Yannis Schumann
| Snapshot Date: 2025-03-17 13:40 -0400 (Mon, 17 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 2025-03-18 11:44 -0400 (Tue, 18 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" | 4537 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4543 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4576 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4528 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4459 |
| 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.3.6.tar.gz |
| StartedAt: 2025-03-17 19:19:43 -0400 (Mon, 17 Mar 2025) |
| EndedAt: 2025-03-17 19:21:15 -0400 (Mon, 17 Mar 2025) |
| EllapsedTime: 91.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.3.6.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 26.943 1.501 19.346
* 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: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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) (2025-03-02 r87868) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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")
2025-03-17 19:20:52.603667 INFO::Formatting Data.
2025-03-17 19:20:52.608165 INFO::Replacing NaNs with NAs.
2025-03-17 19:20:52.624004 INFO::Removing potential empty rows and columns
2025-03-17 19:20:52.914989 INFO::Found 0 missing values.
2025-03-17 19:20:52.918235 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 19:20:52.9192 INFO::Done
2025-03-17 19:20:52.920059 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 19:20:52.935628 INFO::Starting hierarchical adjustment
2025-03-17 19:20:52.936732 INFO::Found 3 batches.
2025-03-17 19:20:52.937293 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 19:20:52.938421 INFO::Using default BPPARAM
2025-03-17 19:20:52.938929 INFO::Processing subtree level 1
2025-03-17 19:20:53.102077 INFO::Adjusting the last 1 batches sequentially
2025-03-17 19:20:53.108192 INFO::Done
2025-03-17 19:20:53.109873 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 19:20:53.117941 INFO::ASW Batch was -0.106374402372373 prior to batch effect correction and is now -0.106374402372373 .
2025-03-17 19:20:53.120405 INFO::Total function execution time is 0.517477035522461 s and adjustment time is 0.171603202819824 s ( 33.16 )
2025-03-17 19:20:53.151089 INFO::Formatting Data.
2025-03-17 19:20:53.152238 INFO::Replacing NaNs with NAs.
2025-03-17 19:20:53.153666 INFO::Removing potential empty rows and columns
2025-03-17 19:20:53.155443 INFO::Found 0 missing values.
2025-03-17 19:20:53.156471 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.
2025-03-17 19:20:53.170452 INFO::Formatting Data.
2025-03-17 19:20:53.171301 INFO::Replacing NaNs with NAs.
2025-03-17 19:20:53.172595 INFO::Removing potential empty rows and columns
2025-03-17 19:20:53.174209 INFO::Found 0 missing values.
2025-03-17 19:20:53.175614 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.
2025-03-17 19:20:53.198211 INFO::Formatting Data.
2025-03-17 19:20:53.199465 INFO::Replacing NaNs with NAs.
2025-03-17 19:20:53.200825 INFO::Removing potential empty rows and columns
2025-03-17 19:20:53.202216 INFO::Found 0 missing values.
2025-03-17 19:20:53.203472 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.
2025-03-17 19:20:53.208114 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 19:20:53.208748 INFO::Done
2025-03-17 19:20:53.209356 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 19:20:53.211365 INFO::Starting hierarchical adjustment
2025-03-17 19:20:53.21217 INFO::Found 2 batches.
2025-03-17 19:20:53.212743 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 19:20:53.213341 INFO::Using default BPPARAM
2025-03-17 19:20:53.213827 INFO::Adjusting the last 2 batches sequentially
2025-03-17 19:20:53.214963 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 19:20:53.239224 INFO::Done
2025-03-17 19:20:53.240179 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 19:20:53.24224 INFO::ASW Batch was 0.0836049392269856 prior to batch effect correction and is now -0.114450396186086 .
2025-03-17 19:20:53.243322 INFO::Total function execution time is 0.0451929569244385 s and adjustment time is 0.0272560119628906 s ( 60.31 )
2025-03-17 19:20:53.247242 INFO::Formatting Data.
2025-03-17 19:20:53.247929 INFO::Replacing NaNs with NAs.
2025-03-17 19:20:53.256824 INFO::Formatting Data.
2025-03-17 19:20:53.25762 INFO::Replacing NaNs with NAs.
2025-03-17 19:20:53.258858 INFO::Removing potential empty rows and columns
2025-03-17 19:20:53.260059 INFO::Found 0 missing values.
2025-03-17 19:20:53.299985 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 19:20:53.300709 INFO::Done
2025-03-17 19:20:53.301216 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 19:20:53.303868 INFO::Starting hierarchical adjustment
2025-03-17 19:20:53.304679 INFO::Found 2 batches.
2025-03-17 19:20:53.305166 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 19:20:53.305935 INFO::Using default BPPARAM
2025-03-17 19:20:53.306672 INFO::Adjusting the last 2 batches sequentially
2025-03-17 19:20:53.307904 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 19:20:53.325111 INFO::Done
2025-03-17 19:20:53.325929 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 19:20:53.328437 INFO::ASW Batch was -0.0579997345738419 prior to batch effect correction and is now -0.0983660556723463 .
2025-03-17 19:20:53.329783 INFO::Total function execution time is 0.0729918479919434 s and adjustment time is 0.0205390453338623 s ( 28.14 )
2025-03-17 19:20:53.331324 INFO::Formatting Data.
2025-03-17 19:20:53.332197 INFO::Replacing NaNs with NAs.
2025-03-17 19:20:53.333378 INFO::Removing potential empty rows and columns
2025-03-17 19:20:53.334747 INFO::Found 0 missing values.
2025-03-17 19:20:53.338749 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 19:20:53.339318 INFO::Done
2025-03-17 19:20:53.340076 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 19:20:53.34277 INFO::Starting hierarchical adjustment
2025-03-17 19:20:53.343822 INFO::Found 2 batches.
2025-03-17 19:20:53.344596 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 19:20:53.345423 INFO::Using default BPPARAM
2025-03-17 19:20:53.346032 INFO::Adjusting the last 2 batches sequentially
2025-03-17 19:20:53.346909 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 19:20:53.367928 INFO::Done
2025-03-17 19:20:53.368591 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 19:20:53.370711 INFO::ASW Batch was -0.0579997345738419 prior to batch effect correction and is now -0.0983660556723463 .
2025-03-17 19:20:53.372054 INFO::Total function execution time is 0.0408010482788086 s and adjustment time is 0.0243079662322998 s ( 59.58 )
2025-03-17 19:20:56.661326 INFO::Formatting Data.
2025-03-17 19:20:56.662149 INFO::Recognized SummarizedExperiment
2025-03-17 19:20:56.662758 INFO::Typecasting input to dataframe.
2025-03-17 19:20:56.69641 INFO::Replacing NaNs with NAs.
2025-03-17 19:20:56.697498 INFO::Removing potential empty rows and columns
2025-03-17 19:20:56.700315 INFO::Found 0 missing values.
2025-03-17 19:20:56.70963 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 19:20:56.710633 INFO::Done
2025-03-17 19:20:56.711187 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 19:20:56.714453 INFO::Starting hierarchical adjustment
2025-03-17 19:20:56.715127 INFO::Found 2 batches.
2025-03-17 19:20:56.7156 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 19:20:56.716568 INFO::Using default BPPARAM
2025-03-17 19:20:56.717053 INFO::Adjusting the last 2 batches sequentially
2025-03-17 19:20:56.717958 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 19:20:56.784607 INFO::Done
2025-03-17 19:20:56.785533 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 19:20:56.78976 INFO::ASW Batch was 0.0101564433809416 prior to batch effect correction and is now -0.109745373794957 .
2025-03-17 19:20:56.790943 INFO::Total function execution time is 0.129832029342651 s and adjustment time is 0.069580078125 s ( 53.59 )
2025-03-17 19:20:56.812801 INFO::Formatting Data.
2025-03-17 19:20:56.813536 INFO::Recognized SummarizedExperiment
2025-03-17 19:20:56.814062 INFO::Typecasting input to dataframe.
2025-03-17 19:20:56.824498 INFO::Replacing NaNs with NAs.
2025-03-17 19:20:56.826179 INFO::Removing potential empty rows and columns
2025-03-17 19:20:56.831118 INFO::Found 0 missing values.
2025-03-17 19:20:56.839601 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 19:20:56.840322 INFO::Done
2025-03-17 19:20:56.840845 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 19:20:56.844795 INFO::Starting hierarchical adjustment
2025-03-17 19:20:56.845888 INFO::Found 2 batches.
2025-03-17 19:20:56.846552 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 19:20:56.847178 INFO::Using default BPPARAM
2025-03-17 19:20:56.847904 INFO::Adjusting the last 2 batches sequentially
2025-03-17 19:20:56.848985 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 19:20:56.876687 INFO::Done
2025-03-17 19:20:56.877672 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 19:20:56.882157 INFO::ASW Batch was -0.00350780316413988 prior to batch effect correction and is now -0.00350780316413988 .
2025-03-17 19:20:56.883378 INFO::Total function execution time is 0.0704889297485352 s and adjustment time is 0.031080961227417 s ( 44.09 )
2025-03-17 19:20:56.908809 INFO::Formatting Data.
2025-03-17 19:20:56.90959 INFO::Replacing NaNs with NAs.
2025-03-17 19:20:56.91043 INFO::Removing potential empty rows and columns
2025-03-17 19:20:56.911353 INFO::Found 0 missing values.
2025-03-17 19:20:56.914839 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 19:20:56.915438 INFO::Done
2025-03-17 19:20:56.915905 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 19:20:56.91789 INFO::Starting hierarchical adjustment
2025-03-17 19:20:56.91876 INFO::Found 3 batches.
2025-03-17 19:20:56.91949 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 19:20:56.920334 INFO::Using default BPPARAM
2025-03-17 19:20:56.921051 INFO::Processing subtree level 1
2025-03-17 19:20:57.319617 INFO::Adjusting the last 1 batches sequentially
2025-03-17 19:20:57.323976 INFO::Done
2025-03-17 19:20:57.325007 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 19:20:57.354007 INFO::ASW Batch was -0.032918741022837 prior to batch effect correction and is now -0.184179794737656 .
2025-03-17 19:20:57.361076 INFO::Total function execution time is 0.451306819915771 s and adjustment time is 0.405330181121826 s ( 89.81 )
2025-03-17 19:20:57.466481 INFO::Skipping initial DF formatting
2025-03-17 19:20:57.467505 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 19:20:57.472302 INFO::Starting hierarchical adjustment
2025-03-17 19:20:57.473086 INFO::Found 5 batches.
2025-03-17 19:20:57.473596 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 19:20:57.474168 INFO::Using default BPPARAM
2025-03-17 19:20:57.474652 INFO::Processing subtree level 1
2025-03-17 19:20:57.7415 INFO::Adjusting the last 2 batches sequentially
2025-03-17 19:20:57.752524 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 19:20:57.798758 INFO::Done
2025-03-17 19:20:57.799837 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 19:20:57.807538 INFO::ASW Batch was 0.503167298738214 prior to batch effect correction and is now 0.503167298738214 .
2025-03-17 19:20:57.808297 INFO::ASW Label was 0.368631001870298 prior to batch effect correction and is now 0.368631001870298 .
2025-03-17 19:20:57.809279 INFO::Total function execution time is 0.342962026596069 s and adjustment time is 0.325754165649414 s ( 94.98 )
2025-03-17 19:20:57.835957 INFO::Formatting Data.
2025-03-17 19:20:57.836888 INFO::Replacing NaNs with NAs.
2025-03-17 19:20:57.837912 INFO::Removing potential empty rows and columns
2025-03-17 19:20:57.839154 INFO::Found 0 missing values.
2025-03-17 19:20:57.843953 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 19:20:57.844715 INFO::Done
2025-03-17 19:20:57.84539 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 19:20:57.849486 INFO::Starting hierarchical adjustment
2025-03-17 19:20:57.850377 INFO::Found 5 batches.
2025-03-17 19:20:57.850925 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 19:20:57.851548 INFO::Using default BPPARAM
2025-03-17 19:20:57.852084 INFO::Processing subtree level 1
2025-03-17 19:20:58.051381 INFO::Adjusting the last 2 batches sequentially
2025-03-17 19:20:58.060189 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 19:20:58.092664 INFO::Done
2025-03-17 19:20:58.093385 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 19:20:58.098339 INFO::ASW Batch was 0.376583275458924 prior to batch effect correction and is now -0.0816734560912016 .
2025-03-17 19:20:58.099843 INFO::ASW Label was 0.340148382085714 prior to batch effect correction and is now 0.731722503872098 .
2025-03-17 19:20:58.102176 INFO::Total function execution time is 0.26627516746521 s and adjustment time is 0.242402791976929 s ( 91.03 )
2025-03-17 19:20:58.103156 INFO::Formatting Data.
2025-03-17 19:20:58.104373 INFO::Replacing NaNs with NAs.
2025-03-17 19:20:58.105795 INFO::Removing potential empty rows and columns
2025-03-17 19:20:58.107514 INFO::Found 0 missing values.
2025-03-17 19:20:58.11433 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 19:20:58.115223 INFO::Done
2025-03-17 19:20:58.116012 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 19:20:58.119414 INFO::Starting hierarchical adjustment
2025-03-17 19:20:58.120196 INFO::Found 5 batches.
2025-03-17 19:20:58.120724 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 19:20:58.12132 INFO::Using default BPPARAM
2025-03-17 19:20:58.122188 INFO::Processing subtree level 1
2025-03-17 19:20:58.317146 INFO::Adjusting the last 2 batches sequentially
2025-03-17 19:20:58.346354 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 19:20:58.388278 INFO::Done
2025-03-17 19:20:58.389169 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 19:20:58.394439 INFO::ASW Batch was 0.376583275458924 prior to batch effect correction and is now -0.0816734560912016 .
2025-03-17 19:20:58.395962 INFO::ASW Label was 0.340148382085714 prior to batch effect correction and is now 0.731722503872098 .
2025-03-17 19:20:58.398882 INFO::Total function execution time is 0.295048952102661 s and adjustment time is 0.268202066421509 s ( 90.9 )
2025-03-17 19:20:58.422118 INFO::Formatting Data.
2025-03-17 19:20:58.422946 INFO::Replacing NaNs with NAs.
2025-03-17 19:20:58.423965 INFO::Removing potential empty rows and columns
2025-03-17 19:20:58.425484 INFO::Found 0 missing values.
2025-03-17 19:20:58.429889 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 19:20:58.430565 INFO::Done
2025-03-17 19:20:58.431088 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 19:20:58.434589 INFO::Starting hierarchical adjustment
2025-03-17 19:20:58.435736 INFO::Found 5 batches.
2025-03-17 19:20:58.436306 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 19:20:58.437123 INFO::Using default BPPARAM
2025-03-17 19:20:58.438158 INFO::Processing subtree level 1
2025-03-17 19:20:58.647721 INFO::Adjusting the last 2 batches sequentially
2025-03-17 19:20:58.655634 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 19:20:58.688703 INFO::Done
2025-03-17 19:20:58.689461 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 19:20:58.695106 INFO::ASW Batch was 0.447382476298513 prior to batch effect correction and is now 0.00666752738241865 .
2025-03-17 19:20:58.697408 INFO::ASW Label was 0.327137436677751 prior to batch effect correction and is now 0.773688045670254 .
2025-03-17 19:20:58.698878 INFO::Total function execution time is 0.27672290802002 s and adjustment time is 0.253098964691162 s ( 91.46 )
2025-03-17 19:20:58.700868 INFO::Formatting Data.
2025-03-17 19:20:58.701841 INFO::Replacing NaNs with NAs.
2025-03-17 19:20:58.703155 INFO::Removing potential empty rows and columns
2025-03-17 19:20:58.704715 INFO::Found 0 missing values.
2025-03-17 19:20:58.710229 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 19:20:58.710879 INFO::Done
2025-03-17 19:20:58.711389 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 19:20:58.714222 INFO::Starting hierarchical adjustment
2025-03-17 19:20:58.715024 INFO::Found 5 batches.
2025-03-17 19:20:58.715771 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 19:20:58.716378 INFO::Using default BPPARAM
2025-03-17 19:20:58.716883 INFO::Processing subtree level 1
2025-03-17 19:20:58.896643 INFO::Adjusting the last 2 batches sequentially
2025-03-17 19:20:58.903507 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 19:20:58.933483 INFO::Done
2025-03-17 19:20:58.935515 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 19:20:58.941798 INFO::ASW Batch was 0.447382476298513 prior to batch effect correction and is now 0.00666752738241865 .
2025-03-17 19:20:58.942586 INFO::ASW Label was 0.327137436677751 prior to batch effect correction and is now 0.773688045670254 .
2025-03-17 19:20:58.944959 INFO::Total function execution time is 0.243840932846069 s and adjustment time is 0.21863317489624 s ( 89.66 )
2025-03-17 19:20:58.96935 INFO::Formatting Data.
2025-03-17 19:20:58.970374 INFO::Replacing NaNs with NAs.
2025-03-17 19:20:58.971367 INFO::Removing potential empty rows and columns
2025-03-17 19:20:58.972325 INFO::Found 0 missing values.
2025-03-17 19:20:58.975837 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 19:20:58.976685 INFO::Done
2025-03-17 19:20:58.977481 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 19:20:58.981165 INFO::Starting hierarchical adjustment
2025-03-17 19:20:58.982232 INFO::Found 2 batches.
2025-03-17 19:20:58.982965 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 19:20:58.983836 INFO::Using default BPPARAM
2025-03-17 19:20:58.984571 INFO::Adjusting the last 2 batches sequentially
2025-03-17 19:20:58.985826 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 19:20:59.007555 INFO::Done
2025-03-17 19:20:59.008655 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 19:20:59.012228 INFO::ASW Batch was 0.533159451959545 prior to batch effect correction and is now -0.0253911708150124 .
2025-03-17 19:20:59.01326 INFO::ASW Label was 0.546300506082419 prior to batch effect correction and is now 0.931101059346778 .
2025-03-17 19:20:59.014542 INFO::Total function execution time is 0.0452730655670166 s and adjustment time is 0.0255279541015625 s ( 56.39 )
2025-03-17 19:20:59.015681 INFO::Formatting Data.
2025-03-17 19:20:59.016629 INFO::Replacing NaNs with NAs.
2025-03-17 19:20:59.017915 INFO::Removing potential empty rows and columns
2025-03-17 19:20:59.019326 INFO::Found 0 missing values.
2025-03-17 19:20:59.02346 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 19:20:59.024313 INFO::Done
2025-03-17 19:20:59.025055 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 19:20:59.028831 INFO::Starting hierarchical adjustment
2025-03-17 19:20:59.029894 INFO::Found 2 batches.
2025-03-17 19:20:59.030657 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 19:20:59.031504 INFO::Using default BPPARAM
2025-03-17 19:20:59.032328 INFO::Adjusting the last 2 batches sequentially
2025-03-17 19:20:59.034173 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 19:20:59.051174 INFO::Done
2025-03-17 19:20:59.05207 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 19:20:59.056282 INFO::ASW Batch was 0.533159451959545 prior to batch effect correction and is now -0.0253911708150124 .
2025-03-17 19:20:59.057211 INFO::ASW Label was 0.546300506082419 prior to batch effect correction and is now 0.931101059346778 .
2025-03-17 19:20:59.058319 INFO::Total function execution time is 0.0426599979400635 s and adjustment time is 0.021496057510376 s ( 50.39 )
2025-03-17 19:20:59.076432 INFO::Formatting Data.
2025-03-17 19:20:59.077782 INFO::Replacing NaNs with NAs.
2025-03-17 19:20:59.079337 INFO::Removing potential empty rows and columns
2025-03-17 19:20:59.080825 INFO::Found 0 missing values.
2025-03-17 19:20:59.084611 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 19:20:59.085491 INFO::Done
2025-03-17 19:20:59.086236 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 19:20:59.088924 INFO::Starting hierarchical adjustment
2025-03-17 19:20:59.089688 INFO::Found 2 batches.
2025-03-17 19:20:59.090168 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 19:20:59.090719 INFO::Using default BPPARAM
2025-03-17 19:20:59.091202 INFO::Adjusting the last 2 batches sequentially
2025-03-17 19:20:59.092083 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 19:20:59.127651 INFO::Done
2025-03-17 19:20:59.12864 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 19:20:59.131536 INFO::ASW Batch was -0.00437871063358104 prior to batch effect correction and is now -0.159324371359461 .
2025-03-17 19:20:59.132744 INFO::Total function execution time is 0.0564711093902588 s and adjustment time is 0.0380511283874512 s ( 67.38 )
2025-03-17 19:20:59.15225 INFO::Formatting Data.
2025-03-17 19:20:59.152993 INFO::Replacing NaNs with NAs.
2025-03-17 19:20:59.153899 INFO::Removing potential empty rows and columns
2025-03-17 19:20:59.155644 INFO::Found 0 missing values.
2025-03-17 19:20:59.156834 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.
2025-03-17 19:20:59.163433 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 19:20:59.164387 INFO::Done
2025-03-17 19:20:59.165187 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 19:20:59.169552 INFO::Starting hierarchical adjustment
2025-03-17 19:20:59.17068 INFO::Found 2 batches.
2025-03-17 19:20:59.171537 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 19:20:59.172415 INFO::Using default BPPARAM
2025-03-17 19:20:59.174419 INFO::Adjusting the last 2 batches sequentially
2025-03-17 19:20:59.17555 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 19:20:59.197588 INFO::Done
2025-03-17 19:20:59.198449 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 19:20:59.202314 INFO::ASW Batch was 0.682196457283062 prior to batch effect correction and is now -0.0232293382013619 .
2025-03-17 19:20:59.203312 INFO::ASW Label was 0.374222020845591 prior to batch effect correction and is now 0.893161927512476 .
2025-03-17 19:20:59.204539 INFO::Total function execution time is 0.0522968769073486 s and adjustment time is 0.0271289348602295 s ( 51.87 )
2025-03-17 19:20:59.20543 INFO::Formatting Data.
2025-03-17 19:20:59.206784 INFO::Replacing NaNs with NAs.
2025-03-17 19:20:59.208261 INFO::Removing potential empty rows and columns
2025-03-17 19:20:59.210155 INFO::Found 0 missing values.
2025-03-17 19:20:59.21176 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.
2025-03-17 19:20:59.218882 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 19:20:59.219604 INFO::Done
2025-03-17 19:20:59.22014 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 19:20:59.22321 INFO::Starting hierarchical adjustment
2025-03-17 19:20:59.224153 INFO::Found 2 batches.
2025-03-17 19:20:59.224838 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 19:20:59.225625 INFO::Using default BPPARAM
2025-03-17 19:20:59.226241 INFO::Adjusting the last 2 batches sequentially
2025-03-17 19:20:59.22725 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 19:20:59.250353 INFO::Done
2025-03-17 19:20:59.251367 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 19:20:59.255487 INFO::ASW Batch was 0.682196457283062 prior to batch effect correction and is now -0.0232293382013619 .
2025-03-17 19:20:59.256358 INFO::ASW Label was 0.374222020845591 prior to batch effect correction and is now 0.893161927512476 .
2025-03-17 19:20:59.257503 INFO::Total function execution time is 0.0520799160003662 s and adjustment time is 0.0263471603393555 s ( 50.59 )
2025-03-17 19:20:59.517867 INFO::Formatting Data.
2025-03-17 19:20:59.519534 INFO::Replacing NaNs with NAs.
2025-03-17 19:20:59.520811 INFO::Removing potential empty rows and columns
2025-03-17 19:20:59.522216 INFO::Found 0 missing values.
2025-03-17 19:20:59.526601 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 19:20:59.527183 INFO::Done
2025-03-17 19:20:59.527725 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 19:20:59.529612 INFO::Starting hierarchical adjustment
2025-03-17 19:20:59.530577 INFO::Found 3 batches.
2025-03-17 19:20:59.531398 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 19:20:59.532029 INFO::Using default BPPARAM
2025-03-17 19:20:59.532516 INFO::Processing subtree level 1
2025-03-17 19:20:59.665691 INFO::Adjusting the last 1 batches sequentially
2025-03-17 19:20:59.679702 INFO::Done
2025-03-17 19:20:59.681506 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 19:20:59.694306 INFO::ASW Batch was -0.101558527827763 prior to batch effect correction and is now -0.101558527827763 .
2025-03-17 19:20:59.698248 INFO::Total function execution time is 0.180380821228027 s and adjustment time is 0.149311065673828 s ( 82.78 )
2025-03-17 19:20:59.70003 INFO::Formatting Data.
2025-03-17 19:20:59.701097 INFO::Typecasting input to dataframe.
2025-03-17 19:20:59.702261 INFO::Replacing NaNs with NAs.
2025-03-17 19:20:59.703626 INFO::Removing potential empty rows and columns
2025-03-17 19:20:59.705831 INFO::Found 0 missing values.
2025-03-17 19:20:59.71184 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 19:20:59.712766 INFO::Done
2025-03-17 19:20:59.714054 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 19:20:59.716048 INFO::Starting hierarchical adjustment
2025-03-17 19:20:59.716917 INFO::Found 3 batches.
2025-03-17 19:20:59.717672 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 19:20:59.718513 INFO::Using default BPPARAM
2025-03-17 19:20:59.719764 INFO::Processing subtree level 1
2025-03-17 19:20:59.844122 INFO::Adjusting the last 1 batches sequentially
2025-03-17 19:20:59.872347 INFO::Done
2025-03-17 19:20:59.875065 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 19:20:59.885923 INFO::ASW Batch was -0.101558527827763 prior to batch effect correction and is now -0.101558527827763 .
2025-03-17 19:20:59.889447 INFO::Total function execution time is 0.188760995864868 s and adjustment time is 0.155150890350342 s ( 82.19 )
2025-03-17 19:20:59.916593 INFO::Formatting Data.
2025-03-17 19:20:59.917657 INFO::Typecasting input to dataframe.
2025-03-17 19:20:59.918897 INFO::Replacing NaNs with NAs.
2025-03-17 19:20:59.92074 INFO::Removing potential empty rows and columns
2025-03-17 19:20:59.922454 INFO::Found 0 missing values.
2025-03-17 19:20:59.926469 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 19:20:59.927267 INFO::Done
2025-03-17 19:20:59.927977 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 19:20:59.93066 INFO::Starting hierarchical adjustment
2025-03-17 19:20:59.931654 INFO::Found 3 batches.
2025-03-17 19:20:59.932415 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 19:20:59.9333 INFO::Using default BPPARAM
2025-03-17 19:20:59.934051 INFO::Processing subtree level 1
2025-03-17 19:21:00.070382 INFO::Adjusting the last 1 batches sequentially
2025-03-17 19:21:00.08777 INFO::Done
2025-03-17 19:21:00.090325 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 19:21:00.106688 INFO::ASW Batch was -0.0050621732938264 prior to batch effect correction and is now -0.0050621732938264 .
2025-03-17 19:21:00.110442 INFO::Total function execution time is 0.193681001663208 s and adjustment time is 0.156243085861206 s ( 80.67 )
2025-03-17 19:21:00.403916 INFO::Formatting Data.
2025-03-17 19:21:00.404882 INFO::Replacing NaNs with NAs.
2025-03-17 19:21:00.407092 INFO::Removing potential empty rows and columns
2025-03-17 19:21:00.412222 INFO::Found 1000 missing values.
2025-03-17 19:21:00.43322 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 19:21:00.434296 INFO::Done
2025-03-17 19:21:00.435218 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 19:21:00.4431 INFO::Starting hierarchical adjustment
2025-03-17 19:21:00.444596 INFO::Found 10 batches.
2025-03-17 19:21:00.445633 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 19:21:00.446536 INFO::Using default BPPARAM
2025-03-17 19:21:00.447098 INFO::Processing subtree level 1
2025-03-17 19:21:00.618958 INFO::Processing subtree level 2
2025-03-17 19:21:00.856407 INFO::Adjusting the last 1 batches sequentially
2025-03-17 19:21:00.87802 INFO::Done
2025-03-17 19:21:00.88066 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 19:21:00.897797 INFO::ASW Batch was 0.497750592736781 prior to batch effect correction and is now 0.497750592736781 .
2025-03-17 19:21:00.899699 INFO::ASW Label was 0.334464891620959 prior to batch effect correction and is now 0.334464891620959 .
2025-03-17 19:21:00.901838 INFO::Total function execution time is 0.498019933700562 s and adjustment time is 0.433794975280762 s ( 87.1 )
2025-03-17 19:21:00.902902 INFO::Formatting Data.
2025-03-17 19:21:00.903531 INFO::Replacing NaNs with NAs.
2025-03-17 19:21:00.905063 INFO::Removing potential empty rows and columns
2025-03-17 19:21:00.910621 INFO::Found 1000 missing values.
2025-03-17 19:21:00.934963 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 19:21:00.936462 INFO::Done
2025-03-17 19:21:00.937551 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 19:21:00.946676 INFO::Starting hierarchical adjustment
2025-03-17 19:21:00.947833 INFO::Found 10 batches.
2025-03-17 19:21:02.056496 INFO::Set up parallel execution backend with 2 workers
2025-03-17 19:21:02.057504 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-03-17 19:21:03.398369 INFO::Adjusting the last 2 batches sequentially
2025-03-17 19:21:03.40003 INFO::Adjusting sequential tree level 1 with 2 batches
2025-03-17 19:21:03.421018 INFO::Done
2025-03-17 19:21:03.421934 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 19:21:03.428456 INFO::ASW Batch was 0.497750592736781 prior to batch effect correction and is now 0.497750592736781 .
2025-03-17 19:21:03.429262 INFO::ASW Label was 0.334464891620959 prior to batch effect correction and is now 0.334464891620959 .
2025-03-17 19:21:03.430348 INFO::Total function execution time is 2.5274829864502 s and adjustment time is 2.47331213951111 s ( 97.86 )
2025-03-17 19:21:03.727868 INFO::Formatting Data.
2025-03-17 19:21:03.729063 INFO::Replacing NaNs with NAs.
2025-03-17 19:21:03.730528 INFO::Removing potential empty rows and columns
2025-03-17 19:21:03.732203 INFO::Found 0 missing values.
2025-03-17 19:21:03.737932 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 19:21:03.73889 INFO::Done
2025-03-17 19:21:03.739704 INFO::Acquiring quality metrics before batch effect correction.
2025-03-17 19:21:03.743733 INFO::Starting hierarchical adjustment
2025-03-17 19:21:03.744846 INFO::Found 3 batches.
2025-03-17 19:21:03.74588 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-03-17 19:21:03.746942 INFO::Using default BPPARAM
2025-03-17 19:21:03.747615 INFO::Processing subtree level 1
2025-03-17 19:21:03.935042 INFO::Adjusting the last 1 batches sequentially
2025-03-17 19:21:03.946052 INFO::Done
2025-03-17 19:21:03.947794 INFO::Acquiring quality metrics after batch effect correction.
2025-03-17 19:21:03.961558 INFO::ASW Batch was 0.285336900038704 prior to batch effect correction and is now -0.143744475111829 .
2025-03-17 19:21:03.962794 INFO::ASW Label was -0.173013647056886 prior to batch effect correction and is now -0.0774965958096285 .
2025-03-17 19:21:03.966646 INFO::Total function execution time is 0.237870931625366 s and adjustment time is 0.201433897018433 s ( 84.68 )
2025-03-17 19:21:04.18667 INFO::Formatting Data.
2025-03-17 19:21:04.188133 INFO::Replacing NaNs with NAs.
2025-03-17 19:21:04.189617 INFO::Removing potential empty rows and columns
2025-03-17 19:21:04.19141 INFO::Found 2 missing values.
2025-03-17 19:21:04.196164 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-03-17 19:21:04.197145 INFO::Done
2025-03-17 19:21:04.255717 INFO::Found NA in Reference column
2025-03-17 19:21:04.275273 INFO::Require at least two references per batch.
2025-03-17 19:21:04.305818 INFO::Formatting Data.
2025-03-17 19:21:04.306604 INFO::Recognized SummarizedExperiment
2025-03-17 19:21:04.307155 INFO::Typecasting input to dataframe.
2025-03-17 19:21:04.319378 INFO::Replacing NaNs with NAs.
2025-03-17 19:21:04.320958 INFO::Removing potential empty rows and columns
2025-03-17 19:21:04.325447 INFO::Found 0 missing values.
2025-03-17 19:21:04.333645 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 19:21:04.335015 INFO::Done
2025-03-17 19:21:04.355449 INFO::Formatting Data.
2025-03-17 19:21:04.356163 INFO::Recognized SummarizedExperiment
2025-03-17 19:21:04.356886 INFO::Typecasting input to dataframe.
2025-03-17 19:21:04.383487 INFO::Replacing NaNs with NAs.
2025-03-17 19:21:04.385336 INFO::Removing potential empty rows and columns
2025-03-17 19:21:04.390026 INFO::Found 0 missing values.
2025-03-17 19:21:04.402391 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 19:21:04.403082 INFO::Done
2025-03-17 19:21:04.42102 INFO::Formatting Data.
2025-03-17 19:21:04.421839 INFO::Recognized SummarizedExperiment
2025-03-17 19:21:04.422578 INFO::Typecasting input to dataframe.
2025-03-17 19:21:04.443611 INFO::Replacing NaNs with NAs.
2025-03-17 19:21:04.444924 INFO::Removing potential empty rows and columns
2025-03-17 19:21:04.446552 INFO::Found 0 missing values.
2025-03-17 19:21:04.447923 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.
2025-03-17 19:21:04.45364 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 19:21:04.454489 INFO::Done
2025-03-17 19:21:04.47461 INFO::Formatting Data.
2025-03-17 19:21:04.475844 INFO::Replacing NaNs with NAs.
2025-03-17 19:21:04.477014 INFO::Removing potential empty rows and columns
2025-03-17 19:21:04.478551 INFO::Found 0 missing values.
2025-03-17 19:21:04.482065 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 19:21:04.483115 INFO::Done
2025-03-17 19:21:04.504479 INFO::Formatting Data.
2025-03-17 19:21:04.505294 INFO::Replacing NaNs with NAs.
2025-03-17 19:21:04.50633 INFO::Removing potential empty rows and columns
2025-03-17 19:21:04.507935 INFO::Found 0 missing values.
2025-03-17 19:21:04.510616 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 19:21:04.511123 INFO::Done
2025-03-17 19:21:04.562121 INFO::Formatting Data.
2025-03-17 19:21:04.563476 INFO::Replacing NaNs with NAs.
2025-03-17 19:21:04.564852 INFO::Removing potential empty rows and columns
2025-03-17 19:21:04.56671 INFO::Found 1 missing values.
2025-03-17 19:21:04.57094 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 19:21:04.571984 INFO::Done
2025-03-17 19:21:04.630088 INFO::Formatting Data.
2025-03-17 19:21:04.631617 INFO::Replacing NaNs with NAs.
2025-03-17 19:21:04.632879 INFO::Removing potential empty rows and columns
2025-03-17 19:21:04.634302 INFO::Found 2 missing values.
2025-03-17 19:21:04.635754 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.
2025-03-17 19:21:04.638818 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-03-17 19:21:04.640533 INFO::Done
2025-03-17 19:21:04.660506 INFO::Formatting Data.
2025-03-17 19:21:04.66147 INFO::Replacing NaNs with NAs.
2025-03-17 19:21:04.662927 INFO::Removing potential empty rows and columns
2025-03-17 19:21:04.664084 INFO::Found 2 missing values.
2025-03-17 19:21:04.66682 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 19:21:04.667754 INFO::Done
2025-03-17 19:21:04.687285 INFO::Formatting Data.
2025-03-17 19:21:04.688252 INFO::Typecasting input to dataframe.
2025-03-17 19:21:04.689445 INFO::Replacing NaNs with NAs.
2025-03-17 19:21:04.690917 INFO::Removing potential empty rows and columns
2025-03-17 19:21:04.692474 INFO::Found 0 missing values.
2025-03-17 19:21:04.696861 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-03-17 19:21:04.69798 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
20.418 4.520 25.267
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 26.943 | 1.501 | 19.346 | |
| compute_asw | 0.026 | 0.001 | 0.028 | |
| count_existing | 0.015 | 0.001 | 0.017 | |
| generate_data_covariables | 0.013 | 0.000 | 0.013 | |
| generate_dataset | 0.011 | 0.001 | 0.012 | |