Yannis Schumann
| Snapshot Date: 2025-03-31 13:00 -0400 (Mon, 31 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_20 |
| git_last_commit: 9764e3f |
| git_last_commit_date: 2024-10-29 11:26:04 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-04-02 19:31 -0400 (Wed, 02 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4764 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4495 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4522 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4449 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4426 |
| 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 159/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.2.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | 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: 1.2.0 |
| 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_1.2.0.tar.gz |
| StartedAt: 2025-03-31 23:41:57 -0400 (Mon, 31 Mar 2025) |
| EndedAt: 2025-03-31 23:44:19 -0400 (Mon, 31 Mar 2025) |
| EllapsedTime: 142.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* 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 ‘1.2.0’
* 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 ‘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 43.967 2.525 34.584
* 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/4.4-x86_64/Resources/library’ * installing *source* package ‘BERT’ ... ** 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 version 4.4.3 (2025-02-28) -- "Trophy Case"
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")
2025-03-31 23:43:41.86377 INFO::Formatting Data.
2025-03-31 23:43:41.871118 INFO::Replacing NaNs with NAs.
2025-03-31 23:43:41.906568 INFO::Removing potential empty rows and columns
2025-03-31 23:43:42.623858 INFO::Found 0 missing values.
2025-03-31 23:43:42.632952 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:43:42.63454 INFO::Done
2025-03-31 23:43:42.635927 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:43:42.66579 INFO::Starting hierarchical adjustment
2025-03-31 23:43:42.667837 INFO::Found 3 batches.
2025-03-31 23:43:42.669488 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:43:42.67381 INFO::Using default BPPARAM
2025-03-31 23:43:42.675474 INFO::Processing subtree level 1
2025-03-31 23:43:42.958493 INFO::Adjusting the last 1 batches sequentially
2025-03-31 23:43:42.964878 INFO::Done
2025-03-31 23:43:42.966407 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:43:42.97464 INFO::ASW Batch was -0.0327080912911084 prior to batch effect correction and is now -0.0327080912911084 .
2025-03-31 23:43:42.977254 INFO::Total function execution time is 1.11472511291504 s and adjustment time is 0.29747200012207 s ( 26.69 )
2025-03-31 23:43:43.015537 INFO::Formatting Data.
2025-03-31 23:43:43.017155 INFO::Replacing NaNs with NAs.
2025-03-31 23:43:43.019481 INFO::Removing potential empty rows and columns
2025-03-31 23:43:43.022295 INFO::Found 0 missing values.
2025-03-31 23:43:43.024672 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.
2025-03-31 23:43:43.05446 INFO::Formatting Data.
2025-03-31 23:43:43.0562 INFO::Replacing NaNs with NAs.
2025-03-31 23:43:43.058317 INFO::Removing potential empty rows and columns
2025-03-31 23:43:43.061035 INFO::Found 0 missing values.
2025-03-31 23:43:43.063623 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.
2025-03-31 23:43:43.108831 INFO::Formatting Data.
2025-03-31 23:43:43.110401 INFO::Replacing NaNs with NAs.
2025-03-31 23:43:43.112704 INFO::Removing potential empty rows and columns
2025-03-31 23:43:43.116638 INFO::Found 0 missing values.
2025-03-31 23:43:43.119181 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.
2025-03-31 23:43:43.132606 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:43:43.134069 INFO::Done
2025-03-31 23:43:43.1354 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:43:43.140319 INFO::Starting hierarchical adjustment
2025-03-31 23:43:43.142133 INFO::Found 2 batches.
2025-03-31 23:43:43.143465 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:43:43.145043 INFO::Using default BPPARAM
2025-03-31 23:43:43.146467 INFO::Adjusting the last 2 batches sequentially
2025-03-31 23:43:43.148932 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 23:43:43.206764 INFO::Done
2025-03-31 23:43:43.208233 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:43:43.213538 INFO::ASW Batch was -0.0408518508703998 prior to batch effect correction and is now -0.104357911835147 .
2025-03-31 23:43:43.215972 INFO::Total function execution time is 0.107146978378296 s and adjustment time is 0.0649669170379639 s ( 60.63 )
2025-03-31 23:43:43.222483 INFO::Formatting Data.
2025-03-31 23:43:43.224205 INFO::Replacing NaNs with NAs.
2025-03-31 23:43:43.249219 INFO::Formatting Data.
2025-03-31 23:43:43.250781 INFO::Replacing NaNs with NAs.
2025-03-31 23:43:43.252853 INFO::Removing potential empty rows and columns
2025-03-31 23:43:43.255912 INFO::Found 0 missing values.
2025-03-31 23:43:43.263831 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:43:43.265195 INFO::Done
2025-03-31 23:43:43.266538 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:43:43.271253 INFO::Starting hierarchical adjustment
2025-03-31 23:43:43.273102 INFO::Found 2 batches.
2025-03-31 23:43:43.2744 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:43:43.277489 INFO::Using default BPPARAM
2025-03-31 23:43:43.279005 INFO::Adjusting the last 2 batches sequentially
2025-03-31 23:43:43.281604 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 23:43:43.323138 INFO::Done
2025-03-31 23:43:43.324534 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:43:43.329246 INFO::ASW Batch was -0.00904485998620683 prior to batch effect correction and is now -0.0872903567771346 .
2025-03-31 23:43:43.33121 INFO::Total function execution time is 0.0820870399475098 s and adjustment time is 0.0504028797149658 s ( 61.4 )
2025-03-31 23:43:43.333776 INFO::Formatting Data.
2025-03-31 23:43:43.335165 INFO::Replacing NaNs with NAs.
2025-03-31 23:43:43.337235 INFO::Removing potential empty rows and columns
2025-03-31 23:43:43.339897 INFO::Found 0 missing values.
2025-03-31 23:43:43.34931 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:43:43.350728 INFO::Done
2025-03-31 23:43:43.352014 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:43:43.356801 INFO::Starting hierarchical adjustment
2025-03-31 23:43:43.358662 INFO::Found 2 batches.
2025-03-31 23:43:43.360055 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:43:43.361555 INFO::Using default BPPARAM
2025-03-31 23:43:43.362793 INFO::Adjusting the last 2 batches sequentially
2025-03-31 23:43:43.364947 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 23:43:43.404421 INFO::Done
2025-03-31 23:43:43.406755 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:43:43.412513 INFO::ASW Batch was -0.00904485998620683 prior to batch effect correction and is now -0.0872903567771346 .
2025-03-31 23:43:43.414452 INFO::Total function execution time is 0.0806689262390137 s and adjustment time is 0.0461070537567139 s ( 57.16 )
2025-03-31 23:43:49.661142 INFO::Formatting Data.
2025-03-31 23:43:49.662525 INFO::Recognized SummarizedExperiment
2025-03-31 23:43:49.663681 INFO::Typecasting input to dataframe.
2025-03-31 23:43:49.733309 INFO::Replacing NaNs with NAs.
2025-03-31 23:43:49.735637 INFO::Removing potential empty rows and columns
2025-03-31 23:43:49.745149 INFO::Found 0 missing values.
2025-03-31 23:43:49.763665 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:43:49.764976 INFO::Done
2025-03-31 23:43:49.766131 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:43:49.774594 INFO::Starting hierarchical adjustment
2025-03-31 23:43:49.776338 INFO::Found 2 batches.
2025-03-31 23:43:49.777604 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:43:49.779863 INFO::Using default BPPARAM
2025-03-31 23:43:49.781149 INFO::Adjusting the last 2 batches sequentially
2025-03-31 23:43:49.783402 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 23:43:49.920832 INFO::Done
2025-03-31 23:43:49.922087 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:43:49.929877 INFO::ASW Batch was -0.00140011164992173 prior to batch effect correction and is now -0.0986558801011443 .
2025-03-31 23:43:49.931706 INFO::Total function execution time is 0.271288871765137 s and adjustment time is 0.144850969314575 s ( 53.39 )
2025-03-31 23:43:49.978569 INFO::Formatting Data.
2025-03-31 23:43:49.980594 INFO::Recognized SummarizedExperiment
2025-03-31 23:43:49.981842 INFO::Typecasting input to dataframe.
2025-03-31 23:43:50.008421 INFO::Replacing NaNs with NAs.
2025-03-31 23:43:50.011011 INFO::Removing potential empty rows and columns
2025-03-31 23:43:50.024762 INFO::Found 0 missing values.
2025-03-31 23:43:50.050756 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:43:50.052231 INFO::Done
2025-03-31 23:43:50.05352 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:43:50.063094 INFO::Starting hierarchical adjustment
2025-03-31 23:43:50.064901 INFO::Found 2 batches.
2025-03-31 23:43:50.066335 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:43:50.067843 INFO::Using default BPPARAM
2025-03-31 23:43:50.069148 INFO::Adjusting the last 2 batches sequentially
2025-03-31 23:43:50.071681 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 23:43:50.155772 INFO::Done
2025-03-31 23:43:50.157215 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:43:50.169647 INFO::ASW Batch was 0.00655808291427142 prior to batch effect correction and is now 0.00655808291427142 .
2025-03-31 23:43:50.17169 INFO::Total function execution time is 0.193096876144409 s and adjustment time is 0.0912230014801025 s ( 47.24 )
2025-03-31 23:43:50.221171 INFO::Formatting Data.
2025-03-31 23:43:50.222782 INFO::Replacing NaNs with NAs.
2025-03-31 23:43:50.22509 INFO::Removing potential empty rows and columns
2025-03-31 23:43:50.227712 INFO::Found 0 missing values.
2025-03-31 23:43:50.238897 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:43:50.240261 INFO::Done
2025-03-31 23:43:50.241419 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:43:50.246996 INFO::Starting hierarchical adjustment
2025-03-31 23:43:50.248896 INFO::Found 3 batches.
2025-03-31 23:43:50.250167 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:43:50.251512 INFO::Using default BPPARAM
2025-03-31 23:43:50.253958 INFO::Processing subtree level 1
2025-03-31 23:43:50.627557 INFO::Adjusting the last 1 batches sequentially
2025-03-31 23:43:50.636132 INFO::Done
2025-03-31 23:43:50.637698 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:43:50.647304 INFO::ASW Batch was -0.0375167585494246 prior to batch effect correction and is now -0.142805819668526 .
2025-03-31 23:43:50.650815 INFO::Total function execution time is 0.429580926895142 s and adjustment time is 0.387573957443237 s ( 90.22 )
2025-03-31 23:43:50.692135 INFO::Skipping initial DF formatting
2025-03-31 23:43:50.693654 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:43:50.703152 INFO::Starting hierarchical adjustment
2025-03-31 23:43:50.705056 INFO::Found 5 batches.
2025-03-31 23:43:50.706373 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:43:50.707884 INFO::Using default BPPARAM
2025-03-31 23:43:50.709132 INFO::Processing subtree level 1
2025-03-31 23:43:51.022618 INFO::Adjusting the last 2 batches sequentially
2025-03-31 23:43:51.033079 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 23:43:51.100752 INFO::Done
2025-03-31 23:43:51.103274 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:43:51.11706 INFO::ASW Batch was 0.510205197926718 prior to batch effect correction and is now 0.510205197926718 .
2025-03-31 23:43:51.118583 INFO::ASW Label was 0.363445501329664 prior to batch effect correction and is now 0.363445501329664 .
2025-03-31 23:43:51.121342 INFO::Total function execution time is 0.429215908050537 s and adjustment time is 0.396054029464722 s ( 92.27 )
2025-03-31 23:43:51.17646 INFO::Formatting Data.
2025-03-31 23:43:51.178625 INFO::Replacing NaNs with NAs.
2025-03-31 23:43:51.181595 INFO::Removing potential empty rows and columns
2025-03-31 23:43:51.185521 INFO::Found 0 missing values.
2025-03-31 23:43:51.197392 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:43:51.198848 INFO::Done
2025-03-31 23:43:51.20028 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:43:51.207317 INFO::Starting hierarchical adjustment
2025-03-31 23:43:51.209233 INFO::Found 5 batches.
2025-03-31 23:43:51.210622 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:43:51.212212 INFO::Using default BPPARAM
2025-03-31 23:43:51.213533 INFO::Processing subtree level 1
2025-03-31 23:43:51.478358 INFO::Adjusting the last 2 batches sequentially
2025-03-31 23:43:51.488369 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 23:43:51.544042 INFO::Done
2025-03-31 23:43:51.546266 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:43:51.556633 INFO::ASW Batch was 0.423496992448875 prior to batch effect correction and is now -0.013609062762341 .
2025-03-31 23:43:51.558159 INFO::ASW Label was 0.317562414127171 prior to batch effect correction and is now 0.760720380048464 .
2025-03-31 23:43:51.560056 INFO::Total function execution time is 0.383676052093506 s and adjustment time is 0.335205078125 s ( 87.37 )
2025-03-31 23:43:51.562579 INFO::Formatting Data.
2025-03-31 23:43:51.564192 INFO::Replacing NaNs with NAs.
2025-03-31 23:43:51.567224 INFO::Removing potential empty rows and columns
2025-03-31 23:43:51.569786 INFO::Found 0 missing values.
2025-03-31 23:43:51.589347 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:43:51.590904 INFO::Done
2025-03-31 23:43:51.592317 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:43:51.599741 INFO::Starting hierarchical adjustment
2025-03-31 23:43:51.601907 INFO::Found 5 batches.
2025-03-31 23:43:51.603601 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:43:51.605347 INFO::Using default BPPARAM
2025-03-31 23:43:51.6068 INFO::Processing subtree level 1
2025-03-31 23:43:51.874116 INFO::Adjusting the last 2 batches sequentially
2025-03-31 23:43:51.884982 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 23:43:51.938223 INFO::Done
2025-03-31 23:43:51.93998 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:43:51.949953 INFO::ASW Batch was 0.423496992448875 prior to batch effect correction and is now -0.013609062762341 .
2025-03-31 23:43:51.951461 INFO::ASW Label was 0.317562414127171 prior to batch effect correction and is now 0.760720380048464 .
2025-03-31 23:43:51.953495 INFO::Total function execution time is 0.390904903411865 s and adjustment time is 0.336733102798462 s ( 86.14 )
2025-03-31 23:43:51.992489 INFO::Formatting Data.
2025-03-31 23:43:51.994257 INFO::Replacing NaNs with NAs.
2025-03-31 23:43:51.996507 INFO::Removing potential empty rows and columns
2025-03-31 23:43:51.999087 INFO::Found 0 missing values.
2025-03-31 23:43:52.01038 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:43:52.011849 INFO::Done
2025-03-31 23:43:52.013151 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:43:52.021153 INFO::Starting hierarchical adjustment
2025-03-31 23:43:52.023004 INFO::Found 5 batches.
2025-03-31 23:43:52.024309 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:43:52.026084 INFO::Using default BPPARAM
2025-03-31 23:43:52.028046 INFO::Processing subtree level 1
2025-03-31 23:43:52.283882 INFO::Adjusting the last 2 batches sequentially
2025-03-31 23:43:52.29627 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 23:43:52.349224 INFO::Done
2025-03-31 23:43:52.351043 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:43:52.360615 INFO::ASW Batch was 0.151163472386391 prior to batch effect correction and is now -0.107332566513983 .
2025-03-31 23:43:52.362213 INFO::ASW Label was 0.557326367209012 prior to batch effect correction and is now 0.890549860694182 .
2025-03-31 23:43:52.364189 INFO::Total function execution time is 0.371786832809448 s and adjustment time is 0.3265700340271 s ( 87.84 )
2025-03-31 23:43:52.366251 INFO::Formatting Data.
2025-03-31 23:43:52.36776 INFO::Replacing NaNs with NAs.
2025-03-31 23:43:52.369899 INFO::Removing potential empty rows and columns
2025-03-31 23:43:52.372334 INFO::Found 0 missing values.
2025-03-31 23:43:52.383327 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:43:52.384859 INFO::Done
2025-03-31 23:43:52.386654 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:43:52.393583 INFO::Starting hierarchical adjustment
2025-03-31 23:43:52.396762 INFO::Found 5 batches.
2025-03-31 23:43:52.398443 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:43:52.400283 INFO::Using default BPPARAM
2025-03-31 23:43:52.40223 INFO::Processing subtree level 1
2025-03-31 23:43:52.666345 INFO::Adjusting the last 2 batches sequentially
2025-03-31 23:43:52.67462 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 23:43:52.72868 INFO::Done
2025-03-31 23:43:52.730212 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:43:52.73865 INFO::ASW Batch was 0.151163472386391 prior to batch effect correction and is now -0.107332566513983 .
2025-03-31 23:43:52.740138 INFO::ASW Label was 0.557326367209012 prior to batch effect correction and is now 0.890549860694182 .
2025-03-31 23:43:52.742147 INFO::Total function execution time is 0.375831842422485 s and adjustment time is 0.332483053207397 s ( 88.47 )
2025-03-31 23:43:52.786787 INFO::Formatting Data.
2025-03-31 23:43:52.788467 INFO::Replacing NaNs with NAs.
2025-03-31 23:43:52.790608 INFO::Removing potential empty rows and columns
2025-03-31 23:43:52.794988 INFO::Found 0 missing values.
2025-03-31 23:43:52.802634 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:43:52.804153 INFO::Done
2025-03-31 23:43:52.805506 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:43:52.812226 INFO::Starting hierarchical adjustment
2025-03-31 23:43:52.814032 INFO::Found 2 batches.
2025-03-31 23:43:52.8153 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:43:52.816792 INFO::Using default BPPARAM
2025-03-31 23:43:52.818057 INFO::Adjusting the last 2 batches sequentially
2025-03-31 23:43:52.820204 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 23:43:52.860535 INFO::Done
2025-03-31 23:43:52.861928 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:43:52.870043 INFO::ASW Batch was 0.679364003228697 prior to batch effect correction and is now 0.0409991033468395 .
2025-03-31 23:43:52.871815 INFO::ASW Label was 0.362796249130687 prior to batch effect correction and is now 0.852378407055225 .
2025-03-31 23:43:52.873752 INFO::Total function execution time is 0.0871181488037109 s and adjustment time is 0.0468289852142334 s ( 53.75 )
2025-03-31 23:43:52.875602 INFO::Formatting Data.
2025-03-31 23:43:52.877822 INFO::Replacing NaNs with NAs.
2025-03-31 23:43:52.881022 INFO::Removing potential empty rows and columns
2025-03-31 23:43:52.883939 INFO::Found 0 missing values.
2025-03-31 23:43:52.891687 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:43:52.893124 INFO::Done
2025-03-31 23:43:52.89443 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:43:52.903075 INFO::Starting hierarchical adjustment
2025-03-31 23:43:52.904859 INFO::Found 2 batches.
2025-03-31 23:43:52.906084 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:43:52.907493 INFO::Using default BPPARAM
2025-03-31 23:43:52.908723 INFO::Adjusting the last 2 batches sequentially
2025-03-31 23:43:52.911783 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 23:43:52.951729 INFO::Done
2025-03-31 23:43:52.954322 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:43:52.961318 INFO::ASW Batch was 0.679364003228697 prior to batch effect correction and is now 0.0409991033468395 .
2025-03-31 23:43:52.962894 INFO::ASW Label was 0.362796249130687 prior to batch effect correction and is now 0.852378407055225 .
2025-03-31 23:43:52.964795 INFO::Total function execution time is 0.089224100112915 s and adjustment time is 0.0471930503845215 s ( 52.89 )
2025-03-31 23:43:52.998462 INFO::Formatting Data.
2025-03-31 23:43:53.000172 INFO::Replacing NaNs with NAs.
2025-03-31 23:43:53.002738 INFO::Removing potential empty rows and columns
2025-03-31 23:43:53.005031 INFO::Found 0 missing values.
2025-03-31 23:43:53.010891 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:43:53.012153 INFO::Done
2025-03-31 23:43:53.013254 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:43:53.017933 INFO::Starting hierarchical adjustment
2025-03-31 23:43:53.019811 INFO::Found 2 batches.
2025-03-31 23:43:53.021122 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:43:53.022618 INFO::Using default BPPARAM
2025-03-31 23:43:53.023909 INFO::Adjusting the last 2 batches sequentially
2025-03-31 23:43:53.02617 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 23:43:53.114909 INFO::Done
2025-03-31 23:43:53.116367 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:43:53.121412 INFO::ASW Batch was -0.00940250987645777 prior to batch effect correction and is now -0.154596350353956 .
2025-03-31 23:43:53.123431 INFO::Total function execution time is 0.125081062316895 s and adjustment time is 0.0954499244689941 s ( 76.31 )
2025-03-31 23:43:53.156367 INFO::Formatting Data.
2025-03-31 23:43:53.158077 INFO::Replacing NaNs with NAs.
2025-03-31 23:43:53.160047 INFO::Removing potential empty rows and columns
2025-03-31 23:43:53.162718 INFO::Found 0 missing values.
2025-03-31 23:43:53.165362 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.
2025-03-31 23:43:53.177951 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:43:53.179216 INFO::Done
2025-03-31 23:43:53.180595 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:43:53.190231 INFO::Starting hierarchical adjustment
2025-03-31 23:43:53.192145 INFO::Found 2 batches.
2025-03-31 23:43:53.19362 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:43:53.19565 INFO::Using default BPPARAM
2025-03-31 23:43:53.197052 INFO::Adjusting the last 2 batches sequentially
2025-03-31 23:43:53.199218 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 23:43:53.241909 INFO::Done
2025-03-31 23:43:53.243237 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:43:53.250989 INFO::ASW Batch was 0.754239963366211 prior to batch effect correction and is now 0.111014565265116 .
2025-03-31 23:43:53.252633 INFO::ASW Label was 0.337210659760478 prior to batch effect correction and is now 0.802073818514653 .
2025-03-31 23:43:53.254427 INFO::Total function execution time is 0.0981979370117188 s and adjustment time is 0.0501670837402344 s ( 51.09 )
2025-03-31 23:43:53.256279 INFO::Formatting Data.
2025-03-31 23:43:53.259156 INFO::Replacing NaNs with NAs.
2025-03-31 23:43:53.261436 INFO::Removing potential empty rows and columns
2025-03-31 23:43:53.264117 INFO::Found 0 missing values.
2025-03-31 23:43:53.26664 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.
2025-03-31 23:43:53.279898 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:43:53.281382 INFO::Done
2025-03-31 23:43:53.282653 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:43:53.290811 INFO::Starting hierarchical adjustment
2025-03-31 23:43:53.292713 INFO::Found 2 batches.
2025-03-31 23:43:53.294206 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:43:53.295719 INFO::Using default BPPARAM
2025-03-31 23:43:53.296949 INFO::Adjusting the last 2 batches sequentially
2025-03-31 23:43:53.299212 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 23:43:53.345119 INFO::Done
2025-03-31 23:43:53.346621 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:43:53.355132 INFO::ASW Batch was 0.754239963366211 prior to batch effect correction and is now 0.111014565265116 .
2025-03-31 23:43:53.356598 INFO::ASW Label was 0.337210659760478 prior to batch effect correction and is now 0.802073818514653 .
2025-03-31 23:43:53.358452 INFO::Total function execution time is 0.102197885513306 s and adjustment time is 0.0527639389038086 s ( 51.63 )
2025-03-31 23:43:53.973213 INFO::Formatting Data.
2025-03-31 23:43:53.974919 INFO::Replacing NaNs with NAs.
2025-03-31 23:43:53.976969 INFO::Removing potential empty rows and columns
2025-03-31 23:43:53.979464 INFO::Found 0 missing values.
2025-03-31 23:43:53.98767 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:43:53.989212 INFO::Done
2025-03-31 23:43:53.990481 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:43:53.995863 INFO::Starting hierarchical adjustment
2025-03-31 23:43:53.997674 INFO::Found 3 batches.
2025-03-31 23:43:53.998915 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:43:54.000332 INFO::Using default BPPARAM
2025-03-31 23:43:54.0016 INFO::Processing subtree level 1
2025-03-31 23:43:54.247269 INFO::Adjusting the last 1 batches sequentially
2025-03-31 23:43:54.255489 INFO::Done
2025-03-31 23:43:54.257055 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:43:54.268123 INFO::ASW Batch was -0.00848556807330655 prior to batch effect correction and is now -0.00848556807330655 .
2025-03-31 23:43:54.272457 INFO::Total function execution time is 0.298572063446045 s and adjustment time is 0.258118152618408 s ( 86.45 )
2025-03-31 23:43:54.27606 INFO::Formatting Data.
2025-03-31 23:43:54.277707 INFO::Typecasting input to dataframe.
2025-03-31 23:43:54.279505 INFO::Replacing NaNs with NAs.
2025-03-31 23:43:54.284056 INFO::Removing potential empty rows and columns
2025-03-31 23:43:54.290033 INFO::Found 0 missing values.
2025-03-31 23:43:54.300699 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:43:54.302368 INFO::Done
2025-03-31 23:43:54.303776 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:43:54.308525 INFO::Starting hierarchical adjustment
2025-03-31 23:43:54.311631 INFO::Found 3 batches.
2025-03-31 23:43:54.31339 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:43:54.315648 INFO::Using default BPPARAM
2025-03-31 23:43:54.316998 INFO::Processing subtree level 1
2025-03-31 23:43:54.773499 INFO::Adjusting the last 1 batches sequentially
2025-03-31 23:43:54.778853 INFO::Done
2025-03-31 23:43:54.780507 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:43:54.823858 INFO::ASW Batch was -0.00848556807330655 prior to batch effect correction and is now -0.00848556807330655 .
2025-03-31 23:43:54.832919 INFO::Total function execution time is 0.555194139480591 s and adjustment time is 0.468816995620728 s ( 84.44 )
2025-03-31 23:43:54.883408 INFO::Formatting Data.
2025-03-31 23:43:54.885135 INFO::Typecasting input to dataframe.
2025-03-31 23:43:54.887734 INFO::Replacing NaNs with NAs.
2025-03-31 23:43:54.890181 INFO::Removing potential empty rows and columns
2025-03-31 23:43:54.893485 INFO::Found 0 missing values.
2025-03-31 23:43:54.901165 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:43:54.902599 INFO::Done
2025-03-31 23:43:54.903839 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:43:54.908464 INFO::Starting hierarchical adjustment
2025-03-31 23:43:54.910711 INFO::Found 3 batches.
2025-03-31 23:43:54.91198 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:43:54.91334 INFO::Using default BPPARAM
2025-03-31 23:43:54.914572 INFO::Processing subtree level 1
2025-03-31 23:43:55.404674 INFO::Adjusting the last 1 batches sequentially
2025-03-31 23:43:55.410317 INFO::Done
2025-03-31 23:43:55.41202 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:43:55.454291 INFO::ASW Batch was -0.114530193019694 prior to batch effect correction and is now -0.114530193019694 .
2025-03-31 23:43:55.461256 INFO::Total function execution time is 0.576710939407349 s and adjustment time is 0.500363111495972 s ( 86.76 )
2025-03-31 23:43:56.074024 INFO::Formatting Data.
2025-03-31 23:43:56.076971 INFO::Replacing NaNs with NAs.
2025-03-31 23:43:56.080208 INFO::Removing potential empty rows and columns
2025-03-31 23:43:56.088107 INFO::Found 1000 missing values.
2025-03-31 23:43:56.161801 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:43:56.16377 INFO::Done
2025-03-31 23:43:56.165102 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:43:56.179964 INFO::Starting hierarchical adjustment
2025-03-31 23:43:56.181933 INFO::Found 10 batches.
2025-03-31 23:43:56.183234 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:43:56.184785 INFO::Using default BPPARAM
2025-03-31 23:43:56.186094 INFO::Processing subtree level 1
2025-03-31 23:43:56.598036 INFO::Processing subtree level 2
2025-03-31 23:43:57.164432 INFO::Adjusting the last 1 batches sequentially
2025-03-31 23:43:57.179348 INFO::Done
2025-03-31 23:43:57.180781 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:43:57.200147 INFO::ASW Batch was 0.527214523224721 prior to batch effect correction and is now 0.527214523224721 .
2025-03-31 23:43:57.201812 INFO::ASW Label was 0.284944409953099 prior to batch effect correction and is now 0.284944409953099 .
2025-03-31 23:43:57.205586 INFO::Total function execution time is 1.13090801239014 s and adjustment time is 0.997849941253662 s ( 88.23 )
2025-03-31 23:43:57.209189 INFO::Formatting Data.
2025-03-31 23:43:57.210939 INFO::Replacing NaNs with NAs.
2025-03-31 23:43:57.21407 INFO::Removing potential empty rows and columns
2025-03-31 23:43:57.223365 INFO::Found 1000 missing values.
2025-03-31 23:43:57.295772 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:43:57.297403 INFO::Done
2025-03-31 23:43:57.298722 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:43:57.312507 INFO::Starting hierarchical adjustment
2025-03-31 23:43:57.314505 INFO::Found 10 batches.
2025-03-31 23:43:58.672714 INFO::Set up parallel execution backend with 2 workers
2025-03-31 23:43:58.674008 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-03-31 23:44:00.607262 INFO::Adjusting the last 2 batches sequentially
2025-03-31 23:44:00.609652 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-31 23:44:00.659041 INFO::Done
2025-03-31 23:44:00.660328 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:44:00.672843 INFO::ASW Batch was 0.527214523224721 prior to batch effect correction and is now 0.527214523224721 .
2025-03-31 23:44:00.674199 INFO::ASW Label was 0.284944409953099 prior to batch effect correction and is now 0.284944409953099 .
2025-03-31 23:44:00.675854 INFO::Total function execution time is 3.46684694290161 s and adjustment time is 3.34493398666382 s ( 96.48 )
2025-03-31 23:44:01.092756 INFO::Formatting Data.
2025-03-31 23:44:01.09445 INFO::Replacing NaNs with NAs.
2025-03-31 23:44:01.096644 INFO::Removing potential empty rows and columns
2025-03-31 23:44:01.101085 INFO::Found 0 missing values.
2025-03-31 23:44:01.111985 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:44:01.113375 INFO::Done
2025-03-31 23:44:01.11502 INFO::Acquiring quality metrics before batch effect correction.
2025-03-31 23:44:01.121625 INFO::Starting hierarchical adjustment
2025-03-31 23:44:01.123947 INFO::Found 3 batches.
2025-03-31 23:44:01.12525 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-31 23:44:01.12896 INFO::Using default BPPARAM
2025-03-31 23:44:01.130329 INFO::Processing subtree level 1
2025-03-31 23:44:01.481538 INFO::Adjusting the last 1 batches sequentially
2025-03-31 23:44:01.49904 INFO::Done
2025-03-31 23:44:01.501003 INFO::Acquiring quality metrics after batch effect correction.
2025-03-31 23:44:01.515164 INFO::ASW Batch was 0.201720296764909 prior to batch effect correction and is now -0.142663904777041 .
2025-03-31 23:44:01.5165 INFO::ASW Label was -0.174546042719062 prior to batch effect correction and is now 0.0198162814214362 .
2025-03-31 23:44:01.519707 INFO::Total function execution time is 0.42651891708374 s and adjustment time is 0.375430822372437 s ( 88.02 )
2025-03-31 23:44:01.886671 INFO::Formatting Data.
2025-03-31 23:44:01.888689 INFO::Replacing NaNs with NAs.
2025-03-31 23:44:01.890965 INFO::Removing potential empty rows and columns
2025-03-31 23:44:01.893662 INFO::Found 2 missing values.
2025-03-31 23:44:01.901908 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:44:01.903344 INFO::Done
2025-03-31 23:44:01.992206 INFO::Found NA in Reference column
2025-03-31 23:44:02.019544 INFO::Require at least two references per batch.
2025-03-31 23:44:02.083144 INFO::Formatting Data.
2025-03-31 23:44:02.084674 INFO::Recognized SummarizedExperiment
2025-03-31 23:44:02.08593 INFO::Typecasting input to dataframe.
2025-03-31 23:44:02.112524 INFO::Replacing NaNs with NAs.
2025-03-31 23:44:02.11521 INFO::Removing potential empty rows and columns
2025-03-31 23:44:02.130259 INFO::Found 0 missing values.
2025-03-31 23:44:02.154333 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:44:02.155823 INFO::Done
2025-03-31 23:44:02.20098 INFO::Formatting Data.
2025-03-31 23:44:02.202519 INFO::Recognized SummarizedExperiment
2025-03-31 23:44:02.203762 INFO::Typecasting input to dataframe.
2025-03-31 23:44:02.256759 INFO::Replacing NaNs with NAs.
2025-03-31 23:44:02.259468 INFO::Removing potential empty rows and columns
2025-03-31 23:44:02.270941 INFO::Found 0 missing values.
2025-03-31 23:44:02.314665 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:44:02.316192 INFO::Done
2025-03-31 23:44:02.361384 INFO::Formatting Data.
2025-03-31 23:44:02.363831 INFO::Recognized SummarizedExperiment
2025-03-31 23:44:02.365393 INFO::Typecasting input to dataframe.
2025-03-31 23:44:02.413919 INFO::Replacing NaNs with NAs.
2025-03-31 23:44:02.419101 INFO::Removing potential empty rows and columns
2025-03-31 23:44:02.423193 INFO::Found 0 missing values.
2025-03-31 23:44:02.425496 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.
2025-03-31 23:44:02.446848 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:44:02.448372 INFO::Done
2025-03-31 23:44:02.4828 INFO::Formatting Data.
2025-03-31 23:44:02.48505 INFO::Replacing NaNs with NAs.
2025-03-31 23:44:02.487556 INFO::Removing potential empty rows and columns
2025-03-31 23:44:02.491627 INFO::Found 0 missing values.
2025-03-31 23:44:02.499839 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:44:02.502953 INFO::Done
2025-03-31 23:44:02.538384 INFO::Formatting Data.
2025-03-31 23:44:02.540125 INFO::Replacing NaNs with NAs.
2025-03-31 23:44:02.544086 INFO::Removing potential empty rows and columns
2025-03-31 23:44:02.546818 INFO::Found 0 missing values.
2025-03-31 23:44:02.55683 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:44:02.558252 INFO::Done
2025-03-31 23:44:02.652917 INFO::Formatting Data.
2025-03-31 23:44:02.657263 INFO::Replacing NaNs with NAs.
2025-03-31 23:44:02.660711 INFO::Removing potential empty rows and columns
2025-03-31 23:44:02.663907 INFO::Found 1 missing values.
2025-03-31 23:44:02.672046 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:44:02.673537 INFO::Done
2025-03-31 23:44:02.738859 INFO::Formatting Data.
2025-03-31 23:44:02.740725 INFO::Replacing NaNs with NAs.
2025-03-31 23:44:02.743255 INFO::Removing potential empty rows and columns
2025-03-31 23:44:02.745932 INFO::Found 2 missing values.
2025-03-31 23:44:02.748456 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.
2025-03-31 23:44:02.755332 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:44:02.756973 INFO::Done
2025-03-31 23:44:02.786911 INFO::Formatting Data.
2025-03-31 23:44:02.788657 INFO::Replacing NaNs with NAs.
2025-03-31 23:44:02.790628 INFO::Removing potential empty rows and columns
2025-03-31 23:44:02.793134 INFO::Found 2 missing values.
2025-03-31 23:44:02.797526 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:44:02.798933 INFO::Done
2025-03-31 23:44:02.830046 INFO::Formatting Data.
2025-03-31 23:44:02.832084 INFO::Typecasting input to dataframe.
2025-03-31 23:44:02.834061 INFO::Replacing NaNs with NAs.
2025-03-31 23:44:02.83617 INFO::Removing potential empty rows and columns
2025-03-31 23:44:02.839961 INFO::Found 0 missing values.
2025-03-31 23:44:02.848168 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-31 23:44:02.850623 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
35.062 6.760 44.108
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 43.967 | 2.525 | 34.584 | |
| compute_asw | 0.055 | 0.002 | 0.061 | |
| count_existing | 0.028 | 0.003 | 0.036 | |
| generate_data_covariables | 0.026 | 0.003 | 0.030 | |
| generate_dataset | 0.026 | 0.002 | 0.033 | |