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This page was generated on 2023-10-16 11:35:38 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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

Package 1558/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
proBatch 1.16.0  (landing page)
Chloe H. Lee
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/proBatch
git_branch: RELEASE_3_17
git_last_commit: 4de7ad4
git_last_commit_date: 2023-04-25 11:08:46 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for proBatch on nebbiolo1


To the developers/maintainers of the proBatch package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: proBatch
Version: 1.16.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:proBatch.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings proBatch_1.16.0.tar.gz
StartedAt: 2023-10-16 00:00:46 -0400 (Mon, 16 Oct 2023)
EndedAt: 2023-10-16 00:06:40 -0400 (Mon, 16 Oct 2023)
EllapsedTime: 353.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: proBatch.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:proBatch.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings proBatch_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/proBatch.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘proBatch/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘proBatch’ version ‘1.16.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: Package 'proBatch' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.17-bioc/meat/proBatch.Rcheck/00install.out’ for details.
* 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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... 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 ... 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 ...
  ‘proBatch.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/proBatch.Rcheck/00check.log’
for details.


Installation output

proBatch.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL proBatch
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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
Warning: Package 'proBatch' is deprecated and will be removed from Bioconductor
  version 3.18
** testing if installed package can be loaded from final location
Warning: Package 'proBatch' is deprecated and will be removed from Bioconductor
  version 3.18
** testing if installed package keeps a record of temporary installation path
* DONE (proBatch)

Tests output

proBatch.Rcheck/tests/spelling.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
  0.156   0.032   0.180 

proBatch.Rcheck/tests/testthat.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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)

Warning message:
Package 'proBatch' is deprecated and will be removed from Bioconductor
  version 3.18 
> 
> test_check("proBatch")
[ FAIL 0 | WARN 36 | SKIP 0 | PASS 159 ]

[ FAIL 0 | WARN 36 | SKIP 0 | PASS 159 ]
> 
> proc.time()
   user  system elapsed 
 35.105   1.022  36.118 

Example timings

proBatch.Rcheck/proBatch-Ex.timings

nameusersystemelapsed
calculate_PVCA17.323 0.20017.524
calculate_feature_CV0.3770.0420.418
calculate_peptide_corr_distr0.0250.0000.025
calculate_sample_corr_distr0.5800.0120.591
check_sample_consistency0.0150.0000.015
correct_batch_effects7.2510.2047.455
create_peptide_annotation0.0060.0000.006
date_to_sample_order0.1400.0080.148
dates_to_posix0.0060.0000.007
define_sample_order0.0250.0080.033
feature_level_diagnostics5.1940.0765.270
fit_nonlinear0.0040.0030.008
long_to_matrix0.0420.0000.043
matrix_to_long0.0060.0040.011
normalize0.0720.0000.072
plot_CV_distr0.6160.0080.625
plot_PCA0.7510.0000.751
plot_PVCA16.657 0.05216.709
plot_PVCA.df16.605 0.07216.677
plot_corr_matrix0.0370.0000.037
plot_heatmap_diagnostic1.9790.0762.055
plot_heatmap_generic0.5480.0080.556
plot_hierarchical_clustering0.4060.0120.418
plot_peptide_corr_distribution1.1580.0081.166