Yannis Schumann
| Snapshot Date: 2025-03-03 13:00 -0500 (Mon, 03 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_20 |
| git_last_commit: 9764e3f |
| git_last_commit_date: 2024-10-29 11:26:04 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-03-06 12:06 -0500 (Thu, 06 Mar 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" | 4769 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4504 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4527 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4480 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4416 |
| 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: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BERT_1.2.0.tar.gz |
| StartedAt: 2025-03-03 23:26:49 -0500 (Mon, 03 Mar 2025) |
| EndedAt: 2025-03-03 23:29:09 -0500 (Mon, 03 Mar 2025) |
| EllapsedTime: 139.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BERT_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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 8.86 0.61 18.63
* 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: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2025-03-03 23:27:55.858907 INFO::Formatting Data.
2025-03-03 23:27:55.86179 INFO::Replacing NaNs with NAs.
2025-03-03 23:27:55.875516 INFO::Removing potential empty rows and columns
2025-03-03 23:27:56.097123 INFO::Found 0 missing values.
2025-03-03 23:27:56.102391 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-03 23:27:56.103866 INFO::Done
2025-03-03 23:27:56.105268 INFO::Acquiring quality metrics before batch effect correction.
2025-03-03 23:27:56.125455 INFO::Starting hierarchical adjustment
2025-03-03 23:27:56.126725 INFO::Found 3 batches.
2025-03-03 23:27:56.127488 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-03 23:27:56.129103 INFO::Using default BPPARAM
2025-03-03 23:27:56.129867 INFO::Processing subtree level 1
2025-03-03 23:27:59.103979 INFO::Adjusting the last 1 batches sequentially
2025-03-03 23:27:59.106215 INFO::Done
2025-03-03 23:27:59.107529 INFO::Acquiring quality metrics after batch effect correction.
2025-03-03 23:27:59.110933 INFO::ASW Batch was -0.0494487834153844 prior to batch effect correction and is now -0.0494487834153844 .
2025-03-03 23:27:59.112678 INFO::Total function execution time is 3.25440621376038 s and adjustment time is 2.97965788841248 s ( 91.56 )
2025-03-03 23:27:59.135536 INFO::Formatting Data.
2025-03-03 23:27:59.13708 INFO::Replacing NaNs with NAs.
2025-03-03 23:27:59.138832 INFO::Removing potential empty rows and columns
2025-03-03 23:27:59.140778 INFO::Found 0 missing values.
2025-03-03 23:27:59.142537 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-03-03 23:27:59.156855 INFO::Formatting Data.
2025-03-03 23:27:59.158397 INFO::Replacing NaNs with NAs.
2025-03-03 23:27:59.16018 INFO::Removing potential empty rows and columns
2025-03-03 23:27:59.16211 INFO::Found 0 missing values.
2025-03-03 23:27:59.163877 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-03-03 23:27:59.190038 INFO::Formatting Data.
2025-03-03 23:27:59.191535 INFO::Replacing NaNs with NAs.
2025-03-03 23:27:59.193244 INFO::Removing potential empty rows and columns
2025-03-03 23:27:59.195135 INFO::Found 0 missing values.
2025-03-03 23:27:59.196893 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-03-03 23:27:59.203474 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-03 23:27:59.20475 INFO::Done
2025-03-03 23:27:59.205937 INFO::Acquiring quality metrics before batch effect correction.
2025-03-03 23:27:59.209268 INFO::Starting hierarchical adjustment
2025-03-03 23:27:59.210662 INFO::Found 2 batches.
2025-03-03 23:27:59.21196 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-03 23:27:59.213245 INFO::Using default BPPARAM
2025-03-03 23:27:59.214367 INFO::Adjusting the last 2 batches sequentially
2025-03-03 23:27:59.216175 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-03 23:27:59.240635 INFO::Done
2025-03-03 23:27:59.241974 INFO::Acquiring quality metrics after batch effect correction.
2025-03-03 23:27:59.245272 INFO::ASW Batch was -0.0536872257878359 prior to batch effect correction and is now -0.119540130747131 .
2025-03-03 23:27:59.246781 INFO::Total function execution time is 0.0568439960479736 s and adjustment time is 0.0301411151885986 s ( 53.02 )
2025-03-03 23:27:59.251056 INFO::Formatting Data.
2025-03-03 23:27:59.2523 INFO::Replacing NaNs with NAs.
2025-03-03 23:27:59.263094 INFO::Formatting Data.
2025-03-03 23:27:59.264426 INFO::Replacing NaNs with NAs.
2025-03-03 23:27:59.266036 INFO::Removing potential empty rows and columns
2025-03-03 23:27:59.267793 INFO::Found 0 missing values.
2025-03-03 23:27:59.271957 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-03 23:27:59.273114 INFO::Done
2025-03-03 23:27:59.274237 INFO::Acquiring quality metrics before batch effect correction.
2025-03-03 23:27:59.277261 INFO::Starting hierarchical adjustment
2025-03-03 23:27:59.278495 INFO::Found 2 batches.
2025-03-03 23:27:59.279499 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-03 23:27:59.280599 INFO::Using default BPPARAM
2025-03-03 23:27:59.281678 INFO::Adjusting the last 2 batches sequentially
2025-03-03 23:27:59.283351 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-03 23:27:59.303679 INFO::Done
2025-03-03 23:27:59.305023 INFO::Acquiring quality metrics after batch effect correction.
2025-03-03 23:27:59.308303 INFO::ASW Batch was -0.0564618767326696 prior to batch effect correction and is now -0.115136370057033 .
2025-03-03 23:27:59.309779 INFO::Total function execution time is 0.0467031002044678 s and adjustment time is 0.0253040790557861 s ( 54.18 )
2025-03-03 23:27:59.311694 INFO::Formatting Data.
2025-03-03 23:27:59.312908 INFO::Replacing NaNs with NAs.
2025-03-03 23:27:59.314474 INFO::Removing potential empty rows and columns
2025-03-03 23:27:59.316194 INFO::Found 0 missing values.
2025-03-03 23:27:59.320316 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-03 23:27:59.321427 INFO::Done
2025-03-03 23:27:59.322534 INFO::Acquiring quality metrics before batch effect correction.
2025-03-03 23:27:59.325745 INFO::Starting hierarchical adjustment
2025-03-03 23:27:59.327092 INFO::Found 2 batches.
2025-03-03 23:27:59.328186 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-03 23:27:59.329371 INFO::Using default BPPARAM
2025-03-03 23:27:59.330478 INFO::Adjusting the last 2 batches sequentially
2025-03-03 23:27:59.332188 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-03 23:27:59.352804 INFO::Done
2025-03-03 23:27:59.354164 INFO::Acquiring quality metrics after batch effect correction.
2025-03-03 23:27:59.357499 INFO::ASW Batch was -0.0564618767326696 prior to batch effect correction and is now -0.115136370057033 .
2025-03-03 23:27:59.359024 INFO::Total function execution time is 0.0472991466522217 s and adjustment time is 0.0258710384368896 s ( 54.7 )
2025-03-03 23:28:01.652357 INFO::Formatting Data.
2025-03-03 23:28:01.653758 INFO::Recognized SummarizedExperiment
2025-03-03 23:28:01.654964 INFO::Typecasting input to dataframe.
2025-03-03 23:28:01.701299 INFO::Replacing NaNs with NAs.
2025-03-03 23:28:01.703599 INFO::Removing potential empty rows and columns
2025-03-03 23:28:01.709145 INFO::Found 0 missing values.
2025-03-03 23:28:01.718868 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-03 23:28:01.720387 INFO::Done
2025-03-03 23:28:01.721653 INFO::Acquiring quality metrics before batch effect correction.
2025-03-03 23:28:01.72788 INFO::Starting hierarchical adjustment
2025-03-03 23:28:01.729284 INFO::Found 2 batches.
2025-03-03 23:28:01.730376 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-03 23:28:01.732174 INFO::Using default BPPARAM
2025-03-03 23:28:01.733226 INFO::Adjusting the last 2 batches sequentially
2025-03-03 23:28:01.734976 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-03 23:28:01.78737 INFO::Done
2025-03-03 23:28:01.788282 INFO::Acquiring quality metrics after batch effect correction.
2025-03-03 23:28:01.792261 INFO::ASW Batch was 0.0154320595667304 prior to batch effect correction and is now -0.09894130244168 .
2025-03-03 23:28:01.793332 INFO::Total function execution time is 0.141442060470581 s and adjustment time is 0.0583019256591797 s ( 41.22 )
2025-03-03 23:28:02.586165 INFO::Formatting Data.
2025-03-03 23:28:02.587154 INFO::Recognized SummarizedExperiment
2025-03-03 23:28:02.588001 INFO::Typecasting input to dataframe.
2025-03-03 23:28:02.59645 INFO::Replacing NaNs with NAs.
2025-03-03 23:28:02.597853 INFO::Removing potential empty rows and columns
2025-03-03 23:28:02.6008 INFO::Found 0 missing values.
2025-03-03 23:28:02.606302 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-03 23:28:02.607173 INFO::Done
2025-03-03 23:28:02.60795 INFO::Acquiring quality metrics before batch effect correction.
2025-03-03 23:28:02.61174 INFO::Starting hierarchical adjustment
2025-03-03 23:28:02.612654 INFO::Found 2 batches.
2025-03-03 23:28:02.613422 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-03 23:28:02.614202 INFO::Using default BPPARAM
2025-03-03 23:28:02.614892 INFO::Adjusting the last 2 batches sequentially
2025-03-03 23:28:02.616061 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-03 23:28:02.634455 INFO::Done
2025-03-03 23:28:02.635427 INFO::Acquiring quality metrics after batch effect correction.
2025-03-03 23:28:02.639357 INFO::ASW Batch was 0.0176957473987133 prior to batch effect correction and is now 0.0176957473987133 .
2025-03-03 23:28:02.64048 INFO::Total function execution time is 0.0543060302734375 s and adjustment time is 0.0218808650970459 s ( 40.29 )
2025-03-03 23:28:02.66104 INFO::Formatting Data.
2025-03-03 23:28:02.662032 INFO::Replacing NaNs with NAs.
2025-03-03 23:28:02.663095 INFO::Removing potential empty rows and columns
2025-03-03 23:28:02.664204 INFO::Found 0 missing values.
2025-03-03 23:28:02.667781 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-03 23:28:02.668623 INFO::Done
2025-03-03 23:28:02.669628 INFO::Acquiring quality metrics before batch effect correction.
2025-03-03 23:28:02.671785 INFO::Starting hierarchical adjustment
2025-03-03 23:28:02.672722 INFO::Found 3 batches.
2025-03-03 23:28:02.673461 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-03 23:28:02.674281 INFO::Using default BPPARAM
2025-03-03 23:28:02.674989 INFO::Processing subtree level 1
2025-03-03 23:28:13.257344 INFO::Adjusting the last 1 batches sequentially
2025-03-03 23:28:13.259593 INFO::Done
2025-03-03 23:28:13.26085 INFO::Acquiring quality metrics after batch effect correction.
2025-03-03 23:28:13.263986 INFO::ASW Batch was -0.091595595194611 prior to batch effect correction and is now -0.156344364041437 .
2025-03-03 23:28:13.265393 INFO::Total function execution time is 10.6043779850006 s and adjustment time is 10.5869898796082 s ( 99.84 )
2025-03-03 23:28:13.286891 INFO::Skipping initial DF formatting
2025-03-03 23:28:13.288199 INFO::Acquiring quality metrics before batch effect correction.
2025-03-03 23:28:13.294239 INFO::Starting hierarchical adjustment
2025-03-03 23:28:13.295641 INFO::Found 5 batches.
2025-03-03 23:28:13.296693 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-03 23:28:13.297848 INFO::Using default BPPARAM
2025-03-03 23:28:13.298877 INFO::Processing subtree level 1
2025-03-03 23:28:16.293856 INFO::Adjusting the last 2 batches sequentially
2025-03-03 23:28:16.296034 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-03 23:28:16.321352 INFO::Done
2025-03-03 23:28:16.322809 INFO::Acquiring quality metrics after batch effect correction.
2025-03-03 23:28:16.329817 INFO::ASW Batch was 0.50192342806485 prior to batch effect correction and is now 0.50192342806485 .
2025-03-03 23:28:16.331215 INFO::ASW Label was 0.399314961483205 prior to batch effect correction and is now 0.399314961483205 .
2025-03-03 23:28:16.332875 INFO::Total function execution time is 3.04604911804199 s and adjustment time is 3.02586197853088 s ( 99.34 )
2025-03-03 23:28:16.36188 INFO::Formatting Data.
2025-03-03 23:28:16.363493 INFO::Replacing NaNs with NAs.
2025-03-03 23:28:16.365316 INFO::Removing potential empty rows and columns
2025-03-03 23:28:16.367211 INFO::Found 0 missing values.
2025-03-03 23:28:16.37364 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-03 23:28:16.375076 INFO::Done
2025-03-03 23:28:16.376386 INFO::Acquiring quality metrics before batch effect correction.
2025-03-03 23:28:16.380952 INFO::Starting hierarchical adjustment
2025-03-03 23:28:16.382539 INFO::Found 5 batches.
2025-03-03 23:28:16.383755 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-03 23:28:16.385139 INFO::Using default BPPARAM
2025-03-03 23:28:16.3864 INFO::Processing subtree level 1
2025-03-03 23:28:19.731251 INFO::Adjusting the last 2 batches sequentially
2025-03-03 23:28:19.733486 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-03 23:28:19.75205 INFO::Done
2025-03-03 23:28:19.753301 INFO::Acquiring quality metrics after batch effect correction.
2025-03-03 23:28:19.757617 INFO::ASW Batch was 0.631729527764171 prior to batch effect correction and is now -0.0323842073465929 .
2025-03-03 23:28:19.75881 INFO::ASW Label was 0.149994842133538 prior to batch effect correction and is now 0.745442310955983 .
2025-03-03 23:28:19.760247 INFO::Total function execution time is 3.39850497245789 s and adjustment time is 3.36972594261169 s ( 99.15 )
2025-03-03 23:28:19.761679 INFO::Formatting Data.
2025-03-03 23:28:19.762961 INFO::Replacing NaNs with NAs.
2025-03-03 23:28:19.764484 INFO::Removing potential empty rows and columns
2025-03-03 23:28:19.765618 INFO::Found 0 missing values.
2025-03-03 23:28:19.771431 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-03 23:28:19.772741 INFO::Done
2025-03-03 23:28:19.773857 INFO::Acquiring quality metrics before batch effect correction.
2025-03-03 23:28:19.778242 INFO::Starting hierarchical adjustment
2025-03-03 23:28:19.77956 INFO::Found 5 batches.
2025-03-03 23:28:19.780628 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-03 23:28:19.781779 INFO::Using default BPPARAM
2025-03-03 23:28:19.782843 INFO::Processing subtree level 1
2025-03-03 23:28:23.271568 INFO::Adjusting the last 2 batches sequentially
2025-03-03 23:28:23.273128 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-03 23:28:23.290808 INFO::Done
2025-03-03 23:28:23.292066 INFO::Acquiring quality metrics after batch effect correction.
2025-03-03 23:28:23.296517 INFO::ASW Batch was 0.631729527764171 prior to batch effect correction and is now -0.0323842073465929 .
2025-03-03 23:28:23.297766 INFO::ASW Label was 0.149994842133538 prior to batch effect correction and is now 0.745442310955983 .
2025-03-03 23:28:23.299215 INFO::Total function execution time is 3.53753590583801 s and adjustment time is 3.51140904426575 s ( 99.26 )
2025-03-03 23:28:23.320579 INFO::Formatting Data.
2025-03-03 23:28:23.322292 INFO::Replacing NaNs with NAs.
2025-03-03 23:28:23.323959 INFO::Removing potential empty rows and columns
2025-03-03 23:28:23.325651 INFO::Found 0 missing values.
2025-03-03 23:28:23.331413 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-03 23:28:23.332693 INFO::Done
2025-03-03 23:28:23.333973 INFO::Acquiring quality metrics before batch effect correction.
2025-03-03 23:28:23.338573 INFO::Starting hierarchical adjustment
2025-03-03 23:28:23.339536 INFO::Found 5 batches.
2025-03-03 23:28:23.340259 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-03 23:28:23.341027 INFO::Using default BPPARAM
2025-03-03 23:28:23.341724 INFO::Processing subtree level 1
2025-03-03 23:28:26.831136 INFO::Adjusting the last 2 batches sequentially
2025-03-03 23:28:26.833132 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-03 23:28:26.852701 INFO::Done
2025-03-03 23:28:26.853591 INFO::Acquiring quality metrics after batch effect correction.
2025-03-03 23:28:26.856605 INFO::ASW Batch was 0.259089394527433 prior to batch effect correction and is now -0.0969080293190083 .
2025-03-03 23:28:26.857389 INFO::ASW Label was 0.542588429249345 prior to batch effect correction and is now 0.934116868913864 .
2025-03-03 23:28:26.858427 INFO::Total function execution time is 3.53797292709351 s and adjustment time is 3.5132851600647 s ( 99.3 )
2025-03-03 23:28:26.859436 INFO::Formatting Data.
2025-03-03 23:28:26.860212 INFO::Replacing NaNs with NAs.
2025-03-03 23:28:26.861623 INFO::Removing potential empty rows and columns
2025-03-03 23:28:26.863303 INFO::Found 0 missing values.
2025-03-03 23:28:26.868476 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-03 23:28:26.86957 INFO::Done
2025-03-03 23:28:26.870572 INFO::Acquiring quality metrics before batch effect correction.
2025-03-03 23:28:26.874635 INFO::Starting hierarchical adjustment
2025-03-03 23:28:26.875907 INFO::Found 5 batches.
2025-03-03 23:28:26.87692 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-03 23:28:26.878045 INFO::Using default BPPARAM
2025-03-03 23:28:26.879036 INFO::Processing subtree level 1
2025-03-03 23:28:30.162453 INFO::Adjusting the last 2 batches sequentially
2025-03-03 23:28:30.16451 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-03 23:28:30.182091 INFO::Done
2025-03-03 23:28:30.183033 INFO::Acquiring quality metrics after batch effect correction.
2025-03-03 23:28:30.186749 INFO::ASW Batch was 0.259089394527433 prior to batch effect correction and is now -0.0969080293190083 .
2025-03-03 23:28:30.187993 INFO::ASW Label was 0.542588429249345 prior to batch effect correction and is now 0.934116868913864 .
2025-03-03 23:28:30.189566 INFO::Total function execution time is 3.33004212379456 s and adjustment time is 3.3063690662384 s ( 99.29 )
2025-03-03 23:28:30.211509 INFO::Formatting Data.
2025-03-03 23:28:30.213079 INFO::Replacing NaNs with NAs.
2025-03-03 23:28:30.214859 INFO::Removing potential empty rows and columns
2025-03-03 23:28:30.216701 INFO::Found 0 missing values.
2025-03-03 23:28:30.220964 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-03 23:28:30.222225 INFO::Done
2025-03-03 23:28:30.223466 INFO::Acquiring quality metrics before batch effect correction.
2025-03-03 23:28:30.228031 INFO::Starting hierarchical adjustment
2025-03-03 23:28:30.22948 INFO::Found 2 batches.
2025-03-03 23:28:30.230689 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-03 23:28:30.231979 INFO::Using default BPPARAM
2025-03-03 23:28:30.233144 INFO::Adjusting the last 2 batches sequentially
2025-03-03 23:28:30.234946 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-03 23:28:30.255109 INFO::Done
2025-03-03 23:28:30.256552 INFO::Acquiring quality metrics after batch effect correction.
2025-03-03 23:28:30.261455 INFO::ASW Batch was 0.578105497544145 prior to batch effect correction and is now -0.0245637964820222 .
2025-03-03 23:28:30.262804 INFO::ASW Label was 0.513560715981645 prior to batch effect correction and is now 0.933787631704217 .
2025-03-03 23:28:30.264371 INFO::Total function execution time is 0.0529739856719971 s and adjustment time is 0.0257949829101562 s ( 48.69 )
2025-03-03 23:28:30.265921 INFO::Formatting Data.
2025-03-03 23:28:30.267264 INFO::Replacing NaNs with NAs.
2025-03-03 23:28:30.268986 INFO::Removing potential empty rows and columns
2025-03-03 23:28:30.270787 INFO::Found 0 missing values.
2025-03-03 23:28:30.275054 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-03 23:28:30.276292 INFO::Done
2025-03-03 23:28:30.277465 INFO::Acquiring quality metrics before batch effect correction.
2025-03-03 23:28:30.282246 INFO::Starting hierarchical adjustment
2025-03-03 23:28:30.283685 INFO::Found 2 batches.
2025-03-03 23:28:30.284811 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-03 23:28:30.286056 INFO::Using default BPPARAM
2025-03-03 23:28:30.287228 INFO::Adjusting the last 2 batches sequentially
2025-03-03 23:28:30.289077 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-03 23:28:30.308569 INFO::Done
2025-03-03 23:28:30.310073 INFO::Acquiring quality metrics after batch effect correction.
2025-03-03 23:28:30.315068 INFO::ASW Batch was 0.578105497544145 prior to batch effect correction and is now -0.0245637964820222 .
2025-03-03 23:28:30.316407 INFO::ASW Label was 0.513560715981645 prior to batch effect correction and is now 0.933787631704217 .
2025-03-03 23:28:30.317916 INFO::Total function execution time is 0.0520119667053223 s and adjustment time is 0.0250890254974365 s ( 48.24 )
2025-03-03 23:28:30.408552 INFO::Formatting Data.
2025-03-03 23:28:30.409511 INFO::Replacing NaNs with NAs.
2025-03-03 23:28:30.41057 INFO::Removing potential empty rows and columns
2025-03-03 23:28:30.411596 INFO::Found 0 missing values.
2025-03-03 23:28:30.41362 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-03 23:28:30.414331 INFO::Done
2025-03-03 23:28:30.415056 INFO::Acquiring quality metrics before batch effect correction.
2025-03-03 23:28:30.417141 INFO::Starting hierarchical adjustment
2025-03-03 23:28:30.418009 INFO::Found 2 batches.
2025-03-03 23:28:30.41873 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-03 23:28:30.4195 INFO::Using default BPPARAM
2025-03-03 23:28:30.420231 INFO::Adjusting the last 2 batches sequentially
2025-03-03 23:28:30.421577 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-03 23:28:30.448424 INFO::Done
2025-03-03 23:28:30.449316 INFO::Acquiring quality metrics after batch effect correction.
2025-03-03 23:28:30.451468 INFO::ASW Batch was 0.128061663038161 prior to batch effect correction and is now -0.144741276236249 .
2025-03-03 23:28:30.452477 INFO::Total function execution time is 0.0439968109130859 s and adjustment time is 0.0304989814758301 s ( 69.32 )
2025-03-03 23:28:30.467755 INFO::Formatting Data.
2025-03-03 23:28:30.468723 INFO::Replacing NaNs with NAs.
2025-03-03 23:28:30.469851 INFO::Removing potential empty rows and columns
2025-03-03 23:28:30.470989 INFO::Found 0 missing values.
2025-03-03 23:28:30.472443 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-03-03 23:28:30.47662 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-03 23:28:30.477383 INFO::Done
2025-03-03 23:28:30.478103 INFO::Acquiring quality metrics before batch effect correction.
2025-03-03 23:28:30.481133 INFO::Starting hierarchical adjustment
2025-03-03 23:28:30.482048 INFO::Found 2 batches.
2025-03-03 23:28:30.482786 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-03 23:28:30.483631 INFO::Using default BPPARAM
2025-03-03 23:28:30.48439 INFO::Adjusting the last 2 batches sequentially
2025-03-03 23:28:30.485595 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-03 23:28:30.508188 INFO::Done
2025-03-03 23:28:30.509099 INFO::Acquiring quality metrics after batch effect correction.
2025-03-03 23:28:30.512143 INFO::ASW Batch was 0.461130398456719 prior to batch effect correction and is now -0.0369601240451339 .
2025-03-03 23:28:30.512921 INFO::ASW Label was 0.613346681257593 prior to batch effect correction and is now 0.944458937584863 .
2025-03-03 23:28:30.513904 INFO::Total function execution time is 0.0462379455566406 s and adjustment time is 0.0262260437011719 s ( 56.72 )
2025-03-03 23:28:30.514838 INFO::Formatting Data.
2025-03-03 23:28:30.515671 INFO::Replacing NaNs with NAs.
2025-03-03 23:28:30.516747 INFO::Removing potential empty rows and columns
2025-03-03 23:28:30.517861 INFO::Found 0 missing values.
2025-03-03 23:28:30.518949 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-03-03 23:28:30.523069 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-03 23:28:30.523826 INFO::Done
2025-03-03 23:28:30.524537 INFO::Acquiring quality metrics before batch effect correction.
2025-03-03 23:28:30.527612 INFO::Starting hierarchical adjustment
2025-03-03 23:28:30.528493 INFO::Found 2 batches.
2025-03-03 23:28:30.529242 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-03 23:28:30.530037 INFO::Using default BPPARAM
2025-03-03 23:28:30.530761 INFO::Adjusting the last 2 batches sequentially
2025-03-03 23:28:30.531891 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-03 23:28:30.548494 INFO::Done
2025-03-03 23:28:30.549994 INFO::Acquiring quality metrics after batch effect correction.
2025-03-03 23:28:30.555588 INFO::ASW Batch was 0.461130398456719 prior to batch effect correction and is now -0.0369601240451339 .
2025-03-03 23:28:30.557106 INFO::ASW Label was 0.613346681257593 prior to batch effect correction and is now 0.944458937584863 .
2025-03-03 23:28:30.55891 INFO::Total function execution time is 0.0439369678497314 s and adjustment time is 0.0200319290161133 s ( 45.59 )
2025-03-03 23:28:30.816822 INFO::Formatting Data.
2025-03-03 23:28:30.818516 INFO::Replacing NaNs with NAs.
2025-03-03 23:28:30.820495 INFO::Removing potential empty rows and columns
2025-03-03 23:28:30.822635 INFO::Found 0 missing values.
2025-03-03 23:28:30.828097 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-03 23:28:30.829477 INFO::Done
2025-03-03 23:28:30.830783 INFO::Acquiring quality metrics before batch effect correction.
2025-03-03 23:28:30.834528 INFO::Starting hierarchical adjustment
2025-03-03 23:28:30.836059 INFO::Found 3 batches.
2025-03-03 23:28:30.837395 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-03 23:28:30.83875 INFO::Using default BPPARAM
2025-03-03 23:28:30.839969 INFO::Processing subtree level 1
2025-03-03 23:28:33.825826 INFO::Adjusting the last 1 batches sequentially
2025-03-03 23:28:33.827937 INFO::Done
2025-03-03 23:28:33.829128 INFO::Acquiring quality metrics after batch effect correction.
2025-03-03 23:28:33.832296 INFO::ASW Batch was 0.0509431957212867 prior to batch effect correction and is now 0.0509431957212867 .
2025-03-03 23:28:33.833731 INFO::Total function execution time is 3.01708912849426 s and adjustment time is 2.9921190738678 s ( 99.17 )
2025-03-03 23:28:33.835317 INFO::Formatting Data.
2025-03-03 23:28:33.836552 INFO::Typecasting input to dataframe.
2025-03-03 23:28:33.837913 INFO::Replacing NaNs with NAs.
2025-03-03 23:28:33.839423 INFO::Removing potential empty rows and columns
2025-03-03 23:28:33.841089 INFO::Found 0 missing values.
2025-03-03 23:28:33.845121 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-03 23:28:33.846236 INFO::Done
2025-03-03 23:28:33.847303 INFO::Acquiring quality metrics before batch effect correction.
2025-03-03 23:28:33.850477 INFO::Starting hierarchical adjustment
2025-03-03 23:28:33.851855 INFO::Found 3 batches.
2025-03-03 23:28:33.852961 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-03 23:28:33.854124 INFO::Using default BPPARAM
2025-03-03 23:28:33.855206 INFO::Processing subtree level 1
2025-03-03 23:28:36.889158 INFO::Adjusting the last 1 batches sequentially
2025-03-03 23:28:36.891079 INFO::Done
2025-03-03 23:28:36.892357 INFO::Acquiring quality metrics after batch effect correction.
2025-03-03 23:28:36.895612 INFO::ASW Batch was 0.0509431957212867 prior to batch effect correction and is now 0.0509431957212867 .
2025-03-03 23:28:36.89715 INFO::Total function execution time is 3.06183099746704 s and adjustment time is 3.03942799568176 s ( 99.27 )
2025-03-03 23:28:36.918487 INFO::Formatting Data.
2025-03-03 23:28:36.919961 INFO::Typecasting input to dataframe.
2025-03-03 23:28:36.92155 INFO::Replacing NaNs with NAs.
2025-03-03 23:28:36.923202 INFO::Removing potential empty rows and columns
2025-03-03 23:28:36.924964 INFO::Found 0 missing values.
2025-03-03 23:28:36.92943 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-03 23:28:36.930686 INFO::Done
2025-03-03 23:28:36.931849 INFO::Acquiring quality metrics before batch effect correction.
2025-03-03 23:28:36.935121 INFO::Starting hierarchical adjustment
2025-03-03 23:28:36.936534 INFO::Found 3 batches.
2025-03-03 23:28:36.937673 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-03 23:28:36.938918 INFO::Using default BPPARAM
2025-03-03 23:28:36.940071 INFO::Processing subtree level 1
2025-03-03 23:28:40.04551 INFO::Adjusting the last 1 batches sequentially
2025-03-03 23:28:40.047799 INFO::Done
2025-03-03 23:28:40.049109 INFO::Acquiring quality metrics after batch effect correction.
2025-03-03 23:28:40.052425 INFO::ASW Batch was -0.0226866771077504 prior to batch effect correction and is now -0.0226866771077504 .
2025-03-03 23:28:40.053941 INFO::Total function execution time is 3.13556385040283 s and adjustment time is 3.11145782470703 s ( 99.23 )
2025-03-03 23:28:43.140618 INFO::Formatting Data.
2025-03-03 23:28:43.142221 INFO::Replacing NaNs with NAs.
2025-03-03 23:28:43.144309 INFO::Removing potential empty rows and columns
2025-03-03 23:28:43.14822 INFO::Found 1000 missing values.
2025-03-03 23:28:43.17259 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-03 23:28:43.174097 INFO::Done
2025-03-03 23:28:43.175418 INFO::Acquiring quality metrics before batch effect correction.
2025-03-03 23:28:43.185674 INFO::Starting hierarchical adjustment
2025-03-03 23:28:43.187403 INFO::Found 10 batches.
2025-03-03 23:28:43.188696 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-03 23:28:43.190075 INFO::Using default BPPARAM
2025-03-03 23:28:43.191313 INFO::Processing subtree level 1
2025-03-03 23:28:46.343955 INFO::Processing subtree level 2
2025-03-03 23:28:49.462719 INFO::Adjusting the last 1 batches sequentially
2025-03-03 23:28:49.465109 INFO::Done
2025-03-03 23:28:49.466321 INFO::Acquiring quality metrics after batch effect correction.
2025-03-03 23:28:49.474983 INFO::ASW Batch was 0.494561431818555 prior to batch effect correction and is now 0.494561431818555 .
2025-03-03 23:28:49.476217 INFO::ASW Label was 0.312263504261988 prior to batch effect correction and is now 0.312263504261988 .
2025-03-03 23:28:49.477714 INFO::Total function execution time is 6.33724784851074 s and adjustment time is 6.27799820899963 s ( 99.07 )
2025-03-03 23:28:49.479073 INFO::Formatting Data.
2025-03-03 23:28:49.480217 INFO::Replacing NaNs with NAs.
2025-03-03 23:28:49.481963 INFO::Removing potential empty rows and columns
2025-03-03 23:28:49.484186 INFO::Found 1000 missing values.
2025-03-03 23:28:49.497601 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-03 23:28:49.498941 INFO::Done
2025-03-03 23:28:49.500109 INFO::Acquiring quality metrics before batch effect correction.
2025-03-03 23:28:49.509715 INFO::Starting hierarchical adjustment
2025-03-03 23:28:49.511329 INFO::Found 10 batches.
2025-03-03 23:28:50.228321 INFO::Set up parallel execution backend with 2 workers
2025-03-03 23:28:50.229785 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-03-03 23:28:53.278664 INFO::Adjusting the last 2 batches sequentially
2025-03-03 23:28:53.280931 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-03 23:28:53.306568 INFO::Done
2025-03-03 23:28:53.307946 INFO::Acquiring quality metrics after batch effect correction.
2025-03-03 23:28:53.31723 INFO::ASW Batch was 0.494561431818555 prior to batch effect correction and is now 0.494561431818555 .
2025-03-03 23:28:53.318574 INFO::ASW Label was 0.312263504261988 prior to batch effect correction and is now 0.312263504261988 .
2025-03-03 23:28:53.32008 INFO::Total function execution time is 3.84101605415344 s and adjustment time is 3.79545497894287 s ( 98.81 )
2025-03-03 23:28:56.285855 INFO::Formatting Data.
2025-03-03 23:28:56.287452 INFO::Replacing NaNs with NAs.
2025-03-03 23:28:56.289213 INFO::Removing potential empty rows and columns
2025-03-03 23:28:56.291075 INFO::Found 0 missing values.
2025-03-03 23:28:56.296508 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-03 23:28:56.297746 INFO::Done
2025-03-03 23:28:56.29893 INFO::Acquiring quality metrics before batch effect correction.
2025-03-03 23:28:56.303252 INFO::Starting hierarchical adjustment
2025-03-03 23:28:56.30468 INFO::Found 3 batches.
2025-03-03 23:28:56.305855 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-03 23:28:56.307164 INFO::Using default BPPARAM
2025-03-03 23:28:56.308323 INFO::Processing subtree level 1
2025-03-03 23:28:59.419482 INFO::Adjusting the last 1 batches sequentially
2025-03-03 23:28:59.421667 INFO::Done
2025-03-03 23:28:59.422854 INFO::Acquiring quality metrics after batch effect correction.
2025-03-03 23:28:59.426745 INFO::ASW Batch was 0.104128839474988 prior to batch effect correction and is now -0.125711540646771 .
2025-03-03 23:28:59.42786 INFO::ASW Label was -0.189704474537846 prior to batch effect correction and is now 0.0244449522807396 .
2025-03-03 23:28:59.429218 INFO::Total function execution time is 3.14350700378418 s and adjustment time is 3.1171760559082 s ( 99.16 )
2025-03-03 23:28:59.56373 INFO::Formatting Data.
2025-03-03 23:28:59.564726 INFO::Replacing NaNs with NAs.
2025-03-03 23:28:59.565775 INFO::Removing potential empty rows and columns
2025-03-03 23:28:59.566882 INFO::Found 2 missing values.
2025-03-03 23:28:59.569367 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-03-03 23:28:59.570072 INFO::Done
2025-03-03 23:28:59.604649 INFO::Found NA in Reference column
2025-03-03 23:28:59.616746 INFO::Require at least two references per batch.
2025-03-03 23:28:59.636475 INFO::Formatting Data.
2025-03-03 23:28:59.637469 INFO::Recognized SummarizedExperiment
2025-03-03 23:28:59.638189 INFO::Typecasting input to dataframe.
2025-03-03 23:28:59.646322 INFO::Replacing NaNs with NAs.
2025-03-03 23:28:59.647617 INFO::Removing potential empty rows and columns
2025-03-03 23:28:59.650337 INFO::Found 0 missing values.
2025-03-03 23:28:59.655365 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-03 23:28:59.656166 INFO::Done
2025-03-03 23:28:59.669911 INFO::Formatting Data.
2025-03-03 23:28:59.670821 INFO::Recognized SummarizedExperiment
2025-03-03 23:28:59.671516 INFO::Typecasting input to dataframe.
2025-03-03 23:28:59.686475 INFO::Replacing NaNs with NAs.
2025-03-03 23:28:59.687901 INFO::Removing potential empty rows and columns
2025-03-03 23:28:59.690769 INFO::Found 0 missing values.
2025-03-03 23:28:59.698745 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-03 23:28:59.699545 INFO::Done
2025-03-03 23:28:59.713413 INFO::Formatting Data.
2025-03-03 23:28:59.71433 INFO::Recognized SummarizedExperiment
2025-03-03 23:28:59.715026 INFO::Typecasting input to dataframe.
2025-03-03 23:28:59.73004 INFO::Replacing NaNs with NAs.
2025-03-03 23:28:59.73122 INFO::Removing potential empty rows and columns
2025-03-03 23:28:59.732377 INFO::Found 0 missing values.
2025-03-03 23:28:59.733436 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-03-03 23:28:59.738582 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-03 23:28:59.739619 INFO::Done
2025-03-03 23:28:59.759616 INFO::Formatting Data.
2025-03-03 23:28:59.761225 INFO::Replacing NaNs with NAs.
2025-03-03 23:28:59.763014 INFO::Removing potential empty rows and columns
2025-03-03 23:28:59.764951 INFO::Found 0 missing values.
2025-03-03 23:28:59.769549 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-03 23:28:59.770804 INFO::Done
2025-03-03 23:28:59.791502 INFO::Formatting Data.
2025-03-03 23:28:59.792989 INFO::Replacing NaNs with NAs.
2025-03-03 23:28:59.794627 INFO::Removing potential empty rows and columns
2025-03-03 23:28:59.796366 INFO::Found 0 missing values.
2025-03-03 23:28:59.800895 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-03 23:28:59.801964 INFO::Done
2025-03-03 23:28:59.854983 INFO::Formatting Data.
2025-03-03 23:28:59.856552 INFO::Replacing NaNs with NAs.
2025-03-03 23:28:59.858421 INFO::Removing potential empty rows and columns
2025-03-03 23:28:59.860378 INFO::Found 1 missing values.
2025-03-03 23:28:59.864172 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-03 23:28:59.865265 INFO::Done
2025-03-03 23:28:59.901092 INFO::Formatting Data.
2025-03-03 23:28:59.902665 INFO::Replacing NaNs with NAs.
2025-03-03 23:28:59.904349 INFO::Removing potential empty rows and columns
2025-03-03 23:28:59.906133 INFO::Found 2 missing values.
2025-03-03 23:28:59.907828 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-03-03 23:28:59.911505 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-03-03 23:28:59.912703 INFO::Done
2025-03-03 23:28:59.933093 INFO::Formatting Data.
2025-03-03 23:28:59.934636 INFO::Replacing NaNs with NAs.
2025-03-03 23:28:59.935741 INFO::Removing potential empty rows and columns
2025-03-03 23:28:59.936818 INFO::Found 2 missing values.
2025-03-03 23:28:59.938521 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-03 23:28:59.939223 INFO::Done
2025-03-03 23:28:59.952933 INFO::Formatting Data.
2025-03-03 23:28:59.953992 INFO::Typecasting input to dataframe.
2025-03-03 23:28:59.955043 INFO::Replacing NaNs with NAs.
2025-03-03 23:28:59.956146 INFO::Removing potential empty rows and columns
2025-03-03 23:28:59.957322 INFO::Found 0 missing values.
2025-03-03 23:28:59.960062 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-03 23:28:59.960788 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
31.56 1.35 79.98
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 8.86 | 0.61 | 18.63 | |
| compute_asw | 0.04 | 0.00 | 0.05 | |
| count_existing | 0.02 | 0.00 | 0.01 | |
| generate_data_covariables | 0.01 | 0.01 | 0.03 | |
| generate_dataset | 0.02 | 0.00 | 0.02 | |