##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TSAR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TSAR_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/TSAR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TSAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TSAR’ version ‘1.4.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘TSAR’ 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 ... NOTE
Found the following CITATION file in a non-standard place:
  CITATION
Most likely ‘inst/CITATION’ should be used instead.
* checking code 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
TSA_Tms : <anonymous>: no visible binding for global variable ‘well_ID’
TSA_Tms : <anonymous>: no visible binding for global variable ‘Tm’
TSA_Tms : <anonymous>: no visible global function definition for ‘sd’
TSA_Tms: no visible binding for global variable ‘well_ID’
TSA_Tms: no visible binding for global variable ‘Tm’
TSA_Tms: no visible binding for global variable ‘condition_ID’
TSA_Tms: no visible binding for global variable ‘Protein’
TSA_Tms: no visible binding for global variable ‘Ligand’
TSA_average: no visible binding for global variable ‘Temperature’
TSA_average: no visible binding for global variable ‘Fluorescence’
TSA_average: no visible global function definition for ‘sd’
TSA_average: no visible binding for global variable ‘Normalized’
TSA_average: no visible global function definition for ‘predict’
TSA_boxplot: no visible binding for global variable ‘condition_ID’
TSA_boxplot: no visible binding for global variable ‘Tm’
TSA_boxplot: no visible binding for global variable ‘Ligand’
TSA_boxplot: no visible binding for global variable ‘well_ID’
TSA_boxplot: no visible binding for global variable ‘Protein’
TSA_compare_plot: no visible binding for global variable ‘Temperature’
TSA_compare_plot: no visible binding for global variable ‘avg_smooth’
TSA_compare_plot: no visible binding for global variable
  ‘sd_min_smooth’
TSA_compare_plot: no visible binding for global variable
  ‘sd_max_smooth’
TSA_compare_plot: no visible global function definition for
  ‘colorRampPalette’
TSA_wells_plot: no visible binding for global variable ‘Temperature’
TSA_wells_plot: no visible binding for global variable ‘Fluorescence’
TSA_wells_plot: no visible binding for global variable ‘Normalized’
TSA_wells_plot: no visible binding for global variable ‘well_ID’
TSA_wells_plot: no visible binding for global variable ‘sd_min_smooth’
TSA_wells_plot: no visible binding for global variable ‘sd_max_smooth’
TSA_wells_plot: no visible binding for global variable ‘avg_smooth’
TSA_wells_plot: no visible binding for global variable ‘sd_min’
TSA_wells_plot: no visible binding for global variable ‘sd_max’
TSA_wells_plot: no visible binding for global variable ‘average’
build_curves: no visible binding for global variable ‘condition_ID’
build_table: no visible global function definition for ‘head’
build_well: no visible global function definition for ‘head’
dummy_plot: no visible binding for global variable ‘x’
dummy_plot: no visible binding for global variable ‘y’
gam_analysis : process_well: no visible binding for global variable
  ‘Well.Position’
gam_analysis : process_well: no visible global function definition for
  ‘all_of’
join_well_info: no visible binding for global variable ‘Col’
join_well_info: no visible binding for global variable ‘pos’
join_well_info: no visible binding for global variable ‘Well’
join_well_info: no visible binding for global variable ‘Protein’
join_well_info: no visible binding for global variable ‘Ligand’
join_well_info: no visible global function definition for ‘na.omit’
merge_norm : <anonymous>: no visible global function definition for
  ‘read.csv’
merge_norm : <anonymous>: no visible binding for global variable
  ‘Well.Position’
merge_norm : <anonymous>: no visible binding for global variable
  ‘Protein’
merge_norm : <anonymous>: no visible binding for global variable
  ‘Ligand’
merge_norm: no visible binding for global variable ‘tm’
merge_norm: no visible binding for global variable ‘Well.Position’
merge_update: no visible global function definition for ‘na.omit’
model_boltzmann: no visible binding for global variable ‘Temperature’
normalize: no visible global function definition for ‘all_of’
preview_condition: no visible global function definition for ‘head’
preview_model: no visible binding for global variable ‘Well.Position’
read_analysis: no visible global function definition for ‘read.delim’
read_analysis: no visible global function definition for ‘read.csv’
read_raw_data: no visible global function definition for ‘read.delim’
read_raw_data: no visible global function definition for ‘read.csv’
remove_raw: no visible binding for global variable ‘Well.Position’
remove_raw: no visible binding for global variable ‘Well’
remove_selected_graph: no visible binding for global variable
  ‘condition_ID’
remove_selected_graph: no visible binding for global variable ‘well_ID’
screen: no visible binding for global variable ‘Well.Position’
screen: no visible binding for global variable ‘Well’
screen : normalize_by_well: no visible binding for global variable
  ‘Well.Position’
screen: no visible binding for global variable ‘Temperature’
screen: no visible binding for global variable ‘Fluorescence’
view_deriv: no visible binding for global variable ‘Temperature’
view_deriv: no visible binding for global variable ‘norm_deriv’
view_deriv: no visible binding for global variable ‘well_ID’
view_deriv: no visible binding for global variable ‘Tm’
view_model: no visible binding for global variable ‘Temperature’
view_model: no visible binding for global variable ‘Normalized’
view_model: no visible binding for global variable ‘fitted’
view_model: no visible global function definition for ‘na.omit’
view_model: no visible binding for global variable ‘norm_deriv’
view_model: no visible binding for global variable ‘Well.Position’
Undefined global functions or variables:
  Col Fluorescence Ligand Normalized Protein Temperature Tm Well
  Well.Position all_of average avg_smooth colorRampPalette condition_ID
  fitted head na.omit norm_deriv pos predict read.csv read.delim sd
  sd_max sd_max_smooth sd_min sd_min_smooth tm well_ID x y
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "fitted", "na.omit", "predict", "sd")
  importFrom("utils", "head", "read.csv", "read.delim")
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
TSA_wells_plot 15.193  0.176  15.402
gam_analysis    7.612  0.587   8.238
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/TSAR.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TSAR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘TSAR’ ...
** 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 (TSAR)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(TSAR)

Attaching package: 'TSAR'

The following object is masked from 'package:graphics':

    screen

> 
> test_check("TSAR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 16 ]
> 
> proc.time()
   user  system elapsed 
  8.296   0.493   8.831