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CHECK report for proBatch on tokay2

This page was generated on 2020-10-17 11:57:28 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE proBatch PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1352/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
proBatch 1.4.0
Chloe H. Lee
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/proBatch
Branch: RELEASE_3_11
Last Commit: ca86ae5
Last Changed Date: 2020-04-27 15:24:52 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

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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
###
##############################################################################
##############################################################################


* 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


Installation output

proBatch.Rcheck/00install.out

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


  % 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

Tests output

proBatch.Rcheck/tests_i386/spelling.Rout


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 

proBatch.Rcheck/tests_x64/spelling.Rout


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 

proBatch.Rcheck/tests_i386/testthat.Rout


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 

proBatch.Rcheck/tests_x64/testthat.Rout


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 

Example timings

proBatch.Rcheck/examples_i386/proBatch-Ex.timings

nameusersystemelapsed
calculate_PVCA25.90 0.0325.94
calculate_feature_CV1.180.021.19
calculate_peptide_corr_distr0.050.000.05
calculate_sample_corr_distr1.830.061.89
check_sample_consistency0.020.020.03
correct_batch_effects6.390.066.45
create_peptide_annotation000
date_to_sample_order0.150.000.16
dates_to_posix0.020.000.01
define_sample_order0.030.030.07
feature_level_diagnostics4.610.004.61
fit_nonlinear000
long_to_matrix0.050.000.05
matrix_to_long0.010.000.01
normalize0.110.000.11
plot_CV_distr0.630.010.64
plot_PCA0.780.030.82
plot_PVCA23.51 0.0023.51
plot_PVCA.df22.61 0.0222.63
plot_corr_matrix0.080.020.09
plot_heatmap_diagnostic1.950.001.95
plot_heatmap_generic0.880.000.88
plot_hierarchical_clustering0.870.000.87
plot_peptide_corr_distribution4.130.004.12
plot_protein_corrplot0.210.000.22
plot_sample_corr_distribution4.390.004.39
plot_sample_corr_heatmap0.850.010.86
plot_sample_mean_or_boxplot3.550.023.57
prepare_PVCA_df22.65 0.0122.67
sample_annotation_to_colors0.030.000.03
transform_raw_data0.020.000.01

proBatch.Rcheck/examples_x64/proBatch-Ex.timings

nameusersystemelapsed
calculate_PVCA19.03 0.0119.04
calculate_feature_CV0.360.020.38
calculate_peptide_corr_distr0.010.000.01
calculate_sample_corr_distr0.630.010.64
check_sample_consistency0.010.000.01
correct_batch_effects5.940.096.03
create_peptide_annotation000
date_to_sample_order0.170.000.18
dates_to_posix0.020.000.01
define_sample_order0.000.020.02
feature_level_diagnostics5.090.015.11
fit_nonlinear000
long_to_matrix0.030.020.04
matrix_to_long0.020.000.02
normalize0.080.000.08
plot_CV_distr0.630.020.64
plot_PCA1.140.031.18
plot_PVCA18.41 0.0018.40
plot_PVCA.df17.68 0.0317.72
plot_corr_matrix0.100.000.09
plot_heatmap_diagnostic1.730.011.75
plot_heatmap_generic0.740.000.74
plot_hierarchical_clustering0.510.000.51
plot_peptide_corr_distribution1.750.051.80
plot_protein_corrplot0.20.00.2
plot_sample_corr_distribution1.110.081.19
plot_sample_corr_heatmap0.520.010.53
plot_sample_mean_or_boxplot3.050.023.07
prepare_PVCA_df19.32 0.0019.34
sample_annotation_to_colors0.040.000.03
transform_raw_data000