Yannis Schumann
| Snapshot Date: 2024-11-07 13:40 -0500 (Thu, 07 Nov 2024) |
| 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 2024-11-08 12:02 -0500 (Fri, 08 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4505 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4765 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4506 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4538 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| 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
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 2024-11-07 22:28:17 -0500 (Thu, 07 Nov 2024) |
| EndedAt: 2024-11-07 22:29:42 -0500 (Thu, 07 Nov 2024) |
| EllapsedTime: 85.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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 ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 19.157 1.357 15.383
* 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 ‘/media/volume/teran2_disk/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 4.4.1 (2024-06-14) -- "Race for Your Life"
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")
2024-11-07 22:29:05.320237 INFO::Formatting Data.
2024-11-07 22:29:05.321398 INFO::Replacing NaNs with NAs.
2024-11-07 22:29:05.330367 INFO::Removing potential empty rows and columns
2024-11-07 22:29:05.538315 INFO::Found 0 missing values.
2024-11-07 22:29:05.541052 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 22:29:05.541515 INFO::Done
2024-11-07 22:29:05.541915 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 22:29:05.550661 INFO::Starting hierarchical adjustment
2024-11-07 22:29:05.55126 INFO::Found 3 batches.
2024-11-07 22:29:05.551681 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 22:29:05.552614 INFO::Using default BPPARAM
2024-11-07 22:29:05.553093 INFO::Processing subtree level 1
2024-11-07 22:29:05.672817 INFO::Adjusting the last 1 batches sequentially
2024-11-07 22:29:05.674447 INFO::Done
2024-11-07 22:29:05.679016 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 22:29:05.681446 INFO::ASW Batch was -0.0716643751731329 prior to batch effect correction and is now -0.0716643751731329 .
2024-11-07 22:29:05.686353 INFO::Total function execution time is 0.366620302200317 s and adjustment time is 0.123320579528809 s ( 33.64 )
2024-11-07 22:29:05.706347 INFO::Formatting Data.
2024-11-07 22:29:05.706847 INFO::Replacing NaNs with NAs.
2024-11-07 22:29:05.707565 INFO::Removing potential empty rows and columns
2024-11-07 22:29:05.708447 INFO::Found 0 missing values.
2024-11-07 22:29:05.709195 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.
2024-11-07 22:29:05.717889 INFO::Formatting Data.
2024-11-07 22:29:05.718387 INFO::Replacing NaNs with NAs.
2024-11-07 22:29:05.719051 INFO::Removing potential empty rows and columns
2024-11-07 22:29:05.719841 INFO::Found 0 missing values.
2024-11-07 22:29:05.720547 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.
2024-11-07 22:29:05.732768 INFO::Formatting Data.
2024-11-07 22:29:05.733281 INFO::Replacing NaNs with NAs.
2024-11-07 22:29:05.733924 INFO::Removing potential empty rows and columns
2024-11-07 22:29:05.734715 INFO::Found 0 missing values.
2024-11-07 22:29:05.735393 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.
2024-11-07 22:29:05.738927 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 22:29:05.739371 INFO::Done
2024-11-07 22:29:05.739765 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 22:29:05.741447 INFO::Starting hierarchical adjustment
2024-11-07 22:29:05.742097 INFO::Found 2 batches.
2024-11-07 22:29:05.74256 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 22:29:05.743118 INFO::Using default BPPARAM
2024-11-07 22:29:05.743555 INFO::Adjusting the last 2 batches sequentially
2024-11-07 22:29:05.744321 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 22:29:05.764288 INFO::Done
2024-11-07 22:29:05.764784 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 22:29:05.766501 INFO::ASW Batch was -0.0243611387782421 prior to batch effect correction and is now -0.110120096868932 .
2024-11-07 22:29:05.767182 INFO::Total function execution time is 0.0344035625457764 s and adjustment time is 0.0223488807678223 s ( 64.96 )
2024-11-07 22:29:05.769422 INFO::Formatting Data.
2024-11-07 22:29:05.769968 INFO::Replacing NaNs with NAs.
2024-11-07 22:29:05.777447 INFO::Formatting Data.
2024-11-07 22:29:05.778056 INFO::Replacing NaNs with NAs.
2024-11-07 22:29:05.778806 INFO::Removing potential empty rows and columns
2024-11-07 22:29:05.779852 INFO::Found 0 missing values.
2024-11-07 22:29:05.782419 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 22:29:05.782871 INFO::Done
2024-11-07 22:29:05.783383 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 22:29:05.785256 INFO::Starting hierarchical adjustment
2024-11-07 22:29:05.785879 INFO::Found 2 batches.
2024-11-07 22:29:05.786367 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 22:29:05.786853 INFO::Using default BPPARAM
2024-11-07 22:29:05.787357 INFO::Adjusting the last 2 batches sequentially
2024-11-07 22:29:05.78818 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 22:29:05.801056 INFO::Done
2024-11-07 22:29:05.80152 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 22:29:05.80311 INFO::ASW Batch was -0.0427781124495945 prior to batch effect correction and is now -0.107609416525536 .
2024-11-07 22:29:05.803737 INFO::Total function execution time is 0.0263032913208008 s and adjustment time is 0.0153062343597412 s ( 58.19 )
2024-11-07 22:29:05.804607 INFO::Formatting Data.
2024-11-07 22:29:05.805131 INFO::Replacing NaNs with NAs.
2024-11-07 22:29:05.80581 INFO::Removing potential empty rows and columns
2024-11-07 22:29:05.806676 INFO::Found 0 missing values.
2024-11-07 22:29:05.809124 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 22:29:05.809578 INFO::Done
2024-11-07 22:29:05.810016 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 22:29:05.811604 INFO::Starting hierarchical adjustment
2024-11-07 22:29:05.812212 INFO::Found 2 batches.
2024-11-07 22:29:05.812643 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 22:29:05.81317 INFO::Using default BPPARAM
2024-11-07 22:29:05.813586 INFO::Adjusting the last 2 batches sequentially
2024-11-07 22:29:05.814331 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 22:29:05.826802 INFO::Done
2024-11-07 22:29:05.827281 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 22:29:05.828862 INFO::ASW Batch was -0.0427781124495945 prior to batch effect correction and is now -0.107609416525536 .
2024-11-07 22:29:05.829503 INFO::Total function execution time is 0.0248954296112061 s and adjustment time is 0.0147140026092529 s ( 59.1 )
2024-11-07 22:29:07.435677 INFO::Formatting Data.
2024-11-07 22:29:07.436273 INFO::Recognized SummarizedExperiment
2024-11-07 22:29:07.436597 INFO::Typecasting input to dataframe.
2024-11-07 22:29:07.458533 INFO::Replacing NaNs with NAs.
2024-11-07 22:29:07.459271 INFO::Removing potential empty rows and columns
2024-11-07 22:29:07.461797 INFO::Found 0 missing values.
2024-11-07 22:29:07.466457 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 22:29:07.466814 INFO::Done
2024-11-07 22:29:07.467169 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 22:29:07.469572 INFO::Starting hierarchical adjustment
2024-11-07 22:29:07.470068 INFO::Found 2 batches.
2024-11-07 22:29:07.470422 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 22:29:07.47113 INFO::Using default BPPARAM
2024-11-07 22:29:07.471472 INFO::Adjusting the last 2 batches sequentially
2024-11-07 22:29:07.472097 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 22:29:07.509547 INFO::Done
2024-11-07 22:29:07.509961 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 22:29:07.512304 INFO::ASW Batch was -0.00899372123098378 prior to batch effect correction and is now -0.100498960473975 .
2024-11-07 22:29:07.51284 INFO::Total function execution time is 0.0774340629577637 s and adjustment time is 0.0396087169647217 s ( 51.15 )
2024-11-07 22:29:07.525596 INFO::Formatting Data.
2024-11-07 22:29:07.526014 INFO::Recognized SummarizedExperiment
2024-11-07 22:29:07.526343 INFO::Typecasting input to dataframe.
2024-11-07 22:29:07.532199 INFO::Replacing NaNs with NAs.
2024-11-07 22:29:07.53287 INFO::Removing potential empty rows and columns
2024-11-07 22:29:07.535171 INFO::Found 0 missing values.
2024-11-07 22:29:07.539684 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 22:29:07.540057 INFO::Done
2024-11-07 22:29:07.540399 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 22:29:07.542565 INFO::Starting hierarchical adjustment
2024-11-07 22:29:07.543056 INFO::Found 2 batches.
2024-11-07 22:29:07.543405 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 22:29:07.543768 INFO::Using default BPPARAM
2024-11-07 22:29:07.544125 INFO::Adjusting the last 2 batches sequentially
2024-11-07 22:29:07.544731 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 22:29:07.560493 INFO::Done
2024-11-07 22:29:07.560868 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 22:29:07.563026 INFO::ASW Batch was 0.00930603199611931 prior to batch effect correction and is now 0.00930603199611931 .
2024-11-07 22:29:07.563542 INFO::Total function execution time is 0.0379147529602051 s and adjustment time is 0.0175659656524658 s ( 46.33 )
2024-11-07 22:29:07.575076 INFO::Formatting Data.
2024-11-07 22:29:07.575496 INFO::Replacing NaNs with NAs.
2024-11-07 22:29:07.576059 INFO::Removing potential empty rows and columns
2024-11-07 22:29:07.576693 INFO::Found 0 missing values.
2024-11-07 22:29:07.578526 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 22:29:07.578879 INFO::Done
2024-11-07 22:29:07.579224 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 22:29:07.580422 INFO::Starting hierarchical adjustment
2024-11-07 22:29:07.580925 INFO::Found 3 batches.
2024-11-07 22:29:07.581284 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 22:29:07.581642 INFO::Using default BPPARAM
2024-11-07 22:29:07.58198 INFO::Processing subtree level 1
2024-11-07 22:29:07.730738 INFO::Adjusting the last 1 batches sequentially
2024-11-07 22:29:07.732409 INFO::Done
2024-11-07 22:29:07.73291 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 22:29:07.735198 INFO::ASW Batch was -0.154591181733654 prior to batch effect correction and is now -0.198585712346831 .
2024-11-07 22:29:07.740047 INFO::Total function execution time is 0.160886287689209 s and adjustment time is 0.151601791381836 s ( 94.23 )
2024-11-07 22:29:07.766027 INFO::Skipping initial DF formatting
2024-11-07 22:29:07.76651 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 22:29:07.773822 INFO::Starting hierarchical adjustment
2024-11-07 22:29:07.774487 INFO::Found 5 batches.
2024-11-07 22:29:07.774915 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 22:29:07.779514 INFO::Using default BPPARAM
2024-11-07 22:29:07.779963 INFO::Processing subtree level 1
2024-11-07 22:29:08.018028 INFO::Adjusting the last 2 batches sequentially
2024-11-07 22:29:08.022556 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 22:29:08.065724 INFO::Done
2024-11-07 22:29:08.070351 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 22:29:08.078516 INFO::ASW Batch was 0.532189573906251 prior to batch effect correction and is now 0.532189573906251 .
2024-11-07 22:29:08.079236 INFO::ASW Label was 0.378650981228797 prior to batch effect correction and is now 0.378650981228797 .
2024-11-07 22:29:08.080016 INFO::Total function execution time is 0.314003467559814 s and adjustment time is 0.291354179382324 s ( 92.79 )
2024-11-07 22:29:08.10193 INFO::Formatting Data.
2024-11-07 22:29:08.102485 INFO::Replacing NaNs with NAs.
2024-11-07 22:29:08.103221 INFO::Removing potential empty rows and columns
2024-11-07 22:29:08.104046 INFO::Found 0 missing values.
2024-11-07 22:29:08.108721 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 22:29:08.109192 INFO::Done
2024-11-07 22:29:08.109592 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 22:29:08.113257 INFO::Starting hierarchical adjustment
2024-11-07 22:29:08.113838 INFO::Found 5 batches.
2024-11-07 22:29:08.114284 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 22:29:08.114766 INFO::Using default BPPARAM
2024-11-07 22:29:08.11547 INFO::Processing subtree level 1
2024-11-07 22:29:08.329807 INFO::Adjusting the last 2 batches sequentially
2024-11-07 22:29:08.338898 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 22:29:08.379273 INFO::Done
2024-11-07 22:29:08.380075 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 22:29:08.387108 INFO::ASW Batch was 0.183068289868345 prior to batch effect correction and is now -0.0826669433060313 .
2024-11-07 22:29:08.387582 INFO::ASW Label was 0.592241179628365 prior to batch effect correction and is now 0.894489795728843 .
2024-11-07 22:29:08.392286 INFO::Total function execution time is 0.290375709533691 s and adjustment time is 0.265441417694092 s ( 91.41 )
2024-11-07 22:29:08.393021 INFO::Formatting Data.
2024-11-07 22:29:08.39351 INFO::Replacing NaNs with NAs.
2024-11-07 22:29:08.394232 INFO::Removing potential empty rows and columns
2024-11-07 22:29:08.395105 INFO::Found 0 missing values.
2024-11-07 22:29:08.398349 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 22:29:08.398856 INFO::Done
2024-11-07 22:29:08.403378 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 22:29:08.40566 INFO::Starting hierarchical adjustment
2024-11-07 22:29:08.40624 INFO::Found 5 batches.
2024-11-07 22:29:08.406651 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 22:29:08.414222 INFO::Using default BPPARAM
2024-11-07 22:29:08.414659 INFO::Processing subtree level 1
2024-11-07 22:29:08.649971 INFO::Adjusting the last 2 batches sequentially
2024-11-07 22:29:08.651483 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 22:29:08.682302 INFO::Done
2024-11-07 22:29:08.683023 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 22:29:08.686995 INFO::ASW Batch was 0.183068289868345 prior to batch effect correction and is now -0.0826669433060313 .
2024-11-07 22:29:08.687694 INFO::ASW Label was 0.592241179628365 prior to batch effect correction and is now 0.894489795728843 .
2024-11-07 22:29:08.691823 INFO::Total function execution time is 0.297748565673828 s and adjustment time is 0.2760910987854 s ( 92.73 )
2024-11-07 22:29:08.705932 INFO::Formatting Data.
2024-11-07 22:29:08.706672 INFO::Replacing NaNs with NAs.
2024-11-07 22:29:08.707499 INFO::Removing potential empty rows and columns
2024-11-07 22:29:08.708321 INFO::Found 0 missing values.
2024-11-07 22:29:08.712037 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 22:29:08.712461 INFO::Done
2024-11-07 22:29:08.712851 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 22:29:08.715441 INFO::Starting hierarchical adjustment
2024-11-07 22:29:08.716061 INFO::Found 5 batches.
2024-11-07 22:29:08.71647 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 22:29:08.717074 INFO::Using default BPPARAM
2024-11-07 22:29:08.717639 INFO::Processing subtree level 1
2024-11-07 22:29:08.990788 INFO::Adjusting the last 2 batches sequentially
2024-11-07 22:29:08.994605 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 22:29:09.02217 INFO::Done
2024-11-07 22:29:09.022624 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 22:29:09.025204 INFO::ASW Batch was 0.292995487299412 prior to batch effect correction and is now -0.0713135814052583 .
2024-11-07 22:29:09.025651 INFO::ASW Label was 0.426598343231657 prior to batch effect correction and is now 0.84227103827371 .
2024-11-07 22:29:09.026338 INFO::Total function execution time is 0.320605993270874 s and adjustment time is 0.30626916885376 s ( 95.53 )
2024-11-07 22:29:09.027027 INFO::Formatting Data.
2024-11-07 22:29:09.027515 INFO::Replacing NaNs with NAs.
2024-11-07 22:29:09.028225 INFO::Removing potential empty rows and columns
2024-11-07 22:29:09.02905 INFO::Found 0 missing values.
2024-11-07 22:29:09.054585 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 22:29:09.055089 INFO::Done
2024-11-07 22:29:09.055501 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 22:29:09.057895 INFO::Starting hierarchical adjustment
2024-11-07 22:29:09.058494 INFO::Found 5 batches.
2024-11-07 22:29:09.058917 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 22:29:09.059447 INFO::Using default BPPARAM
2024-11-07 22:29:09.059985 INFO::Processing subtree level 1
2024-11-07 22:29:09.24902 INFO::Adjusting the last 2 batches sequentially
2024-11-07 22:29:09.251094 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 22:29:09.28504 INFO::Done
2024-11-07 22:29:09.285604 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 22:29:09.293057 INFO::ASW Batch was 0.292995487299412 prior to batch effect correction and is now -0.0713135814052583 .
2024-11-07 22:29:09.293587 INFO::ASW Label was 0.426598343231657 prior to batch effect correction and is now 0.84227103827371 .
2024-11-07 22:29:09.295698 INFO::Total function execution time is 0.268453359603882 s and adjustment time is 0.226625442504883 s ( 84.42 )
2024-11-07 22:29:09.315914 INFO::Formatting Data.
2024-11-07 22:29:09.316645 INFO::Replacing NaNs with NAs.
2024-11-07 22:29:09.318166 INFO::Removing potential empty rows and columns
2024-11-07 22:29:09.320014 INFO::Found 0 missing values.
2024-11-07 22:29:09.322694 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 22:29:09.323231 INFO::Done
2024-11-07 22:29:09.323683 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 22:29:09.328544 INFO::Starting hierarchical adjustment
2024-11-07 22:29:09.329594 INFO::Found 2 batches.
2024-11-07 22:29:09.330572 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 22:29:09.331173 INFO::Using default BPPARAM
2024-11-07 22:29:09.331606 INFO::Adjusting the last 2 batches sequentially
2024-11-07 22:29:09.33238 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 22:29:09.35198 INFO::Done
2024-11-07 22:29:09.352455 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 22:29:09.356209 INFO::ASW Batch was 0.28794400309428 prior to batch effect correction and is now 0.106024305103748 .
2024-11-07 22:29:09.356705 INFO::ASW Label was 0.785206260253505 prior to batch effect correction and is now 0.872077155874472 .
2024-11-07 22:29:09.357392 INFO::Total function execution time is 0.0415561199188232 s and adjustment time is 0.0225679874420166 s ( 54.31 )
2024-11-07 22:29:09.358042 INFO::Formatting Data.
2024-11-07 22:29:09.358578 INFO::Replacing NaNs with NAs.
2024-11-07 22:29:09.359407 INFO::Removing potential empty rows and columns
2024-11-07 22:29:09.360313 INFO::Found 0 missing values.
2024-11-07 22:29:09.362814 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 22:29:09.363915 INFO::Done
2024-11-07 22:29:09.36577 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 22:29:09.370595 INFO::Starting hierarchical adjustment
2024-11-07 22:29:09.37134 INFO::Found 2 batches.
2024-11-07 22:29:09.371787 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 22:29:09.372343 INFO::Using default BPPARAM
2024-11-07 22:29:09.372749 INFO::Adjusting the last 2 batches sequentially
2024-11-07 22:29:09.373883 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 22:29:09.39328 INFO::Done
2024-11-07 22:29:09.393756 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 22:29:09.397023 INFO::ASW Batch was 0.28794400309428 prior to batch effect correction and is now 0.106024305103748 .
2024-11-07 22:29:09.397477 INFO::ASW Label was 0.785206260253505 prior to batch effect correction and is now 0.872077155874472 .
2024-11-07 22:29:09.398108 INFO::Total function execution time is 0.0400798320770264 s and adjustment time is 0.0220780372619629 s ( 55.09 )
2024-11-07 22:29:09.414173 INFO::Formatting Data.
2024-11-07 22:29:09.414724 INFO::Replacing NaNs with NAs.
2024-11-07 22:29:09.416653 INFO::Removing potential empty rows and columns
2024-11-07 22:29:09.417449 INFO::Found 0 missing values.
2024-11-07 22:29:09.420273 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 22:29:09.420721 INFO::Done
2024-11-07 22:29:09.421214 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 22:29:09.422675 INFO::Starting hierarchical adjustment
2024-11-07 22:29:09.423899 INFO::Found 2 batches.
2024-11-07 22:29:09.424392 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 22:29:09.424906 INFO::Using default BPPARAM
2024-11-07 22:29:09.425366 INFO::Adjusting the last 2 batches sequentially
2024-11-07 22:29:09.426594 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 22:29:09.467511 INFO::Done
2024-11-07 22:29:09.46817 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 22:29:09.47133 INFO::ASW Batch was -0.0954719813615374 prior to batch effect correction and is now -0.155539403548515 .
2024-11-07 22:29:09.47197 INFO::Total function execution time is 0.0577902793884277 s and adjustment time is 0.0440058708190918 s ( 76.15 )
2024-11-07 22:29:09.487139 INFO::Formatting Data.
2024-11-07 22:29:09.487691 INFO::Replacing NaNs with NAs.
2024-11-07 22:29:09.491887 INFO::Removing potential empty rows and columns
2024-11-07 22:29:09.493142 INFO::Found 0 missing values.
2024-11-07 22:29:09.494177 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.
2024-11-07 22:29:09.499203 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 22:29:09.499676 INFO::Done
2024-11-07 22:29:09.500171 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 22:29:09.50674 INFO::Starting hierarchical adjustment
2024-11-07 22:29:09.507395 INFO::Found 2 batches.
2024-11-07 22:29:09.507907 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 22:29:09.510902 INFO::Using default BPPARAM
2024-11-07 22:29:09.51138 INFO::Adjusting the last 2 batches sequentially
2024-11-07 22:29:09.512264 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 22:29:09.534762 INFO::Done
2024-11-07 22:29:09.535992 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 22:29:09.538722 INFO::ASW Batch was 0.605073444182089 prior to batch effect correction and is now -0.0382123778443113 .
2024-11-07 22:29:09.539795 INFO::ASW Label was 0.48623613474199 prior to batch effect correction and is now 0.957877927921733 .
2024-11-07 22:29:09.540459 INFO::Total function execution time is 0.0533268451690674 s and adjustment time is 0.0274968147277832 s ( 51.56 )
2024-11-07 22:29:09.542341 INFO::Formatting Data.
2024-11-07 22:29:09.54341 INFO::Replacing NaNs with NAs.
2024-11-07 22:29:09.544132 INFO::Removing potential empty rows and columns
2024-11-07 22:29:09.544925 INFO::Found 0 missing values.
2024-11-07 22:29:09.545647 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.
2024-11-07 22:29:09.551347 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 22:29:09.551778 INFO::Done
2024-11-07 22:29:09.55227 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 22:29:09.556178 INFO::Starting hierarchical adjustment
2024-11-07 22:29:09.556725 INFO::Found 2 batches.
2024-11-07 22:29:09.557445 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 22:29:09.557914 INFO::Using default BPPARAM
2024-11-07 22:29:09.558334 INFO::Adjusting the last 2 batches sequentially
2024-11-07 22:29:09.559048 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 22:29:09.576506 INFO::Done
2024-11-07 22:29:09.576967 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 22:29:09.580567 INFO::ASW Batch was 0.605073444182089 prior to batch effect correction and is now -0.0382123778443113 .
2024-11-07 22:29:09.581048 INFO::ASW Label was 0.48623613474199 prior to batch effect correction and is now 0.957877927921733 .
2024-11-07 22:29:09.581647 INFO::Total function execution time is 0.0405910015106201 s and adjustment time is 0.0198912620544434 s ( 49 )
2024-11-07 22:29:09.832536 INFO::Formatting Data.
2024-11-07 22:29:09.833203 INFO::Replacing NaNs with NAs.
2024-11-07 22:29:09.833888 INFO::Removing potential empty rows and columns
2024-11-07 22:29:09.835383 INFO::Found 0 missing values.
2024-11-07 22:29:09.838467 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 22:29:09.838887 INFO::Done
2024-11-07 22:29:09.840169 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 22:29:09.843111 INFO::Starting hierarchical adjustment
2024-11-07 22:29:09.843681 INFO::Found 3 batches.
2024-11-07 22:29:09.844279 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 22:29:09.844764 INFO::Using default BPPARAM
2024-11-07 22:29:09.845219 INFO::Processing subtree level 1
2024-11-07 22:29:10.008507 INFO::Adjusting the last 1 batches sequentially
2024-11-07 22:29:10.017852 INFO::Done
2024-11-07 22:29:10.018375 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 22:29:10.029634 INFO::ASW Batch was -0.0699025828435697 prior to batch effect correction and is now -0.0699025828435697 .
2024-11-07 22:29:10.030434 INFO::Total function execution time is 0.197952747344971 s and adjustment time is 0.174306631088257 s ( 88.05 )
2024-11-07 22:29:10.036774 INFO::Formatting Data.
2024-11-07 22:29:10.037362 INFO::Typecasting input to dataframe.
2024-11-07 22:29:10.041998 INFO::Replacing NaNs with NAs.
2024-11-07 22:29:10.042729 INFO::Removing potential empty rows and columns
2024-11-07 22:29:10.043658 INFO::Found 0 missing values.
2024-11-07 22:29:10.050302 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 22:29:10.050744 INFO::Done
2024-11-07 22:29:10.051191 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 22:29:10.05282 INFO::Starting hierarchical adjustment
2024-11-07 22:29:10.053426 INFO::Found 3 batches.
2024-11-07 22:29:10.053851 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 22:29:10.054346 INFO::Using default BPPARAM
2024-11-07 22:29:10.05477 INFO::Processing subtree level 1
2024-11-07 22:29:10.363348 INFO::Adjusting the last 1 batches sequentially
2024-11-07 22:29:10.369001 INFO::Done
2024-11-07 22:29:10.369509 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 22:29:10.371782 INFO::ASW Batch was -0.0699025828435697 prior to batch effect correction and is now -0.0699025828435697 .
2024-11-07 22:29:10.372617 INFO::Total function execution time is 0.335807800292969 s and adjustment time is 0.315690755844116 s ( 94.01 )
2024-11-07 22:29:10.396245 INFO::Formatting Data.
2024-11-07 22:29:10.39677 INFO::Typecasting input to dataframe.
2024-11-07 22:29:10.397469 INFO::Replacing NaNs with NAs.
2024-11-07 22:29:10.39818 INFO::Removing potential empty rows and columns
2024-11-07 22:29:10.403109 INFO::Found 0 missing values.
2024-11-07 22:29:10.437778 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 22:29:10.44245 INFO::Done
2024-11-07 22:29:10.442956 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 22:29:10.444829 INFO::Starting hierarchical adjustment
2024-11-07 22:29:10.4495 INFO::Found 3 batches.
2024-11-07 22:29:10.449924 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 22:29:10.450459 INFO::Using default BPPARAM
2024-11-07 22:29:10.450902 INFO::Processing subtree level 1
2024-11-07 22:29:10.682405 INFO::Adjusting the last 1 batches sequentially
2024-11-07 22:29:10.684474 INFO::Done
2024-11-07 22:29:10.689012 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 22:29:10.691646 INFO::ASW Batch was -0.119010948441905 prior to batch effect correction and is now -0.119010948441905 .
2024-11-07 22:29:10.692571 INFO::Total function execution time is 0.296285390853882 s and adjustment time is 0.235107421875 s ( 79.35 )
2024-11-07 22:29:11.025073 INFO::Formatting Data.
2024-11-07 22:29:11.025648 INFO::Replacing NaNs with NAs.
2024-11-07 22:29:11.026695 INFO::Removing potential empty rows and columns
2024-11-07 22:29:11.033579 INFO::Found 1000 missing values.
2024-11-07 22:29:11.066503 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 22:29:11.071055 INFO::Done
2024-11-07 22:29:11.071479 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 22:29:11.079754 INFO::Starting hierarchical adjustment
2024-11-07 22:29:11.080352 INFO::Found 10 batches.
2024-11-07 22:29:11.080776 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 22:29:11.08534 INFO::Using default BPPARAM
2024-11-07 22:29:11.085787 INFO::Processing subtree level 1
2024-11-07 22:29:11.419432 INFO::Processing subtree level 2
2024-11-07 22:29:11.69048 INFO::Adjusting the last 1 batches sequentially
2024-11-07 22:29:11.696718 INFO::Done
2024-11-07 22:29:11.697425 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 22:29:11.707146 INFO::ASW Batch was 0.501999418418464 prior to batch effect correction and is now 0.501999418418464 .
2024-11-07 22:29:11.707711 INFO::ASW Label was 0.320327305134566 prior to batch effect correction and is now 0.320327305134566 .
2024-11-07 22:29:11.708555 INFO::Total function execution time is 0.683486223220825 s and adjustment time is 0.616445302963257 s ( 90.19 )
2024-11-07 22:29:11.709351 INFO::Formatting Data.
2024-11-07 22:29:11.70993 INFO::Replacing NaNs with NAs.
2024-11-07 22:29:11.715228 INFO::Removing potential empty rows and columns
2024-11-07 22:29:11.72101 INFO::Found 1000 missing values.
2024-11-07 22:29:11.759932 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 22:29:11.760477 INFO::Done
2024-11-07 22:29:11.764963 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 22:29:11.76976 INFO::Starting hierarchical adjustment
2024-11-07 22:29:11.770459 INFO::Found 10 batches.
2024-11-07 22:29:12.863226 INFO::Set up parallel execution backend with 2 workers
2024-11-07 22:29:12.865164 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-11-07 22:29:14.315594 INFO::Adjusting the last 2 batches sequentially
2024-11-07 22:29:14.317061 INFO::Adjusting sequential tree level 1 with 2 batches
2024-11-07 22:29:14.329615 INFO::Done
2024-11-07 22:29:14.330015 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 22:29:14.333552 INFO::ASW Batch was 0.501999418418464 prior to batch effect correction and is now 0.501999418418464 .
2024-11-07 22:29:14.333926 INFO::ASW Label was 0.320327305134566 prior to batch effect correction and is now 0.320327305134566 .
2024-11-07 22:29:14.334463 INFO::Total function execution time is 2.62514424324036 s and adjustment time is 2.55932521820068 s ( 97.49 )
2024-11-07 22:29:14.492789 INFO::Formatting Data.
2024-11-07 22:29:14.49344 INFO::Replacing NaNs with NAs.
2024-11-07 22:29:14.494165 INFO::Removing potential empty rows and columns
2024-11-07 22:29:14.49793 INFO::Found 0 missing values.
2024-11-07 22:29:14.501051 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 22:29:14.501465 INFO::Done
2024-11-07 22:29:14.501872 INFO::Acquiring quality metrics before batch effect correction.
2024-11-07 22:29:14.504076 INFO::Starting hierarchical adjustment
2024-11-07 22:29:14.504629 INFO::Found 3 batches.
2024-11-07 22:29:14.505071 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-11-07 22:29:14.505546 INFO::Using default BPPARAM
2024-11-07 22:29:14.505922 INFO::Processing subtree level 1
2024-11-07 22:29:14.608958 INFO::Adjusting the last 1 batches sequentially
2024-11-07 22:29:14.610584 INFO::Done
2024-11-07 22:29:14.611095 INFO::Acquiring quality metrics after batch effect correction.
2024-11-07 22:29:14.613848 INFO::ASW Batch was 0.277820441721848 prior to batch effect correction and is now -0.169658896411981 .
2024-11-07 22:29:14.614372 INFO::ASW Label was -0.181176326939362 prior to batch effect correction and is now -0.00728155637154724 .
2024-11-07 22:29:14.619147 INFO::Total function execution time is 0.122332811355591 s and adjustment time is 0.106078147888184 s ( 86.71 )
2024-11-07 22:29:14.730014 INFO::Formatting Data.
2024-11-07 22:29:14.730698 INFO::Replacing NaNs with NAs.
2024-11-07 22:29:14.731429 INFO::Removing potential empty rows and columns
2024-11-07 22:29:14.732305 INFO::Found 2 missing values.
2024-11-07 22:29:14.734604 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-11-07 22:29:14.735036 INFO::Done
2024-11-07 22:29:14.756428 INFO::Found NA in Reference column
2024-11-07 22:29:14.764183 INFO::Require at least two references per batch.
2024-11-07 22:29:14.781418 INFO::Formatting Data.
2024-11-07 22:29:14.781886 INFO::Recognized SummarizedExperiment
2024-11-07 22:29:14.782314 INFO::Typecasting input to dataframe.
2024-11-07 22:29:14.790476 INFO::Replacing NaNs with NAs.
2024-11-07 22:29:14.791292 INFO::Removing potential empty rows and columns
2024-11-07 22:29:14.794376 INFO::Found 0 missing values.
2024-11-07 22:29:14.80023 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 22:29:14.800696 INFO::Done
2024-11-07 22:29:14.812594 INFO::Formatting Data.
2024-11-07 22:29:14.813086 INFO::Recognized SummarizedExperiment
2024-11-07 22:29:14.813471 INFO::Typecasting input to dataframe.
2024-11-07 22:29:14.826997 INFO::Replacing NaNs with NAs.
2024-11-07 22:29:14.827793 INFO::Removing potential empty rows and columns
2024-11-07 22:29:14.830746 INFO::Found 0 missing values.
2024-11-07 22:29:14.840568 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 22:29:14.841068 INFO::Done
2024-11-07 22:29:14.853347 INFO::Formatting Data.
2024-11-07 22:29:14.853847 INFO::Recognized SummarizedExperiment
2024-11-07 22:29:14.854287 INFO::Typecasting input to dataframe.
2024-11-07 22:29:14.867415 INFO::Replacing NaNs with NAs.
2024-11-07 22:29:14.86812 INFO::Removing potential empty rows and columns
2024-11-07 22:29:14.868964 INFO::Found 0 missing values.
2024-11-07 22:29:14.869678 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.
2024-11-07 22:29:14.873607 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 22:29:14.874051 INFO::Done
2024-11-07 22:29:14.882057 INFO::Formatting Data.
2024-11-07 22:29:14.882552 INFO::Replacing NaNs with NAs.
2024-11-07 22:29:14.883279 INFO::Removing potential empty rows and columns
2024-11-07 22:29:14.884555 INFO::Found 0 missing values.
2024-11-07 22:29:14.88718 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 22:29:14.887605 INFO::Done
2024-11-07 22:29:14.897005 INFO::Formatting Data.
2024-11-07 22:29:14.897497 INFO::Replacing NaNs with NAs.
2024-11-07 22:29:14.89815 INFO::Removing potential empty rows and columns
2024-11-07 22:29:14.89891 INFO::Found 0 missing values.
2024-11-07 22:29:14.901279 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 22:29:14.901693 INFO::Done
2024-11-07 22:29:14.924985 INFO::Formatting Data.
2024-11-07 22:29:14.925511 INFO::Replacing NaNs with NAs.
2024-11-07 22:29:14.926437 INFO::Removing potential empty rows and columns
2024-11-07 22:29:14.927463 INFO::Found 1 missing values.
2024-11-07 22:29:14.929532 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 22:29:14.929966 INFO::Done
2024-11-07 22:29:14.944828 INFO::Formatting Data.
2024-11-07 22:29:14.94537 INFO::Replacing NaNs with NAs.
2024-11-07 22:29:14.946014 INFO::Removing potential empty rows and columns
2024-11-07 22:29:14.946738 INFO::Found 2 missing values.
2024-11-07 22:29:14.947488 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.
2024-11-07 22:29:14.949378 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-11-07 22:29:14.94981 INFO::Done
2024-11-07 22:29:14.95815 INFO::Formatting Data.
2024-11-07 22:29:14.958654 INFO::Replacing NaNs with NAs.
2024-11-07 22:29:14.959364 INFO::Removing potential empty rows and columns
2024-11-07 22:29:14.960118 INFO::Found 2 missing values.
2024-11-07 22:29:14.961449 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 22:29:14.961859 INFO::Done
2024-11-07 22:29:14.970877 INFO::Formatting Data.
2024-11-07 22:29:14.971413 INFO::Typecasting input to dataframe.
2024-11-07 22:29:14.972096 INFO::Replacing NaNs with NAs.
2024-11-07 22:29:14.972742 INFO::Removing potential empty rows and columns
2024-11-07 22:29:14.973579 INFO::Found 0 missing values.
2024-11-07 22:29:14.976032 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-11-07 22:29:14.976491 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
13.889 3.867 19.856
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 19.157 | 1.357 | 15.383 | |
| compute_asw | 0.015 | 0.000 | 0.016 | |
| count_existing | 0.008 | 0.001 | 0.008 | |
| generate_data_covariables | 0.007 | 0.001 | 0.008 | |
| generate_dataset | 0.007 | 0.001 | 0.007 | |