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This page was generated on 2021-11-30 13:55:37 -0500 (Tue, 30 Nov 2021).

CHECK results for proBatch on merida1

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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:proBatch.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings proBatch_1.11.0.tar.gz
StartedAt: 2021-11-30 06:38:18 -0500 (Tue, 30 Nov 2021)
EndedAt: 2021-11-30 06:46:02 -0500 (Tue, 30 Nov 2021)
EllapsedTime: 464.7 seconds
RetCode: 0
Status:   OK  
CheckDir: proBatch.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:proBatch.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings proBatch_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/proBatch.Rcheck’
* using R Under development (unstable) (2021-11-01 r81125)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
calculate_PVCA              28.430  0.144  28.626
prepare_PVCA_df             27.487  0.066  27.585
plot_PVCA                   27.307  0.071  27.412
plot_PVCA.df                26.792  0.069  26.911
correct_batch_effects        8.481  0.129   8.621
plot_sample_mean_or_boxplot  6.055  0.117   6.180
feature_level_diagnostics    5.826  0.029   5.866
* 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL proBatch
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* 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
** 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
* DONE (proBatch)

Tests output

proBatch.Rcheck/tests/spelling.Rout


R Under development (unstable) (2021-11-01 r81125) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 
  0.303   0.072   0.354 

proBatch.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-01 r81125) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 
 51.683   0.923  52.643 

Example timings

proBatch.Rcheck/proBatch-Ex.timings

nameusersystemelapsed
calculate_PVCA28.430 0.14428.626
calculate_feature_CV1.1570.0231.182
calculate_peptide_corr_distr0.0420.0000.042
calculate_sample_corr_distr1.4560.0291.486
check_sample_consistency0.0220.0000.022
correct_batch_effects8.4810.1298.621
create_peptide_annotation0.0080.0000.008
date_to_sample_order0.3160.0010.317
dates_to_posix0.0150.0000.016
define_sample_order0.0360.0040.040
feature_level_diagnostics5.8260.0295.866
fit_nonlinear0.0130.0010.015
long_to_matrix0.0730.0020.075
matrix_to_long0.0200.0010.021
normalize0.1120.0030.115
plot_CV_distr1.0620.0131.079
plot_PCA1.0620.0251.089
plot_PVCA27.307 0.07127.412
plot_PVCA.df26.792 0.06926.911
plot_corr_matrix0.0650.0020.066
plot_heatmap_diagnostic2.1560.0752.239
plot_heatmap_generic0.8890.0340.928
plot_hierarchical_clustering0.6590.0220.685
plot_peptide_corr_distribution2.4230.0302.455
plot_protein_corrplot0.3120.0030.316
plot_sample_corr_distribution1.8860.0251.913
plot_sample_corr_heatmap0.7940.0210.814
plot_sample_mean_or_boxplot6.0550.1176.180
prepare_PVCA_df27.487 0.06627.585
sample_annotation_to_colors0.0470.0000.047
transform_raw_data0.0080.0000.009