Yannis Schumann
| Snapshot Date: 2025-03-21 13:40 -0400 (Fri, 21 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: f785e17 |
| git_last_commit_date: 2025-01-29 01:54:20 -0400 (Wed, 29 Jan 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-03-22 11:43 -0400 (Sat, 22 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" | 4777 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4547 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4576 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4528 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4458 |
| 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 161/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.3.6 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.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. |
| Package: BERT |
| Version: 1.3.6 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.3.6.tar.gz |
| StartedAt: 2025-03-21 19:32:52 -0400 (Fri, 21 Mar 2025) |
| EndedAt: 2025-03-21 19:34:18 -0400 (Fri, 21 Mar 2025) |
| EllapsedTime: 85.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.3.6.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.3.6’
* 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 ‘BERT’ 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 26.871 1.537 19.421
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.3.6’ ** using staged installation ** R ** 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 (BERT)
BERT.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2025-03-21 19:33:55.310116 INFO::Formatting Data.
2025-03-21 19:33:55.31439 INFO::Replacing NaNs with NAs.
2025-03-21 19:33:55.330093 INFO::Removing potential empty rows and columns
2025-03-21 19:33:55.646016 INFO::Found 0 missing values.
2025-03-21 19:33:55.650554 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-21 19:33:55.651359 INFO::Done
2025-03-21 19:33:55.651904 INFO::Acquiring quality metrics before batch effect correction.
2025-03-21 19:33:55.667477 INFO::Starting hierarchical adjustment
2025-03-21 19:33:55.668307 INFO::Found 3 batches.
2025-03-21 19:33:55.668833 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-21 19:33:55.669852 INFO::Using default BPPARAM
2025-03-21 19:33:55.670341 INFO::Processing subtree level 1
2025-03-21 19:33:55.838373 INFO::Adjusting the last 1 batches sequentially
2025-03-21 19:33:55.845337 INFO::Done
2025-03-21 19:33:55.847887 INFO::Acquiring quality metrics after batch effect correction.
2025-03-21 19:33:55.857325 INFO::ASW Batch was -0.0252190783097246 prior to batch effect correction and is now -0.0252190783097246 .
2025-03-21 19:33:55.859149 INFO::Total function execution time is 0.549540042877197 s and adjustment time is 0.177118062973022 s ( 32.23 )
2025-03-21 19:33:55.883935 INFO::Formatting Data.
2025-03-21 19:33:55.884925 INFO::Replacing NaNs with NAs.
2025-03-21 19:33:55.886152 INFO::Removing potential empty rows and columns
2025-03-21 19:33:55.887543 INFO::Found 0 missing values.
2025-03-21 19:33:55.888708 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-03-21 19:33:55.903574 INFO::Formatting Data.
2025-03-21 19:33:55.904731 INFO::Replacing NaNs with NAs.
2025-03-21 19:33:55.90586 INFO::Removing potential empty rows and columns
2025-03-21 19:33:55.90733 INFO::Found 0 missing values.
2025-03-21 19:33:55.908621 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-03-21 19:33:55.929634 INFO::Formatting Data.
2025-03-21 19:33:55.930823 INFO::Replacing NaNs with NAs.
2025-03-21 19:33:55.932156 INFO::Removing potential empty rows and columns
2025-03-21 19:33:55.933518 INFO::Found 0 missing values.
2025-03-21 19:33:55.934663 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-03-21 19:33:55.938689 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-21 19:33:55.939314 INFO::Done
2025-03-21 19:33:55.939843 INFO::Acquiring quality metrics before batch effect correction.
2025-03-21 19:33:55.942141 INFO::Starting hierarchical adjustment
2025-03-21 19:33:55.942952 INFO::Found 2 batches.
2025-03-21 19:33:55.943621 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-21 19:33:55.944247 INFO::Using default BPPARAM
2025-03-21 19:33:55.944973 INFO::Adjusting the last 2 batches sequentially
2025-03-21 19:33:55.946131 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-21 19:33:55.97011 INFO::Done
2025-03-21 19:33:55.970859 INFO::Acquiring quality metrics after batch effect correction.
2025-03-21 19:33:55.972797 INFO::ASW Batch was 0.0509662962381302 prior to batch effect correction and is now -0.121315955089458 .
2025-03-21 19:33:55.973559 INFO::Total function execution time is 0.0440030097961426 s and adjustment time is 0.0272989273071289 s ( 62.04 )
2025-03-21 19:33:55.97702 INFO::Formatting Data.
2025-03-21 19:33:55.977941 INFO::Replacing NaNs with NAs.
2025-03-21 19:33:55.987206 INFO::Formatting Data.
2025-03-21 19:33:55.987983 INFO::Replacing NaNs with NAs.
2025-03-21 19:33:55.98893 INFO::Removing potential empty rows and columns
2025-03-21 19:33:55.989946 INFO::Found 0 missing values.
2025-03-21 19:33:56.028188 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-21 19:33:56.02912 INFO::Done
2025-03-21 19:33:56.029923 INFO::Acquiring quality metrics before batch effect correction.
2025-03-21 19:33:56.032834 INFO::Starting hierarchical adjustment
2025-03-21 19:33:56.03396 INFO::Found 2 batches.
2025-03-21 19:33:56.034612 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-21 19:33:56.035169 INFO::Using default BPPARAM
2025-03-21 19:33:56.035632 INFO::Adjusting the last 2 batches sequentially
2025-03-21 19:33:56.036621 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-21 19:33:56.054851 INFO::Done
2025-03-21 19:33:56.055775 INFO::Acquiring quality metrics after batch effect correction.
2025-03-21 19:33:56.058096 INFO::ASW Batch was -0.050428503067377 prior to batch effect correction and is now -0.108968152693804 .
2025-03-21 19:33:56.058865 INFO::Total function execution time is 0.0717577934265137 s and adjustment time is 0.0210819244384766 s ( 29.38 )
2025-03-21 19:33:56.059793 INFO::Formatting Data.
2025-03-21 19:33:56.06031 INFO::Replacing NaNs with NAs.
2025-03-21 19:33:56.061056 INFO::Removing potential empty rows and columns
2025-03-21 19:33:56.062193 INFO::Found 0 missing values.
2025-03-21 19:33:56.065332 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-21 19:33:56.065827 INFO::Done
2025-03-21 19:33:56.06628 INFO::Acquiring quality metrics before batch effect correction.
2025-03-21 19:33:56.068201 INFO::Starting hierarchical adjustment
2025-03-21 19:33:56.06894 INFO::Found 2 batches.
2025-03-21 19:33:56.069407 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-21 19:33:56.069923 INFO::Using default BPPARAM
2025-03-21 19:33:56.070395 INFO::Adjusting the last 2 batches sequentially
2025-03-21 19:33:56.07122 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-21 19:33:56.088216 INFO::Done
2025-03-21 19:33:56.089051 INFO::Acquiring quality metrics after batch effect correction.
2025-03-21 19:33:56.09178 INFO::ASW Batch was -0.050428503067377 prior to batch effect correction and is now -0.108968152693804 .
2025-03-21 19:33:56.092947 INFO::Total function execution time is 0.0330259799957275 s and adjustment time is 0.0193181037902832 s ( 58.49 )
2025-03-21 19:33:59.473406 INFO::Formatting Data.
2025-03-21 19:33:59.474124 INFO::Recognized SummarizedExperiment
2025-03-21 19:33:59.47458 INFO::Typecasting input to dataframe.
2025-03-21 19:33:59.510368 INFO::Replacing NaNs with NAs.
2025-03-21 19:33:59.512378 INFO::Removing potential empty rows and columns
2025-03-21 19:33:59.516557 INFO::Found 0 missing values.
2025-03-21 19:33:59.526771 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-21 19:33:59.527751 INFO::Done
2025-03-21 19:33:59.528523 INFO::Acquiring quality metrics before batch effect correction.
2025-03-21 19:33:59.533352 INFO::Starting hierarchical adjustment
2025-03-21 19:33:59.534349 INFO::Found 2 batches.
2025-03-21 19:33:59.534965 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-21 19:33:59.536249 INFO::Using default BPPARAM
2025-03-21 19:33:59.536982 INFO::Adjusting the last 2 batches sequentially
2025-03-21 19:33:59.538336 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-21 19:33:59.599393 INFO::Done
2025-03-21 19:33:59.600267 INFO::Acquiring quality metrics after batch effect correction.
2025-03-21 19:33:59.604578 INFO::ASW Batch was -0.00282175219423705 prior to batch effect correction and is now -0.107192137254859 .
2025-03-21 19:33:59.605905 INFO::Total function execution time is 0.132772922515869 s and adjustment time is 0.0650382041931152 s ( 48.98 )
2025-03-21 19:33:59.634359 INFO::Formatting Data.
2025-03-21 19:33:59.635082 INFO::Recognized SummarizedExperiment
2025-03-21 19:33:59.635664 INFO::Typecasting input to dataframe.
2025-03-21 19:33:59.647702 INFO::Replacing NaNs with NAs.
2025-03-21 19:33:59.649617 INFO::Removing potential empty rows and columns
2025-03-21 19:33:59.654389 INFO::Found 0 missing values.
2025-03-21 19:33:59.663048 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-21 19:33:59.664083 INFO::Done
2025-03-21 19:33:59.664737 INFO::Acquiring quality metrics before batch effect correction.
2025-03-21 19:33:59.668116 INFO::Starting hierarchical adjustment
2025-03-21 19:33:59.669027 INFO::Found 2 batches.
2025-03-21 19:33:59.66967 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-21 19:33:59.670542 INFO::Using default BPPARAM
2025-03-21 19:33:59.671303 INFO::Adjusting the last 2 batches sequentially
2025-03-21 19:33:59.672816 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-21 19:33:59.708242 INFO::Done
2025-03-21 19:33:59.709459 INFO::Acquiring quality metrics after batch effect correction.
2025-03-21 19:33:59.714124 INFO::ASW Batch was -0.00206009194570065 prior to batch effect correction and is now -0.00206009194570065 .
2025-03-21 19:33:59.715565 INFO::Total function execution time is 0.0810220241546631 s and adjustment time is 0.0394880771636963 s ( 48.74 )
2025-03-21 19:33:59.743705 INFO::Formatting Data.
2025-03-21 19:33:59.744812 INFO::Replacing NaNs with NAs.
2025-03-21 19:33:59.746044 INFO::Removing potential empty rows and columns
2025-03-21 19:33:59.74762 INFO::Found 0 missing values.
2025-03-21 19:33:59.751272 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-21 19:33:59.751941 INFO::Done
2025-03-21 19:33:59.752901 INFO::Acquiring quality metrics before batch effect correction.
2025-03-21 19:33:59.755199 INFO::Starting hierarchical adjustment
2025-03-21 19:33:59.756183 INFO::Found 3 batches.
2025-03-21 19:33:59.756797 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-21 19:33:59.757615 INFO::Using default BPPARAM
2025-03-21 19:33:59.758152 INFO::Processing subtree level 1
2025-03-21 19:34:00.195957 INFO::Adjusting the last 1 batches sequentially
2025-03-21 19:34:00.199155 INFO::Done
2025-03-21 19:34:00.199897 INFO::Acquiring quality metrics after batch effect correction.
2025-03-21 19:34:00.203784 INFO::ASW Batch was 0.0967629816464054 prior to batch effect correction and is now -0.18718964581114 .
2025-03-21 19:34:00.234319 INFO::Total function execution time is 0.487284183502197 s and adjustment time is 0.443145036697388 s ( 90.94 )
2025-03-21 19:34:00.36836 INFO::Skipping initial DF formatting
2025-03-21 19:34:00.369216 INFO::Acquiring quality metrics before batch effect correction.
2025-03-21 19:34:00.374173 INFO::Starting hierarchical adjustment
2025-03-21 19:34:00.375133 INFO::Found 5 batches.
2025-03-21 19:34:00.375967 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-21 19:34:00.376977 INFO::Using default BPPARAM
2025-03-21 19:34:00.377803 INFO::Processing subtree level 1
2025-03-21 19:34:00.652766 INFO::Adjusting the last 2 batches sequentially
2025-03-21 19:34:00.770787 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-21 19:34:00.81785 INFO::Done
2025-03-21 19:34:00.819852 INFO::Acquiring quality metrics after batch effect correction.
2025-03-21 19:34:00.828594 INFO::ASW Batch was 0.48519848360751 prior to batch effect correction and is now 0.48519848360751 .
2025-03-21 19:34:00.829596 INFO::ASW Label was 0.418370835988627 prior to batch effect correction and is now 0.418370835988627 .
2025-03-21 19:34:00.832527 INFO::Total function execution time is 0.464195966720581 s and adjustment time is 0.442953109741211 s ( 95.42 )
2025-03-21 19:34:00.86376 INFO::Formatting Data.
2025-03-21 19:34:00.864957 INFO::Replacing NaNs with NAs.
2025-03-21 19:34:00.866335 INFO::Removing potential empty rows and columns
2025-03-21 19:34:00.86752 INFO::Found 0 missing values.
2025-03-21 19:34:00.873907 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-21 19:34:00.874885 INFO::Done
2025-03-21 19:34:00.875892 INFO::Acquiring quality metrics before batch effect correction.
2025-03-21 19:34:00.880577 INFO::Starting hierarchical adjustment
2025-03-21 19:34:00.881559 INFO::Found 5 batches.
2025-03-21 19:34:00.882591 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-21 19:34:00.883595 INFO::Using default BPPARAM
2025-03-21 19:34:00.884474 INFO::Processing subtree level 1
2025-03-21 19:34:01.106065 INFO::Adjusting the last 2 batches sequentially
2025-03-21 19:34:01.118706 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-21 19:34:01.156247 INFO::Done
2025-03-21 19:34:01.156944 INFO::Acquiring quality metrics after batch effect correction.
2025-03-21 19:34:01.160297 INFO::ASW Batch was 0.23898054607685 prior to batch effect correction and is now -0.0559961150712292 .
2025-03-21 19:34:01.16115 INFO::ASW Label was 0.448159078059189 prior to batch effect correction and is now 0.875985226759131 .
2025-03-21 19:34:01.162343 INFO::Total function execution time is 0.298680067062378 s and adjustment time is 0.274933815002441 s ( 92.05 )
2025-03-21 19:34:01.164091 INFO::Formatting Data.
2025-03-21 19:34:01.164995 INFO::Replacing NaNs with NAs.
2025-03-21 19:34:01.166279 INFO::Removing potential empty rows and columns
2025-03-21 19:34:01.167722 INFO::Found 0 missing values.
2025-03-21 19:34:01.173635 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-21 19:34:01.17474 INFO::Done
2025-03-21 19:34:01.175592 INFO::Acquiring quality metrics before batch effect correction.
2025-03-21 19:34:01.179978 INFO::Starting hierarchical adjustment
2025-03-21 19:34:01.181067 INFO::Found 5 batches.
2025-03-21 19:34:01.182062 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-21 19:34:01.183031 INFO::Using default BPPARAM
2025-03-21 19:34:01.183861 INFO::Processing subtree level 1
2025-03-21 19:34:01.378014 INFO::Adjusting the last 2 batches sequentially
2025-03-21 19:34:01.43216 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-21 19:34:01.472755 INFO::Done
2025-03-21 19:34:01.473859 INFO::Acquiring quality metrics after batch effect correction.
2025-03-21 19:34:01.479218 INFO::ASW Batch was 0.23898054607685 prior to batch effect correction and is now -0.0559961150712292 .
2025-03-21 19:34:01.480164 INFO::ASW Label was 0.448159078059189 prior to batch effect correction and is now 0.875985226759131 .
2025-03-21 19:34:01.48196 INFO::Total function execution time is 0.31787896156311 s and adjustment time is 0.291937112808228 s ( 91.84 )
2025-03-21 19:34:01.507227 INFO::Formatting Data.
2025-03-21 19:34:01.508179 INFO::Replacing NaNs with NAs.
2025-03-21 19:34:01.509616 INFO::Removing potential empty rows and columns
2025-03-21 19:34:01.511365 INFO::Found 0 missing values.
2025-03-21 19:34:01.517395 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-21 19:34:01.518353 INFO::Done
2025-03-21 19:34:01.519199 INFO::Acquiring quality metrics before batch effect correction.
2025-03-21 19:34:01.523346 INFO::Starting hierarchical adjustment
2025-03-21 19:34:01.524564 INFO::Found 5 batches.
2025-03-21 19:34:01.525398 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-21 19:34:01.526345 INFO::Using default BPPARAM
2025-03-21 19:34:01.527205 INFO::Processing subtree level 1
2025-03-21 19:34:01.735072 INFO::Adjusting the last 2 batches sequentially
2025-03-21 19:34:01.742673 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-21 19:34:01.773734 INFO::Done
2025-03-21 19:34:01.774576 INFO::Acquiring quality metrics after batch effect correction.
2025-03-21 19:34:01.779417 INFO::ASW Batch was 0.386611507796911 prior to batch effect correction and is now -0.0832857608183622 .
2025-03-21 19:34:01.78031 INFO::ASW Label was 0.415904144761464 prior to batch effect correction and is now 0.809788543517963 .
2025-03-21 19:34:01.782124 INFO::Total function execution time is 0.274399042129517 s and adjustment time is 0.249423980712891 s ( 90.9 )
2025-03-21 19:34:01.783119 INFO::Formatting Data.
2025-03-21 19:34:01.784023 INFO::Replacing NaNs with NAs.
2025-03-21 19:34:01.785327 INFO::Removing potential empty rows and columns
2025-03-21 19:34:01.787173 INFO::Found 0 missing values.
2025-03-21 19:34:01.793201 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-21 19:34:01.794718 INFO::Done
2025-03-21 19:34:01.795582 INFO::Acquiring quality metrics before batch effect correction.
2025-03-21 19:34:01.800836 INFO::Starting hierarchical adjustment
2025-03-21 19:34:01.802086 INFO::Found 5 batches.
2025-03-21 19:34:01.802959 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-21 19:34:01.803893 INFO::Using default BPPARAM
2025-03-21 19:34:01.804704 INFO::Processing subtree level 1
2025-03-21 19:34:01.997868 INFO::Adjusting the last 2 batches sequentially
2025-03-21 19:34:02.012233 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-21 19:34:02.044982 INFO::Done
2025-03-21 19:34:02.046046 INFO::Acquiring quality metrics after batch effect correction.
2025-03-21 19:34:02.051694 INFO::ASW Batch was 0.386611507796911 prior to batch effect correction and is now -0.0832857608183622 .
2025-03-21 19:34:02.053152 INFO::ASW Label was 0.415904144761464 prior to batch effect correction and is now 0.809788543517963 .
2025-03-21 19:34:02.054492 INFO::Total function execution time is 0.271338939666748 s and adjustment time is 0.243106126785278 s ( 89.6 )
2025-03-21 19:34:02.079878 INFO::Formatting Data.
2025-03-21 19:34:02.08106 INFO::Replacing NaNs with NAs.
2025-03-21 19:34:02.082563 INFO::Removing potential empty rows and columns
2025-03-21 19:34:02.084732 INFO::Found 0 missing values.
2025-03-21 19:34:02.088504 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-21 19:34:02.089101 INFO::Done
2025-03-21 19:34:02.089627 INFO::Acquiring quality metrics before batch effect correction.
2025-03-21 19:34:02.092841 INFO::Starting hierarchical adjustment
2025-03-21 19:34:02.093561 INFO::Found 2 batches.
2025-03-21 19:34:02.094074 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-21 19:34:02.094673 INFO::Using default BPPARAM
2025-03-21 19:34:02.095289 INFO::Adjusting the last 2 batches sequentially
2025-03-21 19:34:02.096165 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-21 19:34:02.113361 INFO::Done
2025-03-21 19:34:02.114115 INFO::Acquiring quality metrics after batch effect correction.
2025-03-21 19:34:02.118286 INFO::ASW Batch was 0.537562635808278 prior to batch effect correction and is now -0.0372425071379702 .
2025-03-21 19:34:02.119125 INFO::ASW Label was 0.51216908167028 prior to batch effect correction and is now 0.943159116507048 .
2025-03-21 19:34:02.120048 INFO::Total function execution time is 0.040553092956543 s and adjustment time is 0.0198709964752197 s ( 49 )
2025-03-21 19:34:02.121124 INFO::Formatting Data.
2025-03-21 19:34:02.121799 INFO::Replacing NaNs with NAs.
2025-03-21 19:34:02.122861 INFO::Removing potential empty rows and columns
2025-03-21 19:34:02.123809 INFO::Found 0 missing values.
2025-03-21 19:34:02.12733 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-21 19:34:02.128195 INFO::Done
2025-03-21 19:34:02.129204 INFO::Acquiring quality metrics before batch effect correction.
2025-03-21 19:34:02.133039 INFO::Starting hierarchical adjustment
2025-03-21 19:34:02.133812 INFO::Found 2 batches.
2025-03-21 19:34:02.134533 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-21 19:34:02.135106 INFO::Using default BPPARAM
2025-03-21 19:34:02.135857 INFO::Adjusting the last 2 batches sequentially
2025-03-21 19:34:02.136803 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-21 19:34:02.153613 INFO::Done
2025-03-21 19:34:02.154328 INFO::Acquiring quality metrics after batch effect correction.
2025-03-21 19:34:02.158799 INFO::ASW Batch was 0.537562635808278 prior to batch effect correction and is now -0.0372425071379702 .
2025-03-21 19:34:02.159787 INFO::ASW Label was 0.51216908167028 prior to batch effect correction and is now 0.943159116507048 .
2025-03-21 19:34:02.160994 INFO::Total function execution time is 0.0398740768432617 s and adjustment time is 0.0199391841888428 s ( 50.01 )
2025-03-21 19:34:02.179949 INFO::Formatting Data.
2025-03-21 19:34:02.180868 INFO::Replacing NaNs with NAs.
2025-03-21 19:34:02.18289 INFO::Removing potential empty rows and columns
2025-03-21 19:34:02.184455 INFO::Found 0 missing values.
2025-03-21 19:34:02.187708 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-21 19:34:02.188539 INFO::Done
2025-03-21 19:34:02.189311 INFO::Acquiring quality metrics before batch effect correction.
2025-03-21 19:34:02.192057 INFO::Starting hierarchical adjustment
2025-03-21 19:34:02.193214 INFO::Found 2 batches.
2025-03-21 19:34:02.194261 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-21 19:34:02.195161 INFO::Using default BPPARAM
2025-03-21 19:34:02.195914 INFO::Adjusting the last 2 batches sequentially
2025-03-21 19:34:02.197205 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-21 19:34:02.235368 INFO::Done
2025-03-21 19:34:02.236408 INFO::Acquiring quality metrics after batch effect correction.
2025-03-21 19:34:02.253129 INFO::ASW Batch was 0.119372493588319 prior to batch effect correction and is now -0.12223397053443 .
2025-03-21 19:34:02.25461 INFO::Total function execution time is 0.0746378898620605 s and adjustment time is 0.0423159599304199 s ( 56.7 )
2025-03-21 19:34:02.289345 INFO::Formatting Data.
2025-03-21 19:34:02.290497 INFO::Replacing NaNs with NAs.
2025-03-21 19:34:02.291982 INFO::Removing potential empty rows and columns
2025-03-21 19:34:02.293301 INFO::Found 0 missing values.
2025-03-21 19:34:02.295223 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-03-21 19:34:02.302089 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-21 19:34:02.302939 INFO::Done
2025-03-21 19:34:02.303827 INFO::Acquiring quality metrics before batch effect correction.
2025-03-21 19:34:02.308376 INFO::Starting hierarchical adjustment
2025-03-21 19:34:02.309162 INFO::Found 2 batches.
2025-03-21 19:34:02.30986 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-21 19:34:02.310436 INFO::Using default BPPARAM
2025-03-21 19:34:02.310931 INFO::Adjusting the last 2 batches sequentially
2025-03-21 19:34:02.311916 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-21 19:34:02.336032 INFO::Done
2025-03-21 19:34:02.336913 INFO::Acquiring quality metrics after batch effect correction.
2025-03-21 19:34:02.341702 INFO::ASW Batch was 0.494071664501453 prior to batch effect correction and is now -0.0267785161990549 .
2025-03-21 19:34:02.342523 INFO::ASW Label was 0.56887709052843 prior to batch effect correction and is now 0.919867244449216 .
2025-03-21 19:34:02.343734 INFO::Total function execution time is 0.0543978214263916 s and adjustment time is 0.0269520282745361 s ( 49.55 )
2025-03-21 19:34:02.344973 INFO::Formatting Data.
2025-03-21 19:34:02.345941 INFO::Replacing NaNs with NAs.
2025-03-21 19:34:02.347369 INFO::Removing potential empty rows and columns
2025-03-21 19:34:02.348649 INFO::Found 0 missing values.
2025-03-21 19:34:02.349924 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-03-21 19:34:02.355632 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-21 19:34:02.356588 INFO::Done
2025-03-21 19:34:02.357383 INFO::Acquiring quality metrics before batch effect correction.
2025-03-21 19:34:02.361413 INFO::Starting hierarchical adjustment
2025-03-21 19:34:02.362587 INFO::Found 2 batches.
2025-03-21 19:34:02.363385 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-21 19:34:02.364252 INFO::Using default BPPARAM
2025-03-21 19:34:02.364987 INFO::Adjusting the last 2 batches sequentially
2025-03-21 19:34:02.366291 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-21 19:34:02.386772 INFO::Done
2025-03-21 19:34:02.38782 INFO::Acquiring quality metrics after batch effect correction.
2025-03-21 19:34:02.391773 INFO::ASW Batch was 0.494071664501453 prior to batch effect correction and is now -0.0267785161990549 .
2025-03-21 19:34:02.392439 INFO::ASW Label was 0.56887709052843 prior to batch effect correction and is now 0.919867244449216 .
2025-03-21 19:34:02.393214 INFO::Total function execution time is 0.0484559535980225 s and adjustment time is 0.0244050025939941 s ( 50.37 )
2025-03-21 19:34:02.664377 INFO::Formatting Data.
2025-03-21 19:34:02.665718 INFO::Replacing NaNs with NAs.
2025-03-21 19:34:02.667003 INFO::Removing potential empty rows and columns
2025-03-21 19:34:02.668563 INFO::Found 0 missing values.
2025-03-21 19:34:02.673242 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-21 19:34:02.673886 INFO::Done
2025-03-21 19:34:02.674385 INFO::Acquiring quality metrics before batch effect correction.
2025-03-21 19:34:02.676729 INFO::Starting hierarchical adjustment
2025-03-21 19:34:02.677747 INFO::Found 3 batches.
2025-03-21 19:34:02.67849 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-21 19:34:02.679321 INFO::Using default BPPARAM
2025-03-21 19:34:02.680058 INFO::Processing subtree level 1
2025-03-21 19:34:02.817624 INFO::Adjusting the last 1 batches sequentially
2025-03-21 19:34:02.834257 INFO::Done
2025-03-21 19:34:02.836416 INFO::Acquiring quality metrics after batch effect correction.
2025-03-21 19:34:02.843513 INFO::ASW Batch was -0.0287776702267531 prior to batch effect correction and is now -0.0287776702267531 .
2025-03-21 19:34:02.845519 INFO::Total function execution time is 0.180917978286743 s and adjustment time is 0.156158208847046 s ( 86.31 )
2025-03-21 19:34:02.849341 INFO::Formatting Data.
2025-03-21 19:34:02.850713 INFO::Typecasting input to dataframe.
2025-03-21 19:34:02.852369 INFO::Replacing NaNs with NAs.
2025-03-21 19:34:02.854468 INFO::Removing potential empty rows and columns
2025-03-21 19:34:02.858483 INFO::Found 0 missing values.
2025-03-21 19:34:02.864356 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-21 19:34:02.865383 INFO::Done
2025-03-21 19:34:02.866354 INFO::Acquiring quality metrics before batch effect correction.
2025-03-21 19:34:02.869496 INFO::Starting hierarchical adjustment
2025-03-21 19:34:02.870821 INFO::Found 3 batches.
2025-03-21 19:34:02.87167 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-21 19:34:02.8729 INFO::Using default BPPARAM
2025-03-21 19:34:02.873545 INFO::Processing subtree level 1
2025-03-21 19:34:03.021208 INFO::Adjusting the last 1 batches sequentially
2025-03-21 19:34:03.034378 INFO::Done
2025-03-21 19:34:03.036634 INFO::Acquiring quality metrics after batch effect correction.
2025-03-21 19:34:03.044071 INFO::ASW Batch was -0.0287776702267531 prior to batch effect correction and is now -0.0287776702267531 .
2025-03-21 19:34:03.045583 INFO::Total function execution time is 0.196046113967896 s and adjustment time is 0.16376805305481 s ( 83.54 )
2025-03-21 19:34:03.074158 INFO::Formatting Data.
2025-03-21 19:34:03.075128 INFO::Typecasting input to dataframe.
2025-03-21 19:34:03.076657 INFO::Replacing NaNs with NAs.
2025-03-21 19:34:03.078119 INFO::Removing potential empty rows and columns
2025-03-21 19:34:03.081718 INFO::Found 0 missing values.
2025-03-21 19:34:03.085931 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-21 19:34:03.086539 INFO::Done
2025-03-21 19:34:03.087053 INFO::Acquiring quality metrics before batch effect correction.
2025-03-21 19:34:03.089286 INFO::Starting hierarchical adjustment
2025-03-21 19:34:03.091009 INFO::Found 3 batches.
2025-03-21 19:34:03.091816 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-21 19:34:03.09264 INFO::Using default BPPARAM
2025-03-21 19:34:03.09327 INFO::Processing subtree level 1
2025-03-21 19:34:03.218614 INFO::Adjusting the last 1 batches sequentially
2025-03-21 19:34:03.250407 INFO::Done
2025-03-21 19:34:03.254566 INFO::Acquiring quality metrics after batch effect correction.
2025-03-21 19:34:03.265521 INFO::ASW Batch was -0.0280738062524422 prior to batch effect correction and is now -0.0280738062524422 .
2025-03-21 19:34:03.268502 INFO::Total function execution time is 0.193233966827393 s and adjustment time is 0.159593820571899 s ( 82.59 )
2025-03-21 19:34:03.561592 INFO::Formatting Data.
2025-03-21 19:34:03.562985 INFO::Replacing NaNs with NAs.
2025-03-21 19:34:03.565369 INFO::Removing potential empty rows and columns
2025-03-21 19:34:03.571354 INFO::Found 1000 missing values.
2025-03-21 19:34:03.594569 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-21 19:34:03.595691 INFO::Done
2025-03-21 19:34:03.596407 INFO::Acquiring quality metrics before batch effect correction.
2025-03-21 19:34:03.603761 INFO::Starting hierarchical adjustment
2025-03-21 19:34:03.605147 INFO::Found 10 batches.
2025-03-21 19:34:03.606051 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-21 19:34:03.606962 INFO::Using default BPPARAM
2025-03-21 19:34:03.607734 INFO::Processing subtree level 1
2025-03-21 19:34:03.811429 INFO::Processing subtree level 2
2025-03-21 19:34:04.053832 INFO::Adjusting the last 1 batches sequentially
2025-03-21 19:34:04.069573 INFO::Done
2025-03-21 19:34:04.071744 INFO::Acquiring quality metrics after batch effect correction.
2025-03-21 19:34:04.082958 INFO::ASW Batch was 0.483516821463114 prior to batch effect correction and is now 0.483516821463114 .
2025-03-21 19:34:04.084277 INFO::ASW Label was 0.351589575385349 prior to batch effect correction and is now 0.351589575385349 .
2025-03-21 19:34:04.085971 INFO::Total function execution time is 0.524072885513306 s and adjustment time is 0.464575052261353 s ( 88.65 )
2025-03-21 19:34:04.08755 INFO::Formatting Data.
2025-03-21 19:34:04.089458 INFO::Replacing NaNs with NAs.
2025-03-21 19:34:04.092013 INFO::Removing potential empty rows and columns
2025-03-21 19:34:04.096896 INFO::Found 1000 missing values.
2025-03-21 19:34:04.119923 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-21 19:34:04.121394 INFO::Done
2025-03-21 19:34:04.122485 INFO::Acquiring quality metrics before batch effect correction.
2025-03-21 19:34:04.129778 INFO::Starting hierarchical adjustment
2025-03-21 19:34:04.131648 INFO::Found 10 batches.
2025-03-21 19:34:05.240707 INFO::Set up parallel execution backend with 2 workers
2025-03-21 19:34:05.242041 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-03-21 19:34:06.524662 INFO::Adjusting the last 2 batches sequentially
2025-03-21 19:34:06.52608 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-21 19:34:06.549216 INFO::Done
2025-03-21 19:34:06.549861 INFO::Acquiring quality metrics after batch effect correction.
2025-03-21 19:34:06.555357 INFO::ASW Batch was 0.483516821463114 prior to batch effect correction and is now 0.483516821463114 .
2025-03-21 19:34:06.556328 INFO::ASW Label was 0.351589575385349 prior to batch effect correction and is now 0.351589575385349 .
2025-03-21 19:34:06.557306 INFO::Total function execution time is 2.46978521347046 s and adjustment time is 2.41780400276184 s ( 97.9 )
2025-03-21 19:34:06.814894 INFO::Formatting Data.
2025-03-21 19:34:06.815923 INFO::Replacing NaNs with NAs.
2025-03-21 19:34:06.817355 INFO::Removing potential empty rows and columns
2025-03-21 19:34:06.819252 INFO::Found 0 missing values.
2025-03-21 19:34:06.824991 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-21 19:34:06.826004 INFO::Done
2025-03-21 19:34:06.826757 INFO::Acquiring quality metrics before batch effect correction.
2025-03-21 19:34:06.83104 INFO::Starting hierarchical adjustment
2025-03-21 19:34:06.832325 INFO::Found 3 batches.
2025-03-21 19:34:06.833207 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-21 19:34:06.834138 INFO::Using default BPPARAM
2025-03-21 19:34:06.83465 INFO::Processing subtree level 1
2025-03-21 19:34:07.029742 INFO::Adjusting the last 1 batches sequentially
2025-03-21 19:34:07.039337 INFO::Done
2025-03-21 19:34:07.042039 INFO::Acquiring quality metrics after batch effect correction.
2025-03-21 19:34:07.05089 INFO::ASW Batch was 0.288828967975597 prior to batch effect correction and is now -0.143404113401252 .
2025-03-21 19:34:07.052038 INFO::ASW Label was -0.180140548980253 prior to batch effect correction and is now 0.0239727931697382 .
2025-03-21 19:34:07.053918 INFO::Total function execution time is 0.238704919815063 s and adjustment time is 0.207234144210815 s ( 86.82 )
2025-03-21 19:34:07.258578 INFO::Formatting Data.
2025-03-21 19:34:07.259793 INFO::Replacing NaNs with NAs.
2025-03-21 19:34:07.261253 INFO::Removing potential empty rows and columns
2025-03-21 19:34:07.262855 INFO::Found 2 missing values.
2025-03-21 19:34:07.267569 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-03-21 19:34:07.268698 INFO::Done
2025-03-21 19:34:07.317882 INFO::Found NA in Reference column
2025-03-21 19:34:07.335411 INFO::Require at least two references per batch.
2025-03-21 19:34:07.366225 INFO::Formatting Data.
2025-03-21 19:34:07.367245 INFO::Recognized SummarizedExperiment
2025-03-21 19:34:07.368056 INFO::Typecasting input to dataframe.
2025-03-21 19:34:07.380115 INFO::Replacing NaNs with NAs.
2025-03-21 19:34:07.381765 INFO::Removing potential empty rows and columns
2025-03-21 19:34:07.386893 INFO::Found 0 missing values.
2025-03-21 19:34:07.396142 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-21 19:34:07.397114 INFO::Done
2025-03-21 19:34:07.4181 INFO::Formatting Data.
2025-03-21 19:34:07.419265 INFO::Recognized SummarizedExperiment
2025-03-21 19:34:07.420132 INFO::Typecasting input to dataframe.
2025-03-21 19:34:07.445077 INFO::Replacing NaNs with NAs.
2025-03-21 19:34:07.446831 INFO::Removing potential empty rows and columns
2025-03-21 19:34:07.451717 INFO::Found 0 missing values.
2025-03-21 19:34:07.465803 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-21 19:34:07.466725 INFO::Done
2025-03-21 19:34:07.485872 INFO::Formatting Data.
2025-03-21 19:34:07.486852 INFO::Recognized SummarizedExperiment
2025-03-21 19:34:07.487631 INFO::Typecasting input to dataframe.
2025-03-21 19:34:07.508025 INFO::Replacing NaNs with NAs.
2025-03-21 19:34:07.509497 INFO::Removing potential empty rows and columns
2025-03-21 19:34:07.511046 INFO::Found 0 missing values.
2025-03-21 19:34:07.512306 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-03-21 19:34:07.518076 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-21 19:34:07.518695 INFO::Done
2025-03-21 19:34:07.535062 INFO::Formatting Data.
2025-03-21 19:34:07.536059 INFO::Replacing NaNs with NAs.
2025-03-21 19:34:07.537307 INFO::Removing potential empty rows and columns
2025-03-21 19:34:07.538632 INFO::Found 0 missing values.
2025-03-21 19:34:07.541782 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-21 19:34:07.542314 INFO::Done
2025-03-21 19:34:07.561355 INFO::Formatting Data.
2025-03-21 19:34:07.562195 INFO::Replacing NaNs with NAs.
2025-03-21 19:34:07.563054 INFO::Removing potential empty rows and columns
2025-03-21 19:34:07.56395 INFO::Found 0 missing values.
2025-03-21 19:34:07.566672 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-21 19:34:07.567288 INFO::Done
2025-03-21 19:34:07.637805 INFO::Formatting Data.
2025-03-21 19:34:07.638613 INFO::Replacing NaNs with NAs.
2025-03-21 19:34:07.640763 INFO::Removing potential empty rows and columns
2025-03-21 19:34:07.642782 INFO::Found 1 missing values.
2025-03-21 19:34:07.646433 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-21 19:34:07.647111 INFO::Done
2025-03-21 19:34:07.683718 INFO::Formatting Data.
2025-03-21 19:34:07.68487 INFO::Replacing NaNs with NAs.
2025-03-21 19:34:07.686141 INFO::Removing potential empty rows and columns
2025-03-21 19:34:07.687502 INFO::Found 2 missing values.
2025-03-21 19:34:07.688848 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-03-21 19:34:07.692117 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-03-21 19:34:07.692898 INFO::Done
2025-03-21 19:34:07.71066 INFO::Formatting Data.
2025-03-21 19:34:07.711626 INFO::Replacing NaNs with NAs.
2025-03-21 19:34:07.712515 INFO::Removing potential empty rows and columns
2025-03-21 19:34:07.713388 INFO::Found 2 missing values.
2025-03-21 19:34:07.715487 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-21 19:34:07.716228 INFO::Done
2025-03-21 19:34:07.735526 INFO::Formatting Data.
2025-03-21 19:34:07.736387 INFO::Typecasting input to dataframe.
2025-03-21 19:34:07.737177 INFO::Replacing NaNs with NAs.
2025-03-21 19:34:07.738356 INFO::Removing potential empty rows and columns
2025-03-21 19:34:07.73932 INFO::Found 0 missing values.
2025-03-21 19:34:07.743487 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-21 19:34:07.744084 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
20.261 4.715 25.395
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 26.871 | 1.537 | 19.421 | |
| compute_asw | 0.027 | 0.001 | 0.028 | |
| count_existing | 0.016 | 0.001 | 0.018 | |
| generate_data_covariables | 0.014 | 0.001 | 0.015 | |
| generate_dataset | 0.012 | 0.001 | 0.012 | |