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### Running command:
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### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:synergyfinder.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings synergyfinder_3.2.10.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/synergyfinder.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'synergyfinder/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'synergyfinder' version '3.2.10'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 '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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
CalculateSensitivity 24.48 0.22 24.70
PlotMultiDrugSurface 9.58 0.29 9.95
PlotMultiDrugBar 5.89 0.13 6.01
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
CalculateSensitivity 21.54 0.08 21.60
PlotMultiDrugSurface 8.43 0.24 8.67
PlotMultiDrugBar 5.66 0.03 5.69
* 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
'C:/Users/biocbuild/bbs-3.14-bioc/meat/synergyfinder.Rcheck/00check.log'
for details.
