Yannis Schumann
| Snapshot Date: 2025-02-14 13:40 -0500 (Fri, 14 Feb 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: f785e17 |
| git_last_commit_date: 2025-01-29 01:54:20 -0500 (Wed, 29 Jan 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-02-15 11:40 -0500 (Sat, 15 Feb 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4720 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4482 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4493 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4446 |
| 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 159/2295 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.3.6 (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 | | ||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.3.6 |
| Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings BERT_1.3.6.tar.gz |
| StartedAt: 2025-02-14 22:55:33 -0500 (Fri, 14 Feb 2025) |
| EndedAt: 2025-02-14 22:57:51 -0500 (Fri, 14 Feb 2025) |
| EllapsedTime: 137.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings BERT_1.3.6.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck'
* using R Under development (unstable) (2025-01-21 r87610 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BERT/DESCRIPTION' ... OK
* this is package 'BERT' version '1.3.6'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'BERT' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 8.78 0.59 18.72
* 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: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'BERT' ... ** this is package 'BERT' version '1.3.6' ** 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) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2025-02-14 22:56:37.599192 INFO::Formatting Data.
2025-02-14 22:56:37.601395 INFO::Replacing NaNs with NAs.
2025-02-14 22:56:37.610964 INFO::Removing potential empty rows and columns
2025-02-14 22:56:37.820242 INFO::Found 0 missing values.
2025-02-14 22:56:37.824178 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 22:56:37.825382 INFO::Done
2025-02-14 22:56:37.826548 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 22:56:37.844948 INFO::Starting hierarchical adjustment
2025-02-14 22:56:37.846157 INFO::Found 3 batches.
2025-02-14 22:56:37.847385 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 22:56:37.849454 INFO::Using default BPPARAM
2025-02-14 22:56:37.850387 INFO::Processing subtree level 1
2025-02-14 22:56:40.428639 INFO::Adjusting the last 1 batches sequentially
2025-02-14 22:56:40.430966 INFO::Done
2025-02-14 22:56:40.432278 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 22:56:40.435623 INFO::ASW Batch was -0.0541875891450463 prior to batch effect correction and is now -0.0541875891450463 .
2025-02-14 22:56:40.437383 INFO::Total function execution time is 2.83859586715698 s and adjustment time is 2.58499097824097 s ( 91.07 )
2025-02-14 22:56:40.459123 INFO::Formatting Data.
2025-02-14 22:56:40.460125 INFO::Replacing NaNs with NAs.
2025-02-14 22:56:40.461296 INFO::Removing potential empty rows and columns
2025-02-14 22:56:40.462483 INFO::Found 0 missing values.
2025-02-14 22:56:40.463579 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.
2025-02-14 22:56:40.477105 INFO::Formatting Data.
2025-02-14 22:56:40.478677 INFO::Replacing NaNs with NAs.
2025-02-14 22:56:40.480483 INFO::Removing potential empty rows and columns
2025-02-14 22:56:40.482437 INFO::Found 0 missing values.
2025-02-14 22:56:40.484214 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.
2025-02-14 22:56:40.509812 INFO::Formatting Data.
2025-02-14 22:56:40.511376 INFO::Replacing NaNs with NAs.
2025-02-14 22:56:40.513152 INFO::Removing potential empty rows and columns
2025-02-14 22:56:40.515028 INFO::Found 0 missing values.
2025-02-14 22:56:40.516824 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.
2025-02-14 22:56:40.523108 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 22:56:40.524445 INFO::Done
2025-02-14 22:56:40.525759 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 22:56:40.529078 INFO::Starting hierarchical adjustment
2025-02-14 22:56:40.530679 INFO::Found 2 batches.
2025-02-14 22:56:40.531967 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 22:56:40.533288 INFO::Using default BPPARAM
2025-02-14 22:56:40.534509 INFO::Adjusting the last 2 batches sequentially
2025-02-14 22:56:40.536351 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 22:56:40.562602 INFO::Done
2025-02-14 22:56:40.564037 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 22:56:40.567384 INFO::ASW Batch was -0.0667295521714242 prior to batch effect correction and is now -0.122637228211823 .
2025-02-14 22:56:40.568979 INFO::Total function execution time is 0.0592341423034668 s and adjustment time is 0.032139778137207 s ( 54.26 )
2025-02-14 22:56:40.573383 INFO::Formatting Data.
2025-02-14 22:56:40.574705 INFO::Replacing NaNs with NAs.
2025-02-14 22:56:40.586287 INFO::Formatting Data.
2025-02-14 22:56:40.58775 INFO::Replacing NaNs with NAs.
2025-02-14 22:56:40.589462 INFO::Removing potential empty rows and columns
2025-02-14 22:56:40.591259 INFO::Found 0 missing values.
2025-02-14 22:56:40.595329 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 22:56:40.596529 INFO::Done
2025-02-14 22:56:40.597674 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 22:56:40.600808 INFO::Starting hierarchical adjustment
2025-02-14 22:56:40.602189 INFO::Found 2 batches.
2025-02-14 22:56:40.603338 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 22:56:40.604565 INFO::Using default BPPARAM
2025-02-14 22:56:40.605692 INFO::Adjusting the last 2 batches sequentially
2025-02-14 22:56:40.607395 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 22:56:40.626885 INFO::Done
2025-02-14 22:56:40.628276 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 22:56:40.631542 INFO::ASW Batch was 0.0945277953393418 prior to batch effect correction and is now -0.119874337557148 .
2025-02-14 22:56:40.633124 INFO::Total function execution time is 0.0469000339508057 s and adjustment time is 0.0248560905456543 s ( 53 )
2025-02-14 22:56:40.635028 INFO::Formatting Data.
2025-02-14 22:56:40.636286 INFO::Replacing NaNs with NAs.
2025-02-14 22:56:40.637903 INFO::Removing potential empty rows and columns
2025-02-14 22:56:40.639659 INFO::Found 0 missing values.
2025-02-14 22:56:40.643712 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 22:56:40.644873 INFO::Done
2025-02-14 22:56:40.646059 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 22:56:40.649234 INFO::Starting hierarchical adjustment
2025-02-14 22:56:40.650631 INFO::Found 2 batches.
2025-02-14 22:56:40.651772 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 22:56:40.653023 INFO::Using default BPPARAM
2025-02-14 22:56:40.654161 INFO::Adjusting the last 2 batches sequentially
2025-02-14 22:56:40.655852 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 22:56:40.675139 INFO::Done
2025-02-14 22:56:40.676507 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 22:56:40.679706 INFO::ASW Batch was 0.0945277953393418 prior to batch effect correction and is now -0.119874337557148 .
2025-02-14 22:56:40.681219 INFO::Total function execution time is 0.0461828708648682 s and adjustment time is 0.0246729850769043 s ( 53.42 )
2025-02-14 22:56:43.237441 INFO::Formatting Data.
2025-02-14 22:56:43.238407 INFO::Recognized SummarizedExperiment
2025-02-14 22:56:43.239122 INFO::Typecasting input to dataframe.
2025-02-14 22:56:43.284104 INFO::Replacing NaNs with NAs.
2025-02-14 22:56:43.28621 INFO::Removing potential empty rows and columns
2025-02-14 22:56:43.291168 INFO::Found 0 missing values.
2025-02-14 22:56:43.3001 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 22:56:43.30155 INFO::Done
2025-02-14 22:56:43.302801 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 22:56:43.309263 INFO::Starting hierarchical adjustment
2025-02-14 22:56:43.310829 INFO::Found 2 batches.
2025-02-14 22:56:43.312092 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 22:56:43.313948 INFO::Using default BPPARAM
2025-02-14 22:56:43.315154 INFO::Adjusting the last 2 batches sequentially
2025-02-14 22:56:43.31706 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 22:56:44.19307 INFO::Done
2025-02-14 22:56:44.194409 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 22:56:44.20069 INFO::ASW Batch was 0.0142740625913151 prior to batch effect correction and is now -0.09111694571968 .
2025-02-14 22:56:44.202466 INFO::Total function execution time is 0.965175867080688 s and adjustment time is 0.88244891166687 s ( 91.43 )
2025-02-14 22:56:44.232212 INFO::Formatting Data.
2025-02-14 22:56:44.233708 INFO::Recognized SummarizedExperiment
2025-02-14 22:56:44.234974 INFO::Typecasting input to dataframe.
2025-02-14 22:56:44.248264 INFO::Replacing NaNs with NAs.
2025-02-14 22:56:44.25043 INFO::Removing potential empty rows and columns
2025-02-14 22:56:44.255311 INFO::Found 0 missing values.
2025-02-14 22:56:44.264606 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 22:56:44.266044 INFO::Done
2025-02-14 22:56:44.267321 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 22:56:44.273537 INFO::Starting hierarchical adjustment
2025-02-14 22:56:44.275044 INFO::Found 2 batches.
2025-02-14 22:56:44.276254 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 22:56:44.277528 INFO::Using default BPPARAM
2025-02-14 22:56:44.27874 INFO::Adjusting the last 2 batches sequentially
2025-02-14 22:56:44.280662 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 22:56:44.314291 INFO::Done
2025-02-14 22:56:44.315781 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 22:56:44.32203 INFO::ASW Batch was 0.0139872304385338 prior to batch effect correction and is now 0.0139872304385338 .
2025-02-14 22:56:44.323789 INFO::Total function execution time is 0.0915119647979736 s and adjustment time is 0.0394141674041748 s ( 43.07 )
2025-02-14 22:56:44.35684 INFO::Formatting Data.
2025-02-14 22:56:44.358417 INFO::Replacing NaNs with NAs.
2025-02-14 22:56:44.360179 INFO::Removing potential empty rows and columns
2025-02-14 22:56:44.362198 INFO::Found 0 missing values.
2025-02-14 22:56:44.366979 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 22:56:44.368307 INFO::Done
2025-02-14 22:56:44.369495 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 22:56:44.372467 INFO::Starting hierarchical adjustment
2025-02-14 22:56:44.373875 INFO::Found 3 batches.
2025-02-14 22:56:44.375038 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 22:56:44.376352 INFO::Using default BPPARAM
2025-02-14 22:56:44.37753 INFO::Processing subtree level 1
2025-02-14 22:56:54.295362 INFO::Adjusting the last 1 batches sequentially
2025-02-14 22:56:54.297519 INFO::Done
2025-02-14 22:56:54.29878 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 22:56:54.302413 INFO::ASW Batch was -0.0622944226553301 prior to batch effect correction and is now -0.152938462724216 .
2025-02-14 22:56:54.304188 INFO::Total function execution time is 9.94740009307861 s and adjustment time is 9.92386794090271 s ( 99.76 )
2025-02-14 22:56:54.328954 INFO::Skipping initial DF formatting
2025-02-14 22:56:54.330418 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 22:56:54.336657 INFO::Starting hierarchical adjustment
2025-02-14 22:56:54.338135 INFO::Found 5 batches.
2025-02-14 22:56:54.339263 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 22:56:54.340449 INFO::Using default BPPARAM
2025-02-14 22:56:54.341519 INFO::Processing subtree level 1
2025-02-14 22:56:57.681331 INFO::Adjusting the last 2 batches sequentially
2025-02-14 22:56:57.683543 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 22:56:57.705513 INFO::Done
2025-02-14 22:56:57.70649 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 22:56:57.710853 INFO::ASW Batch was 0.56948019539393 prior to batch effect correction and is now 0.56948019539393 .
2025-02-14 22:56:57.7122 INFO::ASW Label was 0.319437755071612 prior to batch effect correction and is now 0.319437755071612 .
2025-02-14 22:56:57.713815 INFO::Total function execution time is 3.38497185707092 s and adjustment time is 3.3676130771637 s ( 99.49 )
2025-02-14 22:56:57.734552 INFO::Formatting Data.
2025-02-14 22:56:57.735679 INFO::Replacing NaNs with NAs.
2025-02-14 22:56:57.736814 INFO::Removing potential empty rows and columns
2025-02-14 22:56:57.738051 INFO::Found 0 missing values.
2025-02-14 22:56:57.741828 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 22:56:57.742656 INFO::Done
2025-02-14 22:56:57.74344 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 22:56:57.747935 INFO::Starting hierarchical adjustment
2025-02-14 22:56:57.749476 INFO::Found 5 batches.
2025-02-14 22:56:57.750726 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 22:56:57.752026 INFO::Using default BPPARAM
2025-02-14 22:56:57.753188 INFO::Processing subtree level 1
2025-02-14 22:57:01.175809 INFO::Adjusting the last 2 batches sequentially
2025-02-14 22:57:01.177908 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 22:57:01.197457 INFO::Done
2025-02-14 22:57:01.198885 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 22:57:01.203796 INFO::ASW Batch was 0.617953114322513 prior to batch effect correction and is now -0.090755376935952 .
2025-02-14 22:57:01.205156 INFO::ASW Label was 0.16423050185732 prior to batch effect correction and is now 0.804410920534419 .
2025-02-14 22:57:01.206702 INFO::Total function execution time is 3.47223401069641 s and adjustment time is 3.44816493988037 s ( 99.31 )
2025-02-14 22:57:01.208315 INFO::Formatting Data.
2025-02-14 22:57:01.209685 INFO::Replacing NaNs with NAs.
2025-02-14 22:57:01.21137 INFO::Removing potential empty rows and columns
2025-02-14 22:57:01.213154 INFO::Found 0 missing values.
2025-02-14 22:57:01.217802 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 22:57:01.219005 INFO::Done
2025-02-14 22:57:01.220108 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 22:57:01.22446 INFO::Starting hierarchical adjustment
2025-02-14 22:57:01.225856 INFO::Found 5 batches.
2025-02-14 22:57:01.226963 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 22:57:01.228282 INFO::Using default BPPARAM
2025-02-14 22:57:01.229391 INFO::Processing subtree level 1
2025-02-14 22:57:04.525118 INFO::Adjusting the last 2 batches sequentially
2025-02-14 22:57:04.527266 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 22:57:04.545491 INFO::Done
2025-02-14 22:57:04.546849 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 22:57:04.55132 INFO::ASW Batch was 0.617953114322513 prior to batch effect correction and is now -0.090755376935952 .
2025-02-14 22:57:04.552562 INFO::ASW Label was 0.16423050185732 prior to batch effect correction and is now 0.804410920534419 .
2025-02-14 22:57:04.554179 INFO::Total function execution time is 3.34588408470154 s and adjustment time is 3.31979084014893 s ( 99.22 )
2025-02-14 22:57:04.578326 INFO::Formatting Data.
2025-02-14 22:57:04.579893 INFO::Replacing NaNs with NAs.
2025-02-14 22:57:04.581662 INFO::Removing potential empty rows and columns
2025-02-14 22:57:04.583549 INFO::Found 0 missing values.
2025-02-14 22:57:04.589542 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 22:57:04.590893 INFO::Done
2025-02-14 22:57:04.592095 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 22:57:04.596883 INFO::Starting hierarchical adjustment
2025-02-14 22:57:04.598419 INFO::Found 5 batches.
2025-02-14 22:57:04.599658 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 22:57:04.60094 INFO::Using default BPPARAM
2025-02-14 22:57:04.602141 INFO::Processing subtree level 1
2025-02-14 22:57:07.853083 INFO::Adjusting the last 2 batches sequentially
2025-02-14 22:57:07.855124 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 22:57:07.875414 INFO::Done
2025-02-14 22:57:07.876857 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 22:57:07.881615 INFO::ASW Batch was 0.224289837225616 prior to batch effect correction and is now -0.0939899438364585 .
2025-02-14 22:57:07.882927 INFO::ASW Label was 0.455939500353417 prior to batch effect correction and is now 0.916548379382784 .
2025-02-14 22:57:07.884461 INFO::Total function execution time is 3.30622506141663 s and adjustment time is 3.27719497680664 s ( 99.12 )
2025-02-14 22:57:07.886432 INFO::Formatting Data.
2025-02-14 22:57:07.88776 INFO::Replacing NaNs with NAs.
2025-02-14 22:57:07.889383 INFO::Removing potential empty rows and columns
2025-02-14 22:57:07.890978 INFO::Found 0 missing values.
2025-02-14 22:57:07.895826 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 22:57:07.896826 INFO::Done
2025-02-14 22:57:07.897794 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 22:57:07.901874 INFO::Starting hierarchical adjustment
2025-02-14 22:57:07.903069 INFO::Found 5 batches.
2025-02-14 22:57:07.904026 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 22:57:07.905084 INFO::Using default BPPARAM
2025-02-14 22:57:07.906264 INFO::Processing subtree level 1
2025-02-14 22:57:11.345285 INFO::Adjusting the last 2 batches sequentially
2025-02-14 22:57:11.347019 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 22:57:11.358543 INFO::Done
2025-02-14 22:57:11.359434 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 22:57:11.362516 INFO::ASW Batch was 0.224289837225616 prior to batch effect correction and is now -0.0939899438364585 .
2025-02-14 22:57:11.363331 INFO::ASW Label was 0.455939500353417 prior to batch effect correction and is now 0.916548379382784 .
2025-02-14 22:57:11.364289 INFO::Total function execution time is 3.47843408584595 s and adjustment time is 3.4556348323822 s ( 99.34 )
2025-02-14 22:57:11.383352 INFO::Formatting Data.
2025-02-14 22:57:11.384821 INFO::Replacing NaNs with NAs.
2025-02-14 22:57:11.386472 INFO::Removing potential empty rows and columns
2025-02-14 22:57:11.388165 INFO::Found 0 missing values.
2025-02-14 22:57:11.391803 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 22:57:11.393028 INFO::Done
2025-02-14 22:57:11.394157 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 22:57:11.398494 INFO::Starting hierarchical adjustment
2025-02-14 22:57:11.399918 INFO::Found 2 batches.
2025-02-14 22:57:11.401053 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 22:57:11.402277 INFO::Using default BPPARAM
2025-02-14 22:57:11.403403 INFO::Adjusting the last 2 batches sequentially
2025-02-14 22:57:11.405066 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 22:57:11.422764 INFO::Done
2025-02-14 22:57:11.424229 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 22:57:11.428636 INFO::ASW Batch was 0.319596111671946 prior to batch effect correction and is now -0.0216761810404123 .
2025-02-14 22:57:11.429936 INFO::ASW Label was 0.743426079883667 prior to batch effect correction and is now 0.951541571685748 .
2025-02-14 22:57:11.43141 INFO::Total function execution time is 0.0481641292572021 s and adjustment time is 0.0230071544647217 s ( 47.77 )
2025-02-14 22:57:11.432844 INFO::Formatting Data.
2025-02-14 22:57:11.43408 INFO::Replacing NaNs with NAs.
2025-02-14 22:57:11.435665 INFO::Removing potential empty rows and columns
2025-02-14 22:57:11.437321 INFO::Found 0 missing values.
2025-02-14 22:57:11.441111 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 22:57:11.442286 INFO::Done
2025-02-14 22:57:11.443435 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 22:57:11.447754 INFO::Starting hierarchical adjustment
2025-02-14 22:57:11.44918 INFO::Found 2 batches.
2025-02-14 22:57:11.450348 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 22:57:11.45162 INFO::Using default BPPARAM
2025-02-14 22:57:11.452833 INFO::Adjusting the last 2 batches sequentially
2025-02-14 22:57:11.454503 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 22:57:11.473159 INFO::Done
2025-02-14 22:57:11.474617 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 22:57:11.479608 INFO::ASW Batch was 0.319596111671946 prior to batch effect correction and is now -0.0216761810404123 .
2025-02-14 22:57:11.481021 INFO::ASW Label was 0.743426079883667 prior to batch effect correction and is now 0.951541571685748 .
2025-02-14 22:57:11.482756 INFO::Total function execution time is 0.0498650074005127 s and adjustment time is 0.0241129398345947 s ( 48.36 )
2025-02-14 22:57:11.505359 INFO::Formatting Data.
2025-02-14 22:57:11.506925 INFO::Replacing NaNs with NAs.
2025-02-14 22:57:11.508605 INFO::Removing potential empty rows and columns
2025-02-14 22:57:11.510327 INFO::Found 0 missing values.
2025-02-14 22:57:11.513696 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 22:57:11.514923 INFO::Done
2025-02-14 22:57:11.516126 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 22:57:11.519489 INFO::Starting hierarchical adjustment
2025-02-14 22:57:11.521057 INFO::Found 2 batches.
2025-02-14 22:57:11.5223 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 22:57:11.523632 INFO::Using default BPPARAM
2025-02-14 22:57:11.524822 INFO::Adjusting the last 2 batches sequentially
2025-02-14 22:57:11.526582 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 22:57:11.567683 INFO::Done
2025-02-14 22:57:11.569134 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 22:57:11.572466 INFO::ASW Batch was -0.0999412583965926 prior to batch effect correction and is now -0.142117531157356 .
2025-02-14 22:57:11.574058 INFO::Total function execution time is 0.0687839984893799 s and adjustment time is 0.0468049049377441 s ( 68.05 )
2025-02-14 22:57:11.597758 INFO::Formatting Data.
2025-02-14 22:57:11.599299 INFO::Replacing NaNs with NAs.
2025-02-14 22:57:11.60105 INFO::Removing potential empty rows and columns
2025-02-14 22:57:11.602888 INFO::Found 0 missing values.
2025-02-14 22:57:11.604897 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.
2025-02-14 22:57:11.611621 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 22:57:11.612952 INFO::Done
2025-02-14 22:57:11.614186 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 22:57:11.618636 INFO::Starting hierarchical adjustment
2025-02-14 22:57:11.62007 INFO::Found 2 batches.
2025-02-14 22:57:11.621199 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 22:57:11.622404 INFO::Using default BPPARAM
2025-02-14 22:57:11.623567 INFO::Adjusting the last 2 batches sequentially
2025-02-14 22:57:11.625202 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 22:57:11.639712 INFO::Done
2025-02-14 22:57:11.640609 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 22:57:11.64368 INFO::ASW Batch was 0.535579713342225 prior to batch effect correction and is now -0.0362319106922115 .
2025-02-14 22:57:11.644501 INFO::ASW Label was 0.494931707688459 prior to batch effect correction and is now 0.927466376329478 .
2025-02-14 22:57:11.645472 INFO::Total function execution time is 0.047896146774292 s and adjustment time is 0.0198829174041748 s ( 41.51 )
2025-02-14 22:57:11.646435 INFO::Formatting Data.
2025-02-14 22:57:11.647238 INFO::Replacing NaNs with NAs.
2025-02-14 22:57:11.648332 INFO::Removing potential empty rows and columns
2025-02-14 22:57:11.649473 INFO::Found 0 missing values.
2025-02-14 22:57:11.650576 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.
2025-02-14 22:57:11.654725 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 22:57:11.65552 INFO::Done
2025-02-14 22:57:11.65626 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 22:57:11.659293 INFO::Starting hierarchical adjustment
2025-02-14 22:57:11.660217 INFO::Found 2 batches.
2025-02-14 22:57:11.660982 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 22:57:11.661793 INFO::Using default BPPARAM
2025-02-14 22:57:11.662546 INFO::Adjusting the last 2 batches sequentially
2025-02-14 22:57:11.66369 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 22:57:11.684501 INFO::Done
2025-02-14 22:57:11.68545 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 22:57:11.688865 INFO::ASW Batch was 0.535579713342225 prior to batch effect correction and is now -0.0362319106922115 .
2025-02-14 22:57:11.689731 INFO::ASW Label was 0.494931707688459 prior to batch effect correction and is now 0.927466376329478 .
2025-02-14 22:57:11.69078 INFO::Total function execution time is 0.0443410873413086 s and adjustment time is 0.0243799686431885 s ( 54.98 )
2025-02-14 22:57:11.938293 INFO::Formatting Data.
2025-02-14 22:57:11.940135 INFO::Replacing NaNs with NAs.
2025-02-14 22:57:11.942299 INFO::Removing potential empty rows and columns
2025-02-14 22:57:11.944559 INFO::Found 0 missing values.
2025-02-14 22:57:11.949941 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 22:57:11.951414 INFO::Done
2025-02-14 22:57:11.952872 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 22:57:11.956681 INFO::Starting hierarchical adjustment
2025-02-14 22:57:11.957685 INFO::Found 3 batches.
2025-02-14 22:57:11.958473 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 22:57:11.959329 INFO::Using default BPPARAM
2025-02-14 22:57:11.960094 INFO::Processing subtree level 1
2025-02-14 22:57:15.104126 INFO::Adjusting the last 1 batches sequentially
2025-02-14 22:57:15.10637 INFO::Done
2025-02-14 22:57:15.107694 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 22:57:15.110889 INFO::ASW Batch was -0.0555373097891787 prior to batch effect correction and is now -0.0555373097891787 .
2025-02-14 22:57:15.112482 INFO::Total function execution time is 3.17433500289917 s and adjustment time is 3.14879393577576 s ( 99.2 )
2025-02-14 22:57:15.114249 INFO::Formatting Data.
2025-02-14 22:57:15.115551 INFO::Typecasting input to dataframe.
2025-02-14 22:57:15.117061 INFO::Replacing NaNs with NAs.
2025-02-14 22:57:15.118725 INFO::Removing potential empty rows and columns
2025-02-14 22:57:15.120551 INFO::Found 0 missing values.
2025-02-14 22:57:15.124921 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 22:57:15.126115 INFO::Done
2025-02-14 22:57:15.127005 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 22:57:15.129298 INFO::Starting hierarchical adjustment
2025-02-14 22:57:15.130155 INFO::Found 3 batches.
2025-02-14 22:57:15.13084 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 22:57:15.131586 INFO::Using default BPPARAM
2025-02-14 22:57:15.132288 INFO::Processing subtree level 1
2025-02-14 22:57:17.792237 INFO::Adjusting the last 1 batches sequentially
2025-02-14 22:57:17.793938 INFO::Done
2025-02-14 22:57:17.79494 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 22:57:17.797062 INFO::ASW Batch was -0.0555373097891787 prior to batch effect correction and is now -0.0555373097891787 .
2025-02-14 22:57:17.798102 INFO::Total function execution time is 2.68393707275391 s and adjustment time is 2.66389513015747 s ( 99.25 )
2025-02-14 22:57:17.813355 INFO::Formatting Data.
2025-02-14 22:57:17.814337 INFO::Typecasting input to dataframe.
2025-02-14 22:57:17.81536 INFO::Replacing NaNs with NAs.
2025-02-14 22:57:17.81641 INFO::Removing potential empty rows and columns
2025-02-14 22:57:17.817513 INFO::Found 0 missing values.
2025-02-14 22:57:17.820028 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 22:57:17.820754 INFO::Done
2025-02-14 22:57:17.821444 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 22:57:17.823926 INFO::Starting hierarchical adjustment
2025-02-14 22:57:17.825427 INFO::Found 3 batches.
2025-02-14 22:57:17.826615 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 22:57:17.827914 INFO::Using default BPPARAM
2025-02-14 22:57:17.829153 INFO::Processing subtree level 1
2025-02-14 22:57:20.56991 INFO::Adjusting the last 1 batches sequentially
2025-02-14 22:57:20.572069 INFO::Done
2025-02-14 22:57:20.573295 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 22:57:20.576378 INFO::ASW Batch was -0.126564229681552 prior to batch effect correction and is now -0.126564229681552 .
2025-02-14 22:57:20.577848 INFO::Total function execution time is 2.76462912559509 s and adjustment time is 2.74685788154602 s ( 99.36 )
2025-02-14 22:57:23.39757 INFO::Formatting Data.
2025-02-14 22:57:23.399033 INFO::Replacing NaNs with NAs.
2025-02-14 22:57:23.400363 INFO::Removing potential empty rows and columns
2025-02-14 22:57:23.403062 INFO::Found 1000 missing values.
2025-02-14 22:57:23.424436 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 22:57:23.425904 INFO::Done
2025-02-14 22:57:23.427137 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 22:57:23.436936 INFO::Starting hierarchical adjustment
2025-02-14 22:57:23.438535 INFO::Found 10 batches.
2025-02-14 22:57:23.439779 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 22:57:23.441066 INFO::Using default BPPARAM
2025-02-14 22:57:23.442211 INFO::Processing subtree level 1
2025-02-14 22:57:26.463757 INFO::Processing subtree level 2
2025-02-14 22:57:29.453311 INFO::Adjusting the last 1 batches sequentially
2025-02-14 22:57:29.4557 INFO::Done
2025-02-14 22:57:29.456948 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 22:57:29.465515 INFO::ASW Batch was 0.512931267013363 prior to batch effect correction and is now 0.512931267013363 .
2025-02-14 22:57:29.46682 INFO::ASW Label was 0.309887916551887 prior to batch effect correction and is now 0.309887916551887 .
2025-02-14 22:57:29.468381 INFO::Total function execution time is 6.07091903686523 s and adjustment time is 6.017413854599 s ( 99.12 )
2025-02-14 22:57:29.469743 INFO::Formatting Data.
2025-02-14 22:57:29.470886 INFO::Replacing NaNs with NAs.
2025-02-14 22:57:29.472637 INFO::Removing potential empty rows and columns
2025-02-14 22:57:29.474937 INFO::Found 1000 missing values.
2025-02-14 22:57:29.492136 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 22:57:29.493651 INFO::Done
2025-02-14 22:57:29.494943 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 22:57:29.505138 INFO::Starting hierarchical adjustment
2025-02-14 22:57:29.506713 INFO::Found 10 batches.
2025-02-14 22:57:30.306117 INFO::Set up parallel execution backend with 2 workers
2025-02-14 22:57:30.307582 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-02-14 22:57:33.407466 INFO::Adjusting the last 2 batches sequentially
2025-02-14 22:57:33.40957 INFO::Adjusting sequential tree level 1 with 2 batches
2025-02-14 22:57:33.432522 INFO::Done
2025-02-14 22:57:33.433832 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 22:57:33.442484 INFO::ASW Batch was 0.512931267013363 prior to batch effect correction and is now 0.512931267013363 .
2025-02-14 22:57:33.443774 INFO::ASW Label was 0.309887916551887 prior to batch effect correction and is now 0.309887916551887 .
2025-02-14 22:57:33.445275 INFO::Total function execution time is 3.97551703453064 s and adjustment time is 3.9260561466217 s ( 98.76 )
2025-02-14 22:57:36.450122 INFO::Formatting Data.
2025-02-14 22:57:36.451153 INFO::Replacing NaNs with NAs.
2025-02-14 22:57:36.45229 INFO::Removing potential empty rows and columns
2025-02-14 22:57:36.453432 INFO::Found 0 missing values.
2025-02-14 22:57:36.456576 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 22:57:36.457355 INFO::Done
2025-02-14 22:57:36.458095 INFO::Acquiring quality metrics before batch effect correction.
2025-02-14 22:57:36.460842 INFO::Starting hierarchical adjustment
2025-02-14 22:57:36.461774 INFO::Found 3 batches.
2025-02-14 22:57:36.462494 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-02-14 22:57:36.463287 INFO::Using default BPPARAM
2025-02-14 22:57:36.464018 INFO::Processing subtree level 1
2025-02-14 22:57:39.638729 INFO::Adjusting the last 1 batches sequentially
2025-02-14 22:57:39.641042 INFO::Done
2025-02-14 22:57:39.642349 INFO::Acquiring quality metrics after batch effect correction.
2025-02-14 22:57:39.647103 INFO::ASW Batch was 0.190485075538189 prior to batch effect correction and is now -0.170919350969544 .
2025-02-14 22:57:39.648593 INFO::ASW Label was -0.210844886054125 prior to batch effect correction and is now -0.0771984165966705 .
2025-02-14 22:57:39.650237 INFO::Total function execution time is 3.20012593269348 s and adjustment time is 3.17935299873352 s ( 99.35 )
2025-02-14 22:57:39.846069 INFO::Formatting Data.
2025-02-14 22:57:39.847612 INFO::Replacing NaNs with NAs.
2025-02-14 22:57:39.849273 INFO::Removing potential empty rows and columns
2025-02-14 22:57:39.851061 INFO::Found 2 missing values.
2025-02-14 22:57:39.855262 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-02-14 22:57:39.856521 INFO::Done
2025-02-14 22:57:39.913682 INFO::Found NA in Reference column
2025-02-14 22:57:39.9316 INFO::Require at least two references per batch.
2025-02-14 22:57:39.95247 INFO::Formatting Data.
2025-02-14 22:57:39.953412 INFO::Recognized SummarizedExperiment
2025-02-14 22:57:39.954137 INFO::Typecasting input to dataframe.
2025-02-14 22:57:39.961994 INFO::Replacing NaNs with NAs.
2025-02-14 22:57:39.96331 INFO::Removing potential empty rows and columns
2025-02-14 22:57:39.966052 INFO::Found 0 missing values.
2025-02-14 22:57:39.971225 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 22:57:39.972031 INFO::Done
2025-02-14 22:57:39.985955 INFO::Formatting Data.
2025-02-14 22:57:39.986854 INFO::Recognized SummarizedExperiment
2025-02-14 22:57:39.987557 INFO::Typecasting input to dataframe.
2025-02-14 22:57:40.001866 INFO::Replacing NaNs with NAs.
2025-02-14 22:57:40.003228 INFO::Removing potential empty rows and columns
2025-02-14 22:57:40.006151 INFO::Found 0 missing values.
2025-02-14 22:57:40.013885 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 22:57:40.014737 INFO::Done
2025-02-14 22:57:40.029311 INFO::Formatting Data.
2025-02-14 22:57:40.030356 INFO::Recognized SummarizedExperiment
2025-02-14 22:57:40.03141 INFO::Typecasting input to dataframe.
2025-02-14 22:57:40.048004 INFO::Replacing NaNs with NAs.
2025-02-14 22:57:40.04928 INFO::Removing potential empty rows and columns
2025-02-14 22:57:40.050532 INFO::Found 0 missing values.
2025-02-14 22:57:40.051617 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.
2025-02-14 22:57:40.055897 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 22:57:40.056675 INFO::Done
2025-02-14 22:57:40.071211 INFO::Formatting Data.
2025-02-14 22:57:40.072216 INFO::Replacing NaNs with NAs.
2025-02-14 22:57:40.073293 INFO::Removing potential empty rows and columns
2025-02-14 22:57:40.074555 INFO::Found 0 missing values.
2025-02-14 22:57:40.077157 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 22:57:40.077892 INFO::Done
2025-02-14 22:57:40.092981 INFO::Formatting Data.
2025-02-14 22:57:40.093971 INFO::Replacing NaNs with NAs.
2025-02-14 22:57:40.095023 INFO::Removing potential empty rows and columns
2025-02-14 22:57:40.096174 INFO::Found 0 missing values.
2025-02-14 22:57:40.098781 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 22:57:40.099497 INFO::Done
2025-02-14 22:57:40.137626 INFO::Formatting Data.
2025-02-14 22:57:40.138605 INFO::Replacing NaNs with NAs.
2025-02-14 22:57:40.139776 INFO::Removing potential empty rows and columns
2025-02-14 22:57:40.140969 INFO::Found 1 missing values.
2025-02-14 22:57:40.143422 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 22:57:40.144375 INFO::Done
2025-02-14 22:57:40.172343 INFO::Formatting Data.
2025-02-14 22:57:40.173477 INFO::Replacing NaNs with NAs.
2025-02-14 22:57:40.175151 INFO::Removing potential empty rows and columns
2025-02-14 22:57:40.176901 INFO::Found 2 missing values.
2025-02-14 22:57:40.178628 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.
2025-02-14 22:57:40.182149 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-02-14 22:57:40.183324 INFO::Done
2025-02-14 22:57:40.200201 INFO::Formatting Data.
2025-02-14 22:57:40.201183 INFO::Replacing NaNs with NAs.
2025-02-14 22:57:40.202215 INFO::Removing potential empty rows and columns
2025-02-14 22:57:40.203278 INFO::Found 2 missing values.
2025-02-14 22:57:40.204899 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 22:57:40.205635 INFO::Done
2025-02-14 22:57:40.221721 INFO::Formatting Data.
2025-02-14 22:57:40.222723 INFO::Typecasting input to dataframe.
2025-02-14 22:57:40.22373 INFO::Replacing NaNs with NAs.
2025-02-14 22:57:40.224769 INFO::Removing potential empty rows and columns
2025-02-14 22:57:40.225869 INFO::Found 0 missing values.
2025-02-14 22:57:40.228472 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-02-14 22:57:40.229228 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
30.98 1.53 78.10
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 8.78 | 0.59 | 18.72 | |
| compute_asw | 0.04 | 0.00 | 0.04 | |
| count_existing | 0.02 | 0.00 | 0.01 | |
| generate_data_covariables | 0.01 | 0.00 | 0.02 | |
| generate_dataset | 0.02 | 0.00 | 0.02 | |