Multiple platform build/check report for BioC 3.9 - CHECK report for proBatch on tokay2

Package: proBatch

Version: 0.99.25

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:proBatch.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings proBatch_0.99.25.tar.gz

StartedAt: 2019-04-09 05:04:20 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 05:09:12 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 292.1 seconds

RetCode: 0

Status: OK

CheckDir: proBatch.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:proBatch.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings proBatch_0.99.25.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/proBatch.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* 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 '0.99.25'
* 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 or elapsed time > 5s
                        user system elapsed
correct_batch_effects   6.88   0.13    7.00
plot_with_fitting_curve 5.64   0.09    5.73
plot_PVCA               5.61   0.08    5.78
adjust_batch_trend      5.41   0.19    5.59
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
correct_batch_effects   7.97   0.08    8.05
adjust_batch_trend      6.80   0.21    7.00
plot_with_fitting_curve 5.40   0.08    5.49
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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/3.9/bioc/src/contrib/proBatch_0.99.25.tar.gz && rm -rf proBatch.buildbin-libdir && mkdir proBatch.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=proBatch.buildbin-libdir proBatch_0.99.25.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL proBatch_0.99.25.zip && rm proBatch_0.99.25.tar.gz proBatch_0.99.25.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
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1299k  100 1299k    0     0  17.2M      0 --:--:-- --:--:-- --:--:-- 18.6M

install for i386

* installing *source* package 'proBatch' ...
** 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
    adjust_batch_trend                      html  
    center_peptide_batch_medians            html  
    color_list_to_df                        html  
    correct_batch_effects                   html  
    correct_with_ComBat                     html  
    create_peptide_annotation               html  
    date_to_sample_order                    html  
    dates_to_posix                          html  
    dot-corr_distribution                   html  
    dot-corr_distribution_prot              html  
    example_peptide_annotation              html  
    example_proteome                        html  
    example_proteome_matrix                 html  
    example_sample_annotation               html  
    fit_nonlinear                           html  
    generate_colors_for_numeric             html  
    get_peptide_corr_df                     html  
    get_sample_corr_distrib                 html  
    log_transform                           html  
    long_to_matrix                          html  
    matrix_to_long                          html  
    merge_rare_levels                       html  
    normalize                               html  
    normalize_data                          html  
    normalize_sample_medians                html  
    plot_PCA                                html  
    plot_PVCA                               html  
    plot_corr_matrix                        html  
    plot_heatmap                            html  
    plot_hierarchical_clustering            html  
    plot_iRT                                html  
    plot_peptide_corr_distribution          html  
    plot_peptides_of_one_protein            html  
    plot_protein_corrplot                   html  
    plot_sample_corr_distribution           html  
    plot_sample_corr_heatmap                html  
    plot_sample_mean_or_boxplot             html  
    plot_single_feature                     html  
    plot_spike_in                           html  
    plot_with_fitting_curve                 html  
    proBatch                                html  
    quantile_normalize                      html  
    sample_annotation_to_colors             html  
    sample_color_scheme                     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_0.99.25.zip
* DONE (proBatch)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'proBatch' successfully unpacked and MD5 sums checked


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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")
Standardizing Data across genes
== testthat results  ===========================================================
OK: 145 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  15.04    0.98   16.01


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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")
Standardizing Data across genes
== testthat results  ===========================================================
OK: 144 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  18.21    0.85   19.14

name	user	system	elapsed
adjust_batch_trend	5.41	0.19	5.59
center_peptide_batch_medians	1.39	0.04	1.44
correct_batch_effects	6.88	0.13	7.00
correct_with_ComBat	0.64	0.03	0.67
create_peptide_annotation	0	0	0
date_to_sample_order	0.09	0.00	0.10
dates_to_posix	0.02	0.00	0.01
log_transform	0	0	0
long_to_matrix	0.06	0.02	0.08
matrix_to_long	0.56	0.04	0.61
normalize_data	0.08	0.00	0.08
normalize_sample_medians	0.12	0.00	0.12
plot_PCA	0.41	0.00	0.41
plot_PVCA	5.61	0.08	5.78
plot_corr_matrix	0.03	0.00	0.03
plot_heatmap	1.86	0.07	1.94
plot_hierarchical_clustering	0.32	0.02	0.35
plot_iRT	0.61	0.00	0.61
plot_peptide_corr_distribution	3.03	0.09	3.12
plot_peptides_of_one_protein	0.08	0.00	0.08
plot_protein_corrplot	0.06	0.00	0.06
plot_sample_corr_distribution	0.38	0.03	0.41
plot_sample_corr_heatmap	0.03	0.00	0.03
plot_sample_mean_or_boxplot	0.67	0.02	0.69
plot_single_feature	0.02	0.00	0.01
plot_spike_in	0.05	0.00	0.05
plot_with_fitting_curve	5.64	0.09	5.73
quantile_normalize	0.03	0.00	0.03
sample_annotation_to_colors	0.01	0.00	0.02

name	user	system	elapsed
adjust_batch_trend	6.80	0.21	7.00
center_peptide_batch_medians	1.31	0.01	1.32
correct_batch_effects	7.97	0.08	8.05
correct_with_ComBat	0.83	0.06	0.89
create_peptide_annotation	0	0	0
date_to_sample_order	0.13	0.00	0.12
dates_to_posix	0.02	0.00	0.01
log_transform	0	0	0
long_to_matrix	0.12	0.02	0.14
matrix_to_long	0.52	0.02	0.54
normalize_data	0.03	0.00	0.03
normalize_sample_medians	0.12	0.01	0.14
plot_PCA	0.19	0.00	0.19
plot_PVCA	4.61	0.02	4.63
plot_corr_matrix	0.01	0.00	0.01
plot_heatmap	1.49	0.04	1.53
plot_hierarchical_clustering	0.75	0.02	0.77
plot_iRT	0.04	0.00	0.05
plot_peptide_corr_distribution	3.28	0.14	3.42
plot_peptides_of_one_protein	0.05	0.00	0.04
plot_protein_corrplot	0.11	0.00	0.11
plot_sample_corr_distribution	0.70	0.05	0.75
plot_sample_corr_heatmap	0.05	0.00	0.05
plot_sample_mean_or_boxplot	0.90	0.01	0.92
plot_single_feature	0.02	0.00	0.01
plot_spike_in	0.08	0.00	0.08
plot_with_fitting_curve	5.40	0.08	5.49
quantile_normalize	0.03	0.00	0.03
sample_annotation_to_colors	0.03	0.00	0.03

CHECK report for proBatch on tokay2

Summary

Command output

Installation output

Tests output

Example timings