Multiple platform build/check report for BioC 3.12 - CHECK report for proBatch on tokay1

Package: proBatch

Version: 1.6.0

Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:proBatch.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings proBatch_1.6.0.tar.gz

StartedAt: 2021-05-06 05:42:18 -0400 (Thu, 06 May 2021)

EndedAt: 2021-05-06 05:52:13 -0400 (Thu, 06 May 2021)

EllapsedTime: 595.9 seconds

RetCode: 0

Status: OK

CheckDir: proBatch.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:proBatch.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings proBatch_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/proBatch.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.6.0'
* 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        28.67   0.01   28.69
plot_PVCA.df          28.52   0.02   28.53
prepare_PVCA_df       28.11   0.00   28.12
plot_PVCA             27.11   0.05   27.18
correct_batch_effects  7.22   0.08    7.29
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
prepare_PVCA_df           22.06   0.00   22.06
calculate_PVCA            21.19   0.02   21.21
plot_PVCA                 20.78   0.01   20.79
plot_PVCA.df              19.94   0.02   19.96
correct_batch_effects      5.89   0.00    5.89
feature_level_diagnostics  5.32   0.00    5.31
* 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 http://172.29.0.3/BBS/3.12/bioc/src/contrib/proBatch_1.6.0.tar.gz && rm -rf proBatch.buildbin-libdir && mkdir proBatch.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=proBatch.buildbin-libdir proBatch_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL proBatch_1.6.0.zip && rm proBatch_1.6.0.tar.gz proBatch_1.6.0.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  834k  100  834k    0     0  3570k      0 --:--:-- --:--:-- --:--:-- 3595k

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_1.6.0.zip
* DONE (proBatch)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'proBatch' successfully unpacked and MD5 sums checked


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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 
   0.18    0.00    0.17


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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 
   0.21    0.09    0.29


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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")
[ FAIL 0 | WARN 30 | SKIP 0 | PASS 159 ]
> 
> proc.time()
   user  system elapsed 
  40.76    0.70   41.53


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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")
[ FAIL 0 | WARN 30 | SKIP 0 | PASS 159 ]
> 
> proc.time()
   user  system elapsed 
  44.57    0.73   45.39

name	user	system	elapsed
calculate_PVCA	28.67	0.01	28.69
calculate_feature_CV	1.12	0.05	1.17
calculate_peptide_corr_distr	0.03	0.00	0.03
calculate_sample_corr_distr	2.20	0.04	2.25
check_sample_consistency	0.02	0.00	0.02
correct_batch_effects	7.22	0.08	7.29
create_peptide_annotation	0.00	0.02	0.02
date_to_sample_order	0.2	0.0	0.2
dates_to_posix	0.03	0.00	0.03
define_sample_order	0.03	0.01	0.05
feature_level_diagnostics	4.90	0.02	4.91
fit_nonlinear	0.01	0.00	0.01
long_to_matrix	0.08	0.00	0.08
matrix_to_long	0.02	0.00	0.01
normalize	0.16	0.00	0.16
plot_CV_distr	0.79	0.03	0.83
plot_PCA	1.00	0.06	1.07
plot_PVCA	27.11	0.05	27.18
plot_PVCA.df	28.52	0.02	28.53
plot_corr_matrix	0.14	0.00	0.14
plot_heatmap_diagnostic	3.58	0.09	3.67
plot_heatmap_generic	1.11	0.03	1.15
plot_hierarchical_clustering	0.72	0.01	0.73
plot_peptide_corr_distribution	3.21	0.03	3.25
plot_protein_corrplot	0.27	0.00	0.27
plot_sample_corr_distribution	3.37	0.03	3.41
plot_sample_corr_heatmap	0.67	0.02	0.68
plot_sample_mean_or_boxplot	4.50	0.03	4.54
prepare_PVCA_df	28.11	0.00	28.12
sample_annotation_to_colors	0.05	0.00	0.05
transform_raw_data	0.01	0.00	0.01

name	user	system	elapsed
calculate_PVCA	21.19	0.02	21.21
calculate_feature_CV	0.44	0.02	0.45
calculate_peptide_corr_distr	0.03	0.00	0.04
calculate_sample_corr_distr	0.66	0.01	0.67
check_sample_consistency	0.03	0.00	0.03
correct_batch_effects	5.89	0.00	5.89
create_peptide_annotation	0	0	0
date_to_sample_order	0.16	0.00	0.16
dates_to_posix	0.01	0.00	0.02
define_sample_order	0.00	0.01	0.01
feature_level_diagnostics	5.32	0.00	5.31
fit_nonlinear	0.01	0.00	0.02
long_to_matrix	0.05	0.00	0.05
matrix_to_long	0	0	0
normalize	0.09	0.00	0.09
plot_CV_distr	0.69	0.02	0.70
plot_PCA	0.78	0.03	0.82
plot_PVCA	20.78	0.01	20.79
plot_PVCA.df	19.94	0.02	19.96
plot_corr_matrix	0.09	0.00	0.09
plot_heatmap_diagnostic	1.99	0.08	2.06
plot_heatmap_generic	0.72	0.03	0.75
plot_hierarchical_clustering	0.53	0.02	0.55
plot_peptide_corr_distribution	2.61	0.04	2.66
plot_protein_corrplot	0.22	0.00	0.21
plot_sample_corr_distribution	1.42	0.00	1.43
plot_sample_corr_heatmap	0.56	0.00	0.56
plot_sample_mean_or_boxplot	3.14	0.03	3.17
prepare_PVCA_df	22.06	0.00	22.06
sample_annotation_to_colors	0.05	0.00	0.05
transform_raw_data	0	0	0

CHECK report for proBatch on tokay1

Summary

Command output

Installation output

Tests output

Example timings