Yannis Schumann
| Snapshot Date: 2025-01-10 13:40 -0500 (Fri, 10 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 10fd252 |
| git_last_commit_date: 2024-11-20 10:26:09 -0500 (Wed, 20 Nov 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-11 11:41 -0500 (Sat, 11 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4760 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4479 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4443 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4398 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4391 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 159/2277 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.3.3 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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: 1.3.3 |
| 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_1.3.3.tar.gz |
| StartedAt: 2025-01-10 22:48:51 -0500 (Fri, 10 Jan 2025) |
| EndedAt: 2025-01-10 22:51:06 -0500 (Fri, 10 Jan 2025) |
| EllapsedTime: 135.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BERT.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### 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_1.3.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* 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 '1.3.3'
* 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 ... WARNING
Undocumented code objects:
'generate_truncated_dataset'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 9.21 0.52 18.81
* 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: 1 WARNING
See
'E:/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck/00check.log'
for details.
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' ... ** 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) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 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")
2025-01-10 22:49:55.077272 INFO::Formatting Data.
2025-01-10 22:49:55.080031 INFO::Replacing NaNs with NAs.
2025-01-10 22:49:55.092735 INFO::Removing potential empty rows and columns
2025-01-10 22:49:55.29309 INFO::Found 0 missing values.
2025-01-10 22:49:55.296426 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 22:49:55.297397 INFO::Done
2025-01-10 22:49:55.298276 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 22:49:55.312374 INFO::Starting hierarchical adjustment
2025-01-10 22:49:55.3135 INFO::Found 3 batches.
2025-01-10 22:49:55.314279 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 22:49:55.315592 INFO::Using default BPPARAM
2025-01-10 22:49:55.316321 INFO::Processing subtree level 1
2025-01-10 22:49:57.897684 INFO::Adjusting the last 1 batches sequentially
2025-01-10 22:49:57.899966 INFO::Done
2025-01-10 22:49:57.901272 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 22:49:57.904518 INFO::ASW Batch was -0.122937792850226 prior to batch effect correction and is now -0.122937792850226 .
2025-01-10 22:49:57.906228 INFO::Total function execution time is 2.82937693595886 s and adjustment time is 2.58662605285645 s ( 91.42 )
2025-01-10 22:49:57.925223 INFO::Formatting Data.
2025-01-10 22:49:57.926202 INFO::Replacing NaNs with NAs.
2025-01-10 22:49:57.927301 INFO::Removing potential empty rows and columns
2025-01-10 22:49:57.928559 INFO::Found 0 missing values.
2025-01-10 22:49:57.929746 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.
2025-01-10 22:49:57.941523 INFO::Formatting Data.
2025-01-10 22:49:57.942883 INFO::Replacing NaNs with NAs.
2025-01-10 22:49:57.944484 INFO::Removing potential empty rows and columns
2025-01-10 22:49:57.946188 INFO::Found 0 missing values.
2025-01-10 22:49:57.947781 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.
2025-01-10 22:49:57.972622 INFO::Formatting Data.
2025-01-10 22:49:57.974058 INFO::Replacing NaNs with NAs.
2025-01-10 22:49:57.975762 INFO::Removing potential empty rows and columns
2025-01-10 22:49:57.977508 INFO::Found 0 missing values.
2025-01-10 22:49:57.979163 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.
2025-01-10 22:49:57.985272 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 22:49:57.98652 INFO::Done
2025-01-10 22:49:57.987676 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 22:49:57.99076 INFO::Starting hierarchical adjustment
2025-01-10 22:49:57.992077 INFO::Found 2 batches.
2025-01-10 22:49:57.993248 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 22:49:57.994429 INFO::Using default BPPARAM
2025-01-10 22:49:57.995474 INFO::Adjusting the last 2 batches sequentially
2025-01-10 22:49:57.997115 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-10 22:49:58.02319 INFO::Done
2025-01-10 22:49:58.024484 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 22:49:58.02772 INFO::ASW Batch was -0.0138480396141772 prior to batch effect correction and is now -0.127723479143307 .
2025-01-10 22:49:58.029224 INFO::Total function execution time is 0.0566549301147461 s and adjustment time is 0.0312809944152832 s ( 55.21 )
2025-01-10 22:49:58.033756 INFO::Formatting Data.
2025-01-10 22:49:58.035157 INFO::Replacing NaNs with NAs.
2025-01-10 22:49:58.048643 INFO::Formatting Data.
2025-01-10 22:49:58.050312 INFO::Replacing NaNs with NAs.
2025-01-10 22:49:58.052349 INFO::Removing potential empty rows and columns
2025-01-10 22:49:58.054446 INFO::Found 0 missing values.
2025-01-10 22:49:58.059833 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 22:49:58.061279 INFO::Done
2025-01-10 22:49:58.062677 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 22:49:58.066459 INFO::Starting hierarchical adjustment
2025-01-10 22:49:58.068183 INFO::Found 2 batches.
2025-01-10 22:49:58.069539 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 22:49:58.071069 INFO::Using default BPPARAM
2025-01-10 22:49:58.072379 INFO::Adjusting the last 2 batches sequentially
2025-01-10 22:49:58.074419 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-10 22:49:58.100812 INFO::Done
2025-01-10 22:49:58.102445 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 22:49:58.106699 INFO::ASW Batch was 0.0117847925825791 prior to batch effect correction and is now -0.106293848251069 .
2025-01-10 22:49:58.108618 INFO::Total function execution time is 0.0599980354309082 s and adjustment time is 0.0328590869903564 s ( 54.77 )
2025-01-10 22:49:58.110006 INFO::Formatting Data.
2025-01-10 22:49:58.110871 INFO::Replacing NaNs with NAs.
2025-01-10 22:49:58.111901 INFO::Removing potential empty rows and columns
2025-01-10 22:49:58.11309 INFO::Found 0 missing values.
2025-01-10 22:49:58.115836 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 22:49:58.116592 INFO::Done
2025-01-10 22:49:58.117685 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 22:49:58.120948 INFO::Starting hierarchical adjustment
2025-01-10 22:49:58.122376 INFO::Found 2 batches.
2025-01-10 22:49:58.123539 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 22:49:58.124856 INFO::Using default BPPARAM
2025-01-10 22:49:58.126095 INFO::Adjusting the last 2 batches sequentially
2025-01-10 22:49:58.127364 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-10 22:49:58.140278 INFO::Done
2025-01-10 22:49:58.141177 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 22:49:58.143358 INFO::ASW Batch was 0.0117847925825791 prior to batch effect correction and is now -0.106293848251069 .
2025-01-10 22:49:58.144388 INFO::Total function execution time is 0.0344400405883789 s and adjustment time is 0.018143892288208 s ( 52.68 )
2025-01-10 22:50:01.106913 INFO::Formatting Data.
2025-01-10 22:50:01.10847 INFO::Recognized SummarizedExperiment
2025-01-10 22:50:01.109741 INFO::Typecasting input to dataframe.
2025-01-10 22:50:01.157906 INFO::Replacing NaNs with NAs.
2025-01-10 22:50:01.160272 INFO::Removing potential empty rows and columns
2025-01-10 22:50:01.166597 INFO::Found 0 missing values.
2025-01-10 22:50:01.176091 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 22:50:01.17754 INFO::Done
2025-01-10 22:50:01.178738 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 22:50:01.184672 INFO::Starting hierarchical adjustment
2025-01-10 22:50:01.186132 INFO::Found 2 batches.
2025-01-10 22:50:01.187304 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 22:50:01.189193 INFO::Using default BPPARAM
2025-01-10 22:50:01.190303 INFO::Adjusting the last 2 batches sequentially
2025-01-10 22:50:01.192166 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-10 22:50:01.263145 INFO::Done
2025-01-10 22:50:01.264512 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 22:50:01.269727 INFO::ASW Batch was -0.00142799090483528 prior to batch effect correction and is now -0.0917787511961666 .
2025-01-10 22:50:01.270941 INFO::Total function execution time is 0.164543867111206 s and adjustment time is 0.0772168636322021 s ( 46.93 )
2025-01-10 22:50:01.30196 INFO::Formatting Data.
2025-01-10 22:50:01.303503 INFO::Recognized SummarizedExperiment
2025-01-10 22:50:01.304827 INFO::Typecasting input to dataframe.
2025-01-10 22:50:01.320338 INFO::Replacing NaNs with NAs.
2025-01-10 22:50:01.322818 INFO::Removing potential empty rows and columns
2025-01-10 22:50:01.329002 INFO::Found 0 missing values.
2025-01-10 22:50:01.340318 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 22:50:01.341898 INFO::Done
2025-01-10 22:50:01.343278 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 22:50:01.350196 INFO::Starting hierarchical adjustment
2025-01-10 22:50:01.352002 INFO::Found 2 batches.
2025-01-10 22:50:01.353445 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 22:50:01.354938 INFO::Using default BPPARAM
2025-01-10 22:50:01.356285 INFO::Adjusting the last 2 batches sequentially
2025-01-10 22:50:01.358482 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-10 22:50:01.397358 INFO::Done
2025-01-10 22:50:01.398907 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 22:50:01.405709 INFO::ASW Batch was 0.00471962889351801 prior to batch effect correction and is now 0.00471962889351801 .
2025-01-10 22:50:01.407655 INFO::Total function execution time is 0.105664968490601 s and adjustment time is 0.0456061363220215 s ( 43.16 )
2025-01-10 22:50:01.441837 INFO::Formatting Data.
2025-01-10 22:50:01.44349 INFO::Replacing NaNs with NAs.
2025-01-10 22:50:01.445425 INFO::Removing potential empty rows and columns
2025-01-10 22:50:01.447444 INFO::Found 0 missing values.
2025-01-10 22:50:01.452455 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 22:50:01.45382 INFO::Done
2025-01-10 22:50:01.455124 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 22:50:01.458586 INFO::Starting hierarchical adjustment
2025-01-10 22:50:01.460124 INFO::Found 3 batches.
2025-01-10 22:50:01.461397 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 22:50:01.462722 INFO::Using default BPPARAM
2025-01-10 22:50:01.463975 INFO::Processing subtree level 1
2025-01-10 22:50:12.005126 INFO::Adjusting the last 1 batches sequentially
2025-01-10 22:50:12.007371 INFO::Done
2025-01-10 22:50:12.008734 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 22:50:12.012168 INFO::ASW Batch was -0.000125048515286126 prior to batch effect correction and is now -0.148266564406207 .
2025-01-10 22:50:12.01369 INFO::Total function execution time is 10.5720319747925 s and adjustment time is 10.5474500656128 s ( 99.77 )
2025-01-10 22:50:12.038559 INFO::Skipping initial DF formatting
2025-01-10 22:50:12.039572 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 22:50:12.043965 INFO::Starting hierarchical adjustment
2025-01-10 22:50:12.045013 INFO::Found 5 batches.
2025-01-10 22:50:12.045773 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 22:50:12.046538 INFO::Using default BPPARAM
2025-01-10 22:50:12.047229 INFO::Processing subtree level 1
2025-01-10 22:50:15.134024 INFO::Adjusting the last 2 batches sequentially
2025-01-10 22:50:15.136308 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-10 22:50:15.161956 INFO::Done
2025-01-10 22:50:15.162926 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 22:50:15.167429 INFO::ASW Batch was 0.471232814200128 prior to batch effect correction and is now 0.471232814200128 .
2025-01-10 22:50:15.168293 INFO::ASW Label was 0.383319114060577 prior to batch effect correction and is now 0.383319114060577 .
2025-01-10 22:50:15.169356 INFO::Total function execution time is 3.13094305992126 s and adjustment time is 3.11708784103394 s ( 99.56 )
2025-01-10 22:50:15.191615 INFO::Formatting Data.
2025-01-10 22:50:15.193188 INFO::Replacing NaNs with NAs.
2025-01-10 22:50:15.19504 INFO::Removing potential empty rows and columns
2025-01-10 22:50:15.196909 INFO::Found 0 missing values.
2025-01-10 22:50:15.203088 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 22:50:15.204451 INFO::Done
2025-01-10 22:50:15.20579 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 22:50:15.210777 INFO::Starting hierarchical adjustment
2025-01-10 22:50:15.212389 INFO::Found 5 batches.
2025-01-10 22:50:15.21362 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 22:50:15.214993 INFO::Using default BPPARAM
2025-01-10 22:50:15.21626 INFO::Processing subtree level 1
2025-01-10 22:50:18.541378 INFO::Adjusting the last 2 batches sequentially
2025-01-10 22:50:18.543036 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-10 22:50:18.55496 INFO::Done
2025-01-10 22:50:18.555835 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 22:50:18.558981 INFO::ASW Batch was 0.137496355062451 prior to batch effect correction and is now -0.0800668228969167 .
2025-01-10 22:50:18.559772 INFO::ASW Label was 0.599398970205779 prior to batch effect correction and is now 0.907876593973588 .
2025-01-10 22:50:18.560746 INFO::Total function execution time is 3.3693368434906 s and adjustment time is 3.34283590316772 s ( 99.21 )
2025-01-10 22:50:18.561752 INFO::Formatting Data.
2025-01-10 22:50:18.562565 INFO::Replacing NaNs with NAs.
2025-01-10 22:50:18.56362 INFO::Removing potential empty rows and columns
2025-01-10 22:50:18.564705 INFO::Found 0 missing values.
2025-01-10 22:50:18.568293 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 22:50:18.569051 INFO::Done
2025-01-10 22:50:18.56975 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 22:50:18.573173 INFO::Starting hierarchical adjustment
2025-01-10 22:50:18.574092 INFO::Found 5 batches.
2025-01-10 22:50:18.574771 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 22:50:18.575504 INFO::Using default BPPARAM
2025-01-10 22:50:18.576169 INFO::Processing subtree level 1
2025-01-10 22:50:21.616438 INFO::Adjusting the last 2 batches sequentially
2025-01-10 22:50:21.618308 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-10 22:50:21.630187 INFO::Done
2025-01-10 22:50:21.631084 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 22:50:21.634101 INFO::ASW Batch was 0.137496355062451 prior to batch effect correction and is now -0.0800668228969167 .
2025-01-10 22:50:21.63508 INFO::ASW Label was 0.599398970205779 prior to batch effect correction and is now 0.907876593973588 .
2025-01-10 22:50:21.636141 INFO::Total function execution time is 3.07439708709717 s and adjustment time is 3.05620098114014 s ( 99.41 )
2025-01-10 22:50:21.652803 INFO::Formatting Data.
2025-01-10 22:50:21.653793 INFO::Replacing NaNs with NAs.
2025-01-10 22:50:21.654901 INFO::Removing potential empty rows and columns
2025-01-10 22:50:21.655975 INFO::Found 0 missing values.
2025-01-10 22:50:21.659289 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 22:50:21.660005 INFO::Done
2025-01-10 22:50:21.660722 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 22:50:21.663888 INFO::Starting hierarchical adjustment
2025-01-10 22:50:21.664832 INFO::Found 5 batches.
2025-01-10 22:50:21.665566 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 22:50:21.66634 INFO::Using default BPPARAM
2025-01-10 22:50:21.667028 INFO::Processing subtree level 1
2025-01-10 22:50:24.952211 INFO::Adjusting the last 2 batches sequentially
2025-01-10 22:50:24.954282 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-10 22:50:24.973462 INFO::Done
2025-01-10 22:50:24.974793 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 22:50:24.979253 INFO::ASW Batch was 0.367881318439247 prior to batch effect correction and is now -0.0865133602511676 .
2025-01-10 22:50:24.980481 INFO::ASW Label was 0.39832333110872 prior to batch effect correction and is now 0.879770791186756 .
2025-01-10 22:50:24.981993 INFO::Total function execution time is 3.32922291755676 s and adjustment time is 3.30870699882507 s ( 99.38 )
2025-01-10 22:50:24.983473 INFO::Formatting Data.
2025-01-10 22:50:24.984716 INFO::Replacing NaNs with NAs.
2025-01-10 22:50:24.986409 INFO::Removing potential empty rows and columns
2025-01-10 22:50:24.988218 INFO::Found 0 missing values.
2025-01-10 22:50:24.994008 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 22:50:24.995242 INFO::Done
2025-01-10 22:50:24.996396 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 22:50:25.000895 INFO::Starting hierarchical adjustment
2025-01-10 22:50:25.002302 INFO::Found 5 batches.
2025-01-10 22:50:25.003451 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 22:50:25.004657 INFO::Using default BPPARAM
2025-01-10 22:50:25.005752 INFO::Processing subtree level 1
2025-01-10 22:50:27.938531 INFO::Adjusting the last 2 batches sequentially
2025-01-10 22:50:27.940454 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-10 22:50:27.958853 INFO::Done
2025-01-10 22:50:27.960172 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 22:50:27.964666 INFO::ASW Batch was 0.367881318439247 prior to batch effect correction and is now -0.0865133602511676 .
2025-01-10 22:50:27.965905 INFO::ASW Label was 0.39832333110872 prior to batch effect correction and is now 0.879770791186756 .
2025-01-10 22:50:27.967356 INFO::Total function execution time is 2.98389601707458 s and adjustment time is 2.95672798156738 s ( 99.09 )
2025-01-10 22:50:27.990452 INFO::Formatting Data.
2025-01-10 22:50:27.991918 INFO::Replacing NaNs with NAs.
2025-01-10 22:50:27.993575 INFO::Removing potential empty rows and columns
2025-01-10 22:50:27.995322 INFO::Found 0 missing values.
2025-01-10 22:50:27.999241 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 22:50:28.000297 INFO::Done
2025-01-10 22:50:28.001363 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 22:50:28.005824 INFO::Starting hierarchical adjustment
2025-01-10 22:50:28.007196 INFO::Found 2 batches.
2025-01-10 22:50:28.008326 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 22:50:28.00953 INFO::Using default BPPARAM
2025-01-10 22:50:28.01064 INFO::Adjusting the last 2 batches sequentially
2025-01-10 22:50:28.012314 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-10 22:50:28.03101 INFO::Done
2025-01-10 22:50:28.032367 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 22:50:28.036901 INFO::ASW Batch was 0.7712463475191 prior to batch effect correction and is now -0.0278668752366685 .
2025-01-10 22:50:28.038191 INFO::ASW Label was 0.27464643691735 prior to batch effect correction and is now 0.898177709953415 .
2025-01-10 22:50:28.039671 INFO::Total function execution time is 0.0493099689483643 s and adjustment time is 0.0240030288696289 s ( 48.68 )
2025-01-10 22:50:28.041162 INFO::Formatting Data.
2025-01-10 22:50:28.042355 INFO::Replacing NaNs with NAs.
2025-01-10 22:50:28.043859 INFO::Removing potential empty rows and columns
2025-01-10 22:50:28.045461 INFO::Found 0 missing values.
2025-01-10 22:50:28.049378 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 22:50:28.050502 INFO::Done
2025-01-10 22:50:28.051595 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 22:50:28.054789 INFO::Starting hierarchical adjustment
2025-01-10 22:50:28.055736 INFO::Found 2 batches.
2025-01-10 22:50:28.056548 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 22:50:28.057608 INFO::Using default BPPARAM
2025-01-10 22:50:28.058482 INFO::Adjusting the last 2 batches sequentially
2025-01-10 22:50:28.05977 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-10 22:50:28.072504 INFO::Done
2025-01-10 22:50:28.073402 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 22:50:28.076464 INFO::ASW Batch was 0.7712463475191 prior to batch effect correction and is now -0.0278668752366685 .
2025-01-10 22:50:28.077254 INFO::ASW Label was 0.27464643691735 prior to batch effect correction and is now 0.898177709953415 .
2025-01-10 22:50:28.0782 INFO::Total function execution time is 0.0371429920196533 s and adjustment time is 0.0168850421905518 s ( 45.46 )
2025-01-10 22:50:28.094157 INFO::Formatting Data.
2025-01-10 22:50:28.095758 INFO::Replacing NaNs with NAs.
2025-01-10 22:50:28.097536 INFO::Removing potential empty rows and columns
2025-01-10 22:50:28.099234 INFO::Found 0 missing values.
2025-01-10 22:50:28.10275 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 22:50:28.103988 INFO::Done
2025-01-10 22:50:28.105159 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 22:50:28.108306 INFO::Starting hierarchical adjustment
2025-01-10 22:50:28.109776 INFO::Found 2 batches.
2025-01-10 22:50:28.110981 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 22:50:28.11228 INFO::Using default BPPARAM
2025-01-10 22:50:28.113431 INFO::Adjusting the last 2 batches sequentially
2025-01-10 22:50:28.115118 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-10 22:50:28.150365 INFO::Done
2025-01-10 22:50:28.151816 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 22:50:28.155077 INFO::ASW Batch was 0.143571872772016 prior to batch effect correction and is now -0.0724286191790026 .
2025-01-10 22:50:28.1567 INFO::Total function execution time is 0.0626518726348877 s and adjustment time is 0.0407600402832031 s ( 65.06 )
2025-01-10 22:50:28.176652 INFO::Formatting Data.
2025-01-10 22:50:28.178181 INFO::Replacing NaNs with NAs.
2025-01-10 22:50:28.179903 INFO::Removing potential empty rows and columns
2025-01-10 22:50:28.181316 INFO::Found 0 missing values.
2025-01-10 22:50:28.182634 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.
2025-01-10 22:50:28.186449 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 22:50:28.187198 INFO::Done
2025-01-10 22:50:28.188002 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 22:50:28.191597 INFO::Starting hierarchical adjustment
2025-01-10 22:50:28.192512 INFO::Found 2 batches.
2025-01-10 22:50:28.193268 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 22:50:28.194036 INFO::Using default BPPARAM
2025-01-10 22:50:28.194842 INFO::Adjusting the last 2 batches sequentially
2025-01-10 22:50:28.196138 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-10 22:50:28.21036 INFO::Done
2025-01-10 22:50:28.2113 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 22:50:28.214404 INFO::ASW Batch was 0.371440556056552 prior to batch effect correction and is now -0.0106894216172827 .
2025-01-10 22:50:28.215218 INFO::ASW Label was 0.731915591212793 prior to batch effect correction and is now 0.951553804427604 .
2025-01-10 22:50:28.216167 INFO::Total function execution time is 0.0396938323974609 s and adjustment time is 0.0179281234741211 s ( 45.17 )
2025-01-10 22:50:28.217154 INFO::Formatting Data.
2025-01-10 22:50:28.217965 INFO::Replacing NaNs with NAs.
2025-01-10 22:50:28.219059 INFO::Removing potential empty rows and columns
2025-01-10 22:50:28.220184 INFO::Found 0 missing values.
2025-01-10 22:50:28.221334 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.
2025-01-10 22:50:28.225586 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 22:50:28.226448 INFO::Done
2025-01-10 22:50:28.227175 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 22:50:28.230353 INFO::Starting hierarchical adjustment
2025-01-10 22:50:28.231299 INFO::Found 2 batches.
2025-01-10 22:50:28.232029 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 22:50:28.232886 INFO::Using default BPPARAM
2025-01-10 22:50:28.23368 INFO::Adjusting the last 2 batches sequentially
2025-01-10 22:50:28.234976 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-10 22:50:28.258523 INFO::Done
2025-01-10 22:50:28.26001 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 22:50:28.265031 INFO::ASW Batch was 0.371440556056552 prior to batch effect correction and is now -0.0106894216172827 .
2025-01-10 22:50:28.266479 INFO::ASW Label was 0.731915591212793 prior to batch effect correction and is now 0.951553804427604 .
2025-01-10 22:50:28.26811 INFO::Total function execution time is 0.0508580207824707 s and adjustment time is 0.027289867401123 s ( 53.66 )
2025-01-10 22:50:28.544304 INFO::Formatting Data.
2025-01-10 22:50:28.545763 INFO::Replacing NaNs with NAs.
2025-01-10 22:50:28.54724 INFO::Removing potential empty rows and columns
2025-01-10 22:50:28.548802 INFO::Found 0 missing values.
2025-01-10 22:50:28.552557 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 22:50:28.553589 INFO::Done
2025-01-10 22:50:28.554618 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 22:50:28.557799 INFO::Starting hierarchical adjustment
2025-01-10 22:50:28.559144 INFO::Found 3 batches.
2025-01-10 22:50:28.560234 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 22:50:28.561511 INFO::Using default BPPARAM
2025-01-10 22:50:28.562688 INFO::Processing subtree level 1
2025-01-10 22:50:31.473351 INFO::Adjusting the last 1 batches sequentially
2025-01-10 22:50:31.475693 INFO::Done
2025-01-10 22:50:31.476991 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 22:50:31.480329 INFO::ASW Batch was -0.0242797761602374 prior to batch effect correction and is now -0.0242797761602374 .
2025-01-10 22:50:31.481956 INFO::Total function execution time is 2.93773818016052 s and adjustment time is 2.91670393943787 s ( 99.28 )
2025-01-10 22:50:31.483829 INFO::Formatting Data.
2025-01-10 22:50:31.485193 INFO::Typecasting input to dataframe.
2025-01-10 22:50:31.486706 INFO::Replacing NaNs with NAs.
2025-01-10 22:50:31.488298 INFO::Removing potential empty rows and columns
2025-01-10 22:50:31.490074 INFO::Found 0 missing values.
2025-01-10 22:50:31.494637 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 22:50:31.49586 INFO::Done
2025-01-10 22:50:31.497048 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 22:50:31.500396 INFO::Starting hierarchical adjustment
2025-01-10 22:50:31.501804 INFO::Found 3 batches.
2025-01-10 22:50:31.503034 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 22:50:31.504351 INFO::Using default BPPARAM
2025-01-10 22:50:31.505544 INFO::Processing subtree level 1
2025-01-10 22:50:34.383357 INFO::Adjusting the last 1 batches sequentially
2025-01-10 22:50:34.385613 INFO::Done
2025-01-10 22:50:34.386964 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 22:50:34.390348 INFO::ASW Batch was -0.0242797761602374 prior to batch effect correction and is now -0.0242797761602374 .
2025-01-10 22:50:34.392021 INFO::Total function execution time is 2.90820503234863 s and adjustment time is 2.88399410247803 s ( 99.17 )
2025-01-10 22:50:34.416099 INFO::Formatting Data.
2025-01-10 22:50:34.417639 INFO::Typecasting input to dataframe.
2025-01-10 22:50:34.419287 INFO::Replacing NaNs with NAs.
2025-01-10 22:50:34.420508 INFO::Removing potential empty rows and columns
2025-01-10 22:50:34.421772 INFO::Found 0 missing values.
2025-01-10 22:50:34.4261 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 22:50:34.427305 INFO::Done
2025-01-10 22:50:34.428476 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 22:50:34.431678 INFO::Starting hierarchical adjustment
2025-01-10 22:50:34.432973 INFO::Found 3 batches.
2025-01-10 22:50:34.434095 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 22:50:34.435335 INFO::Using default BPPARAM
2025-01-10 22:50:34.436484 INFO::Processing subtree level 1
2025-01-10 22:50:37.140558 INFO::Adjusting the last 1 batches sequentially
2025-01-10 22:50:37.142882 INFO::Done
2025-01-10 22:50:37.144266 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 22:50:37.147711 INFO::ASW Batch was -0.0711409570652735 prior to batch effect correction and is now -0.0711409570652735 .
2025-01-10 22:50:37.149319 INFO::Total function execution time is 2.73331212997437 s and adjustment time is 2.71008086204529 s ( 99.15 )
2025-01-10 22:50:40.08657 INFO::Formatting Data.
2025-01-10 22:50:40.088375 INFO::Replacing NaNs with NAs.
2025-01-10 22:50:40.090771 INFO::Removing potential empty rows and columns
2025-01-10 22:50:40.094738 INFO::Found 1000 missing values.
2025-01-10 22:50:40.11965 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 22:50:40.121161 INFO::Done
2025-01-10 22:50:40.122559 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 22:50:40.132958 INFO::Starting hierarchical adjustment
2025-01-10 22:50:40.134678 INFO::Found 10 batches.
2025-01-10 22:50:40.135899 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 22:50:40.137201 INFO::Using default BPPARAM
2025-01-10 22:50:40.138359 INFO::Processing subtree level 1
2025-01-10 22:50:43.187921 INFO::Processing subtree level 2
2025-01-10 22:50:46.04941 INFO::Adjusting the last 1 batches sequentially
2025-01-10 22:50:46.05181 INFO::Done
2025-01-10 22:50:46.053008 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 22:50:46.061564 INFO::ASW Batch was 0.53811987411158 prior to batch effect correction and is now 0.53811987411158 .
2025-01-10 22:50:46.06284 INFO::ASW Label was 0.306802577661733 prior to batch effect correction and is now 0.306802577661733 .
2025-01-10 22:50:46.064412 INFO::Total function execution time is 5.97803497314453 s and adjustment time is 5.91742515563965 s ( 98.99 )
2025-01-10 22:50:46.06581 INFO::Formatting Data.
2025-01-10 22:50:46.066996 INFO::Replacing NaNs with NAs.
2025-01-10 22:50:46.068821 INFO::Removing potential empty rows and columns
2025-01-10 22:50:46.071618 INFO::Found 1000 missing values.
2025-01-10 22:50:46.092776 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 22:50:46.094224 INFO::Done
2025-01-10 22:50:46.095008 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 22:50:46.101134 INFO::Starting hierarchical adjustment
2025-01-10 22:50:46.102132 INFO::Found 10 batches.
2025-01-10 22:50:46.825646 INFO::Set up parallel execution backend with 2 workers
2025-01-10 22:50:46.827082 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-01-10 22:50:49.899451 INFO::Adjusting the last 2 batches sequentially
2025-01-10 22:50:49.901663 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-10 22:50:49.925586 INFO::Done
2025-01-10 22:50:49.927004 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 22:50:49.936582 INFO::ASW Batch was 0.53811987411158 prior to batch effect correction and is now 0.53811987411158 .
2025-01-10 22:50:49.938036 INFO::ASW Label was 0.306802577661733 prior to batch effect correction and is now 0.306802577661733 .
2025-01-10 22:50:49.939595 INFO::Total function execution time is 3.87379789352417 s and adjustment time is 3.82351994514465 s ( 98.7 )
2025-01-10 22:50:52.923258 INFO::Formatting Data.
2025-01-10 22:50:52.924278 INFO::Replacing NaNs with NAs.
2025-01-10 22:50:52.925375 INFO::Removing potential empty rows and columns
2025-01-10 22:50:52.926538 INFO::Found 0 missing values.
2025-01-10 22:50:52.929751 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 22:50:52.930528 INFO::Done
2025-01-10 22:50:52.931328 INFO::Acquiring quality metrics before batch effect correction.
2025-01-10 22:50:52.934225 INFO::Starting hierarchical adjustment
2025-01-10 22:50:52.935137 INFO::Found 3 batches.
2025-01-10 22:50:52.935925 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-10 22:50:52.936987 INFO::Using default BPPARAM
2025-01-10 22:50:52.937832 INFO::Processing subtree level 1
2025-01-10 22:50:55.969758 INFO::Adjusting the last 1 batches sequentially
2025-01-10 22:50:55.972176 INFO::Done
2025-01-10 22:50:55.973553 INFO::Acquiring quality metrics after batch effect correction.
2025-01-10 22:50:55.977987 INFO::ASW Batch was 0.169024410741479 prior to batch effect correction and is now -0.154514889068598 .
2025-01-10 22:50:55.979328 INFO::ASW Label was -0.178297905905234 prior to batch effect correction and is now 0.157395963877814 .
2025-01-10 22:50:55.980923 INFO::Total function execution time is 3.05768084526062 s and adjustment time is 3.03711009025574 s ( 99.33 )
2025-01-10 22:50:56.133738 INFO::Formatting Data.
2025-01-10 22:50:56.134837 INFO::Replacing NaNs with NAs.
2025-01-10 22:50:56.136014 INFO::Removing potential empty rows and columns
2025-01-10 22:50:56.13733 INFO::Found 2 missing values.
2025-01-10 22:50:56.140179 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-01-10 22:50:56.141405 INFO::Done
2025-01-10 22:50:56.182636 INFO::Found NA in Reference column
2025-01-10 22:50:56.196143 INFO::Require at least two references per batch.
2025-01-10 22:50:56.216942 INFO::Formatting Data.
2025-01-10 22:50:56.217911 INFO::Recognized SummarizedExperiment
2025-01-10 22:50:56.218656 INFO::Typecasting input to dataframe.
2025-01-10 22:50:56.226579 INFO::Replacing NaNs with NAs.
2025-01-10 22:50:56.227905 INFO::Removing potential empty rows and columns
2025-01-10 22:50:56.230634 INFO::Found 0 missing values.
2025-01-10 22:50:56.235974 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 22:50:56.236794 INFO::Done
2025-01-10 22:50:56.25182 INFO::Formatting Data.
2025-01-10 22:50:56.252742 INFO::Recognized SummarizedExperiment
2025-01-10 22:50:56.25349 INFO::Typecasting input to dataframe.
2025-01-10 22:50:56.267821 INFO::Replacing NaNs with NAs.
2025-01-10 22:50:56.269166 INFO::Removing potential empty rows and columns
2025-01-10 22:50:56.271924 INFO::Found 0 missing values.
2025-01-10 22:50:56.281005 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 22:50:56.281889 INFO::Done
2025-01-10 22:50:56.297836 INFO::Formatting Data.
2025-01-10 22:50:56.299257 INFO::Recognized SummarizedExperiment
2025-01-10 22:50:56.300454 INFO::Typecasting input to dataframe.
2025-01-10 22:50:56.3227 INFO::Replacing NaNs with NAs.
2025-01-10 22:50:56.324499 INFO::Removing potential empty rows and columns
2025-01-10 22:50:56.326335 INFO::Found 0 missing values.
2025-01-10 22:50:56.328048 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.
2025-01-10 22:50:56.334206 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 22:50:56.335465 INFO::Done
2025-01-10 22:50:56.355986 INFO::Formatting Data.
2025-01-10 22:50:56.357509 INFO::Replacing NaNs with NAs.
2025-01-10 22:50:56.359393 INFO::Removing potential empty rows and columns
2025-01-10 22:50:56.36137 INFO::Found 0 missing values.
2025-01-10 22:50:56.366007 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 22:50:56.367289 INFO::Done
2025-01-10 22:50:56.389395 INFO::Formatting Data.
2025-01-10 22:50:56.390898 INFO::Replacing NaNs with NAs.
2025-01-10 22:50:56.392584 INFO::Removing potential empty rows and columns
2025-01-10 22:50:56.394338 INFO::Found 0 missing values.
2025-01-10 22:50:56.39871 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 22:50:56.39995 INFO::Done
2025-01-10 22:50:56.457535 INFO::Formatting Data.
2025-01-10 22:50:56.459112 INFO::Replacing NaNs with NAs.
2025-01-10 22:50:56.461076 INFO::Removing potential empty rows and columns
2025-01-10 22:50:56.46315 INFO::Found 1 missing values.
2025-01-10 22:50:56.467133 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 22:50:56.468421 INFO::Done
2025-01-10 22:50:56.506143 INFO::Formatting Data.
2025-01-10 22:50:56.507702 INFO::Replacing NaNs with NAs.
2025-01-10 22:50:56.509374 INFO::Removing potential empty rows and columns
2025-01-10 22:50:56.511102 INFO::Found 2 missing values.
2025-01-10 22:50:56.512833 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.
2025-01-10 22:50:56.516399 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-01-10 22:50:56.517582 INFO::Done
2025-01-10 22:50:56.538047 INFO::Formatting Data.
2025-01-10 22:50:56.539626 INFO::Replacing NaNs with NAs.
2025-01-10 22:50:56.541324 INFO::Removing potential empty rows and columns
2025-01-10 22:50:56.543056 INFO::Found 2 missing values.
2025-01-10 22:50:56.545755 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 22:50:56.546927 INFO::Done
2025-01-10 22:50:56.568922 INFO::Formatting Data.
2025-01-10 22:50:56.570468 INFO::Typecasting input to dataframe.
2025-01-10 22:50:56.572132 INFO::Replacing NaNs with NAs.
2025-01-10 22:50:56.573795 INFO::Removing potential empty rows and columns
2025-01-10 22:50:56.57551 INFO::Found 0 missing values.
2025-01-10 22:50:56.579775 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-10 22:50:56.580607 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 138 ]
>
> proc.time()
user system elapsed
29.84 1.34 76.07
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 9.21 | 0.52 | 18.81 | |
| compute_asw | 0.05 | 0.00 | 0.05 | |
| count_existing | 0.02 | 0.00 | 0.01 | |
| generate_data_covariables | 0.03 | 0.00 | 0.03 | |
| generate_dataset | 0.00 | 0.01 | 0.02 | |