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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:proBatch.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings proBatch_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/proBatch.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘proBatch/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘proBatch’ version ‘1.16.0’
* 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 ‘proBatch’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'proBatch' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.17-bioc/meat/proBatch.Rcheck/00install.out’ for details.
* 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 startup messages can be suppressed ... 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 ... OK
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘proBatch-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_protein_corrplot
> ### Title: Peptide correlation matrix (heatmap)
> ### Aliases: plot_protein_corrplot
> 
> ### ** Examples
> 
> protein_corrplot_plot <- plot_protein_corrplot(example_proteome_matrix, 
+ protein_name = 'Haao', peptide_annotation = example_peptide_annotation, 
+ protein_col = 'Gene')
Warning in plot_corr_matrix(corr_matrix, annotation = peptide_annotation,  :
  color_list for annotation (cols & rows) not defined, inferring automatically.
            Numeric/factor columns are guessed, for more controlled color mapping use 
            sample_annotation_to_colors()
Warning in sample_annotation_to_colors(sample_annotation = annotation, sample_id_col = annotation_id_col,  :
  The following columns will not be mapped to colors: Gene if these have to be mapped, please assign 
                    them to factor, date or numeric
Warning in sample_annotation_to_colors(sample_annotation = annotation, sample_id_col = annotation_id_col,  :
  numeric columns not specified, 
            extracting numeric columns from factors
converting columns to corresponding classes 
          (factor, numeric)
> 
> protein_corrplot_plot <- plot_protein_corrplot(example_proteome_matrix, 
+  protein_name = c('Haao', 'Dhtkd1'), 
+  peptide_annotation = example_peptide_annotation,
+  protein_col = 'Gene', factors_to_plot = 'Gene')
Warning in plot_corr_matrix(corr_matrix, annotation = peptide_annotation,  :
  color_list for annotation (cols & rows) not defined, inferring automatically.
            Numeric/factor columns are guessed, for more controlled color mapping use 
            sample_annotation_to_colors()
Warning in sample_annotation_to_colors(sample_annotation = annotation, sample_id_col = annotation_id_col,  :
  The following columns will not be mapped to colors: ProteinName if these have to be mapped, please assign 
                    them to factor, date or numeric
Warning in sample_annotation_to_colors(sample_annotation = annotation, sample_id_col = annotation_id_col,  :
  numeric columns not specified, 
            extracting numeric columns from factors
converting columns to corresponding classes 
          (factor, numeric)
Error in if (is.na(main)) { : the condition has length > 1
Calls: plot_protein_corrplot ... plot_heatmap_generic -> pheatmap -> heatmap_motor -> lo
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’
 OK
* 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: 1 ERROR, 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.17-bioc/meat/proBatch.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL proBatch
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘proBatch’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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
Warning: Package 'proBatch' is deprecated and will be removed from Bioconductor
  version 3.18
** testing if installed package can be loaded from final location
Warning: Package 'proBatch' is deprecated and will be removed from Bioconductor
  version 3.18
** testing if installed package keeps a record of temporary installation path
* DONE (proBatch)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)

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.

> if(requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
NULL
> 
> proc.time()
   user  system elapsed 
  0.366   0.119   0.478 

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)

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.

> library(testthat)
> library(proBatch)

Warning message:
Package 'proBatch' is deprecated and will be removed from Bioconductor
  version 3.18 
> 
> test_check("proBatch")
[ FAIL 0 | WARN 36 | SKIP 0 | PASS 159 ]

[ FAIL 0 | WARN 36 | SKIP 0 | PASS 159 ]
> 
> proc.time()
   user  system elapsed 
 63.480   1.676  81.644