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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:synergyfinder.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings synergyfinder_2.4.16.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/synergyfinder.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘synergyfinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘synergyfinder’ version ‘2.4.16’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'drc', 'reshape2', 'tidyverse', 'dplyr', 'tidyr', 'purrr', 'furrr',
  'ggplot2', 'ggforce', 'grid', 'vegan', 'gstat', 'sp',
  'SpatialExtremes', 'ggrepel', 'kriging', 'plotly', 'stringr',
  'future', 'mice', 'lattice', 'nleqslv', 'magrittr', 'pbapply', 'metR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘synergyfinder’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘drc’ ‘reshape2’ ‘tidyverse’ ‘dplyr’ ‘tidyr’ ‘purrr’ ‘furrr’ ‘ggplot2’ ‘ggforce’ ‘grid’ ‘vegan’ ‘gstat’ ‘sp’ ‘methods’ ‘SpatialExtremes’ ‘ggrepel’ ‘kriging’ ‘plotly’ ‘stringr’ ‘future’ ‘mice’ ‘lattice’ ‘nleqslv’ ‘stats’ ‘graphics’ ‘grDevices’ ‘magrittr’ ‘pbapply’ ‘metR’
A package should be listed in only one of these fields.
* 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:
  ‘future’ ‘gstat’ ‘nleqslv’ ‘sp’ ‘tidyverse’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘SpatialExtremes’ ‘dplyr’ ‘drc’ ‘furrr’ ‘future’ ‘ggforce’ ‘ggrepel’
  ‘grid’ ‘gstat’ ‘kriging’ ‘lattice’ ‘metR’ ‘methods’ ‘mice’ ‘nleqslv’
  ‘pbapply’ ‘plotly’ ‘purrr’ ‘reshape2’ ‘sp’ ‘stringr’ ‘tidyr’
  ‘tidyverse’ ‘vegan’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.Extract2DrugPlotData: no visible binding for global variable
  ‘input_type’
.Extract2DrugPlotData: no visible binding for global variable
  ‘block_id’
.Extract2DrugPlotData: no visible binding for global variable ‘value’
.Extract2DrugPlotData: no visible binding for global variable ‘left’
.Extract2DrugPlotData: no visible binding for global variable ‘right’
.Extract2DrugPlotData: no visible binding for global variable ‘conc1’
.Extract2DrugPlotData: no visible binding for global variable ‘conc2’
.Extract2DrugPlotData: no visible binding for global variable ‘text’
.ExtractMultiDrugPlotData: no visible binding for global variable
  ‘block_id’
Bliss: no visible binding for global variable ‘Bliss_ref’
CalculateCSS: no visible binding for global variable ‘data’
CalculateSensitivity: no visible binding for global variable
  ‘response_origin’
CalculateSensitivity: no visible binding for global variable ‘block_id’
CalculateSynergy: no visible binding for global variable
  ‘response_origin’
CalculateSynergy: no visible binding for global variable ‘block_id’
HSA: no visible binding for global variable ‘HSA_ref’
HighlightBarPlot: no visible binding for global variable ‘id’
HighlightBarPlot: no visible binding for global variable ‘value’
HighlightBarPlot: no visible binding for global variable ‘color’
Plot2DrugHeatmap: no visible binding for global variable ‘text’
PlotBarometer: no visible binding for global variable ‘block_id’
PlotBarometer: no visible binding for global variable ‘response_mean’
PlotBarometer: no visible binding for global variable ‘response’
PlotBarometer: no visible binding for global variable ‘r’
PlotBarometer: no visible binding for global variable ‘theta’
PlotBarometer: no visible binding for global variable ‘value’
PlotBarometer: no visible binding for global variable ‘start’
PlotBarometer: no visible binding for global variable ‘end’
PlotBarometer: no visible binding for global variable ‘label’
PlotBarometer: no visible binding for global variable ‘x’
PlotBarometer: no visible binding for global variable ‘y’
PlotBarometer: no visible binding for global variable ‘adjust’
PlotBarometer: no visible binding for global variable ‘angle’
PlotDoseResponse: no visible binding for global variable ‘grid’
PlotDoseResponseCurve: no visible binding for global variable ‘respone’
PlotDoseResponseCurve: no visible binding for global variable
  ‘response_origin’
PlotDoseResponseCurve: no visible binding for global variable
  ‘block_id’
PlotMultiDrugBar: no visible binding for global variable ‘id’
PlotMultiDrugBar: no visible binding for global variable ‘value’
PlotMultiDrugBar: no visible binding for global variable ‘color’
PlotMultiDrugBar: no visible binding for global variable ‘metric’
PlotSensitiveSynergy: no visible binding for global variable ‘block_id’
PlotSensitiveSynergy: no visible binding for global variable ‘css’
PlotSensitiveSynergy: no visible binding for global variable ‘label’
PlotSensitiveSynergy: no visible binding for global variable ‘synergy’
ReshapeData: no visible binding for global variable ‘block_id’
ReshapeData: no visible binding for global variable ‘response_origin’
ReshapeData: no visible binding for global variable ‘n’
ReshapeData: no visible binding for global variable ‘response_sd’
ReshapeData: no visible binding for global variable ‘response_sem’
ReshapeData: no visible binding for global variable ‘response_mean’
ReshapeData: no visible binding for global variable ‘response_CI95’
ReshapeData: no visible binding for global variable
  ‘response_origin_sd’
ReshapeData: no visible binding for global variable
  ‘response_origin_sem’
ReshapeData: no visible binding for global variable
  ‘response_origin_mean’
ReshapeData: no visible binding for global variable
  ‘response_origin_CI95’
ZIP : <anonymous>: no visible binding for global variable ‘data’
ZIP : <anonymous>: no visible binding for global variable ‘pred’
ZIP : <anonymous>: no visible global function definition for ‘:=’
ZIP: no visible binding for global variable ‘.’
ZIP: no visible binding for global variable ‘ZIP_fit’
ZIP: no visible binding for global variable ‘ZIP_ref’
ZIP: no visible binding for global variable ‘ZIP_synergy’
Undefined global functions or variables:
  . := Bliss_ref HSA_ref ZIP_fit ZIP_ref ZIP_synergy adjust angle
  block_id color conc1 conc2 css data end grid id input_type label left
  metric n pred r respone response response_CI95 response_mean
  response_origin response_origin_CI95 response_origin_mean
  response_origin_sd response_origin_sem response_sd response_sem right
  start synergy text theta value x y
Consider adding
  importFrom("graphics", "grid", "text")
  importFrom("stats", "end", "start")
  importFrom("utils", "data")
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 data for ASCII and uncompressed saves ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
PlotMultiDrugSurface 11.476  0.136  11.626
PlotMultiDrugBar      7.596  0.036   7.651
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/synergyfinder.Rcheck/00check.log’
for details.

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###
### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL synergyfinder
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘synergyfinder’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (synergyfinder)