Yannis Schumann
| Snapshot Date: 2025-04-16 13:40 -0400 (Wed, 16 Apr 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_21 |
| git_last_commit: dedce04 |
| git_last_commit_date: 2025-04-15 13:25:40 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-04-17 11:46 -0400 (Thu, 17 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4667 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4573 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4599 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4553 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4570 |
| 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 163/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.4.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | 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: 1.4.0 |
| 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_1.4.0.tar.gz |
| StartedAt: 2025-04-17 04:08:59 -0000 (Thu, 17 Apr 2025) |
| EndedAt: 2025-04-17 04:10:30 -0000 (Thu, 17 Apr 2025) |
| EllapsedTime: 91.1 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.4.0’
* 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 31.005 1.656 22.446
* 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-devel_2025-02-19/site-library’ * installing *source* package ‘BERT’ ... ** this is package ‘BERT’ version ‘1.4.0’ ** 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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 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")
2025-04-17 04:10:13.547716 INFO::Formatting Data.
2025-04-17 04:10:13.549424 INFO::Replacing NaNs with NAs.
2025-04-17 04:10:13.566754 INFO::Removing potential empty rows and columns
2025-04-17 04:10:13.935947 INFO::Found 0 missing values.
2025-04-17 04:10:13.941118 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-17 04:10:13.942054 INFO::Done
2025-04-17 04:10:13.942813 INFO::Acquiring quality metrics before batch effect correction.
2025-04-17 04:10:13.957757 INFO::Starting hierarchical adjustment
2025-04-17 04:10:13.958891 INFO::Found 3 batches.
2025-04-17 04:10:13.959673 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-17 04:10:13.961123 INFO::Using default BPPARAM
2025-04-17 04:10:13.961891 INFO::Processing subtree level 1
2025-04-17 04:10:14.088252 INFO::Adjusting the last 1 batches sequentially
2025-04-17 04:10:14.090706 INFO::Done
2025-04-17 04:10:14.091686 INFO::Acquiring quality metrics after batch effect correction.
2025-04-17 04:10:14.095339 INFO::ASW Batch was -0.0747594576130257 prior to batch effect correction and is now -0.0747594576130257 .
2025-04-17 04:10:14.096946 INFO::Total function execution time is 0.549965620040894 s and adjustment time is 0.132015466690063 s ( 24 )
2025-04-17 04:10:14.11639 INFO::Formatting Data.
2025-04-17 04:10:14.117506 INFO::Replacing NaNs with NAs.
2025-04-17 04:10:14.118814 INFO::Removing potential empty rows and columns
2025-04-17 04:10:14.120603 INFO::Found 0 missing values.
2025-04-17 04:10:14.122185 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.
2025-04-17 04:10:14.137723 INFO::Formatting Data.
2025-04-17 04:10:14.13872 INFO::Replacing NaNs with NAs.
2025-04-17 04:10:14.139982 INFO::Removing potential empty rows and columns
2025-04-17 04:10:14.141445 INFO::Found 0 missing values.
2025-04-17 04:10:14.142709 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.
2025-04-17 04:10:14.164662 INFO::Formatting Data.
2025-04-17 04:10:14.165639 INFO::Replacing NaNs with NAs.
2025-04-17 04:10:14.166847 INFO::Removing potential empty rows and columns
2025-04-17 04:10:14.168319 INFO::Found 0 missing values.
2025-04-17 04:10:14.169663 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.
2025-04-17 04:10:14.176342 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-17 04:10:14.177255 INFO::Done
2025-04-17 04:10:14.177996 INFO::Acquiring quality metrics before batch effect correction.
2025-04-17 04:10:14.180887 INFO::Starting hierarchical adjustment
2025-04-17 04:10:14.181917 INFO::Found 2 batches.
2025-04-17 04:10:14.182672 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-17 04:10:14.183564 INFO::Using default BPPARAM
2025-04-17 04:10:14.184316 INFO::Adjusting the last 2 batches sequentially
2025-04-17 04:10:14.185642 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-17 04:10:14.215463 INFO::Done
2025-04-17 04:10:14.216334 INFO::Acquiring quality metrics after batch effect correction.
2025-04-17 04:10:14.219155 INFO::ASW Batch was 0.000663883077913999 prior to batch effect correction and is now -0.0972273115784772 .
2025-04-17 04:10:14.220249 INFO::Total function execution time is 0.055649995803833 s and adjustment time is 0.0337338447570801 s ( 60.62 )
2025-04-17 04:10:14.223852 INFO::Formatting Data.
2025-04-17 04:10:14.224809 INFO::Replacing NaNs with NAs.
2025-04-17 04:10:14.236986 INFO::Formatting Data.
2025-04-17 04:10:14.237941 INFO::Replacing NaNs with NAs.
2025-04-17 04:10:14.239137 INFO::Removing potential empty rows and columns
2025-04-17 04:10:14.249795 INFO::Found 0 missing values.
2025-04-17 04:10:14.298643 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-17 04:10:14.299923 INFO::Done
2025-04-17 04:10:14.30068 INFO::Acquiring quality metrics before batch effect correction.
2025-04-17 04:10:14.303527 INFO::Starting hierarchical adjustment
2025-04-17 04:10:14.304569 INFO::Found 2 batches.
2025-04-17 04:10:14.305304 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-17 04:10:14.306133 INFO::Using default BPPARAM
2025-04-17 04:10:14.306853 INFO::Adjusting the last 2 batches sequentially
2025-04-17 04:10:14.308098 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-17 04:10:14.329443 INFO::Done
2025-04-17 04:10:14.330322 INFO::Acquiring quality metrics after batch effect correction.
2025-04-17 04:10:14.333081 INFO::ASW Batch was -0.0472112587061442 prior to batch effect correction and is now -0.112080423408545 .
2025-04-17 04:10:14.334287 INFO::Total function execution time is 0.0973947048187256 s and adjustment time is 0.0250842571258545 s ( 25.76 )
2025-04-17 04:10:14.335761 INFO::Formatting Data.
2025-04-17 04:10:14.336605 INFO::Replacing NaNs with NAs.
2025-04-17 04:10:14.337789 INFO::Removing potential empty rows and columns
2025-04-17 04:10:14.339335 INFO::Found 0 missing values.
2025-04-17 04:10:14.343329 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-17 04:10:14.344107 INFO::Done
2025-04-17 04:10:14.344859 INFO::Acquiring quality metrics before batch effect correction.
2025-04-17 04:10:14.347614 INFO::Starting hierarchical adjustment
2025-04-17 04:10:14.348624 INFO::Found 2 batches.
2025-04-17 04:10:14.349366 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-17 04:10:14.350238 INFO::Using default BPPARAM
2025-04-17 04:10:14.351004 INFO::Adjusting the last 2 batches sequentially
2025-04-17 04:10:14.352288 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-17 04:10:14.373178 INFO::Done
2025-04-17 04:10:14.374081 INFO::Acquiring quality metrics after batch effect correction.
2025-04-17 04:10:14.376942 INFO::ASW Batch was -0.0472112587061442 prior to batch effect correction and is now -0.112080423408545 .
2025-04-17 04:10:14.378136 INFO::Total function execution time is 0.0423357486724854 s and adjustment time is 0.0247495174407959 s ( 58.46 )
2025-04-17 04:10:18.423553 INFO::Formatting Data.
2025-04-17 04:10:18.424439 INFO::Recognized SummarizedExperiment
2025-04-17 04:10:18.425166 INFO::Typecasting input to dataframe.
2025-04-17 04:10:18.465809 INFO::Replacing NaNs with NAs.
2025-04-17 04:10:18.467242 INFO::Removing potential empty rows and columns
2025-04-17 04:10:18.472227 INFO::Found 0 missing values.
2025-04-17 04:10:18.482787 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-17 04:10:18.483702 INFO::Done
2025-04-17 04:10:18.484452 INFO::Acquiring quality metrics before batch effect correction.
2025-04-17 04:10:18.489858 INFO::Starting hierarchical adjustment
2025-04-17 04:10:18.491061 INFO::Found 2 batches.
2025-04-17 04:10:18.491941 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-17 04:10:18.493531 INFO::Using default BPPARAM
2025-04-17 04:10:18.494401 INFO::Adjusting the last 2 batches sequentially
2025-04-17 04:10:18.495873 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-17 04:10:18.576253 INFO::Done
2025-04-17 04:10:18.577179 INFO::Acquiring quality metrics after batch effect correction.
2025-04-17 04:10:18.582088 INFO::ASW Batch was -0.0115882552441047 prior to batch effect correction and is now -0.0897795430230827 .
2025-04-17 04:10:18.583309 INFO::Total function execution time is 0.160156011581421 s and adjustment time is 0.0854296684265137 s ( 53.34 )
2025-04-17 04:10:18.607794 INFO::Formatting Data.
2025-04-17 04:10:18.608776 INFO::Recognized SummarizedExperiment
2025-04-17 04:10:18.609506 INFO::Typecasting input to dataframe.
2025-04-17 04:10:18.622701 INFO::Replacing NaNs with NAs.
2025-04-17 04:10:18.62426 INFO::Removing potential empty rows and columns
2025-04-17 04:10:18.62956 INFO::Found 0 missing values.
2025-04-17 04:10:18.640178 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-17 04:10:18.641133 INFO::Done
2025-04-17 04:10:18.641914 INFO::Acquiring quality metrics before batch effect correction.
2025-04-17 04:10:18.646947 INFO::Starting hierarchical adjustment
2025-04-17 04:10:18.648106 INFO::Found 2 batches.
2025-04-17 04:10:18.648945 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-17 04:10:18.649827 INFO::Using default BPPARAM
2025-04-17 04:10:18.650577 INFO::Adjusting the last 2 batches sequentially
2025-04-17 04:10:18.651953 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-17 04:10:18.687541 INFO::Done
2025-04-17 04:10:18.688411 INFO::Acquiring quality metrics after batch effect correction.
2025-04-17 04:10:18.693331 INFO::ASW Batch was 0.00548475966164935 prior to batch effect correction and is now 0.00548475966164935 .
2025-04-17 04:10:18.69458 INFO::Total function execution time is 0.0867552757263184 s and adjustment time is 0.0396585464477539 s ( 45.71 )
2025-04-17 04:10:18.719313 INFO::Formatting Data.
2025-04-17 04:10:18.720316 INFO::Replacing NaNs with NAs.
2025-04-17 04:10:18.721609 INFO::Removing potential empty rows and columns
2025-04-17 04:10:18.723003 INFO::Found 0 missing values.
2025-04-17 04:10:18.727106 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-17 04:10:18.727944 INFO::Done
2025-04-17 04:10:18.728722 INFO::Acquiring quality metrics before batch effect correction.
2025-04-17 04:10:18.731588 INFO::Starting hierarchical adjustment
2025-04-17 04:10:18.732702 INFO::Found 3 batches.
2025-04-17 04:10:18.73348 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-17 04:10:18.734332 INFO::Using default BPPARAM
2025-04-17 04:10:18.735084 INFO::Processing subtree level 1
2025-04-17 04:10:19.057183 INFO::Adjusting the last 1 batches sequentially
2025-04-17 04:10:19.059725 INFO::Done
2025-04-17 04:10:19.060795 INFO::Acquiring quality metrics after batch effect correction.
2025-04-17 04:10:19.064393 INFO::ASW Batch was -0.0397747883436342 prior to batch effect correction and is now -0.15217315260967 .
2025-04-17 04:10:19.065864 INFO::Total function execution time is 0.346514701843262 s and adjustment time is 0.327281951904297 s ( 94.45 )
2025-04-17 04:10:19.169572 INFO::Skipping initial DF formatting
2025-04-17 04:10:19.170584 INFO::Acquiring quality metrics before batch effect correction.
2025-04-17 04:10:19.176757 INFO::Starting hierarchical adjustment
2025-04-17 04:10:19.178021 INFO::Found 5 batches.
2025-04-17 04:10:19.178897 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-17 04:10:19.179888 INFO::Using default BPPARAM
2025-04-17 04:10:19.180788 INFO::Processing subtree level 1
2025-04-17 04:10:19.396959 INFO::Adjusting the last 2 batches sequentially
2025-04-17 04:10:19.399491 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-17 04:10:19.437208 INFO::Done
2025-04-17 04:10:19.438281 INFO::Acquiring quality metrics after batch effect correction.
2025-04-17 04:10:19.445359 INFO::ASW Batch was 0.561667082816179 prior to batch effect correction and is now 0.561667082816179 .
2025-04-17 04:10:19.446431 INFO::ASW Label was 0.330917470786079 prior to batch effect correction and is now 0.330917470786079 .
2025-04-17 04:10:19.447865 INFO::Total function execution time is 0.278312683105469 s and adjustment time is 0.259410381317139 s ( 93.21 )
2025-04-17 04:10:19.477936 INFO::Formatting Data.
2025-04-17 04:10:19.479236 INFO::Replacing NaNs with NAs.
2025-04-17 04:10:19.480846 INFO::Removing potential empty rows and columns
2025-04-17 04:10:19.482577 INFO::Found 0 missing values.
2025-04-17 04:10:19.48981 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-17 04:10:19.490837 INFO::Done
2025-04-17 04:10:19.491832 INFO::Acquiring quality metrics before batch effect correction.
2025-04-17 04:10:19.497042 INFO::Starting hierarchical adjustment
2025-04-17 04:10:19.498373 INFO::Found 5 batches.
2025-04-17 04:10:19.499311 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-17 04:10:19.500363 INFO::Using default BPPARAM
2025-04-17 04:10:19.501277 INFO::Processing subtree level 1
2025-04-17 04:10:19.659371 INFO::Adjusting the last 2 batches sequentially
2025-04-17 04:10:19.661887 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-17 04:10:19.687842 INFO::Done
2025-04-17 04:10:19.688893 INFO::Acquiring quality metrics after batch effect correction.
2025-04-17 04:10:19.694084 INFO::ASW Batch was 0.474168144222694 prior to batch effect correction and is now -0.0452089806784905 .
2025-04-17 04:10:19.695155 INFO::ASW Label was 0.305647782662313 prior to batch effect correction and is now 0.838182913315587 .
2025-04-17 04:10:19.696515 INFO::Total function execution time is 0.2186279296875 s and adjustment time is 0.189718961715698 s ( 86.78 )
2025-04-17 04:10:19.697903 INFO::Formatting Data.
2025-04-17 04:10:19.698904 INFO::Replacing NaNs with NAs.
2025-04-17 04:10:19.700381 INFO::Removing potential empty rows and columns
2025-04-17 04:10:19.702101 INFO::Found 0 missing values.
2025-04-17 04:10:19.709108 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-17 04:10:19.710099 INFO::Done
2025-04-17 04:10:19.710992 INFO::Acquiring quality metrics before batch effect correction.
2025-04-17 04:10:19.71566 INFO::Starting hierarchical adjustment
2025-04-17 04:10:19.716953 INFO::Found 5 batches.
2025-04-17 04:10:19.717885 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-17 04:10:19.718887 INFO::Using default BPPARAM
2025-04-17 04:10:19.719734 INFO::Processing subtree level 1
2025-04-17 04:10:19.87887 INFO::Adjusting the last 2 batches sequentially
2025-04-17 04:10:19.881248 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-17 04:10:19.905599 INFO::Done
2025-04-17 04:10:19.906613 INFO::Acquiring quality metrics after batch effect correction.
2025-04-17 04:10:19.911631 INFO::ASW Batch was 0.474168144222694 prior to batch effect correction and is now -0.0452089806784905 .
2025-04-17 04:10:19.912678 INFO::ASW Label was 0.305647782662313 prior to batch effect correction and is now 0.838182913315587 .
2025-04-17 04:10:19.913982 INFO::Total function execution time is 0.216068029403687 s and adjustment time is 0.188891649246216 s ( 87.42 )
2025-04-17 04:10:19.935407 INFO::Formatting Data.
2025-04-17 04:10:19.936603 INFO::Replacing NaNs with NAs.
2025-04-17 04:10:19.938066 INFO::Removing potential empty rows and columns
2025-04-17 04:10:19.939665 INFO::Found 0 missing values.
2025-04-17 04:10:19.94656 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-17 04:10:19.947588 INFO::Done
2025-04-17 04:10:19.94851 INFO::Acquiring quality metrics before batch effect correction.
2025-04-17 04:10:19.953352 INFO::Starting hierarchical adjustment
2025-04-17 04:10:19.954672 INFO::Found 5 batches.
2025-04-17 04:10:19.955613 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-17 04:10:19.956686 INFO::Using default BPPARAM
2025-04-17 04:10:19.957701 INFO::Processing subtree level 1
2025-04-17 04:10:20.115088 INFO::Adjusting the last 2 batches sequentially
2025-04-17 04:10:20.117457 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-17 04:10:20.141626 INFO::Done
2025-04-17 04:10:20.142654 INFO::Acquiring quality metrics after batch effect correction.
2025-04-17 04:10:20.147798 INFO::ASW Batch was 0.400898433651772 prior to batch effect correction and is now -0.0219156131772401 .
2025-04-17 04:10:20.148892 INFO::ASW Label was 0.37866044997464 prior to batch effect correction and is now 0.759334699685666 .
2025-04-17 04:10:20.150233 INFO::Total function execution time is 0.214864492416382 s and adjustment time is 0.187214612960815 s ( 87.13 )
2025-04-17 04:10:20.151627 INFO::Formatting Data.
2025-04-17 04:10:20.152699 INFO::Replacing NaNs with NAs.
2025-04-17 04:10:20.154138 INFO::Removing potential empty rows and columns
2025-04-17 04:10:20.155768 INFO::Found 0 missing values.
2025-04-17 04:10:20.162761 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-17 04:10:20.163784 INFO::Done
2025-04-17 04:10:20.164758 INFO::Acquiring quality metrics before batch effect correction.
2025-04-17 04:10:20.169504 INFO::Starting hierarchical adjustment
2025-04-17 04:10:20.170735 INFO::Found 5 batches.
2025-04-17 04:10:20.171651 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-17 04:10:20.17272 INFO::Using default BPPARAM
2025-04-17 04:10:20.173685 INFO::Processing subtree level 1
2025-04-17 04:10:20.327178 INFO::Adjusting the last 2 batches sequentially
2025-04-17 04:10:20.329493 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-17 04:10:20.352935 INFO::Done
2025-04-17 04:10:20.353924 INFO::Acquiring quality metrics after batch effect correction.
2025-04-17 04:10:20.358682 INFO::ASW Batch was 0.400898433651772 prior to batch effect correction and is now -0.0219156131772401 .
2025-04-17 04:10:20.359675 INFO::ASW Label was 0.37866044997464 prior to batch effect correction and is now 0.759334699685666 .
2025-04-17 04:10:20.360993 INFO::Total function execution time is 0.209380149841309 s and adjustment time is 0.182436227798462 s ( 87.13 )
2025-04-17 04:10:20.381411 INFO::Formatting Data.
2025-04-17 04:10:20.382545 INFO::Replacing NaNs with NAs.
2025-04-17 04:10:20.383985 INFO::Removing potential empty rows and columns
2025-04-17 04:10:20.38559 INFO::Found 0 missing values.
2025-04-17 04:10:20.389951 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-17 04:10:20.390895 INFO::Done
2025-04-17 04:10:20.391721 INFO::Acquiring quality metrics before batch effect correction.
2025-04-17 04:10:20.396105 INFO::Starting hierarchical adjustment
2025-04-17 04:10:20.397341 INFO::Found 2 batches.
2025-04-17 04:10:20.398174 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-17 04:10:20.399124 INFO::Using default BPPARAM
2025-04-17 04:10:20.399958 INFO::Adjusting the last 2 batches sequentially
2025-04-17 04:10:20.401403 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-17 04:10:20.423318 INFO::Done
2025-04-17 04:10:20.424312 INFO::Acquiring quality metrics after batch effect correction.
2025-04-17 04:10:20.428696 INFO::ASW Batch was 0.74105057870014 prior to batch effect correction and is now -0.0323050194007729 .
2025-04-17 04:10:20.429664 INFO::ASW Label was 0.256184997293805 prior to batch effect correction and is now 0.841509162358642 .
2025-04-17 04:10:20.43085 INFO::Total function execution time is 0.049515962600708 s and adjustment time is 0.0262010097503662 s ( 52.91 )
2025-04-17 04:10:20.432042 INFO::Formatting Data.
2025-04-17 04:10:20.433008 INFO::Replacing NaNs with NAs.
2025-04-17 04:10:20.434301 INFO::Removing potential empty rows and columns
2025-04-17 04:10:20.435819 INFO::Found 0 missing values.
2025-04-17 04:10:20.440128 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-17 04:10:20.44108 INFO::Done
2025-04-17 04:10:20.441908 INFO::Acquiring quality metrics before batch effect correction.
2025-04-17 04:10:20.446169 INFO::Starting hierarchical adjustment
2025-04-17 04:10:20.447335 INFO::Found 2 batches.
2025-04-17 04:10:20.448201 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-17 04:10:20.449158 INFO::Using default BPPARAM
2025-04-17 04:10:20.449965 INFO::Adjusting the last 2 batches sequentially
2025-04-17 04:10:20.45136 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-17 04:10:20.473122 INFO::Done
2025-04-17 04:10:20.474073 INFO::Acquiring quality metrics after batch effect correction.
2025-04-17 04:10:20.478396 INFO::ASW Batch was 0.74105057870014 prior to batch effect correction and is now -0.0323050194007729 .
2025-04-17 04:10:20.479361 INFO::ASW Label was 0.256184997293805 prior to batch effect correction and is now 0.841509162358642 .
2025-04-17 04:10:20.480559 INFO::Total function execution time is 0.0485262870788574 s and adjustment time is 0.0259981155395508 s ( 53.58 )
2025-04-17 04:10:20.497231 INFO::Formatting Data.
2025-04-17 04:10:20.498294 INFO::Replacing NaNs with NAs.
2025-04-17 04:10:20.499568 INFO::Removing potential empty rows and columns
2025-04-17 04:10:20.500969 INFO::Found 0 missing values.
2025-04-17 04:10:20.504229 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-17 04:10:20.50516 INFO::Done
2025-04-17 04:10:20.505987 INFO::Acquiring quality metrics before batch effect correction.
2025-04-17 04:10:20.508806 INFO::Starting hierarchical adjustment
2025-04-17 04:10:20.509945 INFO::Found 2 batches.
2025-04-17 04:10:20.510759 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-17 04:10:20.511695 INFO::Using default BPPARAM
2025-04-17 04:10:20.512527 INFO::Adjusting the last 2 batches sequentially
2025-04-17 04:10:20.513946 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-17 04:10:20.560852 INFO::Done
2025-04-17 04:10:20.561822 INFO::Acquiring quality metrics after batch effect correction.
2025-04-17 04:10:20.564677 INFO::ASW Batch was 0.0356467470493314 prior to batch effect correction and is now -0.163098559953105 .
2025-04-17 04:10:20.56594 INFO::Total function execution time is 0.0687770843505859 s and adjustment time is 0.051124095916748 s ( 74.33 )
2025-04-17 04:10:20.583207 INFO::Formatting Data.
2025-04-17 04:10:20.584324 INFO::Replacing NaNs with NAs.
2025-04-17 04:10:20.585643 INFO::Removing potential empty rows and columns
2025-04-17 04:10:20.587145 INFO::Found 0 missing values.
2025-04-17 04:10:20.58894 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.
2025-04-17 04:10:20.596259 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-17 04:10:20.597257 INFO::Done
2025-04-17 04:10:20.598108 INFO::Acquiring quality metrics before batch effect correction.
2025-04-17 04:10:20.602463 INFO::Starting hierarchical adjustment
2025-04-17 04:10:20.603682 INFO::Found 2 batches.
2025-04-17 04:10:20.604584 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-17 04:10:20.60554 INFO::Using default BPPARAM
2025-04-17 04:10:20.606404 INFO::Adjusting the last 2 batches sequentially
2025-04-17 04:10:20.607888 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-17 04:10:20.632225 INFO::Done
2025-04-17 04:10:20.633181 INFO::Acquiring quality metrics after batch effect correction.
2025-04-17 04:10:20.637363 INFO::ASW Batch was 0.754736030518889 prior to batch effect correction and is now 0.0607683264679022 .
2025-04-17 04:10:20.638308 INFO::ASW Label was 0.307671097286701 prior to batch effect correction and is now 0.820160101862898 .
2025-04-17 04:10:20.639445 INFO::Total function execution time is 0.0563108921051025 s and adjustment time is 0.0287985801696777 s ( 51.14 )
2025-04-17 04:10:20.640611 INFO::Formatting Data.
2025-04-17 04:10:20.641526 INFO::Replacing NaNs with NAs.
2025-04-17 04:10:20.64284 INFO::Removing potential empty rows and columns
2025-04-17 04:10:20.644291 INFO::Found 0 missing values.
2025-04-17 04:10:20.645634 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.
2025-04-17 04:10:20.652526 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-17 04:10:20.653464 INFO::Done
2025-04-17 04:10:20.65424 INFO::Acquiring quality metrics before batch effect correction.
2025-04-17 04:10:20.658418 INFO::Starting hierarchical adjustment
2025-04-17 04:10:20.659562 INFO::Found 2 batches.
2025-04-17 04:10:20.660402 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-17 04:10:20.671033 INFO::Using default BPPARAM
2025-04-17 04:10:20.671984 INFO::Adjusting the last 2 batches sequentially
2025-04-17 04:10:20.67365 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-17 04:10:20.698678 INFO::Done
2025-04-17 04:10:20.699601 INFO::Acquiring quality metrics after batch effect correction.
2025-04-17 04:10:20.703855 INFO::ASW Batch was 0.754736030518889 prior to batch effect correction and is now 0.0607683264679022 .
2025-04-17 04:10:20.704806 INFO::ASW Label was 0.307671097286701 prior to batch effect correction and is now 0.820160101862898 .
2025-04-17 04:10:20.705984 INFO::Total function execution time is 0.0653948783874512 s and adjustment time is 0.039323091506958 s ( 60.13 )
2025-04-17 04:10:20.999755 INFO::Formatting Data.
2025-04-17 04:10:21.00081 INFO::Replacing NaNs with NAs.
2025-04-17 04:10:21.002056 INFO::Removing potential empty rows and columns
2025-04-17 04:10:21.003528 INFO::Found 0 missing values.
2025-04-17 04:10:21.007864 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-17 04:10:21.008761 INFO::Done
2025-04-17 04:10:21.009532 INFO::Acquiring quality metrics before batch effect correction.
2025-04-17 04:10:21.012341 INFO::Starting hierarchical adjustment
2025-04-17 04:10:21.013438 INFO::Found 3 batches.
2025-04-17 04:10:21.014233 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-17 04:10:21.015125 INFO::Using default BPPARAM
2025-04-17 04:10:21.015924 INFO::Processing subtree level 1
2025-04-17 04:10:21.125954 INFO::Adjusting the last 1 batches sequentially
2025-04-17 04:10:21.128392 INFO::Done
2025-04-17 04:10:21.129394 INFO::Acquiring quality metrics after batch effect correction.
2025-04-17 04:10:21.132925 INFO::ASW Batch was -0.138747598223881 prior to batch effect correction and is now -0.138747598223881 .
2025-04-17 04:10:21.134338 INFO::Total function execution time is 0.134599924087524 s and adjustment time is 0.115134239196777 s ( 85.54 )
2025-04-17 04:10:21.135891 INFO::Formatting Data.
2025-04-17 04:10:21.136936 INFO::Typecasting input to dataframe.
2025-04-17 04:10:21.138129 INFO::Replacing NaNs with NAs.
2025-04-17 04:10:21.139535 INFO::Removing potential empty rows and columns
2025-04-17 04:10:21.1412 INFO::Found 0 missing values.
2025-04-17 04:10:21.145795 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-17 04:10:21.146738 INFO::Done
2025-04-17 04:10:21.14759 INFO::Acquiring quality metrics before batch effect correction.
2025-04-17 04:10:21.150473 INFO::Starting hierarchical adjustment
2025-04-17 04:10:21.151623 INFO::Found 3 batches.
2025-04-17 04:10:21.152452 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-17 04:10:21.153462 INFO::Using default BPPARAM
2025-04-17 04:10:21.154276 INFO::Processing subtree level 1
2025-04-17 04:10:21.265261 INFO::Adjusting the last 1 batches sequentially
2025-04-17 04:10:21.267643 INFO::Done
2025-04-17 04:10:21.268609 INFO::Acquiring quality metrics after batch effect correction.
2025-04-17 04:10:21.27218 INFO::ASW Batch was -0.138747598223881 prior to batch effect correction and is now -0.138747598223881 .
2025-04-17 04:10:21.27363 INFO::Total function execution time is 0.137687206268311 s and adjustment time is 0.116256237030029 s ( 84.44 )
2025-04-17 04:10:21.292117 INFO::Formatting Data.
2025-04-17 04:10:21.293276 INFO::Typecasting input to dataframe.
2025-04-17 04:10:21.294794 INFO::Replacing NaNs with NAs.
2025-04-17 04:10:21.29621 INFO::Removing potential empty rows and columns
2025-04-17 04:10:21.297926 INFO::Found 0 missing values.
2025-04-17 04:10:21.302616 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-17 04:10:21.303589 INFO::Done
2025-04-17 04:10:21.30446 INFO::Acquiring quality metrics before batch effect correction.
2025-04-17 04:10:21.307482 INFO::Starting hierarchical adjustment
2025-04-17 04:10:21.308624 INFO::Found 3 batches.
2025-04-17 04:10:21.309484 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-17 04:10:21.310441 INFO::Using default BPPARAM
2025-04-17 04:10:21.311358 INFO::Processing subtree level 1
2025-04-17 04:10:21.418626 INFO::Adjusting the last 1 batches sequentially
2025-04-17 04:10:21.421139 INFO::Done
2025-04-17 04:10:21.422133 INFO::Acquiring quality metrics after batch effect correction.
2025-04-17 04:10:21.426068 INFO::ASW Batch was -0.064783200622402 prior to batch effect correction and is now -0.064783200622402 .
2025-04-17 04:10:21.427584 INFO::Total function execution time is 0.135411500930786 s and adjustment time is 0.112741470336914 s ( 83.26 )
2025-04-17 04:10:21.613799 INFO::Formatting Data.
2025-04-17 04:10:21.615053 INFO::Replacing NaNs with NAs.
2025-04-17 04:10:21.617058 INFO::Removing potential empty rows and columns
2025-04-17 04:10:21.621857 INFO::Found 1000 missing values.
2025-04-17 04:10:21.653632 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-17 04:10:21.654819 INFO::Done
2025-04-17 04:10:21.655949 INFO::Acquiring quality metrics before batch effect correction.
2025-04-17 04:10:21.664831 INFO::Starting hierarchical adjustment
2025-04-17 04:10:21.666277 INFO::Found 10 batches.
2025-04-17 04:10:21.667364 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-17 04:10:21.66849 INFO::Using default BPPARAM
2025-04-17 04:10:21.669508 INFO::Processing subtree level 1
2025-04-17 04:10:21.836563 INFO::Processing subtree level 2
2025-04-17 04:10:22.020352 INFO::Adjusting the last 1 batches sequentially
2025-04-17 04:10:22.023221 INFO::Done
2025-04-17 04:10:22.02427 INFO::Acquiring quality metrics after batch effect correction.
2025-04-17 04:10:22.032758 INFO::ASW Batch was 0.466473245169627 prior to batch effect correction and is now 0.466473245169627 .
2025-04-17 04:10:22.033882 INFO::ASW Label was 0.338725011705528 prior to batch effect correction and is now 0.338725011705528 .
2025-04-17 04:10:22.035389 INFO::Total function execution time is 0.421589136123657 s and adjustment time is 0.357280254364014 s ( 84.75 )
2025-04-17 04:10:22.036696 INFO::Formatting Data.
2025-04-17 04:10:22.037632 INFO::Replacing NaNs with NAs.
2025-04-17 04:10:22.03936 INFO::Removing potential empty rows and columns
2025-04-17 04:10:22.043395 INFO::Found 1000 missing values.
2025-04-17 04:10:22.070684 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-17 04:10:22.071622 INFO::Done
2025-04-17 04:10:22.072391 INFO::Acquiring quality metrics before batch effect correction.
2025-04-17 04:10:22.079912 INFO::Starting hierarchical adjustment
2025-04-17 04:10:22.081212 INFO::Found 10 batches.
2025-04-17 04:10:23.385965 INFO::Set up parallel execution backend with 2 workers
2025-04-17 04:10:23.388121 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-04-17 04:10:24.836859 INFO::Adjusting the last 2 batches sequentially
2025-04-17 04:10:24.839263 INFO::Adjusting sequential tree level 1 with 2 batches
2025-04-17 04:10:24.866174 INFO::Done
2025-04-17 04:10:24.867116 INFO::Acquiring quality metrics after batch effect correction.
2025-04-17 04:10:24.874603 INFO::ASW Batch was 0.466473245169627 prior to batch effect correction and is now 0.466473245169627 .
2025-04-17 04:10:24.875472 INFO::ASW Label was 0.338725011705528 prior to batch effect correction and is now 0.338725011705528 .
2025-04-17 04:10:24.876566 INFO::Total function execution time is 2.8399031162262 s and adjustment time is 2.78520774841309 s ( 98.07 )
2025-04-17 04:10:25.070377 INFO::Formatting Data.
2025-04-17 04:10:25.071517 INFO::Replacing NaNs with NAs.
2025-04-17 04:10:25.072922 INFO::Removing potential empty rows and columns
2025-04-17 04:10:25.074621 INFO::Found 0 missing values.
2025-04-17 04:10:25.081237 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-17 04:10:25.082232 INFO::Done
2025-04-17 04:10:25.083056 INFO::Acquiring quality metrics before batch effect correction.
2025-04-17 04:10:25.087229 INFO::Starting hierarchical adjustment
2025-04-17 04:10:25.088445 INFO::Found 3 batches.
2025-04-17 04:10:25.08931 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-04-17 04:10:25.090286 INFO::Using default BPPARAM
2025-04-17 04:10:25.091122 INFO::Processing subtree level 1
2025-04-17 04:10:25.226809 INFO::Adjusting the last 1 batches sequentially
2025-04-17 04:10:25.229535 INFO::Done
2025-04-17 04:10:25.230606 INFO::Acquiring quality metrics after batch effect correction.
2025-04-17 04:10:25.235702 INFO::ASW Batch was 0.283203127721723 prior to batch effect correction and is now -0.165671142766022 .
2025-04-17 04:10:25.236843 INFO::ASW Label was -0.193063580164869 prior to batch effect correction and is now -0.0175643655220755 .
2025-04-17 04:10:25.238338 INFO::Total function execution time is 0.167948961257935 s and adjustment time is 0.141301393508911 s ( 84.13 )
2025-04-17 04:10:25.42045 INFO::Formatting Data.
2025-04-17 04:10:25.421656 INFO::Replacing NaNs with NAs.
2025-04-17 04:10:25.423021 INFO::Removing potential empty rows and columns
2025-04-17 04:10:25.424649 INFO::Found 2 missing values.
2025-04-17 04:10:25.429228 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-04-17 04:10:25.43021 INFO::Done
2025-04-17 04:10:25.473097 INFO::Found NA in Reference column
2025-04-17 04:10:25.488684 INFO::Require at least two references per batch.
2025-04-17 04:10:25.520619 INFO::Formatting Data.
2025-04-17 04:10:25.521653 INFO::Recognized SummarizedExperiment
2025-04-17 04:10:25.522502 INFO::Typecasting input to dataframe.
2025-04-17 04:10:25.537954 INFO::Replacing NaNs with NAs.
2025-04-17 04:10:25.539734 INFO::Removing potential empty rows and columns
2025-04-17 04:10:25.545999 INFO::Found 0 missing values.
2025-04-17 04:10:25.558042 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-17 04:10:25.559045 INFO::Done
2025-04-17 04:10:25.582497 INFO::Formatting Data.
2025-04-17 04:10:25.583514 INFO::Recognized SummarizedExperiment
2025-04-17 04:10:25.584335 INFO::Typecasting input to dataframe.
2025-04-17 04:10:25.612734 INFO::Replacing NaNs with NAs.
2025-04-17 04:10:25.614538 INFO::Removing potential empty rows and columns
2025-04-17 04:10:25.620673 INFO::Found 0 missing values.
2025-04-17 04:10:25.63988 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-17 04:10:25.640876 INFO::Done
2025-04-17 04:10:25.664287 INFO::Formatting Data.
2025-04-17 04:10:25.66534 INFO::Recognized SummarizedExperiment
2025-04-17 04:10:25.666205 INFO::Typecasting input to dataframe.
2025-04-17 04:10:25.694297 INFO::Replacing NaNs with NAs.
2025-04-17 04:10:25.695758 INFO::Removing potential empty rows and columns
2025-04-17 04:10:25.697464 INFO::Found 0 missing values.
2025-04-17 04:10:25.698885 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.
2025-04-17 04:10:25.706029 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-17 04:10:25.706983 INFO::Done
2025-04-17 04:10:25.723449 INFO::Formatting Data.
2025-04-17 04:10:25.72461 INFO::Replacing NaNs with NAs.
2025-04-17 04:10:25.725909 INFO::Removing potential empty rows and columns
2025-04-17 04:10:25.727446 INFO::Found 0 missing values.
2025-04-17 04:10:25.732089 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-17 04:10:25.733074 INFO::Done
2025-04-17 04:10:25.750584 INFO::Formatting Data.
2025-04-17 04:10:25.75171 INFO::Replacing NaNs with NAs.
2025-04-17 04:10:25.753098 INFO::Removing potential empty rows and columns
2025-04-17 04:10:25.75471 INFO::Found 0 missing values.
2025-04-17 04:10:25.759378 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-17 04:10:25.760368 INFO::Done
2025-04-17 04:10:25.807958 INFO::Formatting Data.
2025-04-17 04:10:25.809156 INFO::Replacing NaNs with NAs.
2025-04-17 04:10:25.810793 INFO::Removing potential empty rows and columns
2025-04-17 04:10:25.812742 INFO::Found 1 missing values.
2025-04-17 04:10:25.817169 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-17 04:10:25.818316 INFO::Done
2025-04-17 04:10:25.848681 INFO::Formatting Data.
2025-04-17 04:10:25.849821 INFO::Replacing NaNs with NAs.
2025-04-17 04:10:25.851251 INFO::Removing potential empty rows and columns
2025-04-17 04:10:25.852842 INFO::Found 2 missing values.
2025-04-17 04:10:25.854381 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.
2025-04-17 04:10:25.858369 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-04-17 04:10:25.85942 INFO::Done
2025-04-17 04:10:25.875581 INFO::Formatting Data.
2025-04-17 04:10:25.876724 INFO::Replacing NaNs with NAs.
2025-04-17 04:10:25.878121 INFO::Removing potential empty rows and columns
2025-04-17 04:10:25.879658 INFO::Found 2 missing values.
2025-04-17 04:10:25.882308 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-17 04:10:25.883233 INFO::Done
2025-04-17 04:10:25.900766 INFO::Formatting Data.
2025-04-17 04:10:25.90196 INFO::Typecasting input to dataframe.
2025-04-17 04:10:25.903335 INFO::Replacing NaNs with NAs.
2025-04-17 04:10:25.90475 INFO::Removing potential empty rows and columns
2025-04-17 04:10:25.906449 INFO::Found 0 missing values.
2025-04-17 04:10:25.911343 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-04-17 04:10:25.912343 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
23.209 4.495 27.276
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 31.005 | 1.656 | 22.446 | |
| compute_asw | 0.032 | 0.004 | 0.036 | |
| count_existing | 0.018 | 0.000 | 0.018 | |
| generate_data_covariables | 0.016 | 0.000 | 0.017 | |
| generate_dataset | 0.012 | 0.004 | 0.016 | |