Yannis Schumann
| Snapshot Date: 2025-02-03 13:00 -0500 (Mon, 03 Feb 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 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-02-06 12:09 -0500 (Thu, 06 Feb 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4753 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4501 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4524 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4476 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4407 |
| 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: 2025-02-04 12:17:22 -0500 (Tue, 04 Feb 2025) |
| EndedAt: 2025-02-04 12:18:32 -0500 (Tue, 04 Feb 2025) |
| EllapsedTime: 70.7 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 4.4.2 (2024-10-31)
* using platform: aarch64-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 Ventura 13.7.1
* 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 17.41 0.639 13.452
* 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-arm64/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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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")
2025-02-04 12:18:11.491492 INFO::Formatting Data.
2025-02-04 12:18:11.496476 INFO::Replacing NaNs with NAs.
2025-02-04 12:18:11.510151 INFO::Removing potential empty rows and columns
2025-02-04 12:18:11.833367 INFO::Found 0 missing values.
2025-02-04 12:18:11.837396 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 12:18:11.838019 INFO::Done
2025-02-04 12:18:11.838565 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 12:18:11.856216 INFO::Starting hierarchical adjustment
2025-02-04 12:18:11.857306 INFO::Found 3 batches.
2025-02-04 12:18:11.857832 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 12:18:11.859208 INFO::Using default BPPARAM
2025-02-04 12:18:11.859714 INFO::Processing subtree level 1
2025-02-04 12:18:12.011311 INFO::Adjusting the last 1 batches sequentially
2025-02-04 12:18:12.01649 INFO::Done
2025-02-04 12:18:12.017695 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 12:18:12.02289 INFO::ASW Batch was -0.0835419721737995 prior to batch effect correction and is now -0.0835419721737995 .
2025-02-04 12:18:12.025108 INFO::Total function execution time is 0.534543037414551 s and adjustment time is 0.159327983856201 s ( 29.81 )
2025-02-04 12:18:12.048613 INFO::Formatting Data.
2025-02-04 12:18:12.049554 INFO::Replacing NaNs with NAs.
2025-02-04 12:18:12.050557 INFO::Removing potential empty rows and columns
2025-02-04 12:18:12.051954 INFO::Found 0 missing values.
2025-02-04 12:18:12.052963 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.
2025-02-04 12:18:12.066854 INFO::Formatting Data.
2025-02-04 12:18:12.067783 INFO::Replacing NaNs with NAs.
2025-02-04 12:18:12.06873 INFO::Removing potential empty rows and columns
2025-02-04 12:18:12.069888 INFO::Found 0 missing values.
2025-02-04 12:18:12.070863 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.
2025-02-04 12:18:12.090509 INFO::Formatting Data.
2025-02-04 12:18:12.091394 INFO::Replacing NaNs with NAs.
2025-02-04 12:18:12.093067 INFO::Removing potential empty rows and columns
2025-02-04 12:18:12.096911 INFO::Found 0 missing values.
2025-02-04 12:18:12.098977 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.
2025-02-04 12:18:12.105898 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 12:18:12.106936 INFO::Done
2025-02-04 12:18:12.107566 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 12:18:12.10994 INFO::Starting hierarchical adjustment
2025-02-04 12:18:12.110816 INFO::Found 2 batches.
2025-02-04 12:18:12.1114 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 12:18:12.112221 INFO::Using default BPPARAM
2025-02-04 12:18:12.112829 INFO::Adjusting the last 2 batches sequentially
2025-02-04 12:18:12.113973 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-04 12:18:12.142572 INFO::Done
2025-02-04 12:18:12.143523 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 12:18:12.146211 INFO::ASW Batch was 0.0684612619269175 prior to batch effect correction and is now -0.115585524228964 .
2025-02-04 12:18:12.147706 INFO::Total function execution time is 0.0572149753570557 s and adjustment time is 0.0318710803985596 s ( 55.7 )
2025-02-04 12:18:12.151604 INFO::Formatting Data.
2025-02-04 12:18:12.152391 INFO::Replacing NaNs with NAs.
2025-02-04 12:18:12.162977 INFO::Formatting Data.
2025-02-04 12:18:12.164024 INFO::Replacing NaNs with NAs.
2025-02-04 12:18:12.165173 INFO::Removing potential empty rows and columns
2025-02-04 12:18:12.166274 INFO::Found 0 missing values.
2025-02-04 12:18:12.169071 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 12:18:12.169797 INFO::Done
2025-02-04 12:18:12.17033 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 12:18:12.172846 INFO::Starting hierarchical adjustment
2025-02-04 12:18:12.173753 INFO::Found 2 batches.
2025-02-04 12:18:12.174288 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 12:18:12.174982 INFO::Using default BPPARAM
2025-02-04 12:18:12.175685 INFO::Adjusting the last 2 batches sequentially
2025-02-04 12:18:12.176795 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-04 12:18:12.193308 INFO::Done
2025-02-04 12:18:12.194107 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 12:18:12.196315 INFO::ASW Batch was 0.0331915118021594 prior to batch effect correction and is now -0.0811529557019522 .
2025-02-04 12:18:12.197267 INFO::Total function execution time is 0.0344181060791016 s and adjustment time is 0.0197248458862305 s ( 57.31 )
2025-02-04 12:18:12.198461 INFO::Formatting Data.
2025-02-04 12:18:12.199112 INFO::Replacing NaNs with NAs.
2025-02-04 12:18:12.200052 INFO::Removing potential empty rows and columns
2025-02-04 12:18:12.20109 INFO::Found 0 missing values.
2025-02-04 12:18:12.203871 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 12:18:12.204526 INFO::Done
2025-02-04 12:18:12.205018 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 12:18:12.207428 INFO::Starting hierarchical adjustment
2025-02-04 12:18:12.208245 INFO::Found 2 batches.
2025-02-04 12:18:12.208785 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 12:18:12.209351 INFO::Using default BPPARAM
2025-02-04 12:18:12.209794 INFO::Adjusting the last 2 batches sequentially
2025-02-04 12:18:12.210629 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-04 12:18:12.227377 INFO::Done
2025-02-04 12:18:12.228268 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 12:18:12.230661 INFO::ASW Batch was 0.0331915118021594 prior to batch effect correction and is now -0.0811529557019522 .
2025-02-04 12:18:12.231657 INFO::Total function execution time is 0.033195972442627 s and adjustment time is 0.0192229747772217 s ( 57.91 )
2025-02-04 12:18:14.935098 INFO::Formatting Data.
2025-02-04 12:18:14.935892 INFO::Recognized SummarizedExperiment
2025-02-04 12:18:14.937002 INFO::Typecasting input to dataframe.
2025-02-04 12:18:14.971088 INFO::Replacing NaNs with NAs.
2025-02-04 12:18:14.972381 INFO::Removing potential empty rows and columns
2025-02-04 12:18:14.97543 INFO::Found 0 missing values.
2025-02-04 12:18:14.981612 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 12:18:14.982226 INFO::Done
2025-02-04 12:18:14.982679 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 12:18:14.987937 INFO::Starting hierarchical adjustment
2025-02-04 12:18:14.989579 INFO::Found 2 batches.
2025-02-04 12:18:14.990455 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 12:18:14.992167 INFO::Using default BPPARAM
2025-02-04 12:18:14.992828 INFO::Adjusting the last 2 batches sequentially
2025-02-04 12:18:14.993947 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-04 12:18:15.045971 INFO::Done
2025-02-04 12:18:15.04669 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 12:18:15.050379 INFO::ASW Batch was -0.011135181010492 prior to batch effect correction and is now -0.0939802291053587 .
2025-02-04 12:18:15.051191 INFO::Total function execution time is 0.116430997848511 s and adjustment time is 0.0569601058959961 s ( 48.92 )
2025-02-04 12:18:15.068722 INFO::Formatting Data.
2025-02-04 12:18:15.069523 INFO::Recognized SummarizedExperiment
2025-02-04 12:18:15.069989 INFO::Typecasting input to dataframe.
2025-02-04 12:18:15.081046 INFO::Replacing NaNs with NAs.
2025-02-04 12:18:15.082275 INFO::Removing potential empty rows and columns
2025-02-04 12:18:15.085609 INFO::Found 0 missing values.
2025-02-04 12:18:15.092191 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 12:18:15.092794 INFO::Done
2025-02-04 12:18:15.093263 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 12:18:15.097076 INFO::Starting hierarchical adjustment
2025-02-04 12:18:15.097779 INFO::Found 2 batches.
2025-02-04 12:18:15.098232 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 12:18:15.098761 INFO::Using default BPPARAM
2025-02-04 12:18:15.09918 INFO::Adjusting the last 2 batches sequentially
2025-02-04 12:18:15.100059 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-04 12:18:15.124513 INFO::Done
2025-02-04 12:18:15.125271 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 12:18:15.128997 INFO::ASW Batch was 0.00160863979300791 prior to batch effect correction and is now 0.00160863979300791 .
2025-02-04 12:18:15.129927 INFO::Total function execution time is 0.0612211227416992 s and adjustment time is 0.0268001556396484 s ( 43.78 )
2025-02-04 12:18:15.15341 INFO::Formatting Data.
2025-02-04 12:18:15.154295 INFO::Replacing NaNs with NAs.
2025-02-04 12:18:15.155185 INFO::Removing potential empty rows and columns
2025-02-04 12:18:15.15637 INFO::Found 0 missing values.
2025-02-04 12:18:15.15893 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 12:18:15.159421 INFO::Done
2025-02-04 12:18:15.159819 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 12:18:15.161685 INFO::Starting hierarchical adjustment
2025-02-04 12:18:15.162236 INFO::Found 3 batches.
2025-02-04 12:18:15.162599 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 12:18:15.163086 INFO::Using default BPPARAM
2025-02-04 12:18:15.163522 INFO::Processing subtree level 1
2025-02-04 12:18:15.342307 INFO::Adjusting the last 1 batches sequentially
2025-02-04 12:18:15.346492 INFO::Done
2025-02-04 12:18:15.347551 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 12:18:15.351813 INFO::ASW Batch was -0.0478807719248058 prior to batch effect correction and is now -0.164334757806964 .
2025-02-04 12:18:15.353525 INFO::Total function execution time is 0.19979190826416 s and adjustment time is 0.184334993362427 s ( 92.26 )
2025-02-04 12:18:15.37649 INFO::Skipping initial DF formatting
2025-02-04 12:18:15.377394 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 12:18:15.381625 INFO::Starting hierarchical adjustment
2025-02-04 12:18:15.382506 INFO::Found 5 batches.
2025-02-04 12:18:15.382999 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 12:18:15.383756 INFO::Using default BPPARAM
2025-02-04 12:18:15.38425 INFO::Processing subtree level 1
2025-02-04 12:18:15.544912 INFO::Adjusting the last 2 batches sequentially
2025-02-04 12:18:15.548668 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-04 12:18:15.574362 INFO::Done
2025-02-04 12:18:15.575687 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 12:18:15.581344 INFO::ASW Batch was 0.615665401633872 prior to batch effect correction and is now 0.615665401633872 .
2025-02-04 12:18:15.582162 INFO::ASW Label was 0.367886318295052 prior to batch effect correction and is now 0.367886318295052 .
2025-02-04 12:18:15.583667 INFO::Total function execution time is 0.207242012023926 s and adjustment time is 0.191949129104614 s ( 92.62 )
2025-02-04 12:18:15.605249 INFO::Formatting Data.
2025-02-04 12:18:15.606169 INFO::Replacing NaNs with NAs.
2025-02-04 12:18:15.607885 INFO::Removing potential empty rows and columns
2025-02-04 12:18:15.60907 INFO::Found 0 missing values.
2025-02-04 12:18:15.612824 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 12:18:15.613459 INFO::Done
2025-02-04 12:18:15.613946 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 12:18:15.619242 INFO::Starting hierarchical adjustment
2025-02-04 12:18:15.620736 INFO::Found 5 batches.
2025-02-04 12:18:15.621344 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 12:18:15.621996 INFO::Using default BPPARAM
2025-02-04 12:18:15.622478 INFO::Processing subtree level 1
2025-02-04 12:18:15.781902 INFO::Adjusting the last 2 batches sequentially
2025-02-04 12:18:15.786348 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-04 12:18:15.811121 INFO::Done
2025-02-04 12:18:15.812017 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 12:18:15.816143 INFO::ASW Batch was 0.48225186366823 prior to batch effect correction and is now -0.0200901324452605 .
2025-02-04 12:18:15.816865 INFO::ASW Label was 0.364174154320967 prior to batch effect correction and is now 0.758178795242746 .
2025-02-04 12:18:15.817737 INFO::Total function execution time is 0.212626934051514 s and adjustment time is 0.190535068511963 s ( 89.61 )
2025-02-04 12:18:15.818541 INFO::Formatting Data.
2025-02-04 12:18:15.819102 INFO::Replacing NaNs with NAs.
2025-02-04 12:18:15.819981 INFO::Removing potential empty rows and columns
2025-02-04 12:18:15.820964 INFO::Found 0 missing values.
2025-02-04 12:18:15.824609 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 12:18:15.825127 INFO::Done
2025-02-04 12:18:15.825572 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 12:18:15.828358 INFO::Starting hierarchical adjustment
2025-02-04 12:18:15.82901 INFO::Found 5 batches.
2025-02-04 12:18:15.829471 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 12:18:15.830098 INFO::Using default BPPARAM
2025-02-04 12:18:15.830552 INFO::Processing subtree level 1
2025-02-04 12:18:15.955919 INFO::Adjusting the last 2 batches sequentially
2025-02-04 12:18:15.968188 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-04 12:18:15.991946 INFO::Done
2025-02-04 12:18:15.993071 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 12:18:15.99706 INFO::ASW Batch was 0.48225186366823 prior to batch effect correction and is now -0.0200901324452605 .
2025-02-04 12:18:15.997674 INFO::ASW Label was 0.364174154320967 prior to batch effect correction and is now 0.758178795242746 .
2025-02-04 12:18:15.999149 INFO::Total function execution time is 0.180538892745972 s and adjustment time is 0.162996053695679 s ( 90.28 )
2025-02-04 12:18:16.020778 INFO::Formatting Data.
2025-02-04 12:18:16.021622 INFO::Replacing NaNs with NAs.
2025-02-04 12:18:16.022917 INFO::Removing potential empty rows and columns
2025-02-04 12:18:16.023947 INFO::Found 0 missing values.
2025-02-04 12:18:16.028039 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 12:18:16.028734 INFO::Done
2025-02-04 12:18:16.02932 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 12:18:16.032895 INFO::Starting hierarchical adjustment
2025-02-04 12:18:16.033861 INFO::Found 5 batches.
2025-02-04 12:18:16.034371 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 12:18:16.035056 INFO::Using default BPPARAM
2025-02-04 12:18:16.03576 INFO::Processing subtree level 1
2025-02-04 12:18:16.171201 INFO::Adjusting the last 2 batches sequentially
2025-02-04 12:18:16.177316 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-04 12:18:16.201427 INFO::Done
2025-02-04 12:18:16.20236 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 12:18:16.206466 INFO::ASW Batch was 0.32146702528157 prior to batch effect correction and is now -0.0530359487924462 .
2025-02-04 12:18:16.207216 INFO::ASW Label was 0.418006478889219 prior to batch effect correction and is now 0.808755385136175 .
2025-02-04 12:18:16.20916 INFO::Total function execution time is 0.18807315826416 s and adjustment time is 0.16767692565918 s ( 89.16 )
2025-02-04 12:18:16.210315 INFO::Formatting Data.
2025-02-04 12:18:16.21172 INFO::Replacing NaNs with NAs.
2025-02-04 12:18:16.214951 INFO::Removing potential empty rows and columns
2025-02-04 12:18:16.216796 INFO::Found 0 missing values.
2025-02-04 12:18:16.222671 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 12:18:16.224697 INFO::Done
2025-02-04 12:18:16.225423 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 12:18:16.228968 INFO::Starting hierarchical adjustment
2025-02-04 12:18:16.229879 INFO::Found 5 batches.
2025-02-04 12:18:16.230394 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 12:18:16.231046 INFO::Using default BPPARAM
2025-02-04 12:18:16.231805 INFO::Processing subtree level 1
2025-02-04 12:18:16.377826 INFO::Adjusting the last 2 batches sequentially
2025-02-04 12:18:16.383736 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-04 12:18:16.410868 INFO::Done
2025-02-04 12:18:16.412732 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 12:18:16.419504 INFO::ASW Batch was 0.32146702528157 prior to batch effect correction and is now -0.0530359487924462 .
2025-02-04 12:18:16.420498 INFO::ASW Label was 0.418006478889219 prior to batch effect correction and is now 0.808755385136175 .
2025-02-04 12:18:16.421964 INFO::Total function execution time is 0.211588859558105 s and adjustment time is 0.180998802185059 s ( 85.54 )
2025-02-04 12:18:16.445559 INFO::Formatting Data.
2025-02-04 12:18:16.446444 INFO::Replacing NaNs with NAs.
2025-02-04 12:18:16.44777 INFO::Removing potential empty rows and columns
2025-02-04 12:18:16.4488 INFO::Found 0 missing values.
2025-02-04 12:18:16.451303 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 12:18:16.452103 INFO::Done
2025-02-04 12:18:16.452604 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 12:18:16.455539 INFO::Starting hierarchical adjustment
2025-02-04 12:18:16.45628 INFO::Found 2 batches.
2025-02-04 12:18:16.456766 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 12:18:16.45749 INFO::Using default BPPARAM
2025-02-04 12:18:16.457953 INFO::Adjusting the last 2 batches sequentially
2025-02-04 12:18:16.458758 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-04 12:18:16.481444 INFO::Done
2025-02-04 12:18:16.482478 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 12:18:16.488256 INFO::ASW Batch was 0.437392254617273 prior to batch effect correction and is now 0.0406175086387112 .
2025-02-04 12:18:16.489383 INFO::ASW Label was 0.639060372350015 prior to batch effect correction and is now 0.912732244970707 .
2025-02-04 12:18:16.490422 INFO::Total function execution time is 0.0449748039245605 s and adjustment time is 0.0252089500427246 s ( 56.05 )
2025-02-04 12:18:16.491187 INFO::Formatting Data.
2025-02-04 12:18:16.49176 INFO::Replacing NaNs with NAs.
2025-02-04 12:18:16.492667 INFO::Removing potential empty rows and columns
2025-02-04 12:18:16.493575 INFO::Found 0 missing values.
2025-02-04 12:18:16.49616 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 12:18:16.496706 INFO::Done
2025-02-04 12:18:16.497174 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 12:18:16.499948 INFO::Starting hierarchical adjustment
2025-02-04 12:18:16.500634 INFO::Found 2 batches.
2025-02-04 12:18:16.501113 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 12:18:16.50165 INFO::Using default BPPARAM
2025-02-04 12:18:16.502128 INFO::Adjusting the last 2 batches sequentially
2025-02-04 12:18:16.502922 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-04 12:18:16.517221 INFO::Done
2025-02-04 12:18:16.517969 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 12:18:16.520849 INFO::ASW Batch was 0.437392254617273 prior to batch effect correction and is now 0.0406175086387112 .
2025-02-04 12:18:16.522136 INFO::ASW Label was 0.639060372350015 prior to batch effect correction and is now 0.912732244970707 .
2025-02-04 12:18:16.523071 INFO::Total function execution time is 0.031836986541748 s and adjustment time is 0.0166778564453125 s ( 52.39 )
2025-02-04 12:18:16.541502 INFO::Formatting Data.
2025-02-04 12:18:16.54337 INFO::Replacing NaNs with NAs.
2025-02-04 12:18:16.544831 INFO::Removing potential empty rows and columns
2025-02-04 12:18:16.545869 INFO::Found 0 missing values.
2025-02-04 12:18:16.549437 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 12:18:16.550161 INFO::Done
2025-02-04 12:18:16.550698 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 12:18:16.552694 INFO::Starting hierarchical adjustment
2025-02-04 12:18:16.553389 INFO::Found 2 batches.
2025-02-04 12:18:16.553836 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 12:18:16.554378 INFO::Using default BPPARAM
2025-02-04 12:18:16.555634 INFO::Adjusting the last 2 batches sequentially
2025-02-04 12:18:16.556894 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-04 12:18:16.596711 INFO::Done
2025-02-04 12:18:16.598147 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 12:18:16.601588 INFO::ASW Batch was -0.0831719256746127 prior to batch effect correction and is now -0.149981311408936 .
2025-02-04 12:18:16.602698 INFO::Total function execution time is 0.0618109703063965 s and adjustment time is 0.0432460308074951 s ( 69.96 )
2025-02-04 12:18:16.616699 INFO::Formatting Data.
2025-02-04 12:18:16.617591 INFO::Replacing NaNs with NAs.
2025-02-04 12:18:16.618513 INFO::Removing potential empty rows and columns
2025-02-04 12:18:16.619517 INFO::Found 0 missing values.
2025-02-04 12:18:16.621052 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.
2025-02-04 12:18:16.625271 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 12:18:16.625867 INFO::Done
2025-02-04 12:18:16.626315 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 12:18:16.629424 INFO::Starting hierarchical adjustment
2025-02-04 12:18:16.630214 INFO::Found 2 batches.
2025-02-04 12:18:16.630708 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 12:18:16.631252 INFO::Using default BPPARAM
2025-02-04 12:18:16.631726 INFO::Adjusting the last 2 batches sequentially
2025-02-04 12:18:16.632683 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-04 12:18:16.651414 INFO::Done
2025-02-04 12:18:16.652231 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 12:18:16.656928 INFO::ASW Batch was 0.401174924553609 prior to batch effect correction and is now -0.0272388889630436 .
2025-02-04 12:18:16.6579 INFO::ASW Label was 0.692121471445988 prior to batch effect correction and is now 0.94453377774602 .
2025-02-04 12:18:16.659781 INFO::Total function execution time is 0.0431368350982666 s and adjustment time is 0.0212860107421875 s ( 49.35 )
2025-02-04 12:18:16.660718 INFO::Formatting Data.
2025-02-04 12:18:16.66132 INFO::Replacing NaNs with NAs.
2025-02-04 12:18:16.66227 INFO::Removing potential empty rows and columns
2025-02-04 12:18:16.663255 INFO::Found 0 missing values.
2025-02-04 12:18:16.664143 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.
2025-02-04 12:18:16.668466 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 12:18:16.669058 INFO::Done
2025-02-04 12:18:16.669528 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 12:18:16.67288 INFO::Starting hierarchical adjustment
2025-02-04 12:18:16.673675 INFO::Found 2 batches.
2025-02-04 12:18:16.6743 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 12:18:16.675466 INFO::Using default BPPARAM
2025-02-04 12:18:16.676539 INFO::Adjusting the last 2 batches sequentially
2025-02-04 12:18:16.677844 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-04 12:18:16.696514 INFO::Done
2025-02-04 12:18:16.69734 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 12:18:16.700257 INFO::ASW Batch was 0.401174924553609 prior to batch effect correction and is now -0.0272388889630436 .
2025-02-04 12:18:16.701215 INFO::ASW Label was 0.692121471445988 prior to batch effect correction and is now 0.94453377774602 .
2025-02-04 12:18:16.702864 INFO::Total function execution time is 0.0420980453491211 s and adjustment time is 0.0229430198669434 s ( 54.5 )
2025-02-04 12:18:16.939521 INFO::Formatting Data.
2025-02-04 12:18:16.940436 INFO::Replacing NaNs with NAs.
2025-02-04 12:18:16.941327 INFO::Removing potential empty rows and columns
2025-02-04 12:18:16.942351 INFO::Found 0 missing values.
2025-02-04 12:18:16.945166 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 12:18:16.945796 INFO::Done
2025-02-04 12:18:16.946274 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 12:18:16.948359 INFO::Starting hierarchical adjustment
2025-02-04 12:18:16.949044 INFO::Found 3 batches.
2025-02-04 12:18:16.949521 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 12:18:16.950083 INFO::Using default BPPARAM
2025-02-04 12:18:16.950526 INFO::Processing subtree level 1
2025-02-04 12:18:17.085263 INFO::Adjusting the last 1 batches sequentially
2025-02-04 12:18:17.087999 INFO::Done
2025-02-04 12:18:17.088593 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 12:18:17.092214 INFO::ASW Batch was -0.132840132317881 prior to batch effect correction and is now -0.132840132317881 .
2025-02-04 12:18:17.09373 INFO::Total function execution time is 0.153950929641724 s and adjustment time is 0.139081954956055 s ( 90.34 )
2025-02-04 12:18:17.09487 INFO::Formatting Data.
2025-02-04 12:18:17.095549 INFO::Typecasting input to dataframe.
2025-02-04 12:18:17.097057 INFO::Replacing NaNs with NAs.
2025-02-04 12:18:17.099663 INFO::Removing potential empty rows and columns
2025-02-04 12:18:17.101299 INFO::Found 0 missing values.
2025-02-04 12:18:17.106534 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 12:18:17.10835 INFO::Done
2025-02-04 12:18:17.109126 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 12:18:17.111489 INFO::Starting hierarchical adjustment
2025-02-04 12:18:17.112291 INFO::Found 3 batches.
2025-02-04 12:18:17.112813 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 12:18:17.113494 INFO::Using default BPPARAM
2025-02-04 12:18:17.114003 INFO::Processing subtree level 1
2025-02-04 12:18:17.238505 INFO::Adjusting the last 1 batches sequentially
2025-02-04 12:18:17.244701 INFO::Done
2025-02-04 12:18:17.245971 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 12:18:17.252001 INFO::ASW Batch was -0.132840132317881 prior to batch effect correction and is now -0.132840132317881 .
2025-02-04 12:18:17.253914 INFO::Total function execution time is 0.158941984176636 s and adjustment time is 0.132361173629761 s ( 83.28 )
2025-02-04 12:18:17.275216 INFO::Formatting Data.
2025-02-04 12:18:17.276104 INFO::Typecasting input to dataframe.
2025-02-04 12:18:17.276896 INFO::Replacing NaNs with NAs.
2025-02-04 12:18:17.278266 INFO::Removing potential empty rows and columns
2025-02-04 12:18:17.279381 INFO::Found 0 missing values.
2025-02-04 12:18:17.282357 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 12:18:17.282975 INFO::Done
2025-02-04 12:18:17.283469 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 12:18:17.28556 INFO::Starting hierarchical adjustment
2025-02-04 12:18:17.286275 INFO::Found 3 batches.
2025-02-04 12:18:17.286733 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 12:18:17.287357 INFO::Using default BPPARAM
2025-02-04 12:18:17.287812 INFO::Processing subtree level 1
2025-02-04 12:18:17.553987 INFO::Adjusting the last 1 batches sequentially
2025-02-04 12:18:17.557127 INFO::Done
2025-02-04 12:18:17.557733 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 12:18:17.561629 INFO::ASW Batch was -0.0447245130537514 prior to batch effect correction and is now -0.0447245130537514 .
2025-02-04 12:18:17.577544 INFO::Total function execution time is 0.298508167266846 s and adjustment time is 0.270987987518311 s ( 90.78 )
2025-02-04 12:18:17.912104 INFO::Formatting Data.
2025-02-04 12:18:17.913036 INFO::Replacing NaNs with NAs.
2025-02-04 12:18:17.914212 INFO::Removing potential empty rows and columns
2025-02-04 12:18:17.917685 INFO::Found 1000 missing values.
2025-02-04 12:18:17.948468 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 12:18:17.949449 INFO::Done
2025-02-04 12:18:17.949995 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 12:18:17.957173 INFO::Starting hierarchical adjustment
2025-02-04 12:18:17.958436 INFO::Found 10 batches.
2025-02-04 12:18:17.959144 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 12:18:17.959884 INFO::Using default BPPARAM
2025-02-04 12:18:17.960463 INFO::Processing subtree level 1
2025-02-04 12:18:18.126513 INFO::Processing subtree level 2
2025-02-04 12:18:18.384128 INFO::Adjusting the last 1 batches sequentially
2025-02-04 12:18:18.387178 INFO::Done
2025-02-04 12:18:18.387903 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 12:18:18.396258 INFO::ASW Batch was 0.5327934563678 prior to batch effect correction and is now 0.5327934563678 .
2025-02-04 12:18:18.397056 INFO::ASW Label was 0.300958382915366 prior to batch effect correction and is now 0.300958382915366 .
2025-02-04 12:18:18.398146 INFO::Total function execution time is 0.486162185668945 s and adjustment time is 0.428992986679077 s ( 88.24 )
2025-02-04 12:18:18.399053 INFO::Formatting Data.
2025-02-04 12:18:18.399644 INFO::Replacing NaNs with NAs.
2025-02-04 12:18:18.401225 INFO::Removing potential empty rows and columns
2025-02-04 12:18:18.404091 INFO::Found 1000 missing values.
2025-02-04 12:18:18.421804 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 12:18:18.422705 INFO::Done
2025-02-04 12:18:18.423192 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 12:18:18.42909 INFO::Starting hierarchical adjustment
2025-02-04 12:18:18.429857 INFO::Found 10 batches.
2025-02-04 12:18:19.689122 INFO::Set up parallel execution backend with 2 workers
2025-02-04 12:18:19.690028 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-02-04 12:18:21.151099 INFO::Adjusting the last 2 batches sequentially
2025-02-04 12:18:21.152873 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-04 12:18:21.173224 INFO::Done
2025-02-04 12:18:21.174057 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 12:18:21.179736 INFO::ASW Batch was 0.5327934563678 prior to batch effect correction and is now 0.5327934563678 .
2025-02-04 12:18:21.180356 INFO::ASW Label was 0.300958382915366 prior to batch effect correction and is now 0.300958382915366 .
2025-02-04 12:18:21.181076 INFO::Total function execution time is 2.78203105926514 s and adjustment time is 2.74346399307251 s ( 98.61 )
2025-02-04 12:18:21.367718 INFO::Formatting Data.
2025-02-04 12:18:21.369013 INFO::Replacing NaNs with NAs.
2025-02-04 12:18:21.370248 INFO::Removing potential empty rows and columns
2025-02-04 12:18:21.371907 INFO::Found 0 missing values.
2025-02-04 12:18:21.376391 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 12:18:21.377105 INFO::Done
2025-02-04 12:18:21.377645 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 12:18:21.381275 INFO::Starting hierarchical adjustment
2025-02-04 12:18:21.382778 INFO::Found 3 batches.
2025-02-04 12:18:21.38431 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 12:18:21.385355 INFO::Using default BPPARAM
2025-02-04 12:18:21.386005 INFO::Processing subtree level 1
2025-02-04 12:18:21.540834 INFO::Adjusting the last 1 batches sequentially
2025-02-04 12:18:21.546455 INFO::Done
2025-02-04 12:18:21.550363 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 12:18:21.557757 INFO::ASW Batch was 0.207280348737712 prior to batch effect correction and is now -0.160955002449769 .
2025-02-04 12:18:21.558675 INFO::ASW Label was -0.183407354366346 prior to batch effect correction and is now -0.0163798514438825 .
2025-02-04 12:18:21.560074 INFO::Total function execution time is 0.192514896392822 s and adjustment time is 0.164229154586792 s ( 85.31 )
2025-02-04 12:18:21.724359 INFO::Formatting Data.
2025-02-04 12:18:21.726441 INFO::Replacing NaNs with NAs.
2025-02-04 12:18:21.727807 INFO::Removing potential empty rows and columns
2025-02-04 12:18:21.729066 INFO::Found 2 missing values.
2025-02-04 12:18:21.732016 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-02-04 12:18:21.732681 INFO::Done
2025-02-04 12:18:21.766464 INFO::Found NA in Reference column
2025-02-04 12:18:21.781014 INFO::Require at least two references per batch.
2025-02-04 12:18:21.803857 INFO::Formatting Data.
2025-02-04 12:18:21.804706 INFO::Recognized SummarizedExperiment
2025-02-04 12:18:21.805201 INFO::Typecasting input to dataframe.
2025-02-04 12:18:21.817883 INFO::Replacing NaNs with NAs.
2025-02-04 12:18:21.819684 INFO::Removing potential empty rows and columns
2025-02-04 12:18:21.824438 INFO::Found 0 missing values.
2025-02-04 12:18:21.833712 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 12:18:21.834472 INFO::Done
2025-02-04 12:18:21.851487 INFO::Formatting Data.
2025-02-04 12:18:21.852418 INFO::Recognized SummarizedExperiment
2025-02-04 12:18:21.85338 INFO::Typecasting input to dataframe.
2025-02-04 12:18:21.876768 INFO::Replacing NaNs with NAs.
2025-02-04 12:18:21.878436 INFO::Removing potential empty rows and columns
2025-02-04 12:18:21.882207 INFO::Found 0 missing values.
2025-02-04 12:18:21.893673 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 12:18:21.894414 INFO::Done
2025-02-04 12:18:21.911267 INFO::Formatting Data.
2025-02-04 12:18:21.912126 INFO::Recognized SummarizedExperiment
2025-02-04 12:18:21.912701 INFO::Typecasting input to dataframe.
2025-02-04 12:18:21.930038 INFO::Replacing NaNs with NAs.
2025-02-04 12:18:21.931287 INFO::Removing potential empty rows and columns
2025-02-04 12:18:21.932408 INFO::Found 0 missing values.
2025-02-04 12:18:21.933416 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.
2025-02-04 12:18:21.93806 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 12:18:21.938731 INFO::Done
2025-02-04 12:18:21.951368 INFO::Formatting Data.
2025-02-04 12:18:21.952372 INFO::Replacing NaNs with NAs.
2025-02-04 12:18:21.953319 INFO::Removing potential empty rows and columns
2025-02-04 12:18:21.954381 INFO::Found 0 missing values.
2025-02-04 12:18:21.957381 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 12:18:21.958103 INFO::Done
2025-02-04 12:18:21.971213 INFO::Formatting Data.
2025-02-04 12:18:21.972108 INFO::Replacing NaNs with NAs.
2025-02-04 12:18:21.972921 INFO::Removing potential empty rows and columns
2025-02-04 12:18:21.973842 INFO::Found 0 missing values.
2025-02-04 12:18:21.976537 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 12:18:21.977162 INFO::Done
2025-02-04 12:18:22.011963 INFO::Formatting Data.
2025-02-04 12:18:22.012905 INFO::Replacing NaNs with NAs.
2025-02-04 12:18:22.013945 INFO::Removing potential empty rows and columns
2025-02-04 12:18:22.015052 INFO::Found 1 missing values.
2025-02-04 12:18:22.017454 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 12:18:22.017996 INFO::Done
2025-02-04 12:18:22.038929 INFO::Formatting Data.
2025-02-04 12:18:22.039902 INFO::Replacing NaNs with NAs.
2025-02-04 12:18:22.040781 INFO::Removing potential empty rows and columns
2025-02-04 12:18:22.041697 INFO::Found 2 missing values.
2025-02-04 12:18:22.04256 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.
2025-02-04 12:18:22.04477 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-02-04 12:18:22.045299 INFO::Done
2025-02-04 12:18:22.058996 INFO::Formatting Data.
2025-02-04 12:18:22.06003 INFO::Replacing NaNs with NAs.
2025-02-04 12:18:22.060963 INFO::Removing potential empty rows and columns
2025-02-04 12:18:22.06212 INFO::Found 2 missing values.
2025-02-04 12:18:22.06415 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 12:18:22.064767 INFO::Done
2025-02-04 12:18:22.079158 INFO::Formatting Data.
2025-02-04 12:18:22.080279 INFO::Typecasting input to dataframe.
2025-02-04 12:18:22.081118 INFO::Replacing NaNs with NAs.
2025-02-04 12:18:22.081998 INFO::Removing potential empty rows and columns
2025-02-04 12:18:22.082988 INFO::Found 0 missing values.
2025-02-04 12:18:22.085933 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 12:18:22.086609 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
20.106 4.096 25.134
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 17.410 | 0.639 | 13.452 | |
| compute_asw | 0.030 | 0.002 | 0.032 | |
| count_existing | 0.016 | 0.001 | 0.017 | |
| generate_data_covariables | 0.014 | 0.001 | 0.015 | |
| generate_dataset | 0.013 | 0.001 | 0.015 | |