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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TADCompare.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TADCompare_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/TADCompare.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TADCompare/DESCRIPTION’ ... OK
* this is package ‘TADCompare’ version ‘1.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘TADCompare’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘cluster’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.Make_Triangles: no visible binding for global variable ‘start’
.Make_Triangles: no visible binding for global variable ‘end’
.Make_Triangles: no visible global function definition for ‘na.omit’
.Make_Triangles: no visible binding for global variable
  ‘boundary_start’
.Make_Triangles: no visible binding for global variable ‘orig_regx’
.Make_Triangles: no visible binding for global variable ‘start1’
.Make_Triangles: no visible binding for global variable ‘boundary_end’
ConsensusTADs : <anonymous>: no visible binding for global variable
  ‘Coordinate’
ConsensusTADs: no visible binding for global variable ‘Sample’
ConsensusTADs: no visible binding for global variable ‘Boundary’
ConsensusTADs: no visible binding for global variable ‘Diff_Score’
ConsensusTADs: no visible global function definition for ‘sd’
ConsensusTADs: no visible binding for global variable ‘Differential’
ConsensusTADs: no visible binding for global variable ‘Coordinate’
ConsensusTADs: no visible binding for global variable ‘TAD_Score’
ConsensusTADs: no visible binding for global variable ‘.’
ConsensusTADs: no visible binding for global variable ‘median’
DiffPlot: no visible binding for global variable ‘Type’
DiffPlot: no visible binding for global variable ‘Differential’
DiffPlot: no visible binding for global variable ‘Boundary’
DiffPlot: no visible binding for global variable ‘Enriched_In’
DiffPlot: no visible global function definition for ‘na.omit’
DiffPlot: no visible binding for global variable ‘boundary_start’
DiffPlot: no visible binding for global variable ‘orig_regx’
DiffPlot: no visible binding for global variable ‘start1’
DiffPlot: no visible binding for global variable ‘boundary_end’
DiffPlot: no visible binding for global variable ‘start2’
DiffPlot: no visible binding for global variable ‘TAD_Score1’
DiffPlot: no visible binding for global variable ‘TAD_Score2’
DiffPlot: no visible binding for global variable ‘Gap_Score’
DiffPlot: no visible binding for global variable ‘variable’
DiffPlot: no visible binding for global variable ‘value’
DiffPlot: no visible binding for global variable ‘line_spot’
DiffPlot: no visible global function definition for ‘complete.cases’
DiffPlot: no visible binding for global variable ‘.’
DiffPlot: no visible binding for global variable ‘x’
DiffPlot: no visible binding for global variable ‘y’
DiffPlot: no visible binding for global variable ‘orig_regy’
TADCompare: no visible global function definition for ‘sd’
TADCompare: no visible binding for global variable ‘Boundary’
TADCompare: no visible binding for global variable ‘Gap_Score’
TADCompare: no visible binding for global variable ‘Differential’
TADCompare: no visible binding for global variable ‘Bound_Dist’
TADCompare: no visible binding for global variable ‘Enriched_In’
TADCompare: no visible binding for global variable ‘Type’
TADCompare: no visible binding for global variable ‘Count’
TimeCompare : <anonymous>: no visible binding for global variable
  ‘Coordinate’
TimeCompare: no visible binding for global variable ‘Sample’
TimeCompare: no visible binding for global variable ‘Groups’
TimeCompare: no visible binding for global variable ‘Coordinate’
TimeCompare: no visible binding for global variable ‘Boundary’
TimeCompare: no visible global function definition for ‘median’
TimeCompare: no visible binding for global variable ‘Diff_Score’
TimeCompare: no visible global function definition for ‘sd’
TimeCompare: no visible binding for global variable ‘Differential’
TimeCompare: no visible binding for global variable ‘TAD_Score’
TimeCompare: no visible binding for global variable ‘.’
TimeCompare: no visible binding for global variable ‘median’
TimeCompare: no visible binding for global variable ‘Sample 1’
TimeCompare: no visible binding for global variable ‘Consensus_Score’
TimeCompare: no visible binding for global variable ‘Category’
TimeCompare: no visible binding for global variable ‘Count’
Undefined global functions or variables:
  . Bound_Dist Boundary Category Consensus_Score Coordinate Count
  Diff_Score Differential Enriched_In Gap_Score Groups Sample Sample 1
  TAD_Score TAD_Score1 TAD_Score2 Type boundary_end boundary_start
  complete.cases end line_spot median na.omit orig_regx orig_regy sd
  start start1 start2 value variable x y
Consider adding
  importFrom("stats", "complete.cases", "end", "median", "na.omit", "sd",
             "start")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/TADCompare.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL TADCompare
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘TADCompare’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (TADCompare)