##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:proBatch.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings proBatch_1.99.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/proBatch.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘proBatch/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘proBatch’ version ‘1.99.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 29 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 code 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 whether 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  correct_with_removeBatchEffect_dm.Rd: removeBatchEffect
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 sizes of PDF files under ‘inst/doc’ ...* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
correct_batch_effects     9.375  0.199   9.574
feature_level_diagnostics 6.054  0.057   6.111
* 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 ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘proBatch.Rmd’ using rmarkdown
Warning: LaTeX Warning: `h' float specifier changed to `ht'.
--- finished re-building ‘proBatch.Rmd’

--- re-building ‘proBatchFeatures.Rmd’ using rmarkdown

Quitting from proBatchFeatures.Rmd:336-362 [plot_PCA]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `grid.arrange()`:
! could not find function "grid.arrange"
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'proBatchFeatures.Rmd' failed with diagnostics:
could not find function "grid.arrange"
--- failed re-building ‘proBatchFeatures.Rmd’

SUMMARY: processing the following file failed:
  ‘proBatchFeatures.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/proBatch.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL proBatch
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘proBatch’ ...
** this is package ‘proBatch’ version ‘1.99.4’
** using staged installation
** R
** data
** 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)

R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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
+     )
+ }
All Done!
> 
> proc.time()
   user  system elapsed 
  0.143   0.040   0.170 

R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(proBatch)

> 
> test_check("proBatch")
sample_id_col is not specified, using FullRunName as default
Cannot calculate CV for 366 peptides with 2 or less measurements, removing those peptides
sample_id_col is not specified, using FullRunName as default
sample_id_col is not specified, using FullRunName as default
sample_id_col is not specified, using FullRunName as default
Cannot calculate CV for 1 peptides with 2 or less measurements, removing those peptides
sample_id_col is not specified, using FullRunName as default
Cannot calculate CV for 366 peptides with 2 or less measurements, removing those peptides
sample_id_col is not specified, using FullRunName as default
Cannot calculate CV for 366 peptides with 2 or less measurements, removing those peptides
reversing log-transformation for CV calculation!
Cannot calculate CV for 366 peptides with 2 or less measurements, removing those peptides
Some CV values are not finite, filtering them out - number of such features: 364
reversing log-transformation for CV calculation!
Cannot calculate CV for 366 peptides with 2 or less measurements, removing those peptides
Saving 7 x 7 in image
Sample annotation has 11 columns and 233 samples.
`assay` not provided, using the most recent assay: feature::raw
Sample annotation has 11 columns and 233 samples.
Sample annotation has 11 columns and 233 samples.
Using stored assay 'feature::raw'.
Checking sample consistency and merging with sample annotation
Checking sample consistency and merging with sample annotation
Sample annotation has 11 columns and 233 samples.
Sample annotation has 11 columns and 233 samples.
Sample annotation has 11 columns and 233 samples.
Sample annotation has 11 columns and 233 samples.
Sample annotation has 3 columns and 2 samples.
Sample annotation has 3 columns and 2 samples.
Sample annotation has 3 columns and 2 samples.
Sample annotation has 3 columns and 3 samples.
Sample annotation has 4 columns and 2 samples.
Sample annotation has 1 columns and 2 samples.
Sample annotation has 1 columns and 2 samples.
Sample annotation has 1 columns and 2 samples.
Sample annotation has 1 columns and 2 samples.
Sample annotation has 1 columns and 2 samples.
Using assay: peptide::raw
Using assay: protein::raw
Sample annotation has 1 columns and 2 samples.
Using assay: peptide::raw
Using assay: peptide::log2_on_raw
Assay 'peptide::log2_on_raw' not stored; computed from operation log.
Checking sample consistency and merging with sample annotation
Checking sample consistency and merging with sample annotation
Checking sample consistency and merging with sample annotation
Sample annotation has 11 columns and 8 samples.
Using assay: feature::raw
Found2batches
Adjusting for0covariate(s) or covariate level(s)
Standardizing Data across genes
Fitting L/S model and finding priors
Finding parametric adjustments
Adjusting the Data

Using assay: feature::raw
Using assay: feature::combat_on_raw
Sample annotation has 11 columns and 126 samples.
Using assay: feature::raw
Using assay: feature::raw
Using assay: feature::limmaRBE_on_raw
converting columns to corresponding classes
          (factor, numeric)
Found4batches
Adjusting for0covariate(s) or covariate level(s)
Standardizing Data across genes
Fitting L/S model and finding priors
Finding parametric adjustments
Adjusting the Data

The following columns are not present in the corrected_df and will be removed from fit_df: order
columns_for_rows is NULL, adding default columns if present
converting columns to corresponding classes
          (factor, numeric)
columns_for_rows is NULL, adding default columns if present
converting columns to corresponding classes
          (factor, numeric)
replaced values in 2 rows and 3 columns
Removing rows with missing values
removed 1 rows and 0 columns
removed 2 rows and 0 columns
removed 1 rows and 0 columns
removed 3 rows and 0 columns
replaced values in 2 rows and 3 columns
Sample ID is kept only if they have a match in annotation data frame,
            otherwise the sample ID is removed from the plot
Sample ID is kept only if they have a match in annotation data frame,
            otherwise the sample ID is removed from the plot
Sample ID is kept only if they have a match in annotation data frame,
            otherwise the sample ID is removed from the plot
converting columns to corresponding classes
          (factor, numeric)
Sample annotation has 11 columns and 233 samples.
Using assay: feature::raw
Sample ID is kept only if they have a match in annotation data frame,
            otherwise the sample ID is removed from the plot
Extracting data from assay: feature::raw
Using stored assay 'feature::raw'.
Checking sample consistency and merging with sample annotation
Extracting data from assay: feature::log2_on_raw
Using stored assay 'feature::log2_on_raw'.
Checking sample consistency and merging with sample annotation
Extracting data from assay: feature::raw
Using stored assay 'feature::raw'.
Checking sample consistency and merging with sample annotation
Extracting data from assay: feature::log2_on_raw
Using stored assay 'feature::log2_on_raw'.
Checking sample consistency and merging with sample annotation
Extracting data from assay: feature::raw
Using stored assay 'feature::raw'.
Checking sample consistency and merging with sample annotation
`pbf_name` not provided, using all assays: feature::raw
Sample annotation has 3 columns and 3 samples.
Using assay: feature::toy
Using assay: feature::toy_alt
Using assay: feature::toy
Using assay: feature::toy_alt
Using assay: feature::toy
Using assay: feature::toy_alt
converting columns to corresponding classes
          (factor, numeric)
replaced values in 5 rows and 157 columns
converting columns to corresponding classes
          (factor, numeric)
replaced values in 10 rows and 202 columns
Column peptide_group_label is not in the data, using default
columns_for_rows is NULL, adding default columns if present
replaced values in 99 rows and 233 columns
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
boundary (singular) fit: see help('isSingular')
replaced values in 254 rows and 233 columns
Using assay: feature::raw
replaced values in 16 rows and 6 columns
Using assay: feature::log2_on_raw
replaced values in 16 rows and 6 columns
Using assay: feature::raw
converting columns to corresponding classes
          (factor, numeric)
converting columns to corresponding classes
          (factor, numeric)
replaced values in 11 rows and 5 columns
Using assay: feature::log2_on_raw
converting columns to corresponding classes
          (factor, numeric)
converting columns to corresponding classes
          (factor, numeric)
replaced values in 11 rows and 5 columns
Using assay: feature::raw
replaced values in 16 rows and 6 columns
Using assay: feature::log2_on_raw
replaced values in 16 rows and 6 columns
Using assay: feature::raw
replaced values in 16 rows and 6 columns
Using assay: feature::raw
converting columns to corresponding classes
          (factor, numeric)
converting columns to corresponding classes
          (factor, numeric)
replaced values in 11 rows and 5 columns
Using assay: feature::log2_on_raw
converting columns to corresponding classes
          (factor, numeric)
converting columns to corresponding classes
          (factor, numeric)
replaced values in 11 rows and 5 columns
Using assay: feature::raw
converting columns to corresponding classes
          (factor, numeric)
converting columns to corresponding classes
          (factor, numeric)
replaced values in 11 rows and 5 columns
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 503 ]
> 
> proc.time()
   user  system elapsed 
 72.149   1.953  74.103