Yannis Schumann
| Snapshot Date: 2025-01-30 13:00 -0500 (Thu, 30 Jan 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 2025-02-03 12:06 -0500 (Mon, 03 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" | 4746 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4494 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4517 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4469 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4400 |
| 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: 2025-01-30 23:40:05 -0500 (Thu, 30 Jan 2025) |
| EndedAt: 2025-01-30 23:42:20 -0500 (Thu, 30 Jan 2025) |
| EllapsedTime: 135.9 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 9.31 0.62 18.77
* 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")
2025-01-30 23:41:07.956394 INFO::Formatting Data.
2025-01-30 23:41:07.959545 INFO::Replacing NaNs with NAs.
2025-01-30 23:41:07.975605 INFO::Removing potential empty rows and columns
2025-01-30 23:41:08.25768 INFO::Found 0 missing values.
2025-01-30 23:41:08.262463 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-30 23:41:08.263861 INFO::Done
2025-01-30 23:41:08.265042 INFO::Acquiring quality metrics before batch effect correction.
2025-01-30 23:41:08.284008 INFO::Starting hierarchical adjustment
2025-01-30 23:41:08.285642 INFO::Found 3 batches.
2025-01-30 23:41:08.286893 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-30 23:41:08.288836 INFO::Using default BPPARAM
2025-01-30 23:41:08.290003 INFO::Processing subtree level 1
2025-01-30 23:41:11.028619 INFO::Adjusting the last 1 batches sequentially
2025-01-30 23:41:11.030922 INFO::Done
2025-01-30 23:41:11.032264 INFO::Acquiring quality metrics after batch effect correction.
2025-01-30 23:41:11.035675 INFO::ASW Batch was -0.137253790386515 prior to batch effect correction and is now -0.137253790386515 .
2025-01-30 23:41:11.037441 INFO::Total function execution time is 3.08177590370178 s and adjustment time is 2.74554204940796 s ( 89.09 )
2025-01-30 23:41:11.06021 INFO::Formatting Data.
2025-01-30 23:41:11.061763 INFO::Replacing NaNs with NAs.
2025-01-30 23:41:11.063504 INFO::Removing potential empty rows and columns
2025-01-30 23:41:11.065494 INFO::Found 0 missing values.
2025-01-30 23:41:11.067228 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.
2025-01-30 23:41:11.081755 INFO::Formatting Data.
2025-01-30 23:41:11.083266 INFO::Replacing NaNs with NAs.
2025-01-30 23:41:11.084966 INFO::Removing potential empty rows and columns
2025-01-30 23:41:11.086847 INFO::Found 0 missing values.
2025-01-30 23:41:11.088564 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.
2025-01-30 23:41:11.114087 INFO::Formatting Data.
2025-01-30 23:41:11.115583 INFO::Replacing NaNs with NAs.
2025-01-30 23:41:11.117341 INFO::Removing potential empty rows and columns
2025-01-30 23:41:11.119212 INFO::Found 0 missing values.
2025-01-30 23:41:11.120837 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.
2025-01-30 23:41:11.12724 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-30 23:41:11.128592 INFO::Done
2025-01-30 23:41:11.129808 INFO::Acquiring quality metrics before batch effect correction.
2025-01-30 23:41:11.132995 INFO::Starting hierarchical adjustment
2025-01-30 23:41:11.134307 INFO::Found 2 batches.
2025-01-30 23:41:11.135555 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-30 23:41:11.136817 INFO::Using default BPPARAM
2025-01-30 23:41:11.137969 INFO::Adjusting the last 2 batches sequentially
2025-01-30 23:41:11.139746 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-30 23:41:11.168424 INFO::Done
2025-01-30 23:41:11.169835 INFO::Acquiring quality metrics after batch effect correction.
2025-01-30 23:41:11.173266 INFO::ASW Batch was -0.0538184255284207 prior to batch effect correction and is now -0.0992864880842614 .
2025-01-30 23:41:11.174919 INFO::Total function execution time is 0.0609071254730225 s and adjustment time is 0.0342659950256348 s ( 56.26 )
2025-01-30 23:41:11.179496 INFO::Formatting Data.
2025-01-30 23:41:11.1809 INFO::Replacing NaNs with NAs.
2025-01-30 23:41:11.193149 INFO::Formatting Data.
2025-01-30 23:41:11.1947 INFO::Replacing NaNs with NAs.
2025-01-30 23:41:11.196514 INFO::Removing potential empty rows and columns
2025-01-30 23:41:11.198468 INFO::Found 0 missing values.
2025-01-30 23:41:11.202836 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-30 23:41:11.204072 INFO::Done
2025-01-30 23:41:11.205249 INFO::Acquiring quality metrics before batch effect correction.
2025-01-30 23:41:11.20866 INFO::Starting hierarchical adjustment
2025-01-30 23:41:11.210032 INFO::Found 2 batches.
2025-01-30 23:41:11.211142 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-30 23:41:11.212402 INFO::Using default BPPARAM
2025-01-30 23:41:11.21353 INFO::Adjusting the last 2 batches sequentially
2025-01-30 23:41:11.215199 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-30 23:41:11.235567 INFO::Done
2025-01-30 23:41:11.236898 INFO::Acquiring quality metrics after batch effect correction.
2025-01-30 23:41:11.239428 INFO::ASW Batch was -0.0628358832436017 prior to batch effect correction and is now -0.123542611426462 .
2025-01-30 23:41:11.240497 INFO::Total function execution time is 0.0475091934204102 s and adjustment time is 0.0256788730621338 s ( 54.05 )
2025-01-30 23:41:11.241728 INFO::Formatting Data.
2025-01-30 23:41:11.242507 INFO::Replacing NaNs with NAs.
2025-01-30 23:41:11.243549 INFO::Removing potential empty rows and columns
2025-01-30 23:41:11.244697 INFO::Found 0 missing values.
2025-01-30 23:41:11.247379 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-30 23:41:11.248145 INFO::Done
2025-01-30 23:41:11.248871 INFO::Acquiring quality metrics before batch effect correction.
2025-01-30 23:41:11.251055 INFO::Starting hierarchical adjustment
2025-01-30 23:41:11.251913 INFO::Found 2 batches.
2025-01-30 23:41:11.252976 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-30 23:41:11.254228 INFO::Using default BPPARAM
2025-01-30 23:41:11.255368 INFO::Adjusting the last 2 batches sequentially
2025-01-30 23:41:11.257097 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-30 23:41:11.278225 INFO::Done
2025-01-30 23:41:11.279633 INFO::Acquiring quality metrics after batch effect correction.
2025-01-30 23:41:11.282944 INFO::ASW Batch was -0.0628358832436017 prior to batch effect correction and is now -0.123542611426462 .
2025-01-30 23:41:11.284523 INFO::Total function execution time is 0.0426859855651855 s and adjustment time is 0.026360034942627 s ( 61.75 )
2025-01-30 23:41:13.84052 INFO::Formatting Data.
2025-01-30 23:41:13.841432 INFO::Recognized SummarizedExperiment
2025-01-30 23:41:13.842167 INFO::Typecasting input to dataframe.
2025-01-30 23:41:13.88208 INFO::Replacing NaNs with NAs.
2025-01-30 23:41:13.884178 INFO::Removing potential empty rows and columns
2025-01-30 23:41:13.889188 INFO::Found 0 missing values.
2025-01-30 23:41:13.898579 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-30 23:41:13.90006 INFO::Done
2025-01-30 23:41:13.901187 INFO::Acquiring quality metrics before batch effect correction.
2025-01-30 23:41:13.906901 INFO::Starting hierarchical adjustment
2025-01-30 23:41:13.908228 INFO::Found 2 batches.
2025-01-30 23:41:13.909289 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-30 23:41:13.911181 INFO::Using default BPPARAM
2025-01-30 23:41:13.912328 INFO::Adjusting the last 2 batches sequentially
2025-01-30 23:41:13.914313 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-30 23:41:13.987226 INFO::Done
2025-01-30 23:41:13.988549 INFO::Acquiring quality metrics after batch effect correction.
2025-01-30 23:41:13.994686 INFO::ASW Batch was -0.0108853759784593 prior to batch effect correction and is now -0.0886694580220533 .
2025-01-30 23:41:13.996275 INFO::Total function execution time is 0.155951976776123 s and adjustment time is 0.079179048538208 s ( 50.77 )
2025-01-30 23:41:14.781871 INFO::Formatting Data.
2025-01-30 23:41:14.783287 INFO::Recognized SummarizedExperiment
2025-01-30 23:41:14.784495 INFO::Typecasting input to dataframe.
2025-01-30 23:41:14.797792 INFO::Replacing NaNs with NAs.
2025-01-30 23:41:14.799832 INFO::Removing potential empty rows and columns
2025-01-30 23:41:14.80471 INFO::Found 0 missing values.
2025-01-30 23:41:14.813796 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-30 23:41:14.815165 INFO::Done
2025-01-30 23:41:14.816424 INFO::Acquiring quality metrics before batch effect correction.
2025-01-30 23:41:14.822587 INFO::Starting hierarchical adjustment
2025-01-30 23:41:14.824144 INFO::Found 2 batches.
2025-01-30 23:41:14.82538 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-30 23:41:14.826668 INFO::Using default BPPARAM
2025-01-30 23:41:14.827822 INFO::Adjusting the last 2 batches sequentially
2025-01-30 23:41:14.829713 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-30 23:41:14.862641 INFO::Done
2025-01-30 23:41:14.864077 INFO::Acquiring quality metrics after batch effect correction.
2025-01-30 23:41:14.870248 INFO::ASW Batch was 0.0117177613938969 prior to batch effect correction and is now 0.0117177613938969 .
2025-01-30 23:41:14.871842 INFO::Total function execution time is 0.0899369716644287 s and adjustment time is 0.0386919975280762 s ( 43.02 )
2025-01-30 23:41:14.902009 INFO::Formatting Data.
2025-01-30 23:41:14.903498 INFO::Replacing NaNs with NAs.
2025-01-30 23:41:14.905229 INFO::Removing potential empty rows and columns
2025-01-30 23:41:14.907048 INFO::Found 0 missing values.
2025-01-30 23:41:14.911479 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-30 23:41:14.912649 INFO::Done
2025-01-30 23:41:14.913784 INFO::Acquiring quality metrics before batch effect correction.
2025-01-30 23:41:14.917066 INFO::Starting hierarchical adjustment
2025-01-30 23:41:14.918438 INFO::Found 3 batches.
2025-01-30 23:41:14.919585 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-30 23:41:14.920874 INFO::Using default BPPARAM
2025-01-30 23:41:14.922058 INFO::Processing subtree level 1
2025-01-30 23:41:25.031681 INFO::Adjusting the last 1 batches sequentially
2025-01-30 23:41:25.034012 INFO::Done
2025-01-30 23:41:25.035311 INFO::Acquiring quality metrics after batch effect correction.
2025-01-30 23:41:25.038596 INFO::ASW Batch was -0.0965986492962669 prior to batch effect correction and is now -0.171661996689613 .
2025-01-30 23:41:25.040066 INFO::Total function execution time is 10.1381678581238 s and adjustment time is 10.1157438755035 s ( 99.78 )
2025-01-30 23:41:25.062045 INFO::Skipping initial DF formatting
2025-01-30 23:41:25.063365 INFO::Acquiring quality metrics before batch effect correction.
2025-01-30 23:41:25.069788 INFO::Starting hierarchical adjustment
2025-01-30 23:41:25.071293 INFO::Found 5 batches.
2025-01-30 23:41:25.072406 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-30 23:41:25.07354 INFO::Using default BPPARAM
2025-01-30 23:41:25.074552 INFO::Processing subtree level 1
2025-01-30 23:41:28.236423 INFO::Adjusting the last 2 batches sequentially
2025-01-30 23:41:28.238163 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-30 23:41:28.26127 INFO::Done
2025-01-30 23:41:28.262693 INFO::Acquiring quality metrics after batch effect correction.
2025-01-30 23:41:28.26953 INFO::ASW Batch was 0.476466057380684 prior to batch effect correction and is now 0.476466057380684 .
2025-01-30 23:41:28.270523 INFO::ASW Label was 0.399545350999683 prior to batch effect correction and is now 0.399545350999683 .
2025-01-30 23:41:28.271625 INFO::Total function execution time is 3.20970702171326 s and adjustment time is 3.190181016922 s ( 99.39 )
2025-01-30 23:41:28.291202 INFO::Formatting Data.
2025-01-30 23:41:28.292204 INFO::Replacing NaNs with NAs.
2025-01-30 23:41:28.293317 INFO::Removing potential empty rows and columns
2025-01-30 23:41:28.294424 INFO::Found 0 missing values.
2025-01-30 23:41:28.298298 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-30 23:41:28.299068 INFO::Done
2025-01-30 23:41:28.299767 INFO::Acquiring quality metrics before batch effect correction.
2025-01-30 23:41:28.302931 INFO::Starting hierarchical adjustment
2025-01-30 23:41:28.303853 INFO::Found 5 batches.
2025-01-30 23:41:28.304552 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-30 23:41:28.305308 INFO::Using default BPPARAM
2025-01-30 23:41:28.305998 INFO::Processing subtree level 1
2025-01-30 23:41:31.684379 INFO::Adjusting the last 2 batches sequentially
2025-01-30 23:41:31.686169 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-30 23:41:31.707777 INFO::Done
2025-01-30 23:41:31.709223 INFO::Acquiring quality metrics after batch effect correction.
2025-01-30 23:41:31.714431 INFO::ASW Batch was 0.712299652257162 prior to batch effect correction and is now -0.0250900863644846 .
2025-01-30 23:41:31.715753 INFO::ASW Label was 0.166034815577234 prior to batch effect correction and is now 0.671071834380722 .
2025-01-30 23:41:31.717294 INFO::Total function execution time is 3.42610692977905 s and adjustment time is 3.40396499633789 s ( 99.35 )
2025-01-30 23:41:31.718669 INFO::Formatting Data.
2025-01-30 23:41:31.719737 INFO::Replacing NaNs with NAs.
2025-01-30 23:41:31.721174 INFO::Removing potential empty rows and columns
2025-01-30 23:41:31.722675 INFO::Found 0 missing values.
2025-01-30 23:41:31.727928 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-30 23:41:31.729044 INFO::Done
2025-01-30 23:41:31.730049 INFO::Acquiring quality metrics before batch effect correction.
2025-01-30 23:41:31.734366 INFO::Starting hierarchical adjustment
2025-01-30 23:41:31.735719 INFO::Found 5 batches.
2025-01-30 23:41:31.736967 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-30 23:41:31.738272 INFO::Using default BPPARAM
2025-01-30 23:41:31.73946 INFO::Processing subtree level 1
2025-01-30 23:41:35.108376 INFO::Adjusting the last 2 batches sequentially
2025-01-30 23:41:35.110402 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-30 23:41:35.12893 INFO::Done
2025-01-30 23:41:35.130287 INFO::Acquiring quality metrics after batch effect correction.
2025-01-30 23:41:35.135155 INFO::ASW Batch was 0.712299652257162 prior to batch effect correction and is now -0.0250900863644846 .
2025-01-30 23:41:35.136465 INFO::ASW Label was 0.166034815577234 prior to batch effect correction and is now 0.671071834380722 .
2025-01-30 23:41:35.137534 INFO::Total function execution time is 3.41891121864319 s and adjustment time is 3.39339399337769 s ( 99.25 )
2025-01-30 23:41:35.157478 INFO::Formatting Data.
2025-01-30 23:41:35.15866 INFO::Replacing NaNs with NAs.
2025-01-30 23:41:35.160408 INFO::Removing potential empty rows and columns
2025-01-30 23:41:35.1622 INFO::Found 0 missing values.
2025-01-30 23:41:35.168333 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-30 23:41:35.16965 INFO::Done
2025-01-30 23:41:35.170894 INFO::Acquiring quality metrics before batch effect correction.
2025-01-30 23:41:35.176023 INFO::Starting hierarchical adjustment
2025-01-30 23:41:35.177579 INFO::Found 5 batches.
2025-01-30 23:41:35.178794 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-30 23:41:35.180058 INFO::Using default BPPARAM
2025-01-30 23:41:35.181223 INFO::Processing subtree level 1
2025-01-30 23:41:38.437791 INFO::Adjusting the last 2 batches sequentially
2025-01-30 23:41:38.439859 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-30 23:41:38.458521 INFO::Done
2025-01-30 23:41:38.459869 INFO::Acquiring quality metrics after batch effect correction.
2025-01-30 23:41:38.464604 INFO::ASW Batch was 0.517718837871039 prior to batch effect correction and is now -0.0979156737120005 .
2025-01-30 23:41:38.465901 INFO::ASW Label was 0.18307723643526 prior to batch effect correction and is now 0.809385161318627 .
2025-01-30 23:41:38.467453 INFO::Total function execution time is 3.30998396873474 s and adjustment time is 3.28115916252136 s ( 99.13 )
2025-01-30 23:41:38.46901 INFO::Formatting Data.
2025-01-30 23:41:38.470259 INFO::Replacing NaNs with NAs.
2025-01-30 23:41:38.471911 INFO::Removing potential empty rows and columns
2025-01-30 23:41:38.473247 INFO::Found 0 missing values.
2025-01-30 23:41:38.478892 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-30 23:41:38.480171 INFO::Done
2025-01-30 23:41:38.481365 INFO::Acquiring quality metrics before batch effect correction.
2025-01-30 23:41:38.486362 INFO::Starting hierarchical adjustment
2025-01-30 23:41:38.487857 INFO::Found 5 batches.
2025-01-30 23:41:38.489023 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-30 23:41:38.490266 INFO::Using default BPPARAM
2025-01-30 23:41:38.491385 INFO::Processing subtree level 1
2025-01-30 23:41:41.733892 INFO::Adjusting the last 2 batches sequentially
2025-01-30 23:41:41.735864 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-30 23:41:41.753917 INFO::Done
2025-01-30 23:41:41.755254 INFO::Acquiring quality metrics after batch effect correction.
2025-01-30 23:41:41.760179 INFO::ASW Batch was 0.517718837871039 prior to batch effect correction and is now -0.0979156737120005 .
2025-01-30 23:41:41.761491 INFO::ASW Label was 0.18307723643526 prior to batch effect correction and is now 0.809385161318627 .
2025-01-30 23:41:41.763053 INFO::Total function execution time is 3.29404783248901 s and adjustment time is 3.266282081604 s ( 99.16 )
2025-01-30 23:41:41.785567 INFO::Formatting Data.
2025-01-30 23:41:41.787102 INFO::Replacing NaNs with NAs.
2025-01-30 23:41:41.788846 INFO::Removing potential empty rows and columns
2025-01-30 23:41:41.790701 INFO::Found 0 missing values.
2025-01-30 23:41:41.795034 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-30 23:41:41.79632 INFO::Done
2025-01-30 23:41:41.797555 INFO::Acquiring quality metrics before batch effect correction.
2025-01-30 23:41:41.802428 INFO::Starting hierarchical adjustment
2025-01-30 23:41:41.80397 INFO::Found 2 batches.
2025-01-30 23:41:41.805193 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-30 23:41:41.806522 INFO::Using default BPPARAM
2025-01-30 23:41:41.807701 INFO::Adjusting the last 2 batches sequentially
2025-01-30 23:41:41.809522 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-30 23:41:41.83076 INFO::Done
2025-01-30 23:41:41.832157 INFO::Acquiring quality metrics after batch effect correction.
2025-01-30 23:41:41.836493 INFO::ASW Batch was 0.609133557457915 prior to batch effect correction and is now -0.023725315444358 .
2025-01-30 23:41:41.837324 INFO::ASW Label was 0.468507561446644 prior to batch effect correction and is now 0.918514819927289 .
2025-01-30 23:41:41.83827 INFO::Total function execution time is 0.0528891086578369 s and adjustment time is 0.0269958972930908 s ( 51.04 )
2025-01-30 23:41:41.83919 INFO::Formatting Data.
2025-01-30 23:41:41.839967 INFO::Replacing NaNs with NAs.
2025-01-30 23:41:41.841 INFO::Removing potential empty rows and columns
2025-01-30 23:41:41.842084 INFO::Found 0 missing values.
2025-01-30 23:41:41.844509 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-30 23:41:41.845216 INFO::Done
2025-01-30 23:41:41.845888 INFO::Acquiring quality metrics before batch effect correction.
2025-01-30 23:41:41.848843 INFO::Starting hierarchical adjustment
2025-01-30 23:41:41.849737 INFO::Found 2 batches.
2025-01-30 23:41:41.850482 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-30 23:41:41.851256 INFO::Using default BPPARAM
2025-01-30 23:41:41.851949 INFO::Adjusting the last 2 batches sequentially
2025-01-30 23:41:41.853019 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-30 23:41:41.865319 INFO::Done
2025-01-30 23:41:41.866221 INFO::Acquiring quality metrics after batch effect correction.
2025-01-30 23:41:41.86932 INFO::ASW Batch was 0.609133557457915 prior to batch effect correction and is now -0.023725315444358 .
2025-01-30 23:41:41.870145 INFO::ASW Label was 0.468507561446644 prior to batch effect correction and is now 0.918514819927289 .
2025-01-30 23:41:41.871085 INFO::Total function execution time is 0.0319020748138428 s and adjustment time is 0.0156779289245605 s ( 49.14 )
2025-01-30 23:41:41.888788 INFO::Formatting Data.
2025-01-30 23:41:41.890404 INFO::Replacing NaNs with NAs.
2025-01-30 23:41:41.89222 INFO::Removing potential empty rows and columns
2025-01-30 23:41:41.894006 INFO::Found 0 missing values.
2025-01-30 23:41:41.897626 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-30 23:41:41.898814 INFO::Done
2025-01-30 23:41:41.900004 INFO::Acquiring quality metrics before batch effect correction.
2025-01-30 23:41:41.903419 INFO::Starting hierarchical adjustment
2025-01-30 23:41:41.904572 INFO::Found 2 batches.
2025-01-30 23:41:41.905292 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-30 23:41:41.906077 INFO::Using default BPPARAM
2025-01-30 23:41:41.906806 INFO::Adjusting the last 2 batches sequentially
2025-01-30 23:41:41.90789 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-30 23:41:41.933666 INFO::Done
2025-01-30 23:41:41.934606 INFO::Acquiring quality metrics after batch effect correction.
2025-01-30 23:41:41.9368 INFO::ASW Batch was -0.0713615347268362 prior to batch effect correction and is now -0.12872179661958 .
2025-01-30 23:41:41.93785 INFO::Total function execution time is 0.0493199825286865 s and adjustment time is 0.0292201042175293 s ( 59.25 )
2025-01-30 23:41:41.952869 INFO::Formatting Data.
2025-01-30 23:41:41.953846 INFO::Replacing NaNs with NAs.
2025-01-30 23:41:41.954936 INFO::Removing potential empty rows and columns
2025-01-30 23:41:41.956079 INFO::Found 0 missing values.
2025-01-30 23:41:41.957375 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.
2025-01-30 23:41:41.962187 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-30 23:41:41.963024 INFO::Done
2025-01-30 23:41:41.963929 INFO::Acquiring quality metrics before batch effect correction.
2025-01-30 23:41:41.967441 INFO::Starting hierarchical adjustment
2025-01-30 23:41:41.968426 INFO::Found 2 batches.
2025-01-30 23:41:41.969178 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-30 23:41:41.970005 INFO::Using default BPPARAM
2025-01-30 23:41:41.971144 INFO::Adjusting the last 2 batches sequentially
2025-01-30 23:41:41.972916 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-30 23:41:41.989238 INFO::Done
2025-01-30 23:41:41.990127 INFO::Acquiring quality metrics after batch effect correction.
2025-01-30 23:41:41.99312 INFO::ASW Batch was 0.373992840988191 prior to batch effect correction and is now -0.0153876973057756 .
2025-01-30 23:41:41.993888 INFO::ASW Label was 0.675050896172555 prior to batch effect correction and is now 0.952080858349893 .
2025-01-30 23:41:41.994828 INFO::Total function execution time is 0.0420670509338379 s and adjustment time is 0.020963191986084 s ( 49.83 )
2025-01-30 23:41:41.99578 INFO::Formatting Data.
2025-01-30 23:41:41.996572 INFO::Replacing NaNs with NAs.
2025-01-30 23:41:41.9978 INFO::Removing potential empty rows and columns
2025-01-30 23:41:41.999432 INFO::Found 0 missing values.
2025-01-30 23:41:42.000921 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.
2025-01-30 23:41:42.005035 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-30 23:41:42.005774 INFO::Done
2025-01-30 23:41:42.006485 INFO::Acquiring quality metrics before batch effect correction.
2025-01-30 23:41:42.011381 INFO::Starting hierarchical adjustment
2025-01-30 23:41:42.012781 INFO::Found 2 batches.
2025-01-30 23:41:42.013953 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-30 23:41:42.015164 INFO::Using default BPPARAM
2025-01-30 23:41:42.016266 INFO::Adjusting the last 2 batches sequentially
2025-01-30 23:41:42.018039 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-30 23:41:42.04233 INFO::Done
2025-01-30 23:41:42.043707 INFO::Acquiring quality metrics after batch effect correction.
2025-01-30 23:41:42.048803 INFO::ASW Batch was 0.373992840988191 prior to batch effect correction and is now -0.0153876973057756 .
2025-01-30 23:41:42.050058 INFO::ASW Label was 0.675050896172555 prior to batch effect correction and is now 0.952080858349893 .
2025-01-30 23:41:42.051624 INFO::Total function execution time is 0.0557558536529541 s and adjustment time is 0.0297160148620605 s ( 53.3 )
2025-01-30 23:41:42.326322 INFO::Formatting Data.
2025-01-30 23:41:42.328055 INFO::Replacing NaNs with NAs.
2025-01-30 23:41:42.33004 INFO::Removing potential empty rows and columns
2025-01-30 23:41:42.332154 INFO::Found 0 missing values.
2025-01-30 23:41:42.337388 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-30 23:41:42.33874 INFO::Done
2025-01-30 23:41:42.339969 INFO::Acquiring quality metrics before batch effect correction.
2025-01-30 23:41:42.343514 INFO::Starting hierarchical adjustment
2025-01-30 23:41:42.345036 INFO::Found 3 batches.
2025-01-30 23:41:42.346259 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-30 23:41:42.347614 INFO::Using default BPPARAM
2025-01-30 23:41:42.348872 INFO::Processing subtree level 1
2025-01-30 23:41:45.35569 INFO::Adjusting the last 1 batches sequentially
2025-01-30 23:41:45.357903 INFO::Done
2025-01-30 23:41:45.35915 INFO::Acquiring quality metrics after batch effect correction.
2025-01-30 23:41:45.362115 INFO::ASW Batch was -0.0796327646845542 prior to batch effect correction and is now -0.0796327646845542 .
2025-01-30 23:41:45.363518 INFO::Total function execution time is 3.03736090660095 s and adjustment time is 3.01309394836426 s ( 99.2 )
2025-01-30 23:41:45.365068 INFO::Formatting Data.
2025-01-30 23:41:45.366229 INFO::Typecasting input to dataframe.
2025-01-30 23:41:45.367501 INFO::Replacing NaNs with NAs.
2025-01-30 23:41:45.36897 INFO::Removing potential empty rows and columns
2025-01-30 23:41:45.370519 INFO::Found 0 missing values.
2025-01-30 23:41:45.374409 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-30 23:41:45.375482 INFO::Done
2025-01-30 23:41:45.376496 INFO::Acquiring quality metrics before batch effect correction.
2025-01-30 23:41:45.379489 INFO::Starting hierarchical adjustment
2025-01-30 23:41:45.380518 INFO::Found 3 batches.
2025-01-30 23:41:45.381268 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-30 23:41:45.382023 INFO::Using default BPPARAM
2025-01-30 23:41:45.382694 INFO::Processing subtree level 1
2025-01-30 23:41:48.358346 INFO::Adjusting the last 1 batches sequentially
2025-01-30 23:41:48.3601 INFO::Done
2025-01-30 23:41:48.36129 INFO::Acquiring quality metrics after batch effect correction.
2025-01-30 23:41:48.364505 INFO::ASW Batch was -0.0796327646845542 prior to batch effect correction and is now -0.0796327646845542 .
2025-01-30 23:41:48.365974 INFO::Total function execution time is 3.0009081363678 s and adjustment time is 2.97968101501465 s ( 99.29 )
2025-01-30 23:41:48.386671 INFO::Formatting Data.
2025-01-30 23:41:48.387686 INFO::Typecasting input to dataframe.
2025-01-30 23:41:48.388683 INFO::Replacing NaNs with NAs.
2025-01-30 23:41:48.389729 INFO::Removing potential empty rows and columns
2025-01-30 23:41:48.391395 INFO::Found 0 missing values.
2025-01-30 23:41:48.395524 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-30 23:41:48.396638 INFO::Done
2025-01-30 23:41:48.397714 INFO::Acquiring quality metrics before batch effect correction.
2025-01-30 23:41:48.400738 INFO::Starting hierarchical adjustment
2025-01-30 23:41:48.402037 INFO::Found 3 batches.
2025-01-30 23:41:48.4031 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-30 23:41:48.404277 INFO::Using default BPPARAM
2025-01-30 23:41:48.405369 INFO::Processing subtree level 1
2025-01-30 23:41:51.131193 INFO::Adjusting the last 1 batches sequentially
2025-01-30 23:41:51.132749 INFO::Done
2025-01-30 23:41:51.133733 INFO::Acquiring quality metrics after batch effect correction.
2025-01-30 23:41:51.135948 INFO::ASW Batch was -0.0711384778903584 prior to batch effect correction and is now -0.0711384778903584 .
2025-01-30 23:41:51.136909 INFO::Total function execution time is 2.75034594535828 s and adjustment time is 2.73091602325439 s ( 99.29 )
2025-01-30 23:41:53.832522 INFO::Formatting Data.
2025-01-30 23:41:53.833913 INFO::Replacing NaNs with NAs.
2025-01-30 23:41:53.835325 INFO::Removing potential empty rows and columns
2025-01-30 23:41:53.83885 INFO::Found 1000 missing values.
2025-01-30 23:41:53.853247 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-30 23:41:53.85427 INFO::Done
2025-01-30 23:41:53.855168 INFO::Acquiring quality metrics before batch effect correction.
2025-01-30 23:41:53.861851 INFO::Starting hierarchical adjustment
2025-01-30 23:41:53.862927 INFO::Found 10 batches.
2025-01-30 23:41:53.863647 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-30 23:41:53.864409 INFO::Using default BPPARAM
2025-01-30 23:41:53.865114 INFO::Processing subtree level 1
2025-01-30 23:41:57.035242 INFO::Processing subtree level 2
2025-01-30 23:41:59.985318 INFO::Adjusting the last 1 batches sequentially
2025-01-30 23:41:59.988081 INFO::Done
2025-01-30 23:41:59.989519 INFO::Acquiring quality metrics after batch effect correction.
2025-01-30 23:41:59.999908 INFO::ASW Batch was 0.483694678310434 prior to batch effect correction and is now 0.483694678310434 .
2025-01-30 23:42:00.001443 INFO::ASW Label was 0.346070190788383 prior to batch effect correction and is now 0.346070190788383 .
2025-01-30 23:42:00.003288 INFO::Total function execution time is 6.17081713676453 s and adjustment time is 6.12524819374084 s ( 99.26 )
2025-01-30 23:42:00.004962 INFO::Formatting Data.
2025-01-30 23:42:00.006386 INFO::Replacing NaNs with NAs.
2025-01-30 23:42:00.008486 INFO::Removing potential empty rows and columns
2025-01-30 23:42:00.012308 INFO::Found 1000 missing values.
2025-01-30 23:42:00.036276 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-30 23:42:00.037737 INFO::Done
2025-01-30 23:42:00.03899 INFO::Acquiring quality metrics before batch effect correction.
2025-01-30 23:42:00.049074 INFO::Starting hierarchical adjustment
2025-01-30 23:42:00.050721 INFO::Found 10 batches.
2025-01-30 23:42:00.782221 INFO::Set up parallel execution backend with 2 workers
2025-01-30 23:42:00.783224 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-01-30 23:42:03.809507 INFO::Adjusting the last 2 batches sequentially
2025-01-30 23:42:03.811538 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-30 23:42:03.833403 INFO::Done
2025-01-30 23:42:03.834696 INFO::Acquiring quality metrics after batch effect correction.
2025-01-30 23:42:03.843805 INFO::ASW Batch was 0.483694678310434 prior to batch effect correction and is now 0.483694678310434 .
2025-01-30 23:42:03.845084 INFO::ASW Label was 0.346070190788383 prior to batch effect correction and is now 0.346070190788383 .
2025-01-30 23:42:03.846502 INFO::Total function execution time is 3.84162616729736 s and adjustment time is 3.78291606903076 s ( 98.47 )
2025-01-30 23:42:06.915915 INFO::Formatting Data.
2025-01-30 23:42:06.917476 INFO::Replacing NaNs with NAs.
2025-01-30 23:42:06.919297 INFO::Removing potential empty rows and columns
2025-01-30 23:42:06.92128 INFO::Found 0 missing values.
2025-01-30 23:42:06.927155 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-30 23:42:06.928409 INFO::Done
2025-01-30 23:42:06.929535 INFO::Acquiring quality metrics before batch effect correction.
2025-01-30 23:42:06.933817 INFO::Starting hierarchical adjustment
2025-01-30 23:42:06.935219 INFO::Found 3 batches.
2025-01-30 23:42:06.936368 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-30 23:42:06.9376 INFO::Using default BPPARAM
2025-01-30 23:42:06.938731 INFO::Processing subtree level 1
2025-01-30 23:42:09.921118 INFO::Adjusting the last 1 batches sequentially
2025-01-30 23:42:09.923257 INFO::Done
2025-01-30 23:42:09.924407 INFO::Acquiring quality metrics after batch effect correction.
2025-01-30 23:42:09.928217 INFO::ASW Batch was 0.218701404632491 prior to batch effect correction and is now -0.191405262047265 .
2025-01-30 23:42:09.929337 INFO::ASW Label was -0.163848511287874 prior to batch effect correction and is now 0.065915667224593 .
2025-01-30 23:42:09.930696 INFO::Total function execution time is 3.01492309570312 s and adjustment time is 2.98824119567871 s ( 99.12 )
2025-01-30 23:42:10.107759 INFO::Formatting Data.
2025-01-30 23:42:10.109298 INFO::Replacing NaNs with NAs.
2025-01-30 23:42:10.110845 INFO::Removing potential empty rows and columns
2025-01-30 23:42:10.11281 INFO::Found 2 missing values.
2025-01-30 23:42:10.115451 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-01-30 23:42:10.117177 INFO::Done
2025-01-30 23:42:10.151916 INFO::Found NA in Reference column
2025-01-30 23:42:10.163871 INFO::Require at least two references per batch.
2025-01-30 23:42:10.183267 INFO::Formatting Data.
2025-01-30 23:42:10.184203 INFO::Recognized SummarizedExperiment
2025-01-30 23:42:10.184928 INFO::Typecasting input to dataframe.
2025-01-30 23:42:10.192756 INFO::Replacing NaNs with NAs.
2025-01-30 23:42:10.194062 INFO::Removing potential empty rows and columns
2025-01-30 23:42:10.196795 INFO::Found 0 missing values.
2025-01-30 23:42:10.201896 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-30 23:42:10.202688 INFO::Done
2025-01-30 23:42:10.216551 INFO::Formatting Data.
2025-01-30 23:42:10.217464 INFO::Recognized SummarizedExperiment
2025-01-30 23:42:10.218214 INFO::Typecasting input to dataframe.
2025-01-30 23:42:10.232877 INFO::Replacing NaNs with NAs.
2025-01-30 23:42:10.234306 INFO::Removing potential empty rows and columns
2025-01-30 23:42:10.237182 INFO::Found 0 missing values.
2025-01-30 23:42:10.245261 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-30 23:42:10.246119 INFO::Done
2025-01-30 23:42:10.260398 INFO::Formatting Data.
2025-01-30 23:42:10.261319 INFO::Recognized SummarizedExperiment
2025-01-30 23:42:10.262074 INFO::Typecasting input to dataframe.
2025-01-30 23:42:10.27681 INFO::Replacing NaNs with NAs.
2025-01-30 23:42:10.278048 INFO::Removing potential empty rows and columns
2025-01-30 23:42:10.279208 INFO::Found 0 missing values.
2025-01-30 23:42:10.280347 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.
2025-01-30 23:42:10.284293 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-30 23:42:10.285056 INFO::Done
2025-01-30 23:42:10.29765 INFO::Formatting Data.
2025-01-30 23:42:10.298601 INFO::Replacing NaNs with NAs.
2025-01-30 23:42:10.299634 INFO::Removing potential empty rows and columns
2025-01-30 23:42:10.300718 INFO::Found 0 missing values.
2025-01-30 23:42:10.30327 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-30 23:42:10.303983 INFO::Done
2025-01-30 23:42:10.317831 INFO::Formatting Data.
2025-01-30 23:42:10.318861 INFO::Replacing NaNs with NAs.
2025-01-30 23:42:10.319968 INFO::Removing potential empty rows and columns
2025-01-30 23:42:10.32115 INFO::Found 0 missing values.
2025-01-30 23:42:10.323826 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-30 23:42:10.324603 INFO::Done
2025-01-30 23:42:10.361799 INFO::Formatting Data.
2025-01-30 23:42:10.362805 INFO::Replacing NaNs with NAs.
2025-01-30 23:42:10.364039 INFO::Removing potential empty rows and columns
2025-01-30 23:42:10.365298 INFO::Found 1 missing values.
2025-01-30 23:42:10.367902 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-30 23:42:10.368663 INFO::Done
2025-01-30 23:42:10.392861 INFO::Formatting Data.
2025-01-30 23:42:10.393853 INFO::Replacing NaNs with NAs.
2025-01-30 23:42:10.394902 INFO::Removing potential empty rows and columns
2025-01-30 23:42:10.395985 INFO::Found 2 missing values.
2025-01-30 23:42:10.397056 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.
2025-01-30 23:42:10.399279 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-01-30 23:42:10.400069 INFO::Done
2025-01-30 23:42:10.413363 INFO::Formatting Data.
2025-01-30 23:42:10.414355 INFO::Replacing NaNs with NAs.
2025-01-30 23:42:10.415434 INFO::Removing potential empty rows and columns
2025-01-30 23:42:10.41651 INFO::Found 2 missing values.
2025-01-30 23:42:10.418179 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-30 23:42:10.418881 INFO::Done
2025-01-30 23:42:10.432868 INFO::Formatting Data.
2025-01-30 23:42:10.433873 INFO::Typecasting input to dataframe.
2025-01-30 23:42:10.434932 INFO::Replacing NaNs with NAs.
2025-01-30 23:42:10.436005 INFO::Removing potential empty rows and columns
2025-01-30 23:42:10.437244 INFO::Found 0 missing values.
2025-01-30 23:42:10.440063 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-30 23:42:10.440803 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
30.57 1.42 77.23
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 9.31 | 0.62 | 18.77 | |
| compute_asw | 0.05 | 0.00 | 0.05 | |
| count_existing | 0.02 | 0.00 | 0.02 | |
| generate_data_covariables | 0.01 | 0.00 | 0.02 | |
| generate_dataset | 0.01 | 0.00 | 0.02 | |