool...
Preparing the data.....
Processing fragment pools.................................................................................................................................................................................................................................
Plotting...
Post-processing the results...

*** Running estimateDistFun...


*** Running estimateBrownianComponent...

s_i factors found - estimating Brownian component...
Reading ProxOE file...
Sampling the dispersion...
Sampling the dispersion...
Sampling the dispersion...
Sampling the dispersion...
Sampling the dispersion...
Getting consensus dispersion estimate...

*** Running getPvals...

Calculating p-values...
Approximating 7 very small p-values.

*** Running getScores...

Calculating p-value weights...
Calculating scores...
Input is a CHiCAGO object...
Filtering out bait2bait interactions...
Removing trans interactions from analysis...
Overlap our reads with Features...
Separate significant interactions from non-significant interactions...
No distance from bait to trim sample was provided...
Removing duplicated other-ends from significant interactions (same will happen with samples)...
Bin non-significant interactions according to distance from bait before drawing random samples...
Draw random samples...
Sum number of overlaps with feature in our significant interactions and in our samples...
Plotting barplot number of overlaps for features and samples...
Returning table with results...

Quitting from lines 277-280 (Chicago.Rmd) 
Error: processing vignette 'Chicago.Rmd' failed with diagnostics:
there is no package called 'GenomicInteractions'
--- failed re-building ‘Chicago.Rmd’

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

Error: Vignette re-building failed.
Execution halted