Yannis Schumann
| Snapshot Date: 2025-02-03 13:00 -0500 (Mon, 03 Feb 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_20 |
| git_last_commit: 9764e3f |
| git_last_commit_date: 2024-10-29 11:26:04 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-02-06 12:04 -0500 (Thu, 06 Feb 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4753 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4501 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4524 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4476 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4407 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 159/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.2.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.2.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BERT_1.2.0.tar.gz |
| StartedAt: 2025-02-03 20:19:27 -0500 (Mon, 03 Feb 2025) |
| EndedAt: 2025-02-03 20:20:55 -0500 (Mon, 03 Feb 2025) |
| EllapsedTime: 88.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BERT_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 24.505 1.263 17.869
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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 20:20:17.894213 INFO::Formatting Data.
2025-02-03 20:20:17.895563 INFO::Replacing NaNs with NAs.
2025-02-03 20:20:17.907076 INFO::Removing potential empty rows and columns
2025-02-03 20:20:18.15889 INFO::Found 0 missing values.
2025-02-03 20:20:18.162251 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 20:20:18.162878 INFO::Done
2025-02-03 20:20:18.163401 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 20:20:18.174897 INFO::Starting hierarchical adjustment
2025-02-03 20:20:18.175726 INFO::Found 3 batches.
2025-02-03 20:20:18.176291 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 20:20:18.177397 INFO::Using default BPPARAM
2025-02-03 20:20:18.177941 INFO::Processing subtree level 1
2025-02-03 20:20:18.276284 INFO::Adjusting the last 1 batches sequentially
2025-02-03 20:20:18.278034 INFO::Done
2025-02-03 20:20:18.278682 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 20:20:18.28138 INFO::ASW Batch was -0.00954092525973248 prior to batch effect correction and is now -0.00954092525973248 .
2025-02-03 20:20:18.282443 INFO::Total function execution time is 0.388908624649048 s and adjustment time is 0.102476119995117 s ( 26.35 )
2025-02-03 20:20:18.296104 INFO::Formatting Data.
2025-02-03 20:20:18.296876 INFO::Replacing NaNs with NAs.
2025-02-03 20:20:18.297776 INFO::Removing potential empty rows and columns
2025-02-03 20:20:18.298879 INFO::Found 0 missing values.
2025-02-03 20:20:18.299845 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 20:20:18.31084 INFO::Formatting Data.
2025-02-03 20:20:18.311583 INFO::Replacing NaNs with NAs.
2025-02-03 20:20:18.312449 INFO::Removing potential empty rows and columns
2025-02-03 20:20:18.313485 INFO::Found 0 missing values.
2025-02-03 20:20:18.314382 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 20:20:18.330536 INFO::Formatting Data.
2025-02-03 20:20:18.331274 INFO::Replacing NaNs with NAs.
2025-02-03 20:20:18.332137 INFO::Removing potential empty rows and columns
2025-02-03 20:20:18.333174 INFO::Found 0 missing values.
2025-02-03 20:20:18.334089 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 20:20:18.338756 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 20:20:18.339339 INFO::Done
2025-02-03 20:20:18.339911 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 20:20:18.342034 INFO::Starting hierarchical adjustment
2025-02-03 20:20:18.342744 INFO::Found 2 batches.
2025-02-03 20:20:18.343267 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 20:20:18.343896 INFO::Using default BPPARAM
2025-02-03 20:20:18.344406 INFO::Adjusting the last 2 batches sequentially
2025-02-03 20:20:18.345324 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-03 20:20:18.368592 INFO::Done
2025-02-03 20:20:18.369496 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 20:20:18.371569 INFO::ASW Batch was -0.0279934135384744 prior to batch effect correction and is now -0.127501418297439 .
2025-02-03 20:20:18.372381 INFO::Total function execution time is 0.0419163703918457 s and adjustment time is 0.0259370803833008 s ( 61.88 )
2025-02-03 20:20:18.375238 INFO::Formatting Data.
2025-02-03 20:20:18.375841 INFO::Replacing NaNs with NAs.
2025-02-03 20:20:18.384888 INFO::Formatting Data.
2025-02-03 20:20:18.385594 INFO::Replacing NaNs with NAs.
2025-02-03 20:20:18.386497 INFO::Removing potential empty rows and columns
2025-02-03 20:20:18.387904 INFO::Found 0 missing values.
2025-02-03 20:20:18.390916 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 20:20:18.391553 INFO::Done
2025-02-03 20:20:18.392052 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 20:20:18.394157 INFO::Starting hierarchical adjustment
2025-02-03 20:20:18.394863 INFO::Found 2 batches.
2025-02-03 20:20:18.395386 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 20:20:18.395973 INFO::Using default BPPARAM
2025-02-03 20:20:18.3965 INFO::Adjusting the last 2 batches sequentially
2025-02-03 20:20:18.397489 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-03 20:20:18.412535 INFO::Done
2025-02-03 20:20:18.413248 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 20:20:18.41529 INFO::ASW Batch was -0.0105097638393095 prior to batch effect correction and is now -0.134340327143282 .
2025-02-03 20:20:18.416064 INFO::Total function execution time is 0.0312302112579346 s and adjustment time is 0.0177910327911377 s ( 56.97 )
2025-02-03 20:20:18.417108 INFO::Formatting Data.
2025-02-03 20:20:18.417673 INFO::Replacing NaNs with NAs.
2025-02-03 20:20:18.418502 INFO::Removing potential empty rows and columns
2025-02-03 20:20:18.419633 INFO::Found 0 missing values.
2025-02-03 20:20:18.422767 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 20:20:18.423275 INFO::Done
2025-02-03 20:20:18.423745 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 20:20:18.425726 INFO::Starting hierarchical adjustment
2025-02-03 20:20:18.426396 INFO::Found 2 batches.
2025-02-03 20:20:18.426896 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 20:20:18.427461 INFO::Using default BPPARAM
2025-02-03 20:20:18.42796 INFO::Adjusting the last 2 batches sequentially
2025-02-03 20:20:18.428829 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-03 20:20:18.443691 INFO::Done
2025-02-03 20:20:18.444378 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 20:20:18.446335 INFO::ASW Batch was -0.0105097638393095 prior to batch effect correction and is now -0.134340327143282 .
2025-02-03 20:20:18.447121 INFO::Total function execution time is 0.0300056934356689 s and adjustment time is 0.0174324512481689 s ( 58.1 )
2025-02-03 20:20:20.578495 INFO::Formatting Data.
2025-02-03 20:20:20.579166 INFO::Recognized SummarizedExperiment
2025-02-03 20:20:20.579603 INFO::Typecasting input to dataframe.
2025-02-03 20:20:20.609083 INFO::Replacing NaNs with NAs.
2025-02-03 20:20:20.610364 INFO::Removing potential empty rows and columns
2025-02-03 20:20:20.613402 INFO::Found 0 missing values.
2025-02-03 20:20:20.618979 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 20:20:20.619495 INFO::Done
2025-02-03 20:20:20.619946 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 20:20:20.623142 INFO::Starting hierarchical adjustment
2025-02-03 20:20:20.623773 INFO::Found 2 batches.
2025-02-03 20:20:20.624235 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 20:20:20.625247 INFO::Using default BPPARAM
2025-02-03 20:20:20.625692 INFO::Adjusting the last 2 batches sequentially
2025-02-03 20:20:20.626544 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-03 20:20:20.675194 INFO::Done
2025-02-03 20:20:20.675862 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 20:20:20.678856 INFO::ASW Batch was 0.00206407603908707 prior to batch effect correction and is now -0.0965667680580503 .
2025-02-03 20:20:20.679597 INFO::Total function execution time is 0.101410388946533 s and adjustment time is 0.051532506942749 s ( 50.82 )
2025-02-03 20:20:20.695682 INFO::Formatting Data.
2025-02-03 20:20:20.696327 INFO::Recognized SummarizedExperiment
2025-02-03 20:20:20.69676 INFO::Typecasting input to dataframe.
2025-02-03 20:20:20.705119 INFO::Replacing NaNs with NAs.
2025-02-03 20:20:20.706253 INFO::Removing potential empty rows and columns
2025-02-03 20:20:20.709233 INFO::Found 0 missing values.
2025-02-03 20:20:20.715116 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 20:20:20.715609 INFO::Done
2025-02-03 20:20:20.716075 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 20:20:20.719173 INFO::Starting hierarchical adjustment
2025-02-03 20:20:20.719785 INFO::Found 2 batches.
2025-02-03 20:20:20.720248 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 20:20:20.720752 INFO::Using default BPPARAM
2025-02-03 20:20:20.721205 INFO::Adjusting the last 2 batches sequentially
2025-02-03 20:20:20.722058 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-03 20:20:20.74498 INFO::Done
2025-02-03 20:20:20.745878 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 20:20:20.749692 INFO::ASW Batch was -0.0117934080647053 prior to batch effect correction and is now -0.0117934080647053 .
2025-02-03 20:20:20.750643 INFO::Total function execution time is 0.0549123287200928 s and adjustment time is 0.0252394676208496 s ( 45.96 )
2025-02-03 20:20:20.770715 INFO::Formatting Data.
2025-02-03 20:20:20.771639 INFO::Replacing NaNs with NAs.
2025-02-03 20:20:20.772599 INFO::Removing potential empty rows and columns
2025-02-03 20:20:20.773626 INFO::Found 0 missing values.
2025-02-03 20:20:20.776409 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 20:20:20.776922 INFO::Done
2025-02-03 20:20:20.777395 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 20:20:20.77944 INFO::Starting hierarchical adjustment
2025-02-03 20:20:20.780163 INFO::Found 3 batches.
2025-02-03 20:20:20.780689 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 20:20:20.781276 INFO::Using default BPPARAM
2025-02-03 20:20:20.781742 INFO::Processing subtree level 1
2025-02-03 20:20:20.948048 INFO::Adjusting the last 1 batches sequentially
2025-02-03 20:20:20.949948 INFO::Done
2025-02-03 20:20:20.950597 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 20:20:20.953145 INFO::ASW Batch was -0.063717710152621 prior to batch effect correction and is now -0.168046355749338 .
2025-02-03 20:20:20.954155 INFO::Total function execution time is 0.183522939682007 s and adjustment time is 0.169915199279785 s ( 92.59 )
2025-02-03 20:20:20.969447 INFO::Skipping initial DF formatting
2025-02-03 20:20:20.97021 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 20:20:20.974191 INFO::Starting hierarchical adjustment
2025-02-03 20:20:20.975001 INFO::Found 5 batches.
2025-02-03 20:20:20.975546 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 20:20:20.976148 INFO::Using default BPPARAM
2025-02-03 20:20:20.976661 INFO::Processing subtree level 1
2025-02-03 20:20:21.143206 INFO::Adjusting the last 2 batches sequentially
2025-02-03 20:20:21.145375 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-03 20:20:21.168502 INFO::Done
2025-02-03 20:20:21.169419 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 20:20:21.176051 INFO::ASW Batch was 0.535979912541641 prior to batch effect correction and is now 0.535979912541641 .
2025-02-03 20:20:21.176895 INFO::ASW Label was 0.343975858765903 prior to batch effect correction and is now 0.343975858765903 .
2025-02-03 20:20:21.177878 INFO::Total function execution time is 0.208469152450562 s and adjustment time is 0.193578720092773 s ( 92.86 )
2025-02-03 20:20:21.196287 INFO::Formatting Data.
2025-02-03 20:20:21.197159 INFO::Replacing NaNs with NAs.
2025-02-03 20:20:21.1981 INFO::Removing potential empty rows and columns
2025-02-03 20:20:21.199124 INFO::Found 0 missing values.
2025-02-03 20:20:21.203218 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 20:20:21.203762 INFO::Done
2025-02-03 20:20:21.204283 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 20:20:21.207362 INFO::Starting hierarchical adjustment
2025-02-03 20:20:21.208091 INFO::Found 5 batches.
2025-02-03 20:20:21.208598 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 20:20:21.209211 INFO::Using default BPPARAM
2025-02-03 20:20:21.209727 INFO::Processing subtree level 1
2025-02-03 20:20:21.361662 INFO::Adjusting the last 2 batches sequentially
2025-02-03 20:20:21.36338 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-03 20:20:21.380446 INFO::Done
2025-02-03 20:20:21.381224 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 20:20:21.384628 INFO::ASW Batch was 0.41761519519042 prior to batch effect correction and is now -0.100170312328506 .
2025-02-03 20:20:21.385292 INFO::ASW Label was 0.170524204370277 prior to batch effect correction and is now 0.810028409560918 .
2025-02-03 20:20:21.38621 INFO::Total function execution time is 0.190001249313354 s and adjustment time is 0.17247462272644 s ( 90.78 )
2025-02-03 20:20:21.387178 INFO::Formatting Data.
2025-02-03 20:20:21.387888 INFO::Replacing NaNs with NAs.
2025-02-03 20:20:21.388834 INFO::Removing potential empty rows and columns
2025-02-03 20:20:21.389819 INFO::Found 0 missing values.
2025-02-03 20:20:21.393778 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 20:20:21.394311 INFO::Done
2025-02-03 20:20:21.39478 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 20:20:21.397888 INFO::Starting hierarchical adjustment
2025-02-03 20:20:21.398575 INFO::Found 5 batches.
2025-02-03 20:20:21.399067 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 20:20:21.399646 INFO::Using default BPPARAM
2025-02-03 20:20:21.400181 INFO::Processing subtree level 1
2025-02-03 20:20:21.538086 INFO::Adjusting the last 2 batches sequentially
2025-02-03 20:20:21.53985 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-03 20:20:21.555518 INFO::Done
2025-02-03 20:20:21.556298 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 20:20:21.559551 INFO::ASW Batch was 0.41761519519042 prior to batch effect correction and is now -0.100170312328506 .
2025-02-03 20:20:21.560172 INFO::ASW Label was 0.170524204370277 prior to batch effect correction and is now 0.810028409560918 .
2025-02-03 20:20:21.560969 INFO::Total function execution time is 0.173824787139893 s and adjustment time is 0.157063722610474 s ( 90.36 )
2025-02-03 20:20:21.574538 INFO::Formatting Data.
2025-02-03 20:20:21.575346 INFO::Replacing NaNs with NAs.
2025-02-03 20:20:21.576246 INFO::Removing potential empty rows and columns
2025-02-03 20:20:21.577246 INFO::Found 0 missing values.
2025-02-03 20:20:21.581282 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 20:20:21.581826 INFO::Done
2025-02-03 20:20:21.582334 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 20:20:21.585273 INFO::Starting hierarchical adjustment
2025-02-03 20:20:21.585976 INFO::Found 5 batches.
2025-02-03 20:20:21.586487 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 20:20:21.587122 INFO::Using default BPPARAM
2025-02-03 20:20:21.587617 INFO::Processing subtree level 1
2025-02-03 20:20:21.783724 INFO::Adjusting the last 2 batches sequentially
2025-02-03 20:20:21.785478 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-03 20:20:21.802339 INFO::Done
2025-02-03 20:20:21.803101 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 20:20:21.806485 INFO::ASW Batch was 0.458518693203321 prior to batch effect correction and is now -0.0488804262228414 .
2025-02-03 20:20:21.807149 INFO::ASW Label was 0.432748481013587 prior to batch effect correction and is now 0.751549846211912 .
2025-02-03 20:20:21.808043 INFO::Total function execution time is 0.233569622039795 s and adjustment time is 0.21649432182312 s ( 92.69 )
2025-02-03 20:20:21.808908 INFO::Formatting Data.
2025-02-03 20:20:21.809554 INFO::Replacing NaNs with NAs.
2025-02-03 20:20:21.810536 INFO::Removing potential empty rows and columns
2025-02-03 20:20:21.811566 INFO::Found 0 missing values.
2025-02-03 20:20:21.815939 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 20:20:21.835467 INFO::Done
2025-02-03 20:20:21.836708 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 20:20:21.839628 INFO::Starting hierarchical adjustment
2025-02-03 20:20:21.84031 INFO::Found 5 batches.
2025-02-03 20:20:21.840784 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 20:20:21.84135 INFO::Using default BPPARAM
2025-02-03 20:20:21.841822 INFO::Processing subtree level 1
2025-02-03 20:20:21.985558 INFO::Adjusting the last 2 batches sequentially
2025-02-03 20:20:21.987552 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-03 20:20:22.016523 INFO::Done
2025-02-03 20:20:22.017551 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 20:20:22.021675 INFO::ASW Batch was 0.458518693203321 prior to batch effect correction and is now -0.0488804262228414 .
2025-02-03 20:20:22.022391 INFO::ASW Label was 0.432748481013587 prior to batch effect correction and is now 0.751549846211912 .
2025-02-03 20:20:22.023364 INFO::Total function execution time is 0.214436769485474 s and adjustment time is 0.176251173019409 s ( 82.19 )
2025-02-03 20:20:22.041989 INFO::Formatting Data.
2025-02-03 20:20:22.04295 INFO::Replacing NaNs with NAs.
2025-02-03 20:20:22.044071 INFO::Removing potential empty rows and columns
2025-02-03 20:20:22.045405 INFO::Found 0 missing values.
2025-02-03 20:20:22.04892 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 20:20:22.049499 INFO::Done
2025-02-03 20:20:22.050047 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 20:20:22.053576 INFO::Starting hierarchical adjustment
2025-02-03 20:20:22.054355 INFO::Found 2 batches.
2025-02-03 20:20:22.05493 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 20:20:22.055632 INFO::Using default BPPARAM
2025-02-03 20:20:22.056242 INFO::Adjusting the last 2 batches sequentially
2025-02-03 20:20:22.057285 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-03 20:20:22.074673 INFO::Done
2025-02-03 20:20:22.075346 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 20:20:22.078567 INFO::ASW Batch was 0.578590364132918 prior to batch effect correction and is now 0.00405146929515911 .
2025-02-03 20:20:22.079171 INFO::ASW Label was 0.458603617327937 prior to batch effect correction and is now 0.852324743065234 .
2025-02-03 20:20:22.079976 INFO::Total function execution time is 0.0381941795349121 s and adjustment time is 0.0204775333404541 s ( 53.61 )
2025-02-03 20:20:22.080784 INFO::Formatting Data.
2025-02-03 20:20:22.081424 INFO::Replacing NaNs with NAs.
2025-02-03 20:20:22.082299 INFO::Removing potential empty rows and columns
2025-02-03 20:20:22.083398 INFO::Found 0 missing values.
2025-02-03 20:20:22.086236 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 20:20:22.086903 INFO::Done
2025-02-03 20:20:22.087443 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 20:20:22.090767 INFO::Starting hierarchical adjustment
2025-02-03 20:20:22.091548 INFO::Found 2 batches.
2025-02-03 20:20:22.092086 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 20:20:22.092733 INFO::Using default BPPARAM
2025-02-03 20:20:22.093337 INFO::Adjusting the last 2 batches sequentially
2025-02-03 20:20:22.094347 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-03 20:20:22.111006 INFO::Done
2025-02-03 20:20:22.111685 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 20:20:22.114983 INFO::ASW Batch was 0.578590364132918 prior to batch effect correction and is now 0.00405146929515911 .
2025-02-03 20:20:22.115581 INFO::ASW Label was 0.458603617327937 prior to batch effect correction and is now 0.852324743065234 .
2025-02-03 20:20:22.116434 INFO::Total function execution time is 0.0356388092041016 s and adjustment time is 0.0196304321289062 s ( 55.08 )
2025-02-03 20:20:22.129756 INFO::Formatting Data.
2025-02-03 20:20:22.130532 INFO::Replacing NaNs with NAs.
2025-02-03 20:20:22.131513 INFO::Removing potential empty rows and columns
2025-02-03 20:20:22.132526 INFO::Found 0 missing values.
2025-02-03 20:20:22.134826 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 20:20:22.135359 INFO::Done
2025-02-03 20:20:22.135887 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 20:20:22.137981 INFO::Starting hierarchical adjustment
2025-02-03 20:20:22.138704 INFO::Found 2 batches.
2025-02-03 20:20:22.139248 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 20:20:22.139853 INFO::Using default BPPARAM
2025-02-03 20:20:22.140361 INFO::Adjusting the last 2 batches sequentially
2025-02-03 20:20:22.141293 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-03 20:20:22.173822 INFO::Done
2025-02-03 20:20:22.174453 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 20:20:22.176453 INFO::ASW Batch was -0.0212978015926902 prior to batch effect correction and is now -0.0731101008628327 .
2025-02-03 20:20:22.177313 INFO::Total function execution time is 0.0476579666137695 s and adjustment time is 0.0352485179901123 s ( 73.96 )
2025-02-03 20:20:22.188692 INFO::Formatting Data.
2025-02-03 20:20:22.189381 INFO::Replacing NaNs with NAs.
2025-02-03 20:20:22.190233 INFO::Removing potential empty rows and columns
2025-02-03 20:20:22.191203 INFO::Found 0 missing values.
2025-02-03 20:20:22.19233 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 20:20:22.196635 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 20:20:22.197147 INFO::Done
2025-02-03 20:20:22.197614 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 20:20:22.200399 INFO::Starting hierarchical adjustment
2025-02-03 20:20:22.201049 INFO::Found 2 batches.
2025-02-03 20:20:22.20154 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 20:20:22.202085 INFO::Using default BPPARAM
2025-02-03 20:20:22.202544 INFO::Adjusting the last 2 batches sequentially
2025-02-03 20:20:22.203457 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-03 20:20:22.222053 INFO::Done
2025-02-03 20:20:22.222816 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 20:20:22.226029 INFO::ASW Batch was 0.571158591569764 prior to batch effect correction and is now 0.17179808858317 .
2025-02-03 20:20:22.226688 INFO::ASW Label was 0.590625228092578 prior to batch effect correction and is now 0.792007950280266 .
2025-02-03 20:20:22.227501 INFO::Total function execution time is 0.0388329029083252 s and adjustment time is 0.0210859775543213 s ( 54.3 )
2025-02-03 20:20:22.22842 INFO::Formatting Data.
2025-02-03 20:20:22.229184 INFO::Replacing NaNs with NAs.
2025-02-03 20:20:22.230293 INFO::Removing potential empty rows and columns
2025-02-03 20:20:22.231309 INFO::Found 0 missing values.
2025-02-03 20:20:22.232172 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 20:20:22.236361 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 20:20:22.236853 INFO::Done
2025-02-03 20:20:22.237312 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 20:20:22.240011 INFO::Starting hierarchical adjustment
2025-02-03 20:20:22.240653 INFO::Found 2 batches.
2025-02-03 20:20:22.241146 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 20:20:22.241691 INFO::Using default BPPARAM
2025-02-03 20:20:22.24217 INFO::Adjusting the last 2 batches sequentially
2025-02-03 20:20:22.243032 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-03 20:20:22.25835 INFO::Done
2025-02-03 20:20:22.258952 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 20:20:22.261684 INFO::ASW Batch was 0.571158591569764 prior to batch effect correction and is now 0.17179808858317 .
2025-02-03 20:20:22.26223 INFO::ASW Label was 0.590625228092578 prior to batch effect correction and is now 0.792007950280266 .
2025-02-03 20:20:22.262957 INFO::Total function execution time is 0.0346124172210693 s and adjustment time is 0.0178172588348389 s ( 51.48 )
2025-02-03 20:20:22.459679 INFO::Formatting Data.
2025-02-03 20:20:22.460404 INFO::Replacing NaNs with NAs.
2025-02-03 20:20:22.461233 INFO::Removing potential empty rows and columns
2025-02-03 20:20:22.462171 INFO::Found 0 missing values.
2025-02-03 20:20:22.464903 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 20:20:22.465385 INFO::Done
2025-02-03 20:20:22.46586 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 20:20:22.467684 INFO::Starting hierarchical adjustment
2025-02-03 20:20:22.468338 INFO::Found 3 batches.
2025-02-03 20:20:22.468827 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 20:20:22.469378 INFO::Using default BPPARAM
2025-02-03 20:20:22.469866 INFO::Processing subtree level 1
2025-02-03 20:20:22.60448 INFO::Adjusting the last 1 batches sequentially
2025-02-03 20:20:22.606171 INFO::Done
2025-02-03 20:20:22.606771 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 20:20:22.609088 INFO::ASW Batch was 0.023030137576381 prior to batch effect correction and is now 0.023030137576381 .
2025-02-03 20:20:22.610001 INFO::Total function execution time is 0.150355100631714 s and adjustment time is 0.137945413589478 s ( 91.75 )
2025-02-03 20:20:22.611017 INFO::Formatting Data.
2025-02-03 20:20:22.611643 INFO::Typecasting input to dataframe.
2025-02-03 20:20:22.612351 INFO::Replacing NaNs with NAs.
2025-02-03 20:20:22.613226 INFO::Removing potential empty rows and columns
2025-02-03 20:20:22.614291 INFO::Found 0 missing values.
2025-02-03 20:20:22.617288 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 20:20:22.617831 INFO::Done
2025-02-03 20:20:22.618343 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 20:20:22.6203 INFO::Starting hierarchical adjustment
2025-02-03 20:20:22.62102 INFO::Found 3 batches.
2025-02-03 20:20:22.621547 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 20:20:22.622188 INFO::Using default BPPARAM
2025-02-03 20:20:22.622704 INFO::Processing subtree level 1
2025-02-03 20:20:22.763344 INFO::Adjusting the last 1 batches sequentially
2025-02-03 20:20:22.7651 INFO::Done
2025-02-03 20:20:22.765749 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 20:20:22.768242 INFO::ASW Batch was 0.023030137576381 prior to batch effect correction and is now 0.023030137576381 .
2025-02-03 20:20:22.769201 INFO::Total function execution time is 0.15816593170166 s and adjustment time is 0.144225835800171 s ( 91.19 )
2025-02-03 20:20:22.782324 INFO::Formatting Data.
2025-02-03 20:20:22.78318 INFO::Typecasting input to dataframe.
2025-02-03 20:20:22.784034 INFO::Replacing NaNs with NAs.
2025-02-03 20:20:22.784989 INFO::Removing potential empty rows and columns
2025-02-03 20:20:22.786068 INFO::Found 0 missing values.
2025-02-03 20:20:22.789037 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 20:20:22.789576 INFO::Done
2025-02-03 20:20:22.790112 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 20:20:22.792135 INFO::Starting hierarchical adjustment
2025-02-03 20:20:22.792845 INFO::Found 3 batches.
2025-02-03 20:20:22.79336 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 20:20:22.79403 INFO::Using default BPPARAM
2025-02-03 20:20:22.794552 INFO::Processing subtree level 1
2025-02-03 20:20:22.955839 INFO::Adjusting the last 1 batches sequentially
2025-02-03 20:20:22.958797 INFO::Done
2025-02-03 20:20:22.959678 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 20:20:22.963204 INFO::ASW Batch was -0.0169694338516286 prior to batch effect correction and is now -0.0169694338516286 .
2025-02-03 20:20:22.964447 INFO::Total function execution time is 0.182119846343994 s and adjustment time is 0.166036128997803 s ( 91.17 )
2025-02-03 20:20:23.152785 INFO::Formatting Data.
2025-02-03 20:20:23.153726 INFO::Replacing NaNs with NAs.
2025-02-03 20:20:23.155077 INFO::Removing potential empty rows and columns
2025-02-03 20:20:23.158154 INFO::Found 1000 missing values.
2025-02-03 20:20:23.177688 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 20:20:23.178464 INFO::Done
2025-02-03 20:20:23.179051 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 20:20:23.184695 INFO::Starting hierarchical adjustment
2025-02-03 20:20:23.185572 INFO::Found 10 batches.
2025-02-03 20:20:23.186236 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 20:20:23.186847 INFO::Using default BPPARAM
2025-02-03 20:20:23.187372 INFO::Processing subtree level 1
2025-02-03 20:20:23.365942 INFO::Processing subtree level 2
2025-02-03 20:20:23.548214 INFO::Adjusting the last 1 batches sequentially
2025-02-03 20:20:23.550622 INFO::Done
2025-02-03 20:20:23.551437 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 20:20:23.558374 INFO::ASW Batch was 0.527088504772776 prior to batch effect correction and is now 0.527088504772776 .
2025-02-03 20:20:23.559161 INFO::ASW Label was 0.300509202179095 prior to batch effect correction and is now 0.300509202179095 .
2025-02-03 20:20:23.560283 INFO::Total function execution time is 0.407562494277954 s and adjustment time is 0.365203619003296 s ( 89.61 )
2025-02-03 20:20:23.561298 INFO::Formatting Data.
2025-02-03 20:20:23.56209 INFO::Replacing NaNs with NAs.
2025-02-03 20:20:23.563924 INFO::Removing potential empty rows and columns
2025-02-03 20:20:23.56764 INFO::Found 1000 missing values.
2025-02-03 20:20:23.598805 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 20:20:23.599673 INFO::Done
2025-02-03 20:20:23.60031 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 20:20:23.606325 INFO::Starting hierarchical adjustment
2025-02-03 20:20:23.607281 INFO::Found 10 batches.
2025-02-03 20:20:24.702817 INFO::Set up parallel execution backend with 2 workers
2025-02-03 20:20:24.704406 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-02-03 20:20:26.371409 INFO::Adjusting the last 2 batches sequentially
2025-02-03 20:20:26.373182 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-03 20:20:26.389922 INFO::Done
2025-02-03 20:20:26.390504 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 20:20:26.395204 INFO::ASW Batch was 0.527088504772776 prior to batch effect correction and is now 0.527088504772776 .
2025-02-03 20:20:26.395727 INFO::ASW Label was 0.300509202179095 prior to batch effect correction and is now 0.300509202179095 .
2025-02-03 20:20:26.396451 INFO::Total function execution time is 2.8352370262146 s and adjustment time is 2.78285598754883 s ( 98.15 )
2025-02-03 20:20:26.542111 INFO::Formatting Data.
2025-02-03 20:20:26.542831 INFO::Replacing NaNs with NAs.
2025-02-03 20:20:26.543719 INFO::Removing potential empty rows and columns
2025-02-03 20:20:26.544771 INFO::Found 0 missing values.
2025-02-03 20:20:26.548353 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 20:20:26.5489 INFO::Done
2025-02-03 20:20:26.549396 INFO::Acquiring quality metrics before batch effect correction.
2025-02-03 20:20:26.55211 INFO::Starting hierarchical adjustment
2025-02-03 20:20:26.552824 INFO::Found 3 batches.
2025-02-03 20:20:26.553393 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-03 20:20:26.553982 INFO::Using default BPPARAM
2025-02-03 20:20:26.554501 INFO::Processing subtree level 1
2025-02-03 20:20:26.661861 INFO::Adjusting the last 1 batches sequentially
2025-02-03 20:20:26.663677 INFO::Done
2025-02-03 20:20:26.664355 INFO::Acquiring quality metrics after batch effect correction.
2025-02-03 20:20:26.66757 INFO::ASW Batch was 0.103496094810453 prior to batch effect correction and is now -0.136457281525082 .
2025-02-03 20:20:26.668216 INFO::ASW Label was -0.213380057483106 prior to batch effect correction and is now -0.175879612381326 .
2025-02-03 20:20:26.669124 INFO::Total function execution time is 0.127021789550781 s and adjustment time is 0.110990047454834 s ( 87.38 )
2025-02-03 20:20:26.78689 INFO::Formatting Data.
2025-02-03 20:20:26.787796 INFO::Replacing NaNs with NAs.
2025-02-03 20:20:26.788768 INFO::Removing potential empty rows and columns
2025-02-03 20:20:26.789873 INFO::Found 2 missing values.
2025-02-03 20:20:26.792769 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-02-03 20:20:26.793334 INFO::Done
2025-02-03 20:20:26.821393 INFO::Found NA in Reference column
2025-02-03 20:20:26.831227 INFO::Require at least two references per batch.
2025-02-03 20:20:26.852201 INFO::Formatting Data.
2025-02-03 20:20:26.853038 INFO::Recognized SummarizedExperiment
2025-02-03 20:20:26.853579 INFO::Typecasting input to dataframe.
2025-02-03 20:20:26.863873 INFO::Replacing NaNs with NAs.
2025-02-03 20:20:26.865178 INFO::Removing potential empty rows and columns
2025-02-03 20:20:26.868755 INFO::Found 0 missing values.
2025-02-03 20:20:26.875834 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 20:20:26.876637 INFO::Done
2025-02-03 20:20:26.893546 INFO::Formatting Data.
2025-02-03 20:20:26.894399 INFO::Recognized SummarizedExperiment
2025-02-03 20:20:26.89494 INFO::Typecasting input to dataframe.
2025-02-03 20:20:26.913188 INFO::Replacing NaNs with NAs.
2025-02-03 20:20:26.91454 INFO::Removing potential empty rows and columns
2025-02-03 20:20:26.91811 INFO::Found 0 missing values.
2025-02-03 20:20:26.929023 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 20:20:26.929798 INFO::Done
2025-02-03 20:20:26.946119 INFO::Formatting Data.
2025-02-03 20:20:26.946884 INFO::Recognized SummarizedExperiment
2025-02-03 20:20:26.947406 INFO::Typecasting input to dataframe.
2025-02-03 20:20:26.965036 INFO::Replacing NaNs with NAs.
2025-02-03 20:20:26.966082 INFO::Removing potential empty rows and columns
2025-02-03 20:20:26.967133 INFO::Found 0 missing values.
2025-02-03 20:20:26.968027 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 20:20:26.972271 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 20:20:26.97278 INFO::Done
2025-02-03 20:20:26.982613 INFO::Formatting Data.
2025-02-03 20:20:26.983348 INFO::Replacing NaNs with NAs.
2025-02-03 20:20:26.984202 INFO::Removing potential empty rows and columns
2025-02-03 20:20:26.985175 INFO::Found 0 missing values.
2025-02-03 20:20:26.988435 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 20:20:26.988995 INFO::Done
2025-02-03 20:20:26.999919 INFO::Formatting Data.
2025-02-03 20:20:27.00073 INFO::Replacing NaNs with NAs.
2025-02-03 20:20:27.001606 INFO::Removing potential empty rows and columns
2025-02-03 20:20:27.00258 INFO::Found 0 missing values.
2025-02-03 20:20:27.005371 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 20:20:27.005875 INFO::Done
2025-02-03 20:20:27.033412 INFO::Formatting Data.
2025-02-03 20:20:27.034231 INFO::Replacing NaNs with NAs.
2025-02-03 20:20:27.035393 INFO::Removing potential empty rows and columns
2025-02-03 20:20:27.036608 INFO::Found 1 missing values.
2025-02-03 20:20:27.039339 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 20:20:27.039839 INFO::Done
2025-02-03 20:20:27.071414 INFO::Formatting Data.
2025-02-03 20:20:27.072459 INFO::Replacing NaNs with NAs.
2025-02-03 20:20:27.073444 INFO::Removing potential empty rows and columns
2025-02-03 20:20:27.074571 INFO::Found 2 missing values.
2025-02-03 20:20:27.075642 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 20:20:27.078294 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-02-03 20:20:27.078904 INFO::Done
2025-02-03 20:20:27.090877 INFO::Formatting Data.
2025-02-03 20:20:27.091711 INFO::Replacing NaNs with NAs.
2025-02-03 20:20:27.092657 INFO::Removing potential empty rows and columns
2025-02-03 20:20:27.093702 INFO::Found 2 missing values.
2025-02-03 20:20:27.09544 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 20:20:27.095992 INFO::Done
2025-02-03 20:20:27.107903 INFO::Formatting Data.
2025-02-03 20:20:27.10875 INFO::Typecasting input to dataframe.
2025-02-03 20:20:27.109828 INFO::Replacing NaNs with NAs.
2025-02-03 20:20:27.110952 INFO::Removing potential empty rows and columns
2025-02-03 20:20:27.112121 INFO::Found 0 missing values.
2025-02-03 20:20:27.115609 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-03 20:20:27.116185 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
16.366 4.591 20.455
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.505 | 1.263 | 17.869 | |
| compute_asw | 0.024 | 0.000 | 0.024 | |
| count_existing | 0.012 | 0.002 | 0.014 | |
| generate_data_covariables | 0.011 | 0.001 | 0.012 | |
| generate_dataset | 0.010 | 0.002 | 0.012 | |