Multiple platform build/check report for BioC 3.13 - CHECK results for proBatch on tokay2

Package: proBatch

Version: 1.8.0

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:proBatch.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings proBatch_1.8.0.tar.gz

StartedAt: 2021-10-15 03:41:53 -0400 (Fri, 15 Oct 2021)

EndedAt: 2021-10-15 03:50:47 -0400 (Fri, 15 Oct 2021)

EllapsedTime: 533.7 seconds

RetCode: 0

Status: OK

CheckDir: proBatch.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:proBatch.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings proBatch_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/proBatch.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.8.0'
* 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 LazyData ... 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  21.81   0.47   22.30
plot_PVCA.df    21.11   0.04   21.15
prepare_PVCA_df 20.91   0.00   20.91
plot_PVCA       20.50   0.02   20.52
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
prepare_PVCA_df           21.61   0.02   21.62
plot_PVCA                 20.32   0.02   20.33
calculate_PVCA            20.19   0.02   20.20
plot_PVCA.df              20.15   0.03   20.19
feature_level_diagnostics  5.67   0.04    5.72
correct_batch_effects      5.55   0.08    5.63
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/proBatch_1.8.0.tar.gz && rm -rf proBatch.buildbin-libdir && mkdir proBatch.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=proBatch.buildbin-libdir proBatch_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL proBatch_1.8.0.zip && rm proBatch_1.8.0.tar.gz proBatch_1.8.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 43  830k   43  357k    0     0  1179k      0 --:--:-- --:--:-- --:--:-- 1179k
100  830k  100  830k    0     0  1704k      0 --:--:-- --:--:-- --:--:-- 1704k

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_1.8.0.zip
* DONE (proBatch)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'proBatch' successfully unpacked and MD5 sums checked


R version 4.1.1 (2021-08-10) -- "Kick Things"
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 
   0.25    0.04    0.28


R version 4.1.1 (2021-08-10) -- "Kick Things"
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    0.07    0.28


R version 4.1.1 (2021-08-10) -- "Kick Things"
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 
  33.10    1.23   34.32


R version 4.1.1 (2021-08-10) -- "Kick Things"
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 
  36.78    0.70   37.46

name	user	system	elapsed
calculate_PVCA	21.81	0.47	22.30
calculate_feature_CV	0.42	0.01	0.43
calculate_peptide_corr_distr	0.03	0.00	0.03
calculate_sample_corr_distr	1.98	0.07	2.05
check_sample_consistency	0.02	0.01	0.03
correct_batch_effects	4.75	0.11	4.86
create_peptide_annotation	0.00	0.02	0.01
date_to_sample_order	0.14	0.00	0.14
dates_to_posix	0.02	0.00	0.02
define_sample_order	0.00	0.01	0.01
feature_level_diagnostics	4.43	0.02	4.46
fit_nonlinear	0.02	0.00	0.01
long_to_matrix	0.03	0.00	0.03
matrix_to_long	0.02	0.00	0.02
normalize	0.09	0.00	0.09
plot_CV_distr	0.66	0.00	0.66
plot_PCA	1.11	0.03	1.14
plot_PVCA	20.50	0.02	20.52
plot_PVCA.df	21.11	0.04	21.15
plot_corr_matrix	0.09	0.00	0.10
plot_heatmap_diagnostic	2.26	0.06	2.32
plot_heatmap_generic	0.88	0.04	0.91
plot_hierarchical_clustering	0.5	0.0	0.5
plot_peptide_corr_distribution	3.54	0.01	3.56
plot_protein_corrplot	0.22	0.00	0.22
plot_sample_corr_distribution	3.17	0.02	3.19
plot_sample_corr_heatmap	0.63	0.00	0.62
plot_sample_mean_or_boxplot	2.87	0.01	2.89
prepare_PVCA_df	20.91	0.00	20.91
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	20.19	0.02	20.20
calculate_feature_CV	0.96	0.01	0.96
calculate_peptide_corr_distr	0.02	0.00	0.02
calculate_sample_corr_distr	0.64	0.00	0.64
check_sample_consistency	0.56	0.02	0.57
correct_batch_effects	5.55	0.08	5.63
create_peptide_annotation	0	0	0
date_to_sample_order	0.16	0.00	0.15
dates_to_posix	0.02	0.00	0.02
define_sample_order	0	0	0
feature_level_diagnostics	5.67	0.04	5.72
fit_nonlinear	0.02	0.00	0.02
long_to_matrix	0.05	0.00	0.04
matrix_to_long	0	0	0
normalize	0.10	0.00	0.09
plot_CV_distr	0.65	0.05	0.71
plot_PCA	0.69	0.04	0.74
plot_PVCA	20.32	0.02	20.33
plot_PVCA.df	20.15	0.03	20.19
plot_corr_matrix	0.08	0.02	0.09
plot_heatmap_diagnostic	1.77	0.06	1.83
plot_heatmap_generic	1.34	0.04	1.39
plot_hierarchical_clustering	0.50	0.02	0.52
plot_peptide_corr_distribution	1.81	0.02	1.82
plot_protein_corrplot	0.21	0.00	0.21
plot_sample_corr_distribution	1.17	0.04	1.22
plot_sample_corr_heatmap	0.56	0.00	0.56
plot_sample_mean_or_boxplot	3.44	0.00	3.44
prepare_PVCA_df	21.61	0.02	21.62
sample_annotation_to_colors	0.06	0.00	0.06
transform_raw_data	0.02	0.00	0.02

CHECK results for proBatch on tokay2

Summary

Command output

Installation output

Tests output

Example timings