Multiple platform build/check report for BioC 3.11 - CHECK report for proBatch on tokay2

Package: proBatch

Version: 1.4.0

Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:proBatch.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings proBatch_1.4.0.tar.gz

StartedAt: 2020-10-17 07:03:23 -0400 (Sat, 17 Oct 2020)

EndedAt: 2020-10-17 07:12:29 -0400 (Sat, 17 Oct 2020)

EllapsedTime: 546.3 seconds

RetCode: 0

Status: OK

CheckDir: proBatch.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:proBatch.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings proBatch_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/proBatch.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'proBatch/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'proBatch' version '1.4.0'
* 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 whether package 'proBatch' 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 ... 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 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
calculate_PVCA        25.90   0.03   25.94
plot_PVCA             23.51   0.00   23.51
prepare_PVCA_df       22.65   0.01   22.67
plot_PVCA.df          22.61   0.02   22.63
correct_batch_effects  6.39   0.06    6.45
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
prepare_PVCA_df           19.32   0.00   19.34
calculate_PVCA            19.03   0.01   19.04
plot_PVCA                 18.41   0.00   18.40
plot_PVCA.df              17.68   0.03   17.72
correct_batch_effects      5.94   0.09    6.03
feature_level_diagnostics  5.09   0.01    5.11
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'spelling.R'
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: OK

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/proBatch_1.4.0.tar.gz && rm -rf proBatch.buildbin-libdir && mkdir proBatch.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=proBatch.buildbin-libdir proBatch_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL proBatch_1.4.0.zip && rm proBatch_1.4.0.tar.gz proBatch_1.4.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  832k  100  832k    0     0  11.5M      0 --:--:-- --:--:-- --:--:-- 12.9M

install for i386

* 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
  converting help for package 'proBatch'
    finding HTML links ... done
    calculate_PVCA                          html  
    calculate_feature_CV                    html  
    calculate_peptide_corr_distr            html  
    calculate_sample_corr_distr             html  
    check_sample_consistency                html  
    color_list_to_df                        html  
    correct_batch_effects                   html  
    create_peptide_annotation               html  
    date_to_sample_order                    html  
    dates_to_posix                          html  
    define_sample_order                     html  
    example_peptide_annotation              html  
    example_proteome                        html  
    example_proteome_matrix                 html  
    example_sample_annotation               html  
    feature_level_diagnostics               html  
    fit_nonlinear                           html  
    generate_colors_for_numeric             html  
    long_to_matrix                          html  
    matrix_to_long                          html  
    merge_rare_levels                       html  
    normalize                               html  
    plot_CV_distr                           html  
    plot_CV_distr.df                        html  
    plot_PCA                                html  
    plot_PVCA                               html  
    plot_PVCA.df                            html  
    plot_corr_matrix                        html  
    plot_heatmap_diagnostic                 html  
    plot_heatmap_generic                    html  
    plot_hierarchical_clustering            html  
    plot_peptide_corr_distribution          html  
    plot_protein_corrplot                   html  
    plot_sample_corr_distribution           html  
    plot_sample_corr_heatmap                html  
    plot_sample_mean_or_boxplot             html  
    plot_split_violin_with_boxplot          html  
    prepare_PVCA_df                         html  
    proBatch                                html  
    sample_annotation_to_colors             html  
    transform_raw_data                      html  
** 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

install for x64

* installing *source* package 'proBatch' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'proBatch' as proBatch_1.4.0.zip
* DONE (proBatch)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'proBatch' successfully unpacked and MD5 sums checked


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
   0.26    0.06    0.29


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
   0.17    0.07    0.25


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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)

> 
> test_check("proBatch")
== testthat results  ===========================================================
[ OK: 159 | SKIPPED: 0 | WARNINGS: 30 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  45.50    1.01   46.53


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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)

> 
> test_check("proBatch")
== testthat results  ===========================================================
[ OK: 159 | SKIPPED: 0 | WARNINGS: 30 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  33.98    0.70   34.67

name	user	system	elapsed
calculate_PVCA	25.90	0.03	25.94
calculate_feature_CV	1.18	0.02	1.19
calculate_peptide_corr_distr	0.05	0.00	0.05
calculate_sample_corr_distr	1.83	0.06	1.89
check_sample_consistency	0.02	0.02	0.03
correct_batch_effects	6.39	0.06	6.45
create_peptide_annotation	0	0	0
date_to_sample_order	0.15	0.00	0.16
dates_to_posix	0.02	0.00	0.01
define_sample_order	0.03	0.03	0.07
feature_level_diagnostics	4.61	0.00	4.61
fit_nonlinear	0	0	0
long_to_matrix	0.05	0.00	0.05
matrix_to_long	0.01	0.00	0.01
normalize	0.11	0.00	0.11
plot_CV_distr	0.63	0.01	0.64
plot_PCA	0.78	0.03	0.82
plot_PVCA	23.51	0.00	23.51
plot_PVCA.df	22.61	0.02	22.63
plot_corr_matrix	0.08	0.02	0.09
plot_heatmap_diagnostic	1.95	0.00	1.95
plot_heatmap_generic	0.88	0.00	0.88
plot_hierarchical_clustering	0.87	0.00	0.87
plot_peptide_corr_distribution	4.13	0.00	4.12
plot_protein_corrplot	0.21	0.00	0.22
plot_sample_corr_distribution	4.39	0.00	4.39
plot_sample_corr_heatmap	0.85	0.01	0.86
plot_sample_mean_or_boxplot	3.55	0.02	3.57
prepare_PVCA_df	22.65	0.01	22.67
sample_annotation_to_colors	0.03	0.00	0.03
transform_raw_data	0.02	0.00	0.01

name	user	system	elapsed
calculate_PVCA	19.03	0.01	19.04
calculate_feature_CV	0.36	0.02	0.38
calculate_peptide_corr_distr	0.01	0.00	0.01
calculate_sample_corr_distr	0.63	0.01	0.64
check_sample_consistency	0.01	0.00	0.01
correct_batch_effects	5.94	0.09	6.03
create_peptide_annotation	0	0	0
date_to_sample_order	0.17	0.00	0.18
dates_to_posix	0.02	0.00	0.01
define_sample_order	0.00	0.02	0.02
feature_level_diagnostics	5.09	0.01	5.11
fit_nonlinear	0	0	0
long_to_matrix	0.03	0.02	0.04
matrix_to_long	0.02	0.00	0.02
normalize	0.08	0.00	0.08
plot_CV_distr	0.63	0.02	0.64
plot_PCA	1.14	0.03	1.18
plot_PVCA	18.41	0.00	18.40
plot_PVCA.df	17.68	0.03	17.72
plot_corr_matrix	0.10	0.00	0.09
plot_heatmap_diagnostic	1.73	0.01	1.75
plot_heatmap_generic	0.74	0.00	0.74
plot_hierarchical_clustering	0.51	0.00	0.51
plot_peptide_corr_distribution	1.75	0.05	1.80
plot_protein_corrplot	0.2	0.0	0.2
plot_sample_corr_distribution	1.11	0.08	1.19
plot_sample_corr_heatmap	0.52	0.01	0.53
plot_sample_mean_or_boxplot	3.05	0.02	3.07
prepare_PVCA_df	19.32	0.00	19.34
sample_annotation_to_colors	0.04	0.00	0.03
transform_raw_data	0	0	0

CHECK report for proBatch on tokay2

Summary

Command output

Installation output

Tests output

Example timings