##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:synergyfinder.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings synergyfinder_3.9.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/synergyfinder.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘synergyfinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘synergyfinder’ version ‘3.9.2’
* 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 loading without being on the library search path ... 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’
CalculateSynergy: no visible global function definition for ‘t.test’
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’
PlotDoseResponseCurve: no visible global function definition for
  ‘dev.list’
PlotDoseResponseCurve: no visible global function definition for
  ‘dev.off’
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 dev.list dev.off 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 t.test text theta value
  x y
Consider adding
  importFrom("grDevices", "dev.list", "dev.off")
  importFrom("graphics", "text")
  importFrom("stats", "end", "start", "t.test")
  importFrom("utils", "data", "head")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) FitDoseResponse.Rd:55: Escaped LaTeX specials: \&
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
CalculateSensitivity 29.796  0.200  29.996
PlotMultiDrugSurface 18.403  0.212  18.617
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘User_tutorual_of_the_SynergyFinder_plus.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/synergyfinder.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL synergyfinder
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.0/site-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)