Yannis Schumann
| Snapshot Date: 2025-02-03 13:40 -0500 (Mon, 03 Feb 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: f785e17 |
| git_last_commit_date: 2025-01-29 01:54:20 -0500 (Wed, 29 Jan 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-02-04 11:44 -0500 (Tue, 04 Feb 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4716 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4478 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4489 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4442 |
| 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 159/2295 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.3.6 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.3.6 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.3.6.tar.gz |
| StartedAt: 2025-02-03 18:48:24 -0500 (Mon, 03 Feb 2025) |
| EndedAt: 2025-02-03 18:48:53 -0500 (Mon, 03 Feb 2025) |
| EllapsedTime: 29.4 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_1.3.6.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.3.6’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 9.389 0.424 6.723
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.3.6’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 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")
2025-02-03 18:48:46.667468 INFO::Formatting Data.
2025-02-03 18:48:46.668973 INFO::Replacing NaNs with NAs.
2025-02-03 18:48:46.673392 INFO::Removing potential empty rows and columns
2025-02-03 18:48:46.776517 INFO::Found 0 missing values.
2025-02-03 18:48:46.778019 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 18:48:46.778271 INFO::Done
2025-02-03 18:48:46.778494 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 18:48:46.785348 INFO::Starting hierarchical adjustment
2025-02-03 18:48:46.7857 INFO::Found 3 batches.
2025-02-03 18:48:46.78589 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 18:48:46.786365 INFO::Using default BPPARAM
2025-02-03 18:48:46.786537 INFO::Processing subtree level 1
2025-02-03 18:48:46.838857 INFO::Adjusting the last 1 batches sequentially
2025-02-03 18:48:46.840422 INFO::Done
2025-02-03 18:48:46.840718 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 18:48:46.842827 INFO::ASW Batch was -0.0694988339375918 prior to batch effect correction and is now -0.0694988339375918 .
2025-02-03 18:48:46.843434 INFO::Total function execution time is 0.176258087158203 s and adjustment time is 0.0547950267791748 s ( 31.09 )
2025-02-03 18:48:46.85146 INFO::Formatting Data.
2025-02-03 18:48:46.851717 INFO::Replacing NaNs with NAs.
2025-02-03 18:48:46.85203 INFO::Removing potential empty rows and columns
2025-02-03 18:48:46.852554 INFO::Found 0 missing values.
2025-02-03 18:48:46.852916 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.
2025-02-03 18:48:46.857054 INFO::Formatting Data.
2025-02-03 18:48:46.857274 INFO::Replacing NaNs with NAs.
2025-02-03 18:48:46.857555 INFO::Removing potential empty rows and columns
2025-02-03 18:48:46.857877 INFO::Found 0 missing values.
2025-02-03 18:48:46.858159 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.
2025-02-03 18:48:46.864306 INFO::Formatting Data.
2025-02-03 18:48:46.864583 INFO::Replacing NaNs with NAs.
2025-02-03 18:48:46.864874 INFO::Removing potential empty rows and columns
2025-02-03 18:48:46.865201 INFO::Found 0 missing values.
2025-02-03 18:48:46.865489 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.
2025-02-03 18:48:46.866901 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 18:48:46.867095 INFO::Done
2025-02-03 18:48:46.867264 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 18:48:46.868011 INFO::Starting hierarchical adjustment
2025-02-03 18:48:46.86822 INFO::Found 2 batches.
2025-02-03 18:48:46.869402 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 18:48:46.869736 INFO::Using default BPPARAM
2025-02-03 18:48:46.869934 INFO::Adjusting the last 2 batches sequentially
2025-02-03 18:48:46.870302 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-03 18:48:46.879271 INFO::Done
2025-02-03 18:48:46.879497 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 18:48:46.880173 INFO::ASW Batch was -0.00423752324335433 prior to batch effect correction and is now -0.118794064581007 .
2025-02-03 18:48:46.88043 INFO::Total function execution time is 0.0161559581756592 s and adjustment time is 0.0110800266265869 s ( 68.58 )
2025-02-03 18:48:46.881486 INFO::Formatting Data.
2025-02-03 18:48:46.881691 INFO::Replacing NaNs with NAs.
2025-02-03 18:48:46.884656 INFO::Formatting Data.
2025-02-03 18:48:46.884904 INFO::Replacing NaNs with NAs.
2025-02-03 18:48:46.885169 INFO::Removing potential empty rows and columns
2025-02-03 18:48:46.885558 INFO::Found 0 missing values.
2025-02-03 18:48:46.899611 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 18:48:46.899864 INFO::Done
2025-02-03 18:48:46.900038 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 18:48:46.900751 INFO::Starting hierarchical adjustment
2025-02-03 18:48:46.900991 INFO::Found 2 batches.
2025-02-03 18:48:46.901162 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 18:48:46.901351 INFO::Using default BPPARAM
2025-02-03 18:48:46.90151 INFO::Adjusting the last 2 batches sequentially
2025-02-03 18:48:46.901775 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-03 18:48:46.906361 INFO::Done
2025-02-03 18:48:46.906572 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 18:48:46.90717 INFO::ASW Batch was 0.0515001039369253 prior to batch effect correction and is now -0.116960320864982 .
2025-02-03 18:48:46.907409 INFO::Total function execution time is 0.0227730274200439 s and adjustment time is 0.00541806221008301 s ( 23.79 )
2025-02-03 18:48:46.907698 INFO::Formatting Data.
2025-02-03 18:48:46.90786 INFO::Replacing NaNs with NAs.
2025-02-03 18:48:46.908108 INFO::Removing potential empty rows and columns
2025-02-03 18:48:46.9084 INFO::Found 0 missing values.
2025-02-03 18:48:46.909178 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 18:48:46.909334 INFO::Done
2025-02-03 18:48:46.909496 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 18:48:46.910053 INFO::Starting hierarchical adjustment
2025-02-03 18:48:46.91024 INFO::Found 2 batches.
2025-02-03 18:48:46.910392 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 18:48:46.910565 INFO::Using default BPPARAM
2025-02-03 18:48:46.910715 INFO::Adjusting the last 2 batches sequentially
2025-02-03 18:48:46.910951 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-03 18:48:46.915382 INFO::Done
2025-02-03 18:48:46.915569 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 18:48:46.916195 INFO::ASW Batch was 0.0515001039369253 prior to batch effect correction and is now -0.116960320864982 .
2025-02-03 18:48:46.91644 INFO::Total function execution time is 0.00873208045959473 s and adjustment time is 0.00516915321350098 s ( 59.2 )
2025-02-03 18:48:47.97491 INFO::Formatting Data.
2025-02-03 18:48:47.975169 INFO::Recognized SummarizedExperiment
2025-02-03 18:48:47.97533 INFO::Typecasting input to dataframe.
2025-02-03 18:48:47.984918 INFO::Replacing NaNs with NAs.
2025-02-03 18:48:47.985275 INFO::Removing potential empty rows and columns
2025-02-03 18:48:47.986314 INFO::Found 0 missing values.
2025-02-03 18:48:47.988301 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 18:48:47.988478 INFO::Done
2025-02-03 18:48:47.988633 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 18:48:47.989861 INFO::Starting hierarchical adjustment
2025-02-03 18:48:47.990073 INFO::Found 2 batches.
2025-02-03 18:48:47.990221 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 18:48:47.990541 INFO::Using default BPPARAM
2025-02-03 18:48:47.990688 INFO::Adjusting the last 2 batches sequentially
2025-02-03 18:48:47.990971 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-03 18:48:48.007618 INFO::Done
2025-02-03 18:48:48.007849 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 18:48:48.009014 INFO::ASW Batch was -0.0322125273440479 prior to batch effect correction and is now -0.0926145875100091 .
2025-02-03 18:48:48.00926 INFO::Total function execution time is 0.0344488620758057 s and adjustment time is 0.017582893371582 s ( 51.04 )
2025-02-03 18:48:48.014975 INFO::Formatting Data.
2025-02-03 18:48:48.015193 INFO::Recognized SummarizedExperiment
2025-02-03 18:48:48.015355 INFO::Typecasting input to dataframe.
2025-02-03 18:48:48.018165 INFO::Replacing NaNs with NAs.
2025-02-03 18:48:48.018504 INFO::Removing potential empty rows and columns
2025-02-03 18:48:48.019594 INFO::Found 0 missing values.
2025-02-03 18:48:48.021628 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 18:48:48.02179 INFO::Done
2025-02-03 18:48:48.021941 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 18:48:48.023084 INFO::Starting hierarchical adjustment
2025-02-03 18:48:48.023297 INFO::Found 2 batches.
2025-02-03 18:48:48.023449 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 18:48:48.023627 INFO::Using default BPPARAM
2025-02-03 18:48:48.023767 INFO::Adjusting the last 2 batches sequentially
2025-02-03 18:48:48.024045 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-03 18:48:48.03174 INFO::Done
2025-02-03 18:48:48.031948 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 18:48:48.033068 INFO::ASW Batch was -0.0191943874499609 prior to batch effect correction and is now -0.0191943874499609 .
2025-02-03 18:48:48.033317 INFO::Total function execution time is 0.0183398723602295 s and adjustment time is 0.00847601890563965 s ( 46.22 )
2025-02-03 18:48:48.039296 INFO::Formatting Data.
2025-02-03 18:48:48.039508 INFO::Replacing NaNs with NAs.
2025-02-03 18:48:48.039762 INFO::Removing potential empty rows and columns
2025-02-03 18:48:48.040052 INFO::Found 0 missing values.
2025-02-03 18:48:48.040857 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 18:48:48.04101 INFO::Done
2025-02-03 18:48:48.041156 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 18:48:48.041717 INFO::Starting hierarchical adjustment
2025-02-03 18:48:48.041907 INFO::Found 3 batches.
2025-02-03 18:48:48.042048 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 18:48:48.042231 INFO::Using default BPPARAM
2025-02-03 18:48:48.042366 INFO::Processing subtree level 1
2025-02-03 18:48:48.097262 INFO::Adjusting the last 1 batches sequentially
2025-02-03 18:48:48.098516 INFO::Done
2025-02-03 18:48:48.098803 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 18:48:48.100173 INFO::ASW Batch was -0.0497277942526786 prior to batch effect correction and is now -0.138293854692901 .
2025-02-03 18:48:48.100761 INFO::Total function execution time is 0.0614418983459473 s and adjustment time is 0.0566449165344238 s ( 92.19 )
2025-02-03 18:48:48.106798 INFO::Skipping initial DF formatting
2025-02-03 18:48:48.107043 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 18:48:48.108327 INFO::Starting hierarchical adjustment
2025-02-03 18:48:48.108605 INFO::Found 5 batches.
2025-02-03 18:48:48.108776 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 18:48:48.109033 INFO::Using default BPPARAM
2025-02-03 18:48:48.109357 INFO::Processing subtree level 1
2025-02-03 18:48:48.160242 INFO::Adjusting the last 2 batches sequentially
2025-02-03 18:48:48.161472 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-03 18:48:48.170631 INFO::Done
2025-02-03 18:48:48.171135 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 18:48:48.173561 INFO::ASW Batch was 0.5171367729452 prior to batch effect correction and is now 0.5171367729452 .
2025-02-03 18:48:48.173879 INFO::ASW Label was 0.378192427766684 prior to batch effect correction and is now 0.378192427766684 .
2025-02-03 18:48:48.174561 INFO::Total function execution time is 0.0677499771118164 s and adjustment time is 0.062075138092041 s ( 91.62 )
2025-02-03 18:48:48.181607 INFO::Formatting Data.
2025-02-03 18:48:48.181852 INFO::Replacing NaNs with NAs.
2025-02-03 18:48:48.18216 INFO::Removing potential empty rows and columns
2025-02-03 18:48:48.182505 INFO::Found 0 missing values.
2025-02-03 18:48:48.183656 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 18:48:48.183832 INFO::Done
2025-02-03 18:48:48.183999 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 18:48:48.1849 INFO::Starting hierarchical adjustment
2025-02-03 18:48:48.185136 INFO::Found 5 batches.
2025-02-03 18:48:48.185309 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 18:48:48.185543 INFO::Using default BPPARAM
2025-02-03 18:48:48.185706 INFO::Processing subtree level 1
2025-02-03 18:48:48.231617 INFO::Adjusting the last 2 batches sequentially
2025-02-03 18:48:48.233581 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-03 18:48:48.241629 INFO::Done
2025-02-03 18:48:48.242052 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 18:48:48.243697 INFO::ASW Batch was 0.544567148898301 prior to batch effect correction and is now -0.0939417517305484 .
2025-02-03 18:48:48.243914 INFO::ASW Label was 0.252072374212514 prior to batch effect correction and is now 0.865217129727677 .
2025-02-03 18:48:48.244458 INFO::Total function execution time is 0.062830924987793 s and adjustment time is 0.0565371513366699 s ( 89.98 )
2025-02-03 18:48:48.244741 INFO::Formatting Data.
2025-02-03 18:48:48.245034 INFO::Replacing NaNs with NAs.
2025-02-03 18:48:48.245328 INFO::Removing potential empty rows and columns
2025-02-03 18:48:48.245688 INFO::Found 0 missing values.
2025-02-03 18:48:48.246937 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 18:48:48.247119 INFO::Done
2025-02-03 18:48:48.247276 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 18:48:48.248145 INFO::Starting hierarchical adjustment
2025-02-03 18:48:48.2485 INFO::Found 5 batches.
2025-02-03 18:48:48.248664 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 18:48:48.248876 INFO::Using default BPPARAM
2025-02-03 18:48:48.249155 INFO::Processing subtree level 1
2025-02-03 18:48:48.28991 INFO::Adjusting the last 2 batches sequentially
2025-02-03 18:48:48.291447 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-03 18:48:48.299746 INFO::Done
2025-02-03 18:48:48.300134 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 18:48:48.301546 INFO::ASW Batch was 0.544567148898301 prior to batch effect correction and is now -0.0939417517305484 .
2025-02-03 18:48:48.301732 INFO::ASW Label was 0.252072374212514 prior to batch effect correction and is now 0.865217129727677 .
2025-02-03 18:48:48.302235 INFO::Total function execution time is 0.0573549270629883 s and adjustment time is 0.0514199733734131 s ( 89.65 )
2025-02-03 18:48:48.307918 INFO::Formatting Data.
2025-02-03 18:48:48.308146 INFO::Replacing NaNs with NAs.
2025-02-03 18:48:48.30843 INFO::Removing potential empty rows and columns
2025-02-03 18:48:48.308744 INFO::Found 0 missing values.
2025-02-03 18:48:48.309861 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 18:48:48.310032 INFO::Done
2025-02-03 18:48:48.310183 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 18:48:48.311024 INFO::Starting hierarchical adjustment
2025-02-03 18:48:48.311239 INFO::Found 5 batches.
2025-02-03 18:48:48.311392 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 18:48:48.311615 INFO::Using default BPPARAM
2025-02-03 18:48:48.311773 INFO::Processing subtree level 1
2025-02-03 18:48:48.357032 INFO::Adjusting the last 2 batches sequentially
2025-02-03 18:48:48.361502 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-03 18:48:48.370835 INFO::Done
2025-02-03 18:48:48.371369 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 18:48:48.373278 INFO::ASW Batch was 0.367519314597897 prior to batch effect correction and is now -0.0591601774913907 .
2025-02-03 18:48:48.373534 INFO::ASW Label was 0.385529027023303 prior to batch effect correction and is now 0.859447210879109 .
2025-02-03 18:48:48.374115 INFO::Total function execution time is 0.0660600662231445 s and adjustment time is 0.0596141815185547 s ( 90.24 )
2025-02-03 18:48:48.374477 INFO::Formatting Data.
2025-02-03 18:48:48.374707 INFO::Replacing NaNs with NAs.
2025-02-03 18:48:48.375046 INFO::Removing potential empty rows and columns
2025-02-03 18:48:48.37547 INFO::Found 0 missing values.
2025-02-03 18:48:48.376716 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 18:48:48.3769 INFO::Done
2025-02-03 18:48:48.377067 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 18:48:48.377961 INFO::Starting hierarchical adjustment
2025-02-03 18:48:48.378376 INFO::Found 5 batches.
2025-02-03 18:48:48.378539 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 18:48:48.378789 INFO::Using default BPPARAM
2025-02-03 18:48:48.379068 INFO::Processing subtree level 1
2025-02-03 18:48:48.422202 INFO::Adjusting the last 2 batches sequentially
2025-02-03 18:48:48.423767 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-03 18:48:48.432979 INFO::Done
2025-02-03 18:48:48.433754 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 18:48:48.437927 INFO::ASW Batch was 0.367519314597897 prior to batch effect correction and is now -0.0591601774913907 .
2025-02-03 18:48:48.438168 INFO::ASW Label was 0.385529027023303 prior to batch effect correction and is now 0.859447210879109 .
2025-02-03 18:48:48.440897 INFO::Total function execution time is 0.0644609928131104 s and adjustment time is 0.0546681880950928 s ( 84.81 )
2025-02-03 18:48:48.449723 INFO::Formatting Data.
2025-02-03 18:48:48.449999 INFO::Replacing NaNs with NAs.
2025-02-03 18:48:48.450297 INFO::Removing potential empty rows and columns
2025-02-03 18:48:48.450641 INFO::Found 0 missing values.
2025-02-03 18:48:48.451447 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 18:48:48.451614 INFO::Done
2025-02-03 18:48:48.451772 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 18:48:48.452665 INFO::Starting hierarchical adjustment
2025-02-03 18:48:48.452987 INFO::Found 2 batches.
2025-02-03 18:48:48.45314 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 18:48:48.453354 INFO::Using default BPPARAM
2025-02-03 18:48:48.453515 INFO::Adjusting the last 2 batches sequentially
2025-02-03 18:48:48.453767 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-03 18:48:48.458231 INFO::Done
2025-02-03 18:48:48.458421 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 18:48:48.486973 INFO::ASW Batch was 0.618004705664874 prior to batch effect correction and is now 0.0964427592347013 .
2025-02-03 18:48:48.487263 INFO::ASW Label was 0.496324951628016 prior to batch effect correction and is now 0.814649154539661 .
2025-02-03 18:48:48.487539 INFO::Total function execution time is 0.0378470420837402 s and adjustment time is 0.00529098510742188 s ( 13.98 )
2025-02-03 18:48:48.487787 INFO::Formatting Data.
2025-02-03 18:48:48.487977 INFO::Replacing NaNs with NAs.
2025-02-03 18:48:48.488276 INFO::Removing potential empty rows and columns
2025-02-03 18:48:48.488593 INFO::Found 0 missing values.
2025-02-03 18:48:48.48949 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 18:48:48.48967 INFO::Done
2025-02-03 18:48:48.489835 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 18:48:48.490787 INFO::Starting hierarchical adjustment
2025-02-03 18:48:48.491023 INFO::Found 2 batches.
2025-02-03 18:48:48.491209 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 18:48:48.491441 INFO::Using default BPPARAM
2025-02-03 18:48:48.491614 INFO::Adjusting the last 2 batches sequentially
2025-02-03 18:48:48.492029 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-03 18:48:48.498161 INFO::Done
2025-02-03 18:48:48.498419 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 18:48:48.499312 INFO::ASW Batch was 0.618004705664874 prior to batch effect correction and is now 0.0964427592347013 .
2025-02-03 18:48:48.499483 INFO::ASW Label was 0.496324951628016 prior to batch effect correction and is now 0.814649154539661 .
2025-02-03 18:48:48.499744 INFO::Total function execution time is 0.0119359493255615 s and adjustment time is 0.00719690322875977 s ( 60.3 )
2025-02-03 18:48:48.503746 INFO::Formatting Data.
2025-02-03 18:48:48.503946 INFO::Replacing NaNs with NAs.
2025-02-03 18:48:48.504194 INFO::Removing potential empty rows and columns
2025-02-03 18:48:48.504443 INFO::Found 0 missing values.
2025-02-03 18:48:48.50503 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 18:48:48.505174 INFO::Done
2025-02-03 18:48:48.505321 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 18:48:48.505838 INFO::Starting hierarchical adjustment
2025-02-03 18:48:48.506015 INFO::Found 2 batches.
2025-02-03 18:48:48.506173 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 18:48:48.506336 INFO::Using default BPPARAM
2025-02-03 18:48:48.506482 INFO::Adjusting the last 2 batches sequentially
2025-02-03 18:48:48.506704 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-03 18:48:48.517667 INFO::Done
2025-02-03 18:48:48.517902 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 18:48:48.518545 INFO::ASW Batch was 0.0618409722246994 prior to batch effect correction and is now -0.145970839926355 .
2025-02-03 18:48:48.518821 INFO::Total function execution time is 0.0150749683380127 s and adjustment time is 0.0116701126098633 s ( 77.41 )
2025-02-03 18:48:48.523569 INFO::Formatting Data.
2025-02-03 18:48:48.523854 INFO::Replacing NaNs with NAs.
2025-02-03 18:48:48.524164 INFO::Removing potential empty rows and columns
2025-02-03 18:48:48.524506 INFO::Found 0 missing values.
2025-02-03 18:48:48.524941 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.
2025-02-03 18:48:48.526687 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 18:48:48.526928 INFO::Done
2025-02-03 18:48:48.527113 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 18:48:48.52803 INFO::Starting hierarchical adjustment
2025-02-03 18:48:48.528271 INFO::Found 2 batches.
2025-02-03 18:48:48.528441 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 18:48:48.528644 INFO::Using default BPPARAM
2025-02-03 18:48:48.528823 INFO::Adjusting the last 2 batches sequentially
2025-02-03 18:48:48.529119 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-03 18:48:48.534292 INFO::Done
2025-02-03 18:48:48.534508 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 18:48:48.53545 INFO::ASW Batch was 0.505099761227874 prior to batch effect correction and is now 0.0854451450938744 .
2025-02-03 18:48:48.535633 INFO::ASW Label was 0.580055499657758 prior to batch effect correction and is now 0.865950098203617 .
2025-02-03 18:48:48.535882 INFO::Total function execution time is 0.012354850769043 s and adjustment time is 0.00606107711791992 s ( 49.06 )
2025-02-03 18:48:48.536117 INFO::Formatting Data.
2025-02-03 18:48:48.536279 INFO::Replacing NaNs with NAs.
2025-02-03 18:48:48.536532 INFO::Removing potential empty rows and columns
2025-02-03 18:48:48.536809 INFO::Found 0 missing values.
2025-02-03 18:48:48.537056 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.
2025-02-03 18:48:48.538287 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 18:48:48.538449 INFO::Done
2025-02-03 18:48:48.538597 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 18:48:48.539391 INFO::Starting hierarchical adjustment
2025-02-03 18:48:48.539592 INFO::Found 2 batches.
2025-02-03 18:48:48.539741 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 18:48:48.539926 INFO::Using default BPPARAM
2025-02-03 18:48:48.540079 INFO::Adjusting the last 2 batches sequentially
2025-02-03 18:48:48.540333 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-03 18:48:48.545732 INFO::Done
2025-02-03 18:48:48.545976 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 18:48:48.546942 INFO::ASW Batch was 0.505099761227874 prior to batch effect correction and is now 0.0854451450938744 .
2025-02-03 18:48:48.547167 INFO::ASW Label was 0.580055499657758 prior to batch effect correction and is now 0.865950098203617 .
2025-02-03 18:48:48.547411 INFO::Total function execution time is 0.0112829208374023 s and adjustment time is 0.00616693496704102 s ( 54.66 )
2025-02-03 18:48:48.615857 INFO::Formatting Data.
2025-02-03 18:48:48.616155 INFO::Replacing NaNs with NAs.
2025-02-03 18:48:48.616455 INFO::Removing potential empty rows and columns
2025-02-03 18:48:48.616807 INFO::Found 0 missing values.
2025-02-03 18:48:48.617728 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 18:48:48.617902 INFO::Done
2025-02-03 18:48:48.618063 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 18:48:48.618726 INFO::Starting hierarchical adjustment
2025-02-03 18:48:48.618929 INFO::Found 3 batches.
2025-02-03 18:48:48.619083 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 18:48:48.619269 INFO::Using default BPPARAM
2025-02-03 18:48:48.619424 INFO::Processing subtree level 1
2025-02-03 18:48:48.663263 INFO::Adjusting the last 1 batches sequentially
2025-02-03 18:48:48.664605 INFO::Done
2025-02-03 18:48:48.664968 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 18:48:48.666767 INFO::ASW Batch was -0.0237970394042793 prior to batch effect correction and is now -0.0237970394042793 .
2025-02-03 18:48:48.667404 INFO::Total function execution time is 0.0515718460083008 s and adjustment time is 0.0457069873809814 s ( 88.63 )
2025-02-03 18:48:48.667792 INFO::Formatting Data.
2025-02-03 18:48:48.668098 INFO::Typecasting input to dataframe.
2025-02-03 18:48:48.668343 INFO::Replacing NaNs with NAs.
2025-02-03 18:48:48.668805 INFO::Removing potential empty rows and columns
2025-02-03 18:48:48.669416 INFO::Found 0 missing values.
2025-02-03 18:48:48.67051 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 18:48:48.670733 INFO::Done
2025-02-03 18:48:48.670912 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 18:48:48.671671 INFO::Starting hierarchical adjustment
2025-02-03 18:48:48.671905 INFO::Found 3 batches.
2025-02-03 18:48:48.67207 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 18:48:48.672299 INFO::Using default BPPARAM
2025-02-03 18:48:48.672466 INFO::Processing subtree level 1
2025-02-03 18:48:48.714796 INFO::Adjusting the last 1 batches sequentially
2025-02-03 18:48:48.716471 INFO::Done
2025-02-03 18:48:48.716716 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 18:48:48.718746 INFO::ASW Batch was -0.0237970394042793 prior to batch effect correction and is now -0.0237970394042793 .
2025-02-03 18:48:48.719515 INFO::Total function execution time is 0.0516998767852783 s and adjustment time is 0.0446131229400635 s ( 86.29 )
2025-02-03 18:48:48.726064 INFO::Formatting Data.
2025-02-03 18:48:48.72635 INFO::Typecasting input to dataframe.
2025-02-03 18:48:48.726659 INFO::Replacing NaNs with NAs.
2025-02-03 18:48:48.726999 INFO::Removing potential empty rows and columns
2025-02-03 18:48:48.727453 INFO::Found 0 missing values.
2025-02-03 18:48:48.728523 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 18:48:48.728734 INFO::Done
2025-02-03 18:48:48.728915 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 18:48:48.729651 INFO::Starting hierarchical adjustment
2025-02-03 18:48:48.729876 INFO::Found 3 batches.
2025-02-03 18:48:48.730051 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 18:48:48.730315 INFO::Using default BPPARAM
2025-02-03 18:48:48.730492 INFO::Processing subtree level 1
2025-02-03 18:48:48.776736 INFO::Adjusting the last 1 batches sequentially
2025-02-03 18:48:48.778159 INFO::Done
2025-02-03 18:48:48.778518 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 18:48:48.780466 INFO::ASW Batch was -0.0723385352649205 prior to batch effect correction and is now -0.0723385352649205 .
2025-02-03 18:48:48.781135 INFO::Total function execution time is 0.0550739765167236 s and adjustment time is 0.0483310222625732 s ( 87.76 )
2025-02-03 18:48:48.852722 INFO::Formatting Data.
2025-02-03 18:48:48.853016 INFO::Replacing NaNs with NAs.
2025-02-03 18:48:48.853488 INFO::Removing potential empty rows and columns
2025-02-03 18:48:48.854617 INFO::Found 1000 missing values.
2025-02-03 18:48:48.862313 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 18:48:48.862571 INFO::Done
2025-02-03 18:48:48.862769 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 18:48:48.864885 INFO::Starting hierarchical adjustment
2025-02-03 18:48:48.865357 INFO::Found 10 batches.
2025-02-03 18:48:48.865778 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 18:48:48.866137 INFO::Using default BPPARAM
2025-02-03 18:48:48.866374 INFO::Processing subtree level 1
2025-02-03 18:48:48.938198 INFO::Processing subtree level 2
2025-02-03 18:48:49.01078 INFO::Adjusting the last 1 batches sequentially
2025-02-03 18:48:49.012521 INFO::Done
2025-02-03 18:48:49.012905 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 18:48:49.016044 INFO::ASW Batch was 0.531679134198791 prior to batch effect correction and is now 0.531679134198791 .
2025-02-03 18:48:49.016308 INFO::ASW Label was 0.32450369318878 prior to batch effect correction and is now 0.32450369318878 .
2025-02-03 18:48:49.016902 INFO::Total function execution time is 0.164167881011963 s and adjustment time is 0.147403955459595 s ( 89.79 )
2025-02-03 18:48:49.017405 INFO::Formatting Data.
2025-02-03 18:48:49.017781 INFO::Replacing NaNs with NAs.
2025-02-03 18:48:49.018481 INFO::Removing potential empty rows and columns
2025-02-03 18:48:49.019582 INFO::Found 1000 missing values.
2025-02-03 18:48:49.026691 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 18:48:49.027008 INFO::Done
2025-02-03 18:48:49.027245 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 18:48:49.029432 INFO::Starting hierarchical adjustment
2025-02-03 18:48:49.029744 INFO::Found 10 batches.
2025-02-03 18:48:49.475635 INFO::Set up parallel execution backend with 2 workers
2025-02-03 18:48:49.475949 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-02-03 18:48:49.995223 INFO::Adjusting the last 2 batches sequentially
2025-02-03 18:48:49.995828 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-03 18:48:50.00129 INFO::Done
2025-02-03 18:48:50.001498 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 18:48:50.003351 INFO::ASW Batch was 0.531679134198791 prior to batch effect correction and is now 0.531679134198791 .
2025-02-03 18:48:50.003521 INFO::ASW Label was 0.32450369318878 prior to batch effect correction and is now 0.32450369318878 .
2025-02-03 18:48:50.003777 INFO::Total function execution time is 0.98638391494751 s and adjustment time is 0.971610069274902 s ( 98.5 )
2025-02-03 18:48:50.070395 INFO::Formatting Data.
2025-02-03 18:48:50.070712 INFO::Replacing NaNs with NAs.
2025-02-03 18:48:50.071055 INFO::Removing potential empty rows and columns
2025-02-03 18:48:50.071495 INFO::Found 0 missing values.
2025-02-03 18:48:50.072773 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 18:48:50.072968 INFO::Done
2025-02-03 18:48:50.073139 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 18:48:50.074169 INFO::Starting hierarchical adjustment
2025-02-03 18:48:50.074425 INFO::Found 3 batches.
2025-02-03 18:48:50.074586 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 18:48:50.074845 INFO::Using default BPPARAM
2025-02-03 18:48:50.075008 INFO::Processing subtree level 1
2025-02-03 18:48:50.12214 INFO::Adjusting the last 1 batches sequentially
2025-02-03 18:48:50.123334 INFO::Done
2025-02-03 18:48:50.123549 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 18:48:50.125422 INFO::ASW Batch was 0.210264033057864 prior to batch effect correction and is now -0.120784858320643 .
2025-02-03 18:48:50.125636 INFO::ASW Label was -0.190938659643244 prior to batch effect correction and is now 0.0424040363326023 .
2025-02-03 18:48:50.126191 INFO::Total function execution time is 0.055837869644165 s and adjustment time is 0.0489659309387207 s ( 87.69 )
2025-02-03 18:48:50.168658 INFO::Formatting Data.
2025-02-03 18:48:50.168967 INFO::Replacing NaNs with NAs.
2025-02-03 18:48:50.169273 INFO::Removing potential empty rows and columns
2025-02-03 18:48:50.169672 INFO::Found 2 missing values.
2025-02-03 18:48:50.170583 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-02-03 18:48:50.17076 INFO::Done
2025-02-03 18:48:50.18017 INFO::Found NA in Reference column
2025-02-03 18:48:50.183243 INFO::Require at least two references per batch.
2025-02-03 18:48:50.190692 INFO::Formatting Data.
2025-02-03 18:48:50.190909 INFO::Recognized SummarizedExperiment
2025-02-03 18:48:50.191073 INFO::Typecasting input to dataframe.
2025-02-03 18:48:50.195012 INFO::Replacing NaNs with NAs.
2025-02-03 18:48:50.195384 INFO::Removing potential empty rows and columns
2025-02-03 18:48:50.196636 INFO::Found 0 missing values.
2025-02-03 18:48:50.19887 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 18:48:50.199059 INFO::Done
2025-02-03 18:48:50.203928 INFO::Formatting Data.
2025-02-03 18:48:50.204137 INFO::Recognized SummarizedExperiment
2025-02-03 18:48:50.20431 INFO::Typecasting input to dataframe.
2025-02-03 18:48:50.209673 INFO::Replacing NaNs with NAs.
2025-02-03 18:48:50.210057 INFO::Removing potential empty rows and columns
2025-02-03 18:48:50.21128 INFO::Found 0 missing values.
2025-02-03 18:48:50.21504 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 18:48:50.215233 INFO::Done
2025-02-03 18:48:50.22043 INFO::Formatting Data.
2025-02-03 18:48:50.220662 INFO::Recognized SummarizedExperiment
2025-02-03 18:48:50.220852 INFO::Typecasting input to dataframe.
2025-02-03 18:48:50.225771 INFO::Replacing NaNs with NAs.
2025-02-03 18:48:50.226065 INFO::Removing potential empty rows and columns
2025-02-03 18:48:50.226395 INFO::Found 0 missing values.
2025-02-03 18:48:50.226672 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.
2025-02-03 18:48:50.227976 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 18:48:50.228149 INFO::Done
2025-02-03 18:48:50.231625 INFO::Formatting Data.
2025-02-03 18:48:50.231838 INFO::Replacing NaNs with NAs.
2025-02-03 18:48:50.232092 INFO::Removing potential empty rows and columns
2025-02-03 18:48:50.232385 INFO::Found 0 missing values.
2025-02-03 18:48:50.233198 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 18:48:50.233363 INFO::Done
2025-02-03 18:48:50.23734 INFO::Formatting Data.
2025-02-03 18:48:50.237553 INFO::Replacing NaNs with NAs.
2025-02-03 18:48:50.237797 INFO::Removing potential empty rows and columns
2025-02-03 18:48:50.238105 INFO::Found 0 missing values.
2025-02-03 18:48:50.238959 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 18:48:50.239119 INFO::Done
2025-02-03 18:48:50.249634 INFO::Formatting Data.
2025-02-03 18:48:50.2499 INFO::Replacing NaNs with NAs.
2025-02-03 18:48:50.25024 INFO::Removing potential empty rows and columns
2025-02-03 18:48:50.250635 INFO::Found 1 missing values.
2025-02-03 18:48:50.251512 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 18:48:50.251681 INFO::Done
2025-02-03 18:48:50.25864 INFO::Formatting Data.
2025-02-03 18:48:50.258889 INFO::Replacing NaNs with NAs.
2025-02-03 18:48:50.259166 INFO::Removing potential empty rows and columns
2025-02-03 18:48:50.259574 INFO::Found 2 missing values.
2025-02-03 18:48:50.259879 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.
2025-02-03 18:48:50.260764 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-02-03 18:48:50.260935 INFO::Done
2025-02-03 18:48:50.265151 INFO::Formatting Data.
2025-02-03 18:48:50.265402 INFO::Replacing NaNs with NAs.
2025-02-03 18:48:50.265671 INFO::Removing potential empty rows and columns
2025-02-03 18:48:50.265991 INFO::Found 2 missing values.
2025-02-03 18:48:50.266463 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 18:48:50.26662 INFO::Done
2025-02-03 18:48:50.270329 INFO::Formatting Data.
2025-02-03 18:48:50.270551 INFO::Typecasting input to dataframe.
2025-02-03 18:48:50.270848 INFO::Replacing NaNs with NAs.
2025-02-03 18:48:50.271093 INFO::Removing potential empty rows and columns
2025-02-03 18:48:50.271385 INFO::Found 0 missing values.
2025-02-03 18:48:50.27231 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 18:48:50.272476 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
6.396 1.422 7.944
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 9.389 | 0.424 | 6.723 | |
| compute_asw | 0.010 | 0.001 | 0.010 | |
| count_existing | 0.006 | 0.000 | 0.006 | |
| generate_data_covariables | 0.004 | 0.000 | 0.005 | |
| generate_dataset | 0.005 | 0.000 | 0.004 | |