Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2021-11-30 13:55:06 -0500 (Tue, 30 Nov 2021).

CHECK results for proBatch on riesling1

To the developers/maintainers of the proBatch package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/proBatch.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1447/2068HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
proBatch 1.11.0  (landing page)
Chloe H. Lee
Snapshot Date: 2021-11-29 14:50:17 -0500 (Mon, 29 Nov 2021)
git_url: https://git.bioconductor.org/packages/proBatch
git_branch: master
git_last_commit: f9dca1a
git_last_commit_date: 2021-10-26 12:50:21 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: proBatch
Version: 1.11.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:proBatch.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings proBatch_1.11.0.tar.gz
StartedAt: 2021-11-30 03:16:37 -0500 (Tue, 30 Nov 2021)
EndedAt: 2021-11-30 03:22:01 -0500 (Tue, 30 Nov 2021)
EllapsedTime: 323.5 seconds
RetCode: 0
Status:   OK  
CheckDir: proBatch.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:proBatch.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings proBatch_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/proBatch.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.11.0'
* 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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
calculate_PVCA  13.47   0.07   13.55
plot_PVCA.df    13.42   0.00   13.42
plot_PVCA       13.40   0.00   13.41
prepare_PVCA_df 13.39   0.00   13.39
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  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 http://155.52.207.165/BBS/3.15/bioc/src/contrib/proBatch_1.11.0.tar.gz && rm -rf proBatch.buildbin-libdir && mkdir proBatch.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=proBatch.buildbin-libdir proBatch_1.11.0.tar.gz && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL proBatch_1.11.0.zip && rm proBatch_1.11.0.tar.gz proBatch_1.11.0.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  831k  100  831k    0     0  2709k      0 --:--:-- --:--:-- --:--:-- 2709k
only one architecture so ignoring '--merge-multiarch'
* 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
* MD5 sums
packaged installation of 'proBatch' as proBatch_1.11.0.zip
* DONE (proBatch)
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
package 'proBatch' successfully unpacked and MD5 sums checked

Tests output

proBatch.Rcheck/tests/spelling.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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 
   0.09    0.04    0.12 

proBatch.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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 
  24.20    0.75   24.96 

Example timings

proBatch.Rcheck/proBatch-Ex.timings

nameusersystemelapsed
calculate_PVCA13.47 0.0713.55
calculate_feature_CV0.670.000.67
calculate_peptide_corr_distr0.010.000.01
calculate_sample_corr_distr0.80.00.8
check_sample_consistency0.020.000.01
correct_batch_effects3.390.053.44
create_peptide_annotation000
date_to_sample_order0.090.000.09
dates_to_posix000
define_sample_order0.000.010.02
feature_level_diagnostics3.560.063.62
fit_nonlinear000
long_to_matrix0.030.000.03
matrix_to_long000
normalize0.060.000.06
plot_CV_distr0.470.020.48
plot_PCA0.490.000.49
plot_PVCA13.40 0.0013.41
plot_PVCA.df13.42 0.0013.42
plot_corr_matrix0.070.000.06
plot_heatmap_diagnostic1.250.021.27
plot_heatmap_generic0.510.030.54
plot_hierarchical_clustering0.740.030.77
plot_peptide_corr_distribution0.840.030.87
plot_protein_corrplot0.130.000.13
plot_sample_corr_distribution0.860.030.89
plot_sample_corr_heatmap0.380.020.39
plot_sample_mean_or_boxplot2.010.072.10
prepare_PVCA_df13.39 0.0013.39
sample_annotation_to_colors0.020.000.01
transform_raw_data0.010.000.02