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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:TSAR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings TSAR_1.9.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/TSAR.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TSAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TSAR’ version ‘1.9.3’
* 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 ‘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 loading without being on the library search path ... 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 binding for global variable ‘RFU’
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 ‘y_plot’
TSA_compare_plot: no visible binding for global variable ‘ymin_rib’
TSA_compare_plot: no visible binding for global variable ‘ymax_rib’
TSA_compare_plot: no visible binding for global variable ‘y_line’
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 ‘RFU’
TSA_wells_plot: no visible binding for global variable ‘well_ID’
TSA_wells_plot: no visible binding for global variable ‘ymin_plot’
TSA_wells_plot: no visible binding for global variable ‘ymax_plot’
TSA_wells_plot: no visible binding for global variable ‘y_avg_plot’
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’
numerical_Tm: no visible global function definition for ‘aggregate’
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 RFU Temperature Tm Well
  Well.Position aggregate all_of condition_ID fitted head na.omit
  norm_deriv pos read.csv read.delim sd tm well_ID x y y_avg_plot
  y_line y_plot ymax_plot ymax_rib ymin_plot ymin_rib
Consider adding
  importFrom("stats", "aggregate", "fitted", "na.omit", "sd")
  importFrom("utils", "head", "read.csv", "read.delim")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  model_gam.Rd: gam
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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’ ... NOTE
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/TSAR_Beta_Method_Introduction.Rmd’
   ‘vignettes/TSAR_Workflow_Beta_Method.Rmd’
(Is a VignetteBuilder field missing?)
* checking examples ... ERROR
Running examples in ‘TSAR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: view_deriv
> ### Title: View Derivative Curves
> ### Aliases: view_deriv
> 
> ### ** Examples
> 
> data("example_tsar_data")
> view_deriv(example_tsar_data, frame_by = "condition_ID")
Error in pm[[2]] : subscript out of bounds
Calls: view_deriv -> ggplotly -> ggplotly.ggplot -> gg2list
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
gam_analysis 13.445  0.327  13.791
* 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: 1 ERROR, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/TSAR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL TSAR
###
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* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘TSAR’ ...
** this is package ‘TSAR’ version ‘1.9.3’
** 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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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 
 14.881   0.687  15.589