Yannis Schumann
| Snapshot Date: 2025-03-23 13:40 -0400 (Sun, 23 Mar 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 -0400 (Wed, 29 Jan 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-03-24 11:41 -0400 (Mon, 24 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" | 4779 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4550 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4578 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4530 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4461 |
| 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 161/2313 | 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 | | ||||||||
| 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. |
| 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: 2025-03-23 23:11:59 -0400 (Sun, 23 Mar 2025) |
| EndedAt: 2025-03-23 23:14:13 -0400 (Sun, 23 Mar 2025) |
| EllapsedTime: 134.2 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) (2025-03-01 r87860 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 8.99 0.49 18.55
* 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) (2025-03-01 r87860 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")
2025-03-23 23:13:02.850207 INFO::Formatting Data.
2025-03-23 23:13:02.853072 INFO::Replacing NaNs with NAs.
2025-03-23 23:13:02.868212 INFO::Removing potential empty rows and columns
2025-03-23 23:13:03.169349 INFO::Found 0 missing values.
2025-03-23 23:13:03.174202 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 23:13:03.175582 INFO::Done
2025-03-23 23:13:03.176893 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 23:13:03.196955 INFO::Starting hierarchical adjustment
2025-03-23 23:13:03.198677 INFO::Found 3 batches.
2025-03-23 23:13:03.199998 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 23:13:03.202036 INFO::Using default BPPARAM
2025-03-23 23:13:03.203266 INFO::Processing subtree level 1
2025-03-23 23:13:05.758309 INFO::Adjusting the last 1 batches sequentially
2025-03-23 23:13:05.760515 INFO::Done
2025-03-23 23:13:05.761768 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 23:13:05.764798 INFO::ASW Batch was -0.0736673954494178 prior to batch effect correction and is now -0.0736673954494178 .
2025-03-23 23:13:05.766367 INFO::Total function execution time is 2.91691708564758 s and adjustment time is 2.56210017204285 s ( 87.84 )
2025-03-23 23:13:05.785717 INFO::Formatting Data.
2025-03-23 23:13:05.786847 INFO::Replacing NaNs with NAs.
2025-03-23 23:13:05.788017 INFO::Removing potential empty rows and columns
2025-03-23 23:13:05.789283 INFO::Found 0 missing values.
2025-03-23 23:13:05.790744 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.
2025-03-23 23:13:05.801529 INFO::Formatting Data.
2025-03-23 23:13:05.802541 INFO::Replacing NaNs with NAs.
2025-03-23 23:13:05.803601 INFO::Removing potential empty rows and columns
2025-03-23 23:13:05.804747 INFO::Found 0 missing values.
2025-03-23 23:13:05.805887 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.
2025-03-23 23:13:05.823115 INFO::Formatting Data.
2025-03-23 23:13:05.824089 INFO::Replacing NaNs with NAs.
2025-03-23 23:13:05.825166 INFO::Removing potential empty rows and columns
2025-03-23 23:13:05.826373 INFO::Found 0 missing values.
2025-03-23 23:13:05.827433 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.
2025-03-23 23:13:05.831324 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 23:13:05.832086 INFO::Done
2025-03-23 23:13:05.832841 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 23:13:05.835063 INFO::Starting hierarchical adjustment
2025-03-23 23:13:05.836053 INFO::Found 2 batches.
2025-03-23 23:13:05.836796 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 23:13:05.837631 INFO::Using default BPPARAM
2025-03-23 23:13:05.838333 INFO::Adjusting the last 2 batches sequentially
2025-03-23 23:13:05.839526 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-23 23:13:05.855903 INFO::Done
2025-03-23 23:13:05.856834 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 23:13:05.858945 INFO::ASW Batch was 0.0723854800067895 prior to batch effect correction and is now -0.128265492650711 .
2025-03-23 23:13:05.859907 INFO::Total function execution time is 0.036876916885376 s and adjustment time is 0.0199611186981201 s ( 54.13 )
2025-03-23 23:13:05.862665 INFO::Formatting Data.
2025-03-23 23:13:05.863456 INFO::Replacing NaNs with NAs.
2025-03-23 23:13:05.870167 INFO::Formatting Data.
2025-03-23 23:13:05.870988 INFO::Replacing NaNs with NAs.
2025-03-23 23:13:05.872012 INFO::Removing potential empty rows and columns
2025-03-23 23:13:05.87308 INFO::Found 0 missing values.
2025-03-23 23:13:05.875469 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 23:13:05.876166 INFO::Done
2025-03-23 23:13:05.876843 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 23:13:05.878852 INFO::Starting hierarchical adjustment
2025-03-23 23:13:05.879703 INFO::Found 2 batches.
2025-03-23 23:13:05.880441 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 23:13:05.881196 INFO::Using default BPPARAM
2025-03-23 23:13:05.881878 INFO::Adjusting the last 2 batches sequentially
2025-03-23 23:13:05.882915 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-23 23:13:05.894702 INFO::Done
2025-03-23 23:13:05.895552 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 23:13:05.897698 INFO::ASW Batch was -0.0239084882156434 prior to batch effect correction and is now -0.12004191261268 .
2025-03-23 23:13:05.898709 INFO::Total function execution time is 0.0285570621490479 s and adjustment time is 0.0151009559631348 s ( 52.88 )
2025-03-23 23:13:05.899924 INFO::Formatting Data.
2025-03-23 23:13:05.900701 INFO::Replacing NaNs with NAs.
2025-03-23 23:13:05.901692 INFO::Removing potential empty rows and columns
2025-03-23 23:13:05.903041 INFO::Found 0 missing values.
2025-03-23 23:13:05.907007 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 23:13:05.908189 INFO::Done
2025-03-23 23:13:05.90935 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 23:13:05.912542 INFO::Starting hierarchical adjustment
2025-03-23 23:13:05.91394 INFO::Found 2 batches.
2025-03-23 23:13:05.915119 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 23:13:05.916362 INFO::Using default BPPARAM
2025-03-23 23:13:05.917527 INFO::Adjusting the last 2 batches sequentially
2025-03-23 23:13:05.919249 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-23 23:13:05.938615 INFO::Done
2025-03-23 23:13:05.940017 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 23:13:05.943296 INFO::ASW Batch was -0.0239084882156434 prior to batch effect correction and is now -0.12004191261268 .
2025-03-23 23:13:05.944879 INFO::Total function execution time is 0.0448620319366455 s and adjustment time is 0.0248310565948486 s ( 55.35 )
2025-03-23 23:13:08.604597 INFO::Formatting Data.
2025-03-23 23:13:08.60551 INFO::Recognized SummarizedExperiment
2025-03-23 23:13:08.606239 INFO::Typecasting input to dataframe.
2025-03-23 23:13:08.648819 INFO::Replacing NaNs with NAs.
2025-03-23 23:13:08.651105 INFO::Removing potential empty rows and columns
2025-03-23 23:13:08.656397 INFO::Found 0 missing values.
2025-03-23 23:13:08.666163 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 23:13:08.667694 INFO::Done
2025-03-23 23:13:08.669007 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 23:13:08.675368 INFO::Starting hierarchical adjustment
2025-03-23 23:13:08.676954 INFO::Found 2 batches.
2025-03-23 23:13:08.678222 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 23:13:08.680234 INFO::Using default BPPARAM
2025-03-23 23:13:08.681483 INFO::Adjusting the last 2 batches sequentially
2025-03-23 23:13:08.683457 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-23 23:13:09.519981 INFO::Done
2025-03-23 23:13:09.521329 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 23:13:09.526895 INFO::ASW Batch was -0.0119815271232231 prior to batch effect correction and is now -0.0892625366374453 .
2025-03-23 23:13:09.528395 INFO::Total function execution time is 0.923992156982422 s and adjustment time is 0.843250036239624 s ( 91.26 )
2025-03-23 23:13:09.555066 INFO::Formatting Data.
2025-03-23 23:13:09.556443 INFO::Recognized SummarizedExperiment
2025-03-23 23:13:09.55761 INFO::Typecasting input to dataframe.
2025-03-23 23:13:09.569503 INFO::Replacing NaNs with NAs.
2025-03-23 23:13:09.571495 INFO::Removing potential empty rows and columns
2025-03-23 23:13:09.575907 INFO::Found 0 missing values.
2025-03-23 23:13:09.58449 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 23:13:09.585756 INFO::Done
2025-03-23 23:13:09.586938 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 23:13:09.59246 INFO::Starting hierarchical adjustment
2025-03-23 23:13:09.593808 INFO::Found 2 batches.
2025-03-23 23:13:09.594925 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 23:13:09.596133 INFO::Using default BPPARAM
2025-03-23 23:13:09.597207 INFO::Adjusting the last 2 batches sequentially
2025-03-23 23:13:09.598945 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-23 23:13:09.630024 INFO::Done
2025-03-23 23:13:09.631435 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 23:13:09.637153 INFO::ASW Batch was -0.00105259576408263 prior to batch effect correction and is now -0.00105259576408263 .
2025-03-23 23:13:09.638692 INFO::Total function execution time is 0.0836100578308105 s and adjustment time is 0.0363659858703613 s ( 43.49 )
2025-03-23 23:13:09.670442 INFO::Formatting Data.
2025-03-23 23:13:09.672228 INFO::Replacing NaNs with NAs.
2025-03-23 23:13:09.674182 INFO::Removing potential empty rows and columns
2025-03-23 23:13:09.676177 INFO::Found 0 missing values.
2025-03-23 23:13:09.681251 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 23:13:09.682642 INFO::Done
2025-03-23 23:13:09.683942 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 23:13:09.687954 INFO::Starting hierarchical adjustment
2025-03-23 23:13:09.689508 INFO::Found 3 batches.
2025-03-23 23:13:09.690831 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 23:13:09.692196 INFO::Using default BPPARAM
2025-03-23 23:13:09.693474 INFO::Processing subtree level 1
2025-03-23 23:13:20.001698 INFO::Adjusting the last 1 batches sequentially
2025-03-23 23:13:20.003979 INFO::Done
2025-03-23 23:13:20.005368 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 23:13:20.008613 INFO::ASW Batch was -0.0811548083659249 prior to batch effect correction and is now -0.151323394517299 .
2025-03-23 23:13:20.010091 INFO::Total function execution time is 10.3398160934448 s and adjustment time is 10.3147280216217 s ( 99.76 )
2025-03-23 23:13:20.033532 INFO::Skipping initial DF formatting
2025-03-23 23:13:20.034825 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 23:13:20.04087 INFO::Starting hierarchical adjustment
2025-03-23 23:13:20.042297 INFO::Found 5 batches.
2025-03-23 23:13:20.043387 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 23:13:20.044526 INFO::Using default BPPARAM
2025-03-23 23:13:20.04554 INFO::Processing subtree level 1
2025-03-23 23:13:22.873725 INFO::Adjusting the last 2 batches sequentially
2025-03-23 23:13:22.875689 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-23 23:13:22.896942 INFO::Done
2025-03-23 23:13:22.897977 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 23:13:22.902239 INFO::ASW Batch was 0.513661533584258 prior to batch effect correction and is now 0.513661533584258 .
2025-03-23 23:13:22.903106 INFO::ASW Label was 0.398392183669133 prior to batch effect correction and is now 0.398392183669133 .
2025-03-23 23:13:22.904108 INFO::Total function execution time is 2.87075185775757 s and adjustment time is 2.85483193397522 s ( 99.45 )
2025-03-23 23:13:22.9251 INFO::Formatting Data.
2025-03-23 23:13:22.926534 INFO::Replacing NaNs with NAs.
2025-03-23 23:13:22.928201 INFO::Removing potential empty rows and columns
2025-03-23 23:13:22.929938 INFO::Found 0 missing values.
2025-03-23 23:13:22.933995 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 23:13:22.934756 INFO::Done
2025-03-23 23:13:22.935543 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 23:13:22.938839 INFO::Starting hierarchical adjustment
2025-03-23 23:13:22.939778 INFO::Found 5 batches.
2025-03-23 23:13:22.940486 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 23:13:22.941344 INFO::Using default BPPARAM
2025-03-23 23:13:22.942122 INFO::Processing subtree level 1
2025-03-23 23:13:26.046748 INFO::Adjusting the last 2 batches sequentially
2025-03-23 23:13:26.048779 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-23 23:13:26.067343 INFO::Done
2025-03-23 23:13:26.068691 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 23:13:26.073685 INFO::ASW Batch was 0.319707688870315 prior to batch effect correction and is now -0.0340882992296604 .
2025-03-23 23:13:26.075048 INFO::ASW Label was 0.461601187510948 prior to batch effect correction and is now 0.869709032223915 .
2025-03-23 23:13:26.076546 INFO::Total function execution time is 3.15155601501465 s and adjustment time is 3.12762188911438 s ( 99.24 )
2025-03-23 23:13:26.078114 INFO::Formatting Data.
2025-03-23 23:13:26.079367 INFO::Replacing NaNs with NAs.
2025-03-23 23:13:26.080675 INFO::Removing potential empty rows and columns
2025-03-23 23:13:26.081752 INFO::Found 0 missing values.
2025-03-23 23:13:26.085201 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 23:13:26.085926 INFO::Done
2025-03-23 23:13:26.086657 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 23:13:26.089757 INFO::Starting hierarchical adjustment
2025-03-23 23:13:26.090655 INFO::Found 5 batches.
2025-03-23 23:13:26.091396 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 23:13:26.092252 INFO::Using default BPPARAM
2025-03-23 23:13:26.093018 INFO::Processing subtree level 1
2025-03-23 23:13:29.058737 INFO::Adjusting the last 2 batches sequentially
2025-03-23 23:13:29.060445 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-23 23:13:29.076481 INFO::Done
2025-03-23 23:13:29.077901 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 23:13:29.082717 INFO::ASW Batch was 0.319707688870315 prior to batch effect correction and is now -0.0340882992296604 .
2025-03-23 23:13:29.084119 INFO::ASW Label was 0.461601187510948 prior to batch effect correction and is now 0.869709032223915 .
2025-03-23 23:13:29.08573 INFO::Total function execution time is 3.0076048374176 s and adjustment time is 2.98590016365051 s ( 99.28 )
2025-03-23 23:13:29.11032 INFO::Formatting Data.
2025-03-23 23:13:29.111868 INFO::Replacing NaNs with NAs.
2025-03-23 23:13:29.113612 INFO::Removing potential empty rows and columns
2025-03-23 23:13:29.115391 INFO::Found 0 missing values.
2025-03-23 23:13:29.121007 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 23:13:29.122294 INFO::Done
2025-03-23 23:13:29.123509 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 23:13:29.127139 INFO::Starting hierarchical adjustment
2025-03-23 23:13:29.128072 INFO::Found 5 batches.
2025-03-23 23:13:29.128796 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 23:13:29.129585 INFO::Using default BPPARAM
2025-03-23 23:13:29.13066 INFO::Processing subtree level 1
2025-03-23 23:13:32.284252 INFO::Adjusting the last 2 batches sequentially
2025-03-23 23:13:32.286251 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-23 23:13:32.301676 INFO::Done
2025-03-23 23:13:32.303001 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 23:13:32.307405 INFO::ASW Batch was 0.698240826939192 prior to batch effect correction and is now -0.095349091769254 .
2025-03-23 23:13:32.308551 INFO::ASW Label was 0.182103937069574 prior to batch effect correction and is now 0.745283980924291 .
2025-03-23 23:13:32.309972 INFO::Total function execution time is 3.19977593421936 s and adjustment time is 3.17366600036621 s ( 99.18 )
2025-03-23 23:13:32.311339 INFO::Formatting Data.
2025-03-23 23:13:32.312126 INFO::Replacing NaNs with NAs.
2025-03-23 23:13:32.313178 INFO::Removing potential empty rows and columns
2025-03-23 23:13:32.314269 INFO::Found 0 missing values.
2025-03-23 23:13:32.317869 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 23:13:32.318663 INFO::Done
2025-03-23 23:13:32.319378 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 23:13:32.322342 INFO::Starting hierarchical adjustment
2025-03-23 23:13:32.323205 INFO::Found 5 batches.
2025-03-23 23:13:32.323907 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 23:13:32.324654 INFO::Using default BPPARAM
2025-03-23 23:13:32.325336 INFO::Processing subtree level 1
2025-03-23 23:13:35.431782 INFO::Adjusting the last 2 batches sequentially
2025-03-23 23:13:35.433915 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-23 23:13:35.453327 INFO::Done
2025-03-23 23:13:35.454727 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 23:13:35.45943 INFO::ASW Batch was 0.698240826939192 prior to batch effect correction and is now -0.095349091769254 .
2025-03-23 23:13:35.460742 INFO::ASW Label was 0.182103937069574 prior to batch effect correction and is now 0.745283980924291 .
2025-03-23 23:13:35.462295 INFO::Total function execution time is 3.15091013908386 s and adjustment time is 3.13016295433044 s ( 99.34 )
2025-03-23 23:13:35.486776 INFO::Formatting Data.
2025-03-23 23:13:35.488325 INFO::Replacing NaNs with NAs.
2025-03-23 23:13:35.490119 INFO::Removing potential empty rows and columns
2025-03-23 23:13:35.491932 INFO::Found 0 missing values.
2025-03-23 23:13:35.496031 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 23:13:35.497274 INFO::Done
2025-03-23 23:13:35.498478 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 23:13:35.503257 INFO::Starting hierarchical adjustment
2025-03-23 23:13:35.504796 INFO::Found 2 batches.
2025-03-23 23:13:35.506022 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 23:13:35.507328 INFO::Using default BPPARAM
2025-03-23 23:13:35.508528 INFO::Adjusting the last 2 batches sequentially
2025-03-23 23:13:35.510303 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-23 23:13:35.523479 INFO::Done
2025-03-23 23:13:35.524367 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 23:13:35.527383 INFO::ASW Batch was 0.509118746489251 prior to batch effect correction and is now -0.0225091814441758 .
2025-03-23 23:13:35.528208 INFO::ASW Label was 0.583100866125194 prior to batch effect correction and is now 0.950183606677177 .
2025-03-23 23:13:35.529152 INFO::Total function execution time is 0.0425620079040527 s and adjustment time is 0.0189270973205566 s ( 44.47 )
2025-03-23 23:13:35.530068 INFO::Formatting Data.
2025-03-23 23:13:35.530845 INFO::Replacing NaNs with NAs.
2025-03-23 23:13:35.531857 INFO::Removing potential empty rows and columns
2025-03-23 23:13:35.532918 INFO::Found 0 missing values.
2025-03-23 23:13:35.535311 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 23:13:35.536031 INFO::Done
2025-03-23 23:13:35.536738 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 23:13:35.541414 INFO::Starting hierarchical adjustment
2025-03-23 23:13:35.54294 INFO::Found 2 batches.
2025-03-23 23:13:35.54419 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 23:13:35.545285 INFO::Using default BPPARAM
2025-03-23 23:13:35.546232 INFO::Adjusting the last 2 batches sequentially
2025-03-23 23:13:35.547367 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-23 23:13:35.559334 INFO::Done
2025-03-23 23:13:35.560196 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 23:13:35.56319 INFO::ASW Batch was 0.509118746489251 prior to batch effect correction and is now -0.0225091814441758 .
2025-03-23 23:13:35.563993 INFO::ASW Label was 0.583100866125194 prior to batch effect correction and is now 0.950183606677177 .
2025-03-23 23:13:35.564939 INFO::Total function execution time is 0.0348711013793945 s and adjustment time is 0.0166628360748291 s ( 47.78 )
2025-03-23 23:13:35.579882 INFO::Formatting Data.
2025-03-23 23:13:35.580859 INFO::Replacing NaNs with NAs.
2025-03-23 23:13:35.581919 INFO::Removing potential empty rows and columns
2025-03-23 23:13:35.582966 INFO::Found 0 missing values.
2025-03-23 23:13:35.584992 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 23:13:35.585723 INFO::Done
2025-03-23 23:13:35.586434 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 23:13:35.588486 INFO::Starting hierarchical adjustment
2025-03-23 23:13:35.589433 INFO::Found 2 batches.
2025-03-23 23:13:35.590162 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 23:13:35.590958 INFO::Using default BPPARAM
2025-03-23 23:13:35.591666 INFO::Adjusting the last 2 batches sequentially
2025-03-23 23:13:35.592738 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-23 23:13:35.623099 INFO::Done
2025-03-23 23:13:35.624365 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 23:13:35.627037 INFO::ASW Batch was 0.0525175342309918 prior to batch effect correction and is now -0.160418965242495 .
2025-03-23 23:13:35.628046 INFO::Total function execution time is 0.0482480525970459 s and adjustment time is 0.0337128639221191 s ( 69.87 )
2025-03-23 23:13:35.643864 INFO::Formatting Data.
2025-03-23 23:13:35.644866 INFO::Replacing NaNs with NAs.
2025-03-23 23:13:35.645954 INFO::Removing potential empty rows and columns
2025-03-23 23:13:35.64709 INFO::Found 0 missing values.
2025-03-23 23:13:35.648355 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.
2025-03-23 23:13:35.654784 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 23:13:35.656139 INFO::Done
2025-03-23 23:13:35.657355 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 23:13:35.662163 INFO::Starting hierarchical adjustment
2025-03-23 23:13:35.663686 INFO::Found 2 batches.
2025-03-23 23:13:35.664957 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 23:13:35.666265 INFO::Using default BPPARAM
2025-03-23 23:13:35.667508 INFO::Adjusting the last 2 batches sequentially
2025-03-23 23:13:35.669263 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-23 23:13:35.683516 INFO::Done
2025-03-23 23:13:35.684482 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 23:13:35.687647 INFO::ASW Batch was 0.376536912457046 prior to batch effect correction and is now -0.0268535557048392 .
2025-03-23 23:13:35.688514 INFO::ASW Label was 0.561209933819352 prior to batch effect correction and is now 0.94129530530937 .
2025-03-23 23:13:35.68952 INFO::Total function execution time is 0.045753002166748 s and adjustment time is 0.0200841426849365 s ( 43.9 )
2025-03-23 23:13:35.690503 INFO::Formatting Data.
2025-03-23 23:13:35.69132 INFO::Replacing NaNs with NAs.
2025-03-23 23:13:35.692436 INFO::Removing potential empty rows and columns
2025-03-23 23:13:35.69358 INFO::Found 0 missing values.
2025-03-23 23:13:35.694693 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.
2025-03-23 23:13:35.69889 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 23:13:35.70004 INFO::Done
2025-03-23 23:13:35.701197 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 23:13:35.706242 INFO::Starting hierarchical adjustment
2025-03-23 23:13:35.707668 INFO::Found 2 batches.
2025-03-23 23:13:35.708938 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 23:13:35.710324 INFO::Using default BPPARAM
2025-03-23 23:13:35.711544 INFO::Adjusting the last 2 batches sequentially
2025-03-23 23:13:35.713459 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-23 23:13:35.734675 INFO::Done
2025-03-23 23:13:35.736396 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 23:13:35.742752 INFO::ASW Batch was 0.376536912457046 prior to batch effect correction and is now -0.0268535557048392 .
2025-03-23 23:13:35.744273 INFO::ASW Label was 0.561209933819352 prior to batch effect correction and is now 0.94129530530937 .
2025-03-23 23:13:35.746225 INFO::Total function execution time is 0.0555520057678223 s and adjustment time is 0.0271461009979248 s ( 48.87 )
2025-03-23 23:13:36.008461 INFO::Formatting Data.
2025-03-23 23:13:36.009585 INFO::Replacing NaNs with NAs.
2025-03-23 23:13:36.010833 INFO::Removing potential empty rows and columns
2025-03-23 23:13:36.012105 INFO::Found 0 missing values.
2025-03-23 23:13:36.0155 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 23:13:36.016302 INFO::Done
2025-03-23 23:13:36.017078 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 23:13:36.019409 INFO::Starting hierarchical adjustment
2025-03-23 23:13:36.020383 INFO::Found 3 batches.
2025-03-23 23:13:36.021171 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 23:13:36.022041 INFO::Using default BPPARAM
2025-03-23 23:13:36.022803 INFO::Processing subtree level 1
2025-03-23 23:13:38.806971 INFO::Adjusting the last 1 batches sequentially
2025-03-23 23:13:38.809116 INFO::Done
2025-03-23 23:13:38.81035 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 23:13:38.813694 INFO::ASW Batch was -0.07186813155357 prior to batch effect correction and is now -0.07186813155357 .
2025-03-23 23:13:38.815288 INFO::Total function execution time is 2.8068699836731 s and adjustment time is 2.78884410858154 s ( 99.36 )
2025-03-23 23:13:38.816943 INFO::Formatting Data.
2025-03-23 23:13:38.818163 INFO::Typecasting input to dataframe.
2025-03-23 23:13:38.819528 INFO::Replacing NaNs with NAs.
2025-03-23 23:13:38.821088 INFO::Removing potential empty rows and columns
2025-03-23 23:13:38.822766 INFO::Found 0 missing values.
2025-03-23 23:13:38.826836 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 23:13:38.827917 INFO::Done
2025-03-23 23:13:38.829082 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 23:13:38.832585 INFO::Starting hierarchical adjustment
2025-03-23 23:13:38.833969 INFO::Found 3 batches.
2025-03-23 23:13:38.835092 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 23:13:38.836243 INFO::Using default BPPARAM
2025-03-23 23:13:38.837015 INFO::Processing subtree level 1
2025-03-23 23:13:41.574917 INFO::Adjusting the last 1 batches sequentially
2025-03-23 23:13:41.577203 INFO::Done
2025-03-23 23:13:41.578533 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 23:13:41.581754 INFO::ASW Batch was -0.07186813155357 prior to batch effect correction and is now -0.07186813155357 .
2025-03-23 23:13:41.583356 INFO::Total function execution time is 2.76639795303345 s and adjustment time is 2.74342107772827 s ( 99.17 )
2025-03-23 23:13:41.605602 INFO::Formatting Data.
2025-03-23 23:13:41.607078 INFO::Typecasting input to dataframe.
2025-03-23 23:13:41.608647 INFO::Replacing NaNs with NAs.
2025-03-23 23:13:41.610254 INFO::Removing potential empty rows and columns
2025-03-23 23:13:41.611958 INFO::Found 0 missing values.
2025-03-23 23:13:41.616171 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 23:13:41.617379 INFO::Done
2025-03-23 23:13:41.618464 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 23:13:41.621603 INFO::Starting hierarchical adjustment
2025-03-23 23:13:41.623005 INFO::Found 3 batches.
2025-03-23 23:13:41.624247 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 23:13:41.6256 INFO::Using default BPPARAM
2025-03-23 23:13:41.6268 INFO::Processing subtree level 1
2025-03-23 23:13:44.556985 INFO::Adjusting the last 1 batches sequentially
2025-03-23 23:13:44.559106 INFO::Done
2025-03-23 23:13:44.560351 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 23:13:44.563337 INFO::ASW Batch was -0.104279719365283 prior to batch effect correction and is now -0.104279719365283 .
2025-03-23 23:13:44.564757 INFO::Total function execution time is 2.95927000045776 s and adjustment time is 2.93629503250122 s ( 99.22 )
2025-03-23 23:13:47.383731 INFO::Formatting Data.
2025-03-23 23:13:47.384755 INFO::Replacing NaNs with NAs.
2025-03-23 23:13:47.386035 INFO::Removing potential empty rows and columns
2025-03-23 23:13:47.388426 INFO::Found 1000 missing values.
2025-03-23 23:13:47.406582 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 23:13:47.408058 INFO::Done
2025-03-23 23:13:47.409428 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 23:13:47.419414 INFO::Starting hierarchical adjustment
2025-03-23 23:13:47.42053 INFO::Found 10 batches.
2025-03-23 23:13:47.42131 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 23:13:47.42213 INFO::Using default BPPARAM
2025-03-23 23:13:47.422842 INFO::Processing subtree level 1
2025-03-23 23:13:50.359947 INFO::Processing subtree level 2
2025-03-23 23:13:53.151698 INFO::Adjusting the last 1 batches sequentially
2025-03-23 23:13:53.154063 INFO::Done
2025-03-23 23:13:53.155258 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 23:13:53.16392 INFO::ASW Batch was 0.528758484453286 prior to batch effect correction and is now 0.528758484453286 .
2025-03-23 23:13:53.165204 INFO::ASW Label was 0.318074905481986 prior to batch effect correction and is now 0.318074905481986 .
2025-03-23 23:13:53.16677 INFO::Total function execution time is 5.78307914733887 s and adjustment time is 5.73369693756104 s ( 99.15 )
2025-03-23 23:13:53.168151 INFO::Formatting Data.
2025-03-23 23:13:53.169333 INFO::Replacing NaNs with NAs.
2025-03-23 23:13:53.170858 INFO::Removing potential empty rows and columns
2025-03-23 23:13:53.173129 INFO::Found 1000 missing values.
2025-03-23 23:13:53.192044 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 23:13:53.193368 INFO::Done
2025-03-23 23:13:53.194515 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 23:13:53.203293 INFO::Starting hierarchical adjustment
2025-03-23 23:13:53.204714 INFO::Found 10 batches.
2025-03-23 23:13:53.945413 INFO::Set up parallel execution backend with 2 workers
2025-03-23 23:13:53.946905 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-03-23 23:13:56.918146 INFO::Adjusting the last 2 batches sequentially
2025-03-23 23:13:56.920407 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-23 23:13:56.945543 INFO::Done
2025-03-23 23:13:56.947001 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 23:13:56.956373 INFO::ASW Batch was 0.528758484453286 prior to batch effect correction and is now 0.528758484453286 .
2025-03-23 23:13:56.957829 INFO::ASW Label was 0.318074905481986 prior to batch effect correction and is now 0.318074905481986 .
2025-03-23 23:13:56.959462 INFO::Total function execution time is 3.79131007194519 s and adjustment time is 3.7410101890564 s ( 98.67 )
2025-03-23 23:13:59.72073 INFO::Formatting Data.
2025-03-23 23:13:59.722127 INFO::Replacing NaNs with NAs.
2025-03-23 23:13:59.72376 INFO::Removing potential empty rows and columns
2025-03-23 23:13:59.725223 INFO::Found 0 missing values.
2025-03-23 23:13:59.728263 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 23:13:59.728984 INFO::Done
2025-03-23 23:13:59.729677 INFO::Acquiring quality metrics before batch effect correction.
2025-03-23 23:13:59.732381 INFO::Starting hierarchical adjustment
2025-03-23 23:13:59.73325 INFO::Found 3 batches.
2025-03-23 23:13:59.733949 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-23 23:13:59.734711 INFO::Using default BPPARAM
2025-03-23 23:13:59.735451 INFO::Processing subtree level 1
2025-03-23 23:14:02.769362 INFO::Adjusting the last 1 batches sequentially
2025-03-23 23:14:02.771635 INFO::Done
2025-03-23 23:14:02.77297 INFO::Acquiring quality metrics after batch effect correction.
2025-03-23 23:14:02.777284 INFO::ASW Batch was 0.152562329707429 prior to batch effect correction and is now -0.152371554333582 .
2025-03-23 23:14:02.778679 INFO::ASW Label was -0.189300948855429 prior to batch effect correction and is now -0.0649252208514599 .
2025-03-23 23:14:02.780208 INFO::Total function execution time is 3.059574842453 s and adjustment time is 3.038419008255 s ( 99.31 )
2025-03-23 23:14:02.993072 INFO::Formatting Data.
2025-03-23 23:14:02.9946 INFO::Replacing NaNs with NAs.
2025-03-23 23:14:02.996229 INFO::Removing potential empty rows and columns
2025-03-23 23:14:02.997972 INFO::Found 2 missing values.
2025-03-23 23:14:03.001833 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-03-23 23:14:03.002976 INFO::Done
2025-03-23 23:14:03.058078 INFO::Found NA in Reference column
2025-03-23 23:14:03.078248 INFO::Require at least two references per batch.
2025-03-23 23:14:03.109448 INFO::Formatting Data.
2025-03-23 23:14:03.110812 INFO::Recognized SummarizedExperiment
2025-03-23 23:14:03.111953 INFO::Typecasting input to dataframe.
2025-03-23 23:14:03.123585 INFO::Replacing NaNs with NAs.
2025-03-23 23:14:03.125517 INFO::Removing potential empty rows and columns
2025-03-23 23:14:03.12962 INFO::Found 0 missing values.
2025-03-23 23:14:03.137581 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 23:14:03.13888 INFO::Done
2025-03-23 23:14:03.161082 INFO::Formatting Data.
2025-03-23 23:14:03.16259 INFO::Recognized SummarizedExperiment
2025-03-23 23:14:03.163766 INFO::Typecasting input to dataframe.
2025-03-23 23:14:03.187306 INFO::Replacing NaNs with NAs.
2025-03-23 23:14:03.188806 INFO::Removing potential empty rows and columns
2025-03-23 23:14:03.191672 INFO::Found 0 missing values.
2025-03-23 23:14:03.199607 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 23:14:03.20056 INFO::Done
2025-03-23 23:14:03.217379 INFO::Formatting Data.
2025-03-23 23:14:03.218416 INFO::Recognized SummarizedExperiment
2025-03-23 23:14:03.219189 INFO::Typecasting input to dataframe.
2025-03-23 23:14:03.234854 INFO::Replacing NaNs with NAs.
2025-03-23 23:14:03.236125 INFO::Removing potential empty rows and columns
2025-03-23 23:14:03.237305 INFO::Found 0 missing values.
2025-03-23 23:14:03.238361 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.
2025-03-23 23:14:03.242074 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 23:14:03.242797 INFO::Done
2025-03-23 23:14:03.256594 INFO::Formatting Data.
2025-03-23 23:14:03.257574 INFO::Replacing NaNs with NAs.
2025-03-23 23:14:03.258634 INFO::Removing potential empty rows and columns
2025-03-23 23:14:03.259765 INFO::Found 0 missing values.
2025-03-23 23:14:03.262401 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 23:14:03.263135 INFO::Done
2025-03-23 23:14:03.283419 INFO::Formatting Data.
2025-03-23 23:14:03.28491 INFO::Replacing NaNs with NAs.
2025-03-23 23:14:03.286553 INFO::Removing potential empty rows and columns
2025-03-23 23:14:03.288305 INFO::Found 0 missing values.
2025-03-23 23:14:03.292335 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 23:14:03.293481 INFO::Done
2025-03-23 23:14:03.348358 INFO::Formatting Data.
2025-03-23 23:14:03.349893 INFO::Replacing NaNs with NAs.
2025-03-23 23:14:03.351732 INFO::Removing potential empty rows and columns
2025-03-23 23:14:03.353629 INFO::Found 1 missing values.
2025-03-23 23:14:03.357401 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 23:14:03.358539 INFO::Done
2025-03-23 23:14:03.396167 INFO::Formatting Data.
2025-03-23 23:14:03.397736 INFO::Replacing NaNs with NAs.
2025-03-23 23:14:03.399447 INFO::Removing potential empty rows and columns
2025-03-23 23:14:03.401171 INFO::Found 2 missing values.
2025-03-23 23:14:03.402861 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.
2025-03-23 23:14:03.406557 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-03-23 23:14:03.407787 INFO::Done
2025-03-23 23:14:03.429338 INFO::Formatting Data.
2025-03-23 23:14:03.430877 INFO::Replacing NaNs with NAs.
2025-03-23 23:14:03.432572 INFO::Removing potential empty rows and columns
2025-03-23 23:14:03.434415 INFO::Found 2 missing values.
2025-03-23 23:14:03.437239 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 23:14:03.438484 INFO::Done
2025-03-23 23:14:03.459745 INFO::Formatting Data.
2025-03-23 23:14:03.461264 INFO::Typecasting input to dataframe.
2025-03-23 23:14:03.462918 INFO::Replacing NaNs with NAs.
2025-03-23 23:14:03.464585 INFO::Removing potential empty rows and columns
2025-03-23 23:14:03.466377 INFO::Found 0 missing values.
2025-03-23 23:14:03.470954 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-23 23:14:03.472251 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
30.39 1.50 75.64
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 8.99 | 0.49 | 18.55 | |
| compute_asw | 0.05 | 0.00 | 0.04 | |
| count_existing | 0.03 | 0.00 | 0.04 | |
| generate_data_covariables | 0.02 | 0.00 | 0.01 | |
| generate_dataset | 0.03 | 0.00 | 0.03 | |