Yannis Schumann
| Snapshot Date: 2025-02-03 13:00 -0500 (Mon, 03 Feb 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_20 |
| git_last_commit: 9764e3f |
| git_last_commit_date: 2024-10-29 11:26:04 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-02-06 12:11 -0500 (Thu, 06 Feb 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4753 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4501 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4524 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4476 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4407 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 159/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.2.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: BERT |
| Version: 1.2.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.2.0.tar.gz |
| StartedAt: 2025-02-04 04:41:16 -0000 (Tue, 04 Feb 2025) |
| EndedAt: 2025-02-04 04:43:13 -0000 (Tue, 04 Feb 2025) |
| EllapsedTime: 116.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 12.3.1 (openEuler 12.3.1-36.oe2403)
* running under: openEuler 24.03 (LTS)
* 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 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 27.062 1.46 29.082
* 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: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.2/site-library’ * installing *source* package ‘BERT’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2025-02-04 04:42:47.144993 INFO::Formatting Data.
2025-02-04 04:42:47.146726 INFO::Replacing NaNs with NAs.
2025-02-04 04:42:47.179051 INFO::Removing potential empty rows and columns
2025-02-04 04:42:47.91971 INFO::Found 0 missing values.
2025-02-04 04:42:47.932813 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 04:42:47.93368 INFO::Done
2025-02-04 04:42:47.934429 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 04:42:47.966098 INFO::Starting hierarchical adjustment
2025-02-04 04:42:47.967243 INFO::Found 3 batches.
2025-02-04 04:42:47.967992 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 04:42:47.973588 INFO::Using default BPPARAM
2025-02-04 04:42:47.974449 INFO::Processing subtree level 1
2025-02-04 04:42:48.22986 INFO::Adjusting the last 1 batches sequentially
2025-02-04 04:42:48.232474 INFO::Done
2025-02-04 04:42:48.23758 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 04:42:48.24555 INFO::ASW Batch was -0.0628847243533644 prior to batch effect correction and is now -0.0628847243533644 .
2025-02-04 04:42:48.24725 INFO::Total function execution time is 1.10704922676086 s and adjustment time is 0.265385627746582 s ( 23.97 )
2025-02-04 04:42:48.288534 INFO::Formatting Data.
2025-02-04 04:42:48.293732 INFO::Replacing NaNs with NAs.
2025-02-04 04:42:48.295213 INFO::Removing potential empty rows and columns
2025-02-04 04:42:48.301069 INFO::Found 0 missing values.
2025-02-04 04:42:48.302664 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-02-04 04:42:48.334572 INFO::Formatting Data.
2025-02-04 04:42:48.335521 INFO::Replacing NaNs with NAs.
2025-02-04 04:42:48.340779 INFO::Removing potential empty rows and columns
2025-02-04 04:42:48.342322 INFO::Found 0 missing values.
2025-02-04 04:42:48.343573 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-02-04 04:42:48.3904 INFO::Formatting Data.
2025-02-04 04:42:48.391343 INFO::Replacing NaNs with NAs.
2025-02-04 04:42:48.392503 INFO::Removing potential empty rows and columns
2025-02-04 04:42:48.397968 INFO::Found 0 missing values.
2025-02-04 04:42:48.399197 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-02-04 04:42:48.413573 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 04:42:48.41439 INFO::Done
2025-02-04 04:42:48.415154 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 04:42:48.421974 INFO::Starting hierarchical adjustment
2025-02-04 04:42:48.423092 INFO::Found 2 batches.
2025-02-04 04:42:48.423842 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 04:42:48.424723 INFO::Using default BPPARAM
2025-02-04 04:42:48.429679 INFO::Adjusting the last 2 batches sequentially
2025-02-04 04:42:48.431077 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-04 04:42:48.494337 INFO::Done
2025-02-04 04:42:48.495187 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 04:42:48.501948 INFO::ASW Batch was 0.0528614553396263 prior to batch effect correction and is now -0.132128255389048 .
2025-02-04 04:42:48.503136 INFO::Total function execution time is 0.112754821777344 s and adjustment time is 0.0714454650878906 s ( 63.36 )
2025-02-04 04:42:48.510696 INFO::Formatting Data.
2025-02-04 04:42:48.511605 INFO::Replacing NaNs with NAs.
2025-02-04 04:42:48.53561 INFO::Formatting Data.
2025-02-04 04:42:48.536587 INFO::Replacing NaNs with NAs.
2025-02-04 04:42:48.541886 INFO::Removing potential empty rows and columns
2025-02-04 04:42:48.543342 INFO::Found 0 missing values.
2025-02-04 04:42:48.551634 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 04:42:48.552613 INFO::Done
2025-02-04 04:42:48.557444 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 04:42:48.560246 INFO::Starting hierarchical adjustment
2025-02-04 04:42:48.56534 INFO::Found 2 batches.
2025-02-04 04:42:48.566118 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 04:42:48.566958 INFO::Using default BPPARAM
2025-02-04 04:42:48.567984 INFO::Adjusting the last 2 batches sequentially
2025-02-04 04:42:48.573609 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-04 04:42:48.614021 INFO::Done
2025-02-04 04:42:48.614905 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 04:42:48.621833 INFO::ASW Batch was 0.00489175965157837 prior to batch effect correction and is now -0.12111088684153 .
2025-02-04 04:42:48.622995 INFO::Total function execution time is 0.0874080657958984 s and adjustment time is 0.048875093460083 s ( 55.92 )
2025-02-04 04:42:48.624553 INFO::Formatting Data.
2025-02-04 04:42:48.62956 INFO::Replacing NaNs with NAs.
2025-02-04 04:42:48.63082 INFO::Removing potential empty rows and columns
2025-02-04 04:42:48.632385 INFO::Found 0 missing values.
2025-02-04 04:42:48.644988 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 04:42:48.645902 INFO::Done
2025-02-04 04:42:48.646681 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 04:42:48.653597 INFO::Starting hierarchical adjustment
2025-02-04 04:42:48.654732 INFO::Found 2 batches.
2025-02-04 04:42:48.655532 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 04:42:48.656411 INFO::Using default BPPARAM
2025-02-04 04:42:48.661318 INFO::Adjusting the last 2 batches sequentially
2025-02-04 04:42:48.662691 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-04 04:42:48.702974 INFO::Done
2025-02-04 04:42:48.70381 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 04:42:48.710584 INFO::ASW Batch was 0.00489175965157837 prior to batch effect correction and is now -0.12111088684153 .
2025-02-04 04:42:48.711746 INFO::Total function execution time is 0.0872621536254883 s and adjustment time is 0.0484840869903564 s ( 55.56 )
2025-02-04 04:42:52.342864 INFO::Formatting Data.
2025-02-04 04:42:52.343622 INFO::Recognized SummarizedExperiment
2025-02-04 04:42:52.344207 INFO::Typecasting input to dataframe.
2025-02-04 04:42:52.382352 INFO::Replacing NaNs with NAs.
2025-02-04 04:42:52.383658 INFO::Removing potential empty rows and columns
2025-02-04 04:42:52.387931 INFO::Found 0 missing values.
2025-02-04 04:42:52.396067 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 04:42:52.396853 INFO::Done
2025-02-04 04:42:52.397493 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 04:42:52.401537 INFO::Starting hierarchical adjustment
2025-02-04 04:42:52.402409 INFO::Found 2 batches.
2025-02-04 04:42:52.403051 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 04:42:52.404324 INFO::Using default BPPARAM
2025-02-04 04:42:52.405003 INFO::Adjusting the last 2 batches sequentially
2025-02-04 04:42:52.406173 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-04 04:42:52.473683 INFO::Done
2025-02-04 04:42:52.474409 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 04:42:52.478327 INFO::ASW Batch was 0.000285769778739984 prior to batch effect correction and is now -0.102723914556494 .
2025-02-04 04:42:52.479297 INFO::Total function execution time is 0.136805534362793 s and adjustment time is 0.0714371204376221 s ( 52.22 )
2025-02-04 04:42:52.499968 INFO::Formatting Data.
2025-02-04 04:42:52.500825 INFO::Recognized SummarizedExperiment
2025-02-04 04:42:52.501462 INFO::Typecasting input to dataframe.
2025-02-04 04:42:52.512327 INFO::Replacing NaNs with NAs.
2025-02-04 04:42:52.513632 INFO::Removing potential empty rows and columns
2025-02-04 04:42:52.517827 INFO::Found 0 missing values.
2025-02-04 04:42:52.526358 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 04:42:52.527123 INFO::Done
2025-02-04 04:42:52.527769 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 04:42:52.531873 INFO::Starting hierarchical adjustment
2025-02-04 04:42:52.532863 INFO::Found 2 batches.
2025-02-04 04:42:52.53353 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 04:42:52.534261 INFO::Using default BPPARAM
2025-02-04 04:42:52.534909 INFO::Adjusting the last 2 batches sequentially
2025-02-04 04:42:52.536124 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-04 04:42:52.565487 INFO::Done
2025-02-04 04:42:52.566223 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 04:42:52.57018 INFO::ASW Batch was 0.0156440997214539 prior to batch effect correction and is now 0.0156440997214539 .
2025-02-04 04:42:52.571166 INFO::Total function execution time is 0.071155309677124 s and adjustment time is 0.0328130722045898 s ( 46.11 )
2025-02-04 04:42:52.592174 INFO::Formatting Data.
2025-02-04 04:42:52.593073 INFO::Replacing NaNs with NAs.
2025-02-04 04:42:52.594084 INFO::Removing potential empty rows and columns
2025-02-04 04:42:52.595268 INFO::Found 0 missing values.
2025-02-04 04:42:52.59885 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 04:42:52.599561 INFO::Done
2025-02-04 04:42:52.600208 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 04:42:52.602504 INFO::Starting hierarchical adjustment
2025-02-04 04:42:52.603378 INFO::Found 3 batches.
2025-02-04 04:42:52.604018 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 04:42:52.6048 INFO::Using default BPPARAM
2025-02-04 04:42:52.605459 INFO::Processing subtree level 1
2025-02-04 04:42:52.961865 INFO::Adjusting the last 1 batches sequentially
2025-02-04 04:42:52.964124 INFO::Done
2025-02-04 04:42:52.969135 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 04:42:52.97248 INFO::ASW Batch was -0.101404795194702 prior to batch effect correction and is now -0.154166292069317 .
2025-02-04 04:42:52.977923 INFO::Total function execution time is 0.38568902015686 s and adjustment time is 0.360911130905151 s ( 93.58 )
2025-02-04 04:42:53.019141 INFO::Skipping initial DF formatting
2025-02-04 04:42:53.020049 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 04:42:53.033827 INFO::Starting hierarchical adjustment
2025-02-04 04:42:53.034962 INFO::Found 5 batches.
2025-02-04 04:42:53.035717 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 04:42:53.0366 INFO::Using default BPPARAM
2025-02-04 04:42:53.041558 INFO::Processing subtree level 1
2025-02-04 04:42:53.373318 INFO::Adjusting the last 2 batches sequentially
2025-02-04 04:42:53.375345 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-04 04:42:53.432641 INFO::Done
2025-02-04 04:42:53.437664 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 04:42:53.44736 INFO::ASW Batch was 0.477144886505505 prior to batch effect correction and is now 0.477144886505505 .
2025-02-04 04:42:53.448217 INFO::ASW Label was 0.396833911458747 prior to batch effect correction and is now 0.396833911458747 .
2025-02-04 04:42:53.453603 INFO::Total function execution time is 0.434454679489136 s and adjustment time is 0.397895812988281 s ( 91.59 )
2025-02-04 04:42:53.502949 INFO::Formatting Data.
2025-02-04 04:42:53.503941 INFO::Replacing NaNs with NAs.
2025-02-04 04:42:53.509316 INFO::Removing potential empty rows and columns
2025-02-04 04:42:53.510818 INFO::Found 0 missing values.
2025-02-04 04:42:53.524956 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 04:42:53.525825 INFO::Done
2025-02-04 04:42:53.526531 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 04:42:53.534629 INFO::Starting hierarchical adjustment
2025-02-04 04:42:53.535718 INFO::Found 5 batches.
2025-02-04 04:42:53.536485 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 04:42:53.541497 INFO::Using default BPPARAM
2025-02-04 04:42:53.542298 INFO::Processing subtree level 1
2025-02-04 04:42:53.814823 INFO::Adjusting the last 2 batches sequentially
2025-02-04 04:42:53.82101 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-04 04:42:53.863728 INFO::Done
2025-02-04 04:42:53.864692 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 04:42:53.877335 INFO::ASW Batch was 0.493305766360952 prior to batch effect correction and is now -0.0740383898279632 .
2025-02-04 04:42:53.878237 INFO::ASW Label was 0.290783882566945 prior to batch effect correction and is now 0.853906001608555 .
2025-02-04 04:42:53.879386 INFO::Total function execution time is 0.376465082168579 s and adjustment time is 0.328204154968262 s ( 87.18 )
2025-02-04 04:42:53.880565 INFO::Formatting Data.
2025-02-04 04:42:53.885651 INFO::Replacing NaNs with NAs.
2025-02-04 04:42:53.886934 INFO::Removing potential empty rows and columns
2025-02-04 04:42:53.888346 INFO::Found 0 missing values.
2025-02-04 04:42:53.90283 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 04:42:53.903683 INFO::Done
2025-02-04 04:42:53.904422 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 04:42:53.912655 INFO::Starting hierarchical adjustment
2025-02-04 04:42:53.917897 INFO::Found 5 batches.
2025-02-04 04:42:53.918671 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 04:42:53.919534 INFO::Using default BPPARAM
2025-02-04 04:42:53.920253 INFO::Processing subtree level 1
2025-02-04 04:42:54.198773 INFO::Adjusting the last 2 batches sequentially
2025-02-04 04:42:54.204987 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-04 04:42:54.24691 INFO::Done
2025-02-04 04:42:54.247806 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 04:42:54.256219 INFO::ASW Batch was 0.493305766360952 prior to batch effect correction and is now -0.0740383898279632 .
2025-02-04 04:42:54.261255 INFO::ASW Label was 0.290783882566945 prior to batch effect correction and is now 0.853906001608555 .
2025-02-04 04:42:54.262439 INFO::Total function execution time is 0.381896734237671 s and adjustment time is 0.329234600067139 s ( 86.21 )
2025-02-04 04:42:54.301832 INFO::Formatting Data.
2025-02-04 04:42:54.302826 INFO::Replacing NaNs with NAs.
2025-02-04 04:42:54.304064 INFO::Removing potential empty rows and columns
2025-02-04 04:42:54.309583 INFO::Found 0 missing values.
2025-02-04 04:42:54.319908 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 04:42:54.324842 INFO::Done
2025-02-04 04:42:54.325742 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 04:42:54.333953 INFO::Starting hierarchical adjustment
2025-02-04 04:42:54.335099 INFO::Found 5 batches.
2025-02-04 04:42:54.335846 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 04:42:54.34079 INFO::Using default BPPARAM
2025-02-04 04:42:54.341683 INFO::Processing subtree level 1
2025-02-04 04:42:54.717741 INFO::Adjusting the last 2 batches sequentially
2025-02-04 04:42:54.719774 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-04 04:42:54.770089 INFO::Done
2025-02-04 04:42:54.77097 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 04:42:54.77939 INFO::ASW Batch was 0.242581456122664 prior to batch effect correction and is now 0.00351690911051945 .
2025-02-04 04:42:54.780274 INFO::ASW Label was 0.497749071977803 prior to batch effect correction and is now 0.780493397619779 .
2025-02-04 04:42:54.78587 INFO::Total function execution time is 0.484040975570679 s and adjustment time is 0.435204267501831 s ( 89.91 )
2025-02-04 04:42:54.787114 INFO::Formatting Data.
2025-02-04 04:42:54.787967 INFO::Replacing NaNs with NAs.
2025-02-04 04:42:54.793392 INFO::Removing potential empty rows and columns
2025-02-04 04:42:54.794875 INFO::Found 0 missing values.
2025-02-04 04:42:54.86561 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 04:42:54.86721 INFO::Done
2025-02-04 04:42:54.867956 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 04:42:54.876043 INFO::Starting hierarchical adjustment
2025-02-04 04:42:54.881284 INFO::Found 5 batches.
2025-02-04 04:42:54.882109 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 04:42:54.882954 INFO::Using default BPPARAM
2025-02-04 04:42:54.883679 INFO::Processing subtree level 1
2025-02-04 04:42:55.193942 INFO::Adjusting the last 2 batches sequentially
2025-02-04 04:42:55.196109 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-04 04:42:55.252937 INFO::Done
2025-02-04 04:42:55.253932 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 04:42:55.263179 INFO::ASW Batch was 0.242581456122664 prior to batch effect correction and is now 0.00351690911051945 .
2025-02-04 04:42:55.264134 INFO::ASW Label was 0.497749071977803 prior to batch effect correction and is now 0.780493397619779 .
2025-02-04 04:42:55.269521 INFO::Total function execution time is 0.482308864593506 s and adjustment time is 0.367843151092529 s ( 76.27 )
2025-02-04 04:42:55.310476 INFO::Formatting Data.
2025-02-04 04:42:55.311495 INFO::Replacing NaNs with NAs.
2025-02-04 04:42:55.31682 INFO::Removing potential empty rows and columns
2025-02-04 04:42:55.318575 INFO::Found 0 missing values.
2025-02-04 04:42:55.326993 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 04:42:55.327868 INFO::Done
2025-02-04 04:42:55.328611 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 04:42:55.341062 INFO::Starting hierarchical adjustment
2025-02-04 04:42:55.342219 INFO::Found 2 batches.
2025-02-04 04:42:55.342955 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 04:42:55.343835 INFO::Using default BPPARAM
2025-02-04 04:42:55.344673 INFO::Adjusting the last 2 batches sequentially
2025-02-04 04:42:55.350143 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-04 04:42:55.392634 INFO::Done
2025-02-04 04:42:55.397623 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 04:42:55.406052 INFO::ASW Batch was 0.503565892905079 prior to batch effect correction and is now 0.161832076697583 .
2025-02-04 04:42:55.406963 INFO::ASW Label was 0.650026251635164 prior to batch effect correction and is now 0.827431468436333 .
2025-02-04 04:42:55.408034 INFO::Total function execution time is 0.097637414932251 s and adjustment time is 0.0506319999694824 s ( 51.86 )
2025-02-04 04:42:55.413277 INFO::Formatting Data.
2025-02-04 04:42:55.414262 INFO::Replacing NaNs with NAs.
2025-02-04 04:42:55.415521 INFO::Removing potential empty rows and columns
2025-02-04 04:42:55.421186 INFO::Found 0 missing values.
2025-02-04 04:42:55.429586 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 04:42:55.430482 INFO::Done
2025-02-04 04:42:55.431185 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 04:42:55.439348 INFO::Starting hierarchical adjustment
2025-02-04 04:42:55.440463 INFO::Found 2 batches.
2025-02-04 04:42:55.445347 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 04:42:55.446266 INFO::Using default BPPARAM
2025-02-04 04:42:55.447034 INFO::Adjusting the last 2 batches sequentially
2025-02-04 04:42:55.448362 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-04 04:42:55.493294 INFO::Done
2025-02-04 04:42:55.494141 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 04:42:55.502292 INFO::ASW Batch was 0.503565892905079 prior to batch effect correction and is now 0.161832076697583 .
2025-02-04 04:42:55.503129 INFO::ASW Label was 0.650026251635164 prior to batch effect correction and is now 0.827431468436333 .
2025-02-04 04:42:55.504154 INFO::Total function execution time is 0.0909347534179688 s and adjustment time is 0.0530450344085693 s ( 58.33 )
2025-02-04 04:42:55.536607 INFO::Formatting Data.
2025-02-04 04:42:55.541662 INFO::Replacing NaNs with NAs.
2025-02-04 04:42:55.542899 INFO::Removing potential empty rows and columns
2025-02-04 04:42:55.544175 INFO::Found 0 missing values.
2025-02-04 04:42:55.551475 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 04:42:55.552246 INFO::Done
2025-02-04 04:42:55.557114 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 04:42:55.559776 INFO::Starting hierarchical adjustment
2025-02-04 04:42:55.564893 INFO::Found 2 batches.
2025-02-04 04:42:55.565726 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 04:42:55.566581 INFO::Using default BPPARAM
2025-02-04 04:42:55.567318 INFO::Adjusting the last 2 batches sequentially
2025-02-04 04:42:55.568672 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-04 04:42:55.705972 INFO::Done
2025-02-04 04:42:55.707103 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 04:42:55.715243 INFO::ASW Batch was -0.107726554742695 prior to batch effect correction and is now -0.153795334634222 .
2025-02-04 04:42:55.720763 INFO::Total function execution time is 0.180179595947266 s and adjustment time is 0.145255565643311 s ( 80.62 )
2025-02-04 04:42:55.763678 INFO::Formatting Data.
2025-02-04 04:42:55.769178 INFO::Replacing NaNs with NAs.
2025-02-04 04:42:55.770849 INFO::Removing potential empty rows and columns
2025-02-04 04:42:55.77263 INFO::Found 0 missing values.
2025-02-04 04:42:55.778771 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-02-04 04:42:55.795905 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 04:42:55.801085 INFO::Done
2025-02-04 04:42:55.802055 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 04:42:55.811503 INFO::Starting hierarchical adjustment
2025-02-04 04:42:55.817062 INFO::Found 2 batches.
2025-02-04 04:42:55.818091 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 04:42:55.819089 INFO::Using default BPPARAM
2025-02-04 04:42:55.819995 INFO::Adjusting the last 2 batches sequentially
2025-02-04 04:42:55.826188 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-04 04:42:55.881843 INFO::Done
2025-02-04 04:42:55.88279 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 04:42:55.891197 INFO::ASW Batch was 0.352610608214748 prior to batch effect correction and is now 0.143017313832533 .
2025-02-04 04:42:55.892122 INFO::ASW Label was 0.736738311923206 prior to batch effect correction and is now 0.830081686925775 .
2025-02-04 04:42:55.897479 INFO::Total function execution time is 0.133856296539307 s and adjustment time is 0.0691723823547363 s ( 51.68 )
2025-02-04 04:42:55.898844 INFO::Formatting Data.
2025-02-04 04:42:55.899786 INFO::Replacing NaNs with NAs.
2025-02-04 04:42:55.905509 INFO::Removing potential empty rows and columns
2025-02-04 04:42:55.907117 INFO::Found 0 missing values.
2025-02-04 04:42:55.908404 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-02-04 04:42:55.92378 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 04:42:55.924673 INFO::Done
2025-02-04 04:42:55.929713 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 04:42:55.938056 INFO::Starting hierarchical adjustment
2025-02-04 04:42:55.939139 INFO::Found 2 batches.
2025-02-04 04:42:55.939905 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 04:42:55.944938 INFO::Using default BPPARAM
2025-02-04 04:42:55.945889 INFO::Adjusting the last 2 batches sequentially
2025-02-04 04:42:55.94728 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-04 04:42:56.000941 INFO::Done
2025-02-04 04:42:56.001903 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 04:42:56.01028 INFO::ASW Batch was 0.352610608214748 prior to batch effect correction and is now 0.143017313832533 .
2025-02-04 04:42:56.011208 INFO::ASW Label was 0.736738311923206 prior to batch effect correction and is now 0.830081686925775 .
2025-02-04 04:42:56.012313 INFO::Total function execution time is 0.113522291183472 s and adjustment time is 0.0579180717468262 s ( 51.02 )
2025-02-04 04:42:56.658576 INFO::Formatting Data.
2025-02-04 04:42:56.659549 INFO::Replacing NaNs with NAs.
2025-02-04 04:42:56.660729 INFO::Removing potential empty rows and columns
2025-02-04 04:42:56.666317 INFO::Found 0 missing values.
2025-02-04 04:42:56.674941 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 04:42:56.675795 INFO::Done
2025-02-04 04:42:56.676571 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 04:42:56.683431 INFO::Starting hierarchical adjustment
2025-02-04 04:42:56.684486 INFO::Found 3 batches.
2025-02-04 04:42:56.689384 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 04:42:56.690279 INFO::Using default BPPARAM
2025-02-04 04:42:56.691065 INFO::Processing subtree level 1
2025-02-04 04:42:57.025576 INFO::Adjusting the last 1 batches sequentially
2025-02-04 04:42:57.028041 INFO::Done
2025-02-04 04:42:57.033167 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 04:42:57.040873 INFO::ASW Batch was -0.0438583237979882 prior to batch effect correction and is now -0.0438583237979882 .
2025-02-04 04:42:57.042417 INFO::Total function execution time is 0.383793354034424 s and adjustment time is 0.343765020370483 s ( 89.57 )
2025-02-04 04:42:57.044013 INFO::Formatting Data.
2025-02-04 04:42:57.049167 INFO::Typecasting input to dataframe.
2025-02-04 04:42:57.050401 INFO::Replacing NaNs with NAs.
2025-02-04 04:42:57.051771 INFO::Removing potential empty rows and columns
2025-02-04 04:42:57.057579 INFO::Found 0 missing values.
2025-02-04 04:42:57.066635 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 04:42:57.067537 INFO::Done
2025-02-04 04:42:57.068352 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 04:42:57.075382 INFO::Starting hierarchical adjustment
2025-02-04 04:42:57.07651 INFO::Found 3 batches.
2025-02-04 04:42:57.081419 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 04:42:57.082344 INFO::Using default BPPARAM
2025-02-04 04:42:57.083143 INFO::Processing subtree level 1
2025-02-04 04:42:57.399556 INFO::Adjusting the last 1 batches sequentially
2025-02-04 04:42:57.406028 INFO::Done
2025-02-04 04:42:57.406934 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 04:42:57.414518 INFO::ASW Batch was -0.0438583237979882 prior to batch effect correction and is now -0.0438583237979882 .
2025-02-04 04:42:57.415858 INFO::Total function execution time is 0.371860265731812 s and adjustment time is 0.329730987548828 s ( 88.67 )
2025-02-04 04:42:57.45473 INFO::Formatting Data.
2025-02-04 04:42:57.455739 INFO::Typecasting input to dataframe.
2025-02-04 04:42:57.461087 INFO::Replacing NaNs with NAs.
2025-02-04 04:42:57.462475 INFO::Removing potential empty rows and columns
2025-02-04 04:42:57.463981 INFO::Found 0 missing values.
2025-02-04 04:42:57.47246 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 04:42:57.477449 INFO::Done
2025-02-04 04:42:57.478207 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 04:42:57.484934 INFO::Starting hierarchical adjustment
2025-02-04 04:42:57.486057 INFO::Found 3 batches.
2025-02-04 04:42:57.486809 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 04:42:57.487641 INFO::Using default BPPARAM
2025-02-04 04:42:57.48838 INFO::Processing subtree level 1
2025-02-04 04:42:57.820914 INFO::Adjusting the last 1 batches sequentially
2025-02-04 04:42:57.823459 INFO::Done
2025-02-04 04:42:57.824442 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 04:42:57.832279 INFO::ASW Batch was -0.105439777988514 prior to batch effect correction and is now -0.105439777988514 .
2025-02-04 04:42:57.837934 INFO::Total function execution time is 0.383139371871948 s and adjustment time is 0.337578535079956 s ( 88.11 )
2025-02-04 04:42:58.24276 INFO::Formatting Data.
2025-02-04 04:42:58.24389 INFO::Replacing NaNs with NAs.
2025-02-04 04:42:58.249838 INFO::Removing potential empty rows and columns
2025-02-04 04:42:58.258902 INFO::Found 1000 missing values.
2025-02-04 04:42:58.32938 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 04:42:58.330302 INFO::Done
2025-02-04 04:42:58.331158 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 04:42:58.347499 INFO::Starting hierarchical adjustment
2025-02-04 04:42:58.353121 INFO::Found 10 batches.
2025-02-04 04:42:58.354078 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 04:42:58.355046 INFO::Using default BPPARAM
2025-02-04 04:42:58.355875 INFO::Processing subtree level 1
2025-02-04 04:42:58.736687 INFO::Processing subtree level 2
2025-02-04 04:42:59.190885 INFO::Adjusting the last 1 batches sequentially
2025-02-04 04:42:59.201603 INFO::Done
2025-02-04 04:42:59.202547 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 04:42:59.218881 INFO::ASW Batch was 0.506563551183544 prior to batch effect correction and is now 0.506563551183544 .
2025-02-04 04:42:59.219891 INFO::ASW Label was 0.344628454911404 prior to batch effect correction and is now 0.344628454911404 .
2025-02-04 04:42:59.225343 INFO::Total function execution time is 0.982564210891724 s and adjustment time is 0.85296368598938 s ( 86.81 )
2025-02-04 04:42:59.226676 INFO::Formatting Data.
2025-02-04 04:42:59.227598 INFO::Replacing NaNs with NAs.
2025-02-04 04:42:59.233667 INFO::Removing potential empty rows and columns
2025-02-04 04:42:59.242586 INFO::Found 1000 missing values.
2025-02-04 04:42:59.306603 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 04:42:59.3075 INFO::Done
2025-02-04 04:42:59.308248 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 04:42:59.324667 INFO::Starting hierarchical adjustment
2025-02-04 04:42:59.33016 INFO::Found 10 batches.
2025-02-04 04:43:00.699172 INFO::Set up parallel execution backend with 2 workers
2025-02-04 04:43:00.700943 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-02-04 04:43:02.78656 INFO::Adjusting the last 2 batches sequentially
2025-02-04 04:43:02.788156 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-04 04:43:02.835634 INFO::Done
2025-02-04 04:43:02.83641 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 04:43:02.85094 INFO::ASW Batch was 0.506563551183544 prior to batch effect correction and is now 0.506563551183544 .
2025-02-04 04:43:02.851714 INFO::ASW Label was 0.344628454911404 prior to batch effect correction and is now 0.344628454911404 .
2025-02-04 04:43:02.856839 INFO::Total function execution time is 3.62612915039062 s and adjustment time is 3.50580382347107 s ( 96.68 )
2025-02-04 04:43:03.241375 INFO::Formatting Data.
2025-02-04 04:43:03.242417 INFO::Replacing NaNs with NAs.
2025-02-04 04:43:03.243654 INFO::Removing potential empty rows and columns
2025-02-04 04:43:03.249431 INFO::Found 0 missing values.
2025-02-04 04:43:03.259367 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 04:43:03.260233 INFO::Done
2025-02-04 04:43:03.265247 INFO::Acquiring quality metrics before batch effect correction.
2025-02-04 04:43:03.273275 INFO::Starting hierarchical adjustment
2025-02-04 04:43:03.274401 INFO::Found 3 batches.
2025-02-04 04:43:03.275242 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-04 04:43:03.276065 INFO::Using default BPPARAM
2025-02-04 04:43:03.280972 INFO::Processing subtree level 1
2025-02-04 04:43:03.545282 INFO::Adjusting the last 1 batches sequentially
2025-02-04 04:43:03.547538 INFO::Done
2025-02-04 04:43:03.548356 INFO::Acquiring quality metrics after batch effect correction.
2025-02-04 04:43:03.560981 INFO::ASW Batch was 0.241670573581546 prior to batch effect correction and is now -0.152460442274788 .
2025-02-04 04:43:03.561989 INFO::ASW Label was -0.160885493797821 prior to batch effect correction and is now 0.206141169988988 .
2025-02-04 04:43:03.563204 INFO::Total function execution time is 0.321889400482178 s and adjustment time is 0.273380517959595 s ( 84.93 )
2025-02-04 04:43:03.914778 INFO::Formatting Data.
2025-02-04 04:43:03.91576 INFO::Replacing NaNs with NAs.
2025-02-04 04:43:03.921147 INFO::Removing potential empty rows and columns
2025-02-04 04:43:03.922826 INFO::Found 2 missing values.
2025-02-04 04:43:03.931246 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-02-04 04:43:03.932095 INFO::Done
2025-02-04 04:43:04.013614 INFO::Found NA in Reference column
2025-02-04 04:43:04.046415 INFO::Require at least two references per batch.
2025-02-04 04:43:04.11779 INFO::Formatting Data.
2025-02-04 04:43:04.118888 INFO::Recognized SummarizedExperiment
2025-02-04 04:43:04.119802 INFO::Typecasting input to dataframe.
2025-02-04 04:43:04.152148 INFO::Replacing NaNs with NAs.
2025-02-04 04:43:04.158097 INFO::Removing potential empty rows and columns
2025-02-04 04:43:04.167831 INFO::Found 0 missing values.
2025-02-04 04:43:04.191423 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 04:43:04.192453 INFO::Done
2025-02-04 04:43:04.239171 INFO::Formatting Data.
2025-02-04 04:43:04.240076 INFO::Recognized SummarizedExperiment
2025-02-04 04:43:04.242546 INFO::Typecasting input to dataframe.
2025-02-04 04:43:04.301736 INFO::Replacing NaNs with NAs.
2025-02-04 04:43:04.303295 INFO::Removing potential empty rows and columns
2025-02-04 04:43:04.312638 INFO::Found 0 missing values.
2025-02-04 04:43:04.349996 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 04:43:04.350859 INFO::Done
2025-02-04 04:43:04.390562 INFO::Formatting Data.
2025-02-04 04:43:04.391475 INFO::Recognized SummarizedExperiment
2025-02-04 04:43:04.392145 INFO::Typecasting input to dataframe.
2025-02-04 04:43:04.446159 INFO::Replacing NaNs with NAs.
2025-02-04 04:43:04.447435 INFO::Removing potential empty rows and columns
2025-02-04 04:43:04.45328 INFO::Found 0 missing values.
2025-02-04 04:43:04.454631 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-02-04 04:43:04.469322 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 04:43:04.470161 INFO::Done
2025-02-04 04:43:04.502041 INFO::Formatting Data.
2025-02-04 04:43:04.50301 INFO::Replacing NaNs with NAs.
2025-02-04 04:43:04.504086 INFO::Removing potential empty rows and columns
2025-02-04 04:43:04.509755 INFO::Found 0 missing values.
2025-02-04 04:43:04.518885 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 04:43:04.519771 INFO::Done
2025-02-04 04:43:04.547405 INFO::Formatting Data.
2025-02-04 04:43:04.548465 INFO::Replacing NaNs with NAs.
2025-02-04 04:43:04.551794 INFO::Removing potential empty rows and columns
2025-02-04 04:43:04.553218 INFO::Found 0 missing values.
2025-02-04 04:43:04.557299 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 04:43:04.558063 INFO::Done
2025-02-04 04:43:04.633956 INFO::Formatting Data.
2025-02-04 04:43:04.634961 INFO::Replacing NaNs with NAs.
2025-02-04 04:43:04.636553 INFO::Removing potential empty rows and columns
2025-02-04 04:43:04.642606 INFO::Found 1 missing values.
2025-02-04 04:43:04.650891 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 04:43:04.651731 INFO::Done
2025-02-04 04:43:04.707887 INFO::Formatting Data.
2025-02-04 04:43:04.71303 INFO::Replacing NaNs with NAs.
2025-02-04 04:43:04.714389 INFO::Removing potential empty rows and columns
2025-02-04 04:43:04.71575 INFO::Found 2 missing values.
2025-02-04 04:43:04.721226 INFO::BERT requires at least 2 numeric values per batch/covariate level. This may reduce the number of adjustable features considerably, depending on the quantification technique.
2025-02-04 04:43:04.728806 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-02-04 04:43:04.729793 INFO::Done
2025-02-04 04:43:04.761969 INFO::Formatting Data.
2025-02-04 04:43:04.76303 INFO::Replacing NaNs with NAs.
2025-02-04 04:43:04.764242 INFO::Removing potential empty rows and columns
2025-02-04 04:43:04.769867 INFO::Found 2 missing values.
2025-02-04 04:43:04.772417 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 04:43:04.7774 INFO::Done
2025-02-04 04:43:04.810739 INFO::Formatting Data.
2025-02-04 04:43:04.811805 INFO::Typecasting input to dataframe.
2025-02-04 04:43:04.81725 INFO::Replacing NaNs with NAs.
2025-02-04 04:43:04.818874 INFO::Removing potential empty rows and columns
2025-02-04 04:43:04.820477 INFO::Found 0 missing values.
2025-02-04 04:43:04.833514 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-04 04:43:04.834435 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
19.324 4.177 36.152
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 27.062 | 1.460 | 29.082 | |
| compute_asw | 0.031 | 0.007 | 0.040 | |
| count_existing | 0.015 | 0.008 | 0.024 | |
| generate_data_covariables | 0.019 | 0.000 | 0.020 | |
| generate_dataset | 0.019 | 0.000 | 0.020 | |