Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:23:30 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

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? 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 1496/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
proBatch 1.12.0  (landing page)
Chloe H. Lee
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/proBatch
git_branch: RELEASE_3_15
git_last_commit: 72e6999
git_last_commit_date: 2022-04-26 11:54:00 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: proBatch
Version: 1.12.0
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_1.12.0.tar.gz
StartedAt: 2022-10-19 06:23:02 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 06:30:55 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 473.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: proBatch.Rcheck
Warnings: NA

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_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/proBatch.Rcheck’
* using R version 4.2.1 (2022-06-23)
* 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 ‘1.12.0’
* 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 ... ERROR
Running examples in ‘proBatch-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_protein_corrplot
> ### Title: Peptide correlation matrix (heatmap)
> ### Aliases: plot_protein_corrplot
> 
> ### ** Examples
> 
> protein_corrplot_plot <- plot_protein_corrplot(example_proteome_matrix, 
+ protein_name = 'Haao', peptide_annotation = example_peptide_annotation, 
+ protein_col = 'Gene')
Warning in plot_corr_matrix(corr_matrix, annotation = peptide_annotation,  :
  color_list for annotation (cols & rows) not defined, inferring automatically.
            Numeric/factor columns are guessed, for more controlled color mapping use 
            sample_annotation_to_colors()
Warning in sample_annotation_to_colors(sample_annotation = annotation, sample_id_col = annotation_id_col,  :
  The following columns will not be mapped to colors: Gene if these have to be mapped, please assign 
                    them to factor, date or numeric
Warning in sample_annotation_to_colors(sample_annotation = annotation, sample_id_col = annotation_id_col,  :
  numeric columns not specified, 
            extracting numeric columns from factors
converting columns to corresponding classes 
          (factor, numeric)
> 
> protein_corrplot_plot <- plot_protein_corrplot(example_proteome_matrix, 
+  protein_name = c('Haao', 'Dhtkd1'), 
+  peptide_annotation = example_peptide_annotation,
+  protein_col = 'Gene', factors_to_plot = 'Gene')
Warning in plot_corr_matrix(corr_matrix, annotation = peptide_annotation,  :
  color_list for annotation (cols & rows) not defined, inferring automatically.
            Numeric/factor columns are guessed, for more controlled color mapping use 
            sample_annotation_to_colors()
Warning in sample_annotation_to_colors(sample_annotation = annotation, sample_id_col = annotation_id_col,  :
  The following columns will not be mapped to colors: ProteinName if these have to be mapped, please assign 
                    them to factor, date or numeric
Warning in sample_annotation_to_colors(sample_annotation = annotation, sample_id_col = annotation_id_col,  :
  numeric columns not specified, 
            extracting numeric columns from factors
converting columns to corresponding classes 
          (factor, numeric)
Error in if (is.na(main)) { : the condition has length > 1
Calls: plot_protein_corrplot ... plot_heatmap_generic -> pheatmap -> heatmap_motor -> lo
Execution halted
* 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: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/proBatch.Rcheck/00check.log’
for details.


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 version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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 
  0.337   0.076   0.391 

proBatch.Rcheck/tests/testthat.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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 32 | SKIP 0 | PASS 159 ]

[ FAIL 0 | WARN 32 | SKIP 0 | PASS 159 ]
> 
> proc.time()
   user  system elapsed 
 56.510   1.091  57.657 

Example timings

proBatch.Rcheck/proBatch-Ex.timings

nameusersystemelapsed
calculate_PVCA29.397 0.22029.668
calculate_feature_CV0.5950.0180.613
calculate_peptide_corr_distr0.0640.0010.064
calculate_sample_corr_distr0.9710.0331.006
check_sample_consistency0.0740.0020.076
correct_batch_effects 9.876 0.15310.046
create_peptide_annotation0.0100.0010.010
date_to_sample_order0.4080.0010.409
dates_to_posix0.0180.0000.018
define_sample_order0.0900.0090.100
feature_level_diagnostics6.1430.0246.174
fit_nonlinear0.0140.0000.015
long_to_matrix0.0720.0050.078
matrix_to_long0.0190.0000.020
normalize0.1180.0020.119
plot_CV_distr1.2390.0161.256
plot_PCA1.3700.0301.403
plot_PVCA28.506 0.08728.635
plot_PVCA.df28.175 0.05128.258
plot_corr_matrix0.0730.0020.076
plot_heatmap_diagnostic3.0360.0723.115
plot_heatmap_generic0.9820.0331.020
plot_hierarchical_clustering0.7180.0230.771
plot_peptide_corr_distribution1.8820.0361.921