Multiple platform build/check report for BioC 3.10 - CHECK report for proBatch on malbec1

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:proBatch.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings proBatch_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/proBatch.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (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 ‘1.2.0’
* 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 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: dates_to_posix
> ### Title: Convert data/time to POSIXct
> ### Aliases: dates_to_posix
> 
> ### ** Examples
> 
> date_to_posix <- dates_to_posix(example_sample_annotation, 
+ time_column = c('RunDate','RunTime'),
+ new_time_column = 'DateTime', 
+ dateTimeFormat = c("%b_%d", "%H:%M:%S"))
Error: Names must be unique.
Backtrace:
     █
  1. ├─proBatch::dates_to_posix(...)
  2. │ └─`%>%`(...)
  3. │   ├─base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  4. │   └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
  5. │     └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
  6. │       └─proBatch:::`_fseq`(`_lhs`)
  7. │         └─magrittr::freduce(value, `_function_list`)
  8. │           ├─base::withVisible(function_list[[k]](value))
  9. │           └─function_list[[k]](value)
 10. │             ├─dplyr::rename(., `:=`(!!new_time_column, dateTime))
 11. │             └─dplyr:::rename.data.frame(., `:=`(!!new_time_column, dateTime))
 12. │               └─tidyselect::vars_rename(names(.data), !!!enquos(...))
 13. │                 └─tidyselect:::rename_impl(NULL, .vars, quo(c(...)), strict = .strict)
 14. │                   ├─tidyselect:::with_subscript_errors(...)
 15. │             
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
  ‘/home/biocbuild/bbs-3.10-bioc/meat/proBatch.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL proBatch
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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 
  0.236   0.032   0.264


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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)

> 
> test_check("proBatch")
Standardizing Data across genes
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 159 | SKIPPED: 0 | WARNINGS: 31 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 45.632   0.692  59.577

name	user	system	elapsed
calculate_PVCA	26.880	0.028	26.970
calculate_feature_CV	1.052	0.012	1.066
calculate_peptide_corr_distr	0.036	0.000	0.036
calculate_sample_corr_distr	1.412	0.012	1.429
check_sample_consistency	0.028	0.000	0.027
correct_batch_effects	15.988	0.304	16.350
create_peptide_annotation	0.008	0.000	0.009
date_to_sample_order	0.164	0.004	0.166

CHECK report for proBatch on malbec1

Summary

Command output

Installation output

Tests output

Example timings