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### Running command:
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###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:synergyfinder.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings synergyfinder_3.4.5.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/synergyfinder.Rcheck’
* using R version 4.2.1 (2022-06-23)
* 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 ‘3.4.5’
* 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 ... 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 ‘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 ... WARNING
'::' or ':::' import not declared from: ‘scales’
Namespaces in Imports field not imported from:
  ‘future’ ‘gstat’ ‘nleqslv’ ‘sp’ ‘tidyverse’
  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
.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’
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’
PlotSensitivitySynergy: no visible binding for global variable
  ‘block_id’
PlotSensitivitySynergy: no visible binding for global variable ‘css’
PlotSensitivitySynergy: no visible binding for global variable ‘label’
PlotSensitivitySynergy: no visible binding for global variable
  ‘synergy’
ReshapeData: no visible binding for global variable ‘block_id’
ReshapeData: no visible binding for global variable ‘n’
ReshapeData: no visible global function definition for ‘head’
ReshapeData: no visible binding for global variable ‘response_origin’
ReshapeData: no visible binding for global variable ‘nn’
ReshapeData: no visible binding for global variable ‘maxn’
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 head id input_type label left
  maxn metric n nn pred r 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", "text")
  importFrom("stats", "end", "start")
  importFrom("utils", "data", "head")
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 ... WARNING
Codoc mismatches from documentation object 'PlotDoseResponse':
PlotDoseResponse
  Code: function(data, block_ids = c(1), drugs = c(1, 2), adjusted =
                 TRUE, statistic = NULL, summary_statistic = "mean",
                 high_value_color = "#FF0000", low_value_color =
                 "#00FF00", point_color = "#C24B40", curve_color =
                 "black", curve_ylim = NULL, curve_grid = TRUE,
                 text_size_scale = 1, heatmap_text_label_size_scale =
                 1, heatmap_text_label_color = "#000000",
                 heatmap_color_range = NULL, curve_plot_title = NULL,
                 heatmap_plot_title = NULL, Emin = NA, Emax = NA,
                 save_file = FALSE, file_type = "pdf", file_name =
                 NULL, width = 12, height = 6)
  Docs: function(data, block_ids = c(1), drugs = c(1, 2), adjusted =
                 TRUE, statistic = NULL, summary_statistic = "mean",
                 high_value_color = "#A90217", low_value_color =
                 "#2166AC", point_color = "#C24B40", curve_color =
                 "black", curve_ylim = NULL, curve_grid = TRUE,
                 text_size_scale = 1, heatmap_text_label_size_scale =
                 1, heatmap_text_label_color = "#000000",
                 heatmap_color_range = NULL, curve_plot_title = NULL,
                 heatmap_plot_title = NULL, Emin = NA, Emax = NA,
                 save_file = FALSE, file_type = "pdf", file_name =
                 NULL, width = 12, height = 6)
  Mismatches in argument default values:
    Name: 'high_value_color' Code: "#FF0000" Docs: "#A90217"
    Name: 'low_value_color' Code: "#00FF00" Docs: "#2166AC"

Codoc mismatches from documentation object 'PlotDoseResponseCurve':
PlotDoseResponseCurve
  Code: function(data, plot_block = 1, drug_index = 1, adjusted = TRUE,
                 Emin = NA, Emax = NA, grid = TRUE, point_color =
                 "#C24B40", curve_color = "black", text_size_scale = 1,
                 plot_title = NULL, plot_subtitle = NULL, plot_setting
                 = list(cex.lab = 1 * text_size_scale, mgp = c(2, 0.5,
                 0), font.main = 2, font.lab = 1, cex.main = 14/12 *
                 text_size_scale, bty = "l", lwd = 1.5), plot_new =
                 TRUE, record_plot = TRUE, ...)
  Docs: function(data, plot_block = 1, drug_index = 1, adjusted = TRUE,
                 Emin = NA, Emax = NA, grid = TRUE, point_color =
                 "#C24B40", curve_color = "black", text_size_scale = 1,
                 plot_title = NULL, plot_subtitle = NULL, plot_setting
                 = list(cex.lab = 1 * text_size_scale, mgp = c(2, 0.5,
                 0), font.main = 2, font.lab = 1, cex.main = 14/12 *
                 text_size_scale, bty = "l", lwd = 1.5), ylim = NULL,
                 plot_new = TRUE, record_plot = TRUE)
  Argument names in code not in docs:
    ...
  Argument names in docs not in code:
    ylim
  Mismatches in argument names:
    Position: 14 Code: plot_new Docs: ylim
    Position: 15 Code: record_plot Docs: plot_new
    Position: 16 Code: ... Docs: record_plot

Codoc mismatches from documentation object 'PlotSynergy':
PlotSynergy
  Code: function(data, type = "2D", method = "ZIP", block_ids = c(1),
                 drugs = c(1, 2), row_range = NULL, col_range = NULL,
                 color_range = NULL, z_range = NULL, axis_line = FALSE,
                 statistic = NULL, summary_statistic = "mean",
                 plot_title = NULL, interpolate_len = 3,
                 high_value_color = "#FF0000", low_value_color =
                 "#00FF00", text_size_scale = 1,
                 heatmap_text_label_size_scale = 1,
                 heatmap_text_label_color = "#000000", grid = TRUE,
                 dynamic = FALSE, display = TRUE, save_file = FALSE,
                 file_type = "pdf", file_name = NULL, file_path = NULL,
                 height = 6, width = 6, units = "in")
  Docs: function(data, type = "2D", method = "ZIP", block_ids = c(1),
                 drugs = c(1, 2), row_range = NULL, col_range = NULL,
                 color_range = NULL, z_range = NULL, axis_line = FALSE,
                 statistic = NULL, summary_statistic = "mean",
                 plot_title = NULL, interpolate_len = 3,
                 high_value_color = "#A90217", low_value_color =
                 "#2166AC", text_size_scale = 1,
                 heatmap_text_label_size_scale = 1,
                 heatmap_text_label_color = "#000000", grid = TRUE,
                 dynamic = FALSE, display = TRUE, save_file = FALSE,
                 file_type = "pdf", file_name = NULL, file_path = NULL,
                 height = 6, width = 6, units = "in")
  Mismatches in argument default values:
    Name: 'high_value_color' Code: "#FF0000" Docs: "#A90217"
    Name: 'low_value_color' Code: "#00FF00" Docs: "#2166AC"

* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
CalculateSensitivity 18.863  0.252  19.114
PlotMultiDrugSurface  9.823  0.228  10.052
* 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: 2 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/synergyfinder.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL synergyfinder
###
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* installing to library ‘/home/biocbuild/bbs-3.15-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
** 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 (synergyfinder)