Yannis Schumann
| Snapshot Date: 2025-01-13 13:00 -0500 (Mon, 13 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_20 |
| git_last_commit: 9764e3f |
| git_last_commit_date: 2024-10-29 11:26:04 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-01-16 12:07 -0500 (Thu, 16 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4746 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4489 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4517 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4469 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4387 |
| 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 159/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.2.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | NA | ||||||||||
|
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: 1.2.0 |
| 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_1.2.0.tar.gz |
| StartedAt: 2025-01-13 23:59:12 -0500 (Mon, 13 Jan 2025) |
| EndedAt: 2025-01-14 00:01:39 -0500 (Tue, 14 Jan 2025) |
| EllapsedTime: 146.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* 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 ‘1.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 45.192 2.673 36.446
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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")
2025-01-14 00:01:04.185474 INFO::Formatting Data.
2025-01-14 00:01:04.192235 INFO::Replacing NaNs with NAs.
2025-01-14 00:01:04.226845 INFO::Removing potential empty rows and columns
2025-01-14 00:01:04.946613 INFO::Found 0 missing values.
2025-01-14 00:01:04.954861 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 00:01:04.956527 INFO::Done
2025-01-14 00:01:04.957901 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 00:01:04.986717 INFO::Starting hierarchical adjustment
2025-01-14 00:01:04.988614 INFO::Found 3 batches.
2025-01-14 00:01:04.989955 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 00:01:04.992517 INFO::Using default BPPARAM
2025-01-14 00:01:04.994085 INFO::Processing subtree level 1
2025-01-14 00:01:05.259331 INFO::Adjusting the last 1 batches sequentially
2025-01-14 00:01:05.265605 INFO::Done
2025-01-14 00:01:05.267379 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 00:01:05.27552 INFO::ASW Batch was -0.010993601665097 prior to batch effect correction and is now -0.010993601665097 .
2025-01-14 00:01:05.278815 INFO::Total function execution time is 1.09404706954956 s and adjustment time is 0.27730393409729 s ( 25.35 )
2025-01-14 00:01:05.326285 INFO::Formatting Data.
2025-01-14 00:01:05.328332 INFO::Replacing NaNs with NAs.
2025-01-14 00:01:05.331094 INFO::Removing potential empty rows and columns
2025-01-14 00:01:05.334781 INFO::Found 0 missing values.
2025-01-14 00:01:05.337764 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.
2025-01-14 00:01:05.371699 INFO::Formatting Data.
2025-01-14 00:01:05.373419 INFO::Replacing NaNs with NAs.
2025-01-14 00:01:05.375597 INFO::Removing potential empty rows and columns
2025-01-14 00:01:05.378466 INFO::Found 0 missing values.
2025-01-14 00:01:05.380981 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.
2025-01-14 00:01:05.432045 INFO::Formatting Data.
2025-01-14 00:01:05.434438 INFO::Replacing NaNs with NAs.
2025-01-14 00:01:05.43794 INFO::Removing potential empty rows and columns
2025-01-14 00:01:05.442502 INFO::Found 0 missing values.
2025-01-14 00:01:05.445479 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.
2025-01-14 00:01:05.46289 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 00:01:05.465277 INFO::Done
2025-01-14 00:01:05.467038 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 00:01:05.473923 INFO::Starting hierarchical adjustment
2025-01-14 00:01:05.476469 INFO::Found 2 batches.
2025-01-14 00:01:05.478332 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 00:01:05.480551 INFO::Using default BPPARAM
2025-01-14 00:01:05.482184 INFO::Adjusting the last 2 batches sequentially
2025-01-14 00:01:05.485529 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-14 00:01:05.564587 INFO::Done
2025-01-14 00:01:05.566292 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 00:01:05.572106 INFO::ASW Batch was -0.0978385153115296 prior to batch effect correction and is now -0.125852095752035 .
2025-01-14 00:01:05.575064 INFO::Total function execution time is 0.142900943756104 s and adjustment time is 0.0886387825012207 s ( 62.03 )
2025-01-14 00:01:05.58269 INFO::Formatting Data.
2025-01-14 00:01:05.584698 INFO::Replacing NaNs with NAs.
2025-01-14 00:01:05.613867 INFO::Formatting Data.
2025-01-14 00:01:05.615778 INFO::Replacing NaNs with NAs.
2025-01-14 00:01:05.618459 INFO::Removing potential empty rows and columns
2025-01-14 00:01:05.62156 INFO::Found 0 missing values.
2025-01-14 00:01:05.63044 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 00:01:05.632043 INFO::Done
2025-01-14 00:01:05.63341 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 00:01:05.638499 INFO::Starting hierarchical adjustment
2025-01-14 00:01:05.640497 INFO::Found 2 batches.
2025-01-14 00:01:05.642007 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 00:01:05.644172 INFO::Using default BPPARAM
2025-01-14 00:01:05.646337 INFO::Adjusting the last 2 batches sequentially
2025-01-14 00:01:05.649228 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-14 00:01:05.696114 INFO::Done
2025-01-14 00:01:05.697801 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 00:01:05.703563 INFO::ASW Batch was -0.0706226908782986 prior to batch effect correction and is now -0.117078562950565 .
2025-01-14 00:01:05.705751 INFO::Total function execution time is 0.0918571949005127 s and adjustment time is 0.0560259819030762 s ( 60.99 )
2025-01-14 00:01:05.709347 INFO::Formatting Data.
2025-01-14 00:01:05.71149 INFO::Replacing NaNs with NAs.
2025-01-14 00:01:05.7141 INFO::Removing potential empty rows and columns
2025-01-14 00:01:05.717268 INFO::Found 0 missing values.
2025-01-14 00:01:05.728041 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 00:01:05.729597 INFO::Done
2025-01-14 00:01:05.7309 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 00:01:05.736318 INFO::Starting hierarchical adjustment
2025-01-14 00:01:05.738455 INFO::Found 2 batches.
2025-01-14 00:01:05.740078 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 00:01:05.741534 INFO::Using default BPPARAM
2025-01-14 00:01:05.742844 INFO::Adjusting the last 2 batches sequentially
2025-01-14 00:01:05.745065 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-14 00:01:05.788145 INFO::Done
2025-01-14 00:01:05.789835 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 00:01:05.795301 INFO::ASW Batch was -0.0706226908782986 prior to batch effect correction and is now -0.117078562950565 .
2025-01-14 00:01:05.797309 INFO::Total function execution time is 0.0880169868469238 s and adjustment time is 0.0501558780670166 s ( 56.98 )
2025-01-14 00:01:11.984681 INFO::Formatting Data.
2025-01-14 00:01:11.98652 INFO::Recognized SummarizedExperiment
2025-01-14 00:01:11.987623 INFO::Typecasting input to dataframe.
2025-01-14 00:01:12.05347 INFO::Replacing NaNs with NAs.
2025-01-14 00:01:12.055745 INFO::Removing potential empty rows and columns
2025-01-14 00:01:12.065011 INFO::Found 0 missing values.
2025-01-14 00:01:12.082127 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 00:01:12.083873 INFO::Done
2025-01-14 00:01:12.084937 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 00:01:12.094505 INFO::Starting hierarchical adjustment
2025-01-14 00:01:12.096119 INFO::Found 2 batches.
2025-01-14 00:01:12.097193 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 00:01:12.099187 INFO::Using default BPPARAM
2025-01-14 00:01:12.100259 INFO::Adjusting the last 2 batches sequentially
2025-01-14 00:01:12.102277 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-14 00:01:12.238656 INFO::Done
2025-01-14 00:01:12.239946 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 00:01:12.248209 INFO::ASW Batch was -0.000810383848534266 prior to batch effect correction and is now -0.0910373516951752 .
2025-01-14 00:01:12.250069 INFO::Total function execution time is 0.265997886657715 s and adjustment time is 0.142855882644653 s ( 53.71 )
2025-01-14 00:01:12.292952 INFO::Formatting Data.
2025-01-14 00:01:12.294466 INFO::Recognized SummarizedExperiment
2025-01-14 00:01:12.295707 INFO::Typecasting input to dataframe.
2025-01-14 00:01:12.319351 INFO::Replacing NaNs with NAs.
2025-01-14 00:01:12.322127 INFO::Removing potential empty rows and columns
2025-01-14 00:01:12.333081 INFO::Found 0 missing values.
2025-01-14 00:01:12.35554 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 00:01:12.356976 INFO::Done
2025-01-14 00:01:12.358464 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 00:01:12.367657 INFO::Starting hierarchical adjustment
2025-01-14 00:01:12.369286 INFO::Found 2 batches.
2025-01-14 00:01:12.370446 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 00:01:12.372175 INFO::Using default BPPARAM
2025-01-14 00:01:12.373438 INFO::Adjusting the last 2 batches sequentially
2025-01-14 00:01:12.375891 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-14 00:01:12.452649 INFO::Done
2025-01-14 00:01:12.454125 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 00:01:12.463552 INFO::ASW Batch was 0.0136107916183256 prior to batch effect correction and is now 0.0136107916183256 .
2025-01-14 00:01:12.4656 INFO::Total function execution time is 0.172600984573364 s and adjustment time is 0.0836281776428223 s ( 48.45 )
2025-01-14 00:01:12.510905 INFO::Formatting Data.
2025-01-14 00:01:12.512248 INFO::Replacing NaNs with NAs.
2025-01-14 00:01:12.514282 INFO::Removing potential empty rows and columns
2025-01-14 00:01:12.516868 INFO::Found 0 missing values.
2025-01-14 00:01:12.52474 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 00:01:12.526196 INFO::Done
2025-01-14 00:01:12.527472 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 00:01:12.532165 INFO::Starting hierarchical adjustment
2025-01-14 00:01:12.534035 INFO::Found 3 batches.
2025-01-14 00:01:12.535301 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 00:01:12.536803 INFO::Using default BPPARAM
2025-01-14 00:01:12.538043 INFO::Processing subtree level 1
2025-01-14 00:01:12.898381 INFO::Adjusting the last 1 batches sequentially
2025-01-14 00:01:12.909195 INFO::Done
2025-01-14 00:01:12.911213 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 00:01:12.923422 INFO::ASW Batch was -0.0334006785557047 prior to batch effect correction and is now -0.173295610079788 .
2025-01-14 00:01:12.926199 INFO::Total function execution time is 0.415194988250732 s and adjustment time is 0.375491142272949 s ( 90.44 )
2025-01-14 00:01:12.973448 INFO::Skipping initial DF formatting
2025-01-14 00:01:12.975025 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 00:01:12.985887 INFO::Starting hierarchical adjustment
2025-01-14 00:01:12.987865 INFO::Found 5 batches.
2025-01-14 00:01:12.989199 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 00:01:12.990683 INFO::Using default BPPARAM
2025-01-14 00:01:12.992028 INFO::Processing subtree level 1
2025-01-14 00:01:13.302642 INFO::Adjusting the last 2 batches sequentially
2025-01-14 00:01:13.315351 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-14 00:01:13.38589 INFO::Done
2025-01-14 00:01:13.387912 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 00:01:13.401707 INFO::ASW Batch was 0.567962199934362 prior to batch effect correction and is now 0.567962199934362 .
2025-01-14 00:01:13.403274 INFO::ASW Label was 0.353258498189474 prior to batch effect correction and is now 0.353258498189474 .
2025-01-14 00:01:13.405512 INFO::Total function execution time is 0.432116031646729 s and adjustment time is 0.39842414855957 s ( 92.2 )
2025-01-14 00:01:13.459201 INFO::Formatting Data.
2025-01-14 00:01:13.461001 INFO::Replacing NaNs with NAs.
2025-01-14 00:01:13.464347 INFO::Removing potential empty rows and columns
2025-01-14 00:01:13.467055 INFO::Found 0 missing values.
2025-01-14 00:01:13.477419 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 00:01:13.478789 INFO::Done
2025-01-14 00:01:13.479979 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 00:01:13.486518 INFO::Starting hierarchical adjustment
2025-01-14 00:01:13.488308 INFO::Found 5 batches.
2025-01-14 00:01:13.489555 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 00:01:13.490975 INFO::Using default BPPARAM
2025-01-14 00:01:13.492239 INFO::Processing subtree level 1
2025-01-14 00:01:13.755444 INFO::Adjusting the last 2 batches sequentially
2025-01-14 00:01:13.772701 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-14 00:01:13.836674 INFO::Done
2025-01-14 00:01:13.839 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 00:01:13.848293 INFO::ASW Batch was 0.704235238691492 prior to batch effect correction and is now -0.0804428940099601 .
2025-01-14 00:01:13.8499 INFO::ASW Label was 0.150196257069905 prior to batch effect correction and is now 0.74729777295868 .
2025-01-14 00:01:13.853392 INFO::Total function execution time is 0.393445014953613 s and adjustment time is 0.348691940307617 s ( 88.63 )
2025-01-14 00:01:13.855813 INFO::Formatting Data.
2025-01-14 00:01:13.857528 INFO::Replacing NaNs with NAs.
2025-01-14 00:01:13.861539 INFO::Removing potential empty rows and columns
2025-01-14 00:01:13.864302 INFO::Found 0 missing values.
2025-01-14 00:01:13.875586 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 00:01:13.877066 INFO::Done
2025-01-14 00:01:13.878529 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 00:01:13.885713 INFO::Starting hierarchical adjustment
2025-01-14 00:01:13.887622 INFO::Found 5 batches.
2025-01-14 00:01:13.890051 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 00:01:13.891565 INFO::Using default BPPARAM
2025-01-14 00:01:13.892853 INFO::Processing subtree level 1
2025-01-14 00:01:14.158308 INFO::Adjusting the last 2 batches sequentially
2025-01-14 00:01:14.172646 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-14 00:01:14.229236 INFO::Done
2025-01-14 00:01:14.231471 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 00:01:14.240985 INFO::ASW Batch was 0.704235238691492 prior to batch effect correction and is now -0.0804428940099601 .
2025-01-14 00:01:14.242682 INFO::ASW Label was 0.150196257069905 prior to batch effect correction and is now 0.74729777295868 .
2025-01-14 00:01:14.245156 INFO::Total function execution time is 0.389366149902344 s and adjustment time is 0.341976165771484 s ( 87.83 )
2025-01-14 00:01:14.285928 INFO::Formatting Data.
2025-01-14 00:01:14.288374 INFO::Replacing NaNs with NAs.
2025-01-14 00:01:14.290717 INFO::Removing potential empty rows and columns
2025-01-14 00:01:14.293377 INFO::Found 0 missing values.
2025-01-14 00:01:14.305086 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 00:01:14.306565 INFO::Done
2025-01-14 00:01:14.307889 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 00:01:14.315273 INFO::Starting hierarchical adjustment
2025-01-14 00:01:14.317239 INFO::Found 5 batches.
2025-01-14 00:01:14.318656 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 00:01:14.320262 INFO::Using default BPPARAM
2025-01-14 00:01:14.321664 INFO::Processing subtree level 1
2025-01-14 00:01:14.571088 INFO::Adjusting the last 2 batches sequentially
2025-01-14 00:01:14.587671 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-14 00:01:14.649334 INFO::Done
2025-01-14 00:01:14.650927 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 00:01:14.661372 INFO::ASW Batch was 0.302934590915139 prior to batch effect correction and is now 0.00233897244099869 .
2025-01-14 00:01:14.663018 INFO::ASW Label was 0.563725992470929 prior to batch effect correction and is now 0.7350446247247 .
2025-01-14 00:01:14.665874 INFO::Total function execution time is 0.380002021789551 s and adjustment time is 0.332488059997559 s ( 87.5 )
2025-01-14 00:01:14.668272 INFO::Formatting Data.
2025-01-14 00:01:14.669935 INFO::Replacing NaNs with NAs.
2025-01-14 00:01:14.674396 INFO::Removing potential empty rows and columns
2025-01-14 00:01:14.676943 INFO::Found 0 missing values.
2025-01-14 00:01:14.688262 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 00:01:14.689813 INFO::Done
2025-01-14 00:01:14.691396 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 00:01:14.698746 INFO::Starting hierarchical adjustment
2025-01-14 00:01:14.700719 INFO::Found 5 batches.
2025-01-14 00:01:14.702178 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 00:01:14.703858 INFO::Using default BPPARAM
2025-01-14 00:01:14.705268 INFO::Processing subtree level 1
2025-01-14 00:01:14.965303 INFO::Adjusting the last 2 batches sequentially
2025-01-14 00:01:14.981128 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-14 00:01:15.043678 INFO::Done
2025-01-14 00:01:15.045328 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 00:01:15.05514 INFO::ASW Batch was 0.302934590915139 prior to batch effect correction and is now 0.00233897244099869 .
2025-01-14 00:01:15.056836 INFO::ASW Label was 0.563725992470929 prior to batch effect correction and is now 0.7350446247247 .
2025-01-14 00:01:15.060436 INFO::Total function execution time is 0.391453981399536 s and adjustment time is 0.343347072601318 s ( 87.71 )
2025-01-14 00:01:15.100805 INFO::Formatting Data.
2025-01-14 00:01:15.102837 INFO::Replacing NaNs with NAs.
2025-01-14 00:01:15.106195 INFO::Removing potential empty rows and columns
2025-01-14 00:01:15.108973 INFO::Found 0 missing values.
2025-01-14 00:01:15.116926 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 00:01:15.118364 INFO::Done
2025-01-14 00:01:15.119793 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 00:01:15.127131 INFO::Starting hierarchical adjustment
2025-01-14 00:01:15.129159 INFO::Found 2 batches.
2025-01-14 00:01:15.130544 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 00:01:15.132088 INFO::Using default BPPARAM
2025-01-14 00:01:15.133389 INFO::Adjusting the last 2 batches sequentially
2025-01-14 00:01:15.135774 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-14 00:01:15.172824 INFO::Done
2025-01-14 00:01:15.174201 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 00:01:15.18077 INFO::ASW Batch was 0.434933262234433 prior to batch effect correction and is now -0.0270881725056314 .
2025-01-14 00:01:15.182214 INFO::ASW Label was 0.50231182551442 prior to batch effect correction and is now 0.911618387801928 .
2025-01-14 00:01:15.18403 INFO::Total function execution time is 0.0833761692047119 s and adjustment time is 0.0441908836364746 s ( 53 )
2025-01-14 00:01:15.186002 INFO::Formatting Data.
2025-01-14 00:01:15.187553 INFO::Replacing NaNs with NAs.
2025-01-14 00:01:15.189674 INFO::Removing potential empty rows and columns
2025-01-14 00:01:15.19215 INFO::Found 0 missing values.
2025-01-14 00:01:15.19918 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 00:01:15.200596 INFO::Done
2025-01-14 00:01:15.201832 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 00:01:15.208551 INFO::Starting hierarchical adjustment
2025-01-14 00:01:15.210333 INFO::Found 2 batches.
2025-01-14 00:01:15.211611 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 00:01:15.213005 INFO::Using default BPPARAM
2025-01-14 00:01:15.214277 INFO::Adjusting the last 2 batches sequentially
2025-01-14 00:01:15.216393 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-14 00:01:15.251512 INFO::Done
2025-01-14 00:01:15.252987 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 00:01:15.260475 INFO::ASW Batch was 0.434933262234433 prior to batch effect correction and is now -0.0270881725056314 .
2025-01-14 00:01:15.261957 INFO::ASW Label was 0.50231182551442 prior to batch effect correction and is now 0.911618387801928 .
2025-01-14 00:01:15.263823 INFO::Total function execution time is 0.0778608322143555 s and adjustment time is 0.0415160655975342 s ( 53.32 )
2025-01-14 00:01:15.296279 INFO::Formatting Data.
2025-01-14 00:01:15.298012 INFO::Replacing NaNs with NAs.
2025-01-14 00:01:15.300056 INFO::Removing potential empty rows and columns
2025-01-14 00:01:15.302285 INFO::Found 0 missing values.
2025-01-14 00:01:15.308006 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 00:01:15.310064 INFO::Done
2025-01-14 00:01:15.311405 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 00:01:15.31593 INFO::Starting hierarchical adjustment
2025-01-14 00:01:15.317847 INFO::Found 2 batches.
2025-01-14 00:01:15.31922 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 00:01:15.320671 INFO::Using default BPPARAM
2025-01-14 00:01:15.321961 INFO::Adjusting the last 2 batches sequentially
2025-01-14 00:01:15.324201 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-14 00:01:15.408462 INFO::Done
2025-01-14 00:01:15.409934 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 00:01:15.414406 INFO::ASW Batch was -0.021674352478668 prior to batch effect correction and is now -0.0694392621667823 .
2025-01-14 00:01:15.41643 INFO::Total function execution time is 0.120204925537109 s and adjustment time is 0.0909719467163086 s ( 75.68 )
2025-01-14 00:01:15.449438 INFO::Formatting Data.
2025-01-14 00:01:15.451079 INFO::Replacing NaNs with NAs.
2025-01-14 00:01:15.453037 INFO::Removing potential empty rows and columns
2025-01-14 00:01:15.455357 INFO::Found 0 missing values.
2025-01-14 00:01:15.458358 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.
2025-01-14 00:01:15.471388 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 00:01:15.472841 INFO::Done
2025-01-14 00:01:15.474118 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 00:01:15.481538 INFO::Starting hierarchical adjustment
2025-01-14 00:01:15.483363 INFO::Found 2 batches.
2025-01-14 00:01:15.484654 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 00:01:15.486105 INFO::Using default BPPARAM
2025-01-14 00:01:15.487362 INFO::Adjusting the last 2 batches sequentially
2025-01-14 00:01:15.489765 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-14 00:01:15.535865 INFO::Done
2025-01-14 00:01:15.537344 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 00:01:15.544437 INFO::ASW Batch was 0.422302528888776 prior to batch effect correction and is now -0.0366474279731805 .
2025-01-14 00:01:15.545975 INFO::ASW Label was 0.579867067887914 prior to batch effect correction and is now 0.940560692649574 .
2025-01-14 00:01:15.547884 INFO::Total function execution time is 0.0985298156738281 s and adjustment time is 0.052854061126709 s ( 53.64 )
2025-01-14 00:01:15.549876 INFO::Formatting Data.
2025-01-14 00:01:15.551416 INFO::Replacing NaNs with NAs.
2025-01-14 00:01:15.553637 INFO::Removing potential empty rows and columns
2025-01-14 00:01:15.556079 INFO::Found 0 missing values.
2025-01-14 00:01:15.558301 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.
2025-01-14 00:01:15.570513 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 00:01:15.571976 INFO::Done
2025-01-14 00:01:15.573232 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 00:01:15.580195 INFO::Starting hierarchical adjustment
2025-01-14 00:01:15.582028 INFO::Found 2 batches.
2025-01-14 00:01:15.583227 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 00:01:15.5848 INFO::Using default BPPARAM
2025-01-14 00:01:15.586233 INFO::Adjusting the last 2 batches sequentially
2025-01-14 00:01:15.588663 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-14 00:01:15.632009 INFO::Done
2025-01-14 00:01:15.633537 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 00:01:15.640605 INFO::ASW Batch was 0.422302528888776 prior to batch effect correction and is now -0.0366474279731805 .
2025-01-14 00:01:15.642232 INFO::ASW Label was 0.579867067887914 prior to batch effect correction and is now 0.940560692649574 .
2025-01-14 00:01:15.644294 INFO::Total function execution time is 0.0944609642028809 s and adjustment time is 0.05031418800354 s ( 53.26 )
2025-01-14 00:01:16.21285 INFO::Formatting Data.
2025-01-14 00:01:16.214559 INFO::Replacing NaNs with NAs.
2025-01-14 00:01:16.216644 INFO::Removing potential empty rows and columns
2025-01-14 00:01:16.21935 INFO::Found 0 missing values.
2025-01-14 00:01:16.227712 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 00:01:16.229173 INFO::Done
2025-01-14 00:01:16.230675 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 00:01:16.235618 INFO::Starting hierarchical adjustment
2025-01-14 00:01:16.237569 INFO::Found 3 batches.
2025-01-14 00:01:16.238907 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 00:01:16.240453 INFO::Using default BPPARAM
2025-01-14 00:01:16.241748 INFO::Processing subtree level 1
2025-01-14 00:01:16.490072 INFO::Adjusting the last 1 batches sequentially
2025-01-14 00:01:16.503618 INFO::Done
2025-01-14 00:01:16.50591 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 00:01:16.519834 INFO::ASW Batch was -0.116449082194613 prior to batch effect correction and is now -0.116449082194613 .
2025-01-14 00:01:16.526838 INFO::Total function execution time is 0.313019990921021 s and adjustment time is 0.266442060470581 s ( 85.12 )
2025-01-14 00:01:16.530824 INFO::Formatting Data.
2025-01-14 00:01:16.534505 INFO::Typecasting input to dataframe.
2025-01-14 00:01:16.53664 INFO::Replacing NaNs with NAs.
2025-01-14 00:01:16.540042 INFO::Removing potential empty rows and columns
2025-01-14 00:01:16.543496 INFO::Found 0 missing values.
2025-01-14 00:01:16.552609 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 00:01:16.554243 INFO::Done
2025-01-14 00:01:16.555792 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 00:01:16.564958 INFO::Starting hierarchical adjustment
2025-01-14 00:01:16.569166 INFO::Found 3 batches.
2025-01-14 00:01:16.570561 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 00:01:16.572095 INFO::Using default BPPARAM
2025-01-14 00:01:16.574955 INFO::Processing subtree level 1
2025-01-14 00:01:16.795438 INFO::Adjusting the last 1 batches sequentially
2025-01-14 00:01:16.813831 INFO::Done
2025-01-14 00:01:16.818221 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 00:01:16.833756 INFO::ASW Batch was -0.116449082194613 prior to batch effect correction and is now -0.116449082194613 .
2025-01-14 00:01:16.839096 INFO::Total function execution time is 0.307482957839966 s and adjustment time is 0.24507999420166 s ( 79.71 )
2025-01-14 00:01:16.885094 INFO::Formatting Data.
2025-01-14 00:01:16.887201 INFO::Typecasting input to dataframe.
2025-01-14 00:01:16.889269 INFO::Replacing NaNs with NAs.
2025-01-14 00:01:16.891463 INFO::Removing potential empty rows and columns
2025-01-14 00:01:16.894207 INFO::Found 0 missing values.
2025-01-14 00:01:16.901897 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 00:01:16.903366 INFO::Done
2025-01-14 00:01:16.904572 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 00:01:16.909169 INFO::Starting hierarchical adjustment
2025-01-14 00:01:16.912018 INFO::Found 3 batches.
2025-01-14 00:01:16.913556 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 00:01:16.915809 INFO::Using default BPPARAM
2025-01-14 00:01:16.918862 INFO::Processing subtree level 1
2025-01-14 00:01:17.408525 INFO::Adjusting the last 1 batches sequentially
2025-01-14 00:01:17.414398 INFO::Done
2025-01-14 00:01:17.416026 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 00:01:17.467779 INFO::ASW Batch was -0.0680938671995059 prior to batch effect correction and is now -0.0680938671995059 .
2025-01-14 00:01:17.476891 INFO::Total function execution time is 0.589364051818848 s and adjustment time is 0.503695011138916 s ( 85.46 )
2025-01-14 00:01:18.10403 INFO::Formatting Data.
2025-01-14 00:01:18.106226 INFO::Replacing NaNs with NAs.
2025-01-14 00:01:18.108903 INFO::Removing potential empty rows and columns
2025-01-14 00:01:18.117069 INFO::Found 1000 missing values.
2025-01-14 00:01:18.188176 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 00:01:18.189728 INFO::Done
2025-01-14 00:01:18.191107 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 00:01:18.204548 INFO::Starting hierarchical adjustment
2025-01-14 00:01:18.206612 INFO::Found 10 batches.
2025-01-14 00:01:18.209215 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 00:01:18.211069 INFO::Using default BPPARAM
2025-01-14 00:01:18.212712 INFO::Processing subtree level 1
2025-01-14 00:01:18.625255 INFO::Processing subtree level 2
2025-01-14 00:01:19.191949 INFO::Adjusting the last 1 batches sequentially
2025-01-14 00:01:19.209779 INFO::Done
2025-01-14 00:01:19.214309 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 00:01:19.243396 INFO::ASW Batch was 0.503146082007307 prior to batch effect correction and is now 0.503146082007307 .
2025-01-14 00:01:19.246129 INFO::ASW Label was 0.317730395968329 prior to batch effect correction and is now 0.317730395968329 .
2025-01-14 00:01:19.251878 INFO::Total function execution time is 1.14644193649292 s and adjustment time is 1.0036039352417 s ( 87.54 )
2025-01-14 00:01:19.254489 INFO::Formatting Data.
2025-01-14 00:01:19.25727 INFO::Replacing NaNs with NAs.
2025-01-14 00:01:19.26342 INFO::Removing potential empty rows and columns
2025-01-14 00:01:19.272612 INFO::Found 1000 missing values.
2025-01-14 00:01:19.339757 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 00:01:19.341312 INFO::Done
2025-01-14 00:01:19.342596 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 00:01:19.354911 INFO::Starting hierarchical adjustment
2025-01-14 00:01:19.357723 INFO::Found 10 batches.
2025-01-14 00:01:20.664173 INFO::Set up parallel execution backend with 2 workers
2025-01-14 00:01:20.665524 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-01-14 00:01:22.554086 INFO::Adjusting the last 2 batches sequentially
2025-01-14 00:01:22.556617 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-14 00:01:22.604327 INFO::Done
2025-01-14 00:01:22.605626 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 00:01:22.616882 INFO::ASW Batch was 0.503146082007307 prior to batch effect correction and is now 0.503146082007307 .
2025-01-14 00:01:22.618247 INFO::ASW Label was 0.317730395968329 prior to batch effect correction and is now 0.317730395968329 .
2025-01-14 00:01:22.619903 INFO::Total function execution time is 3.36562991142273 s and adjustment time is 3.24705719947815 s ( 96.48 )
2025-01-14 00:01:23.059977 INFO::Formatting Data.
2025-01-14 00:01:23.061691 INFO::Replacing NaNs with NAs.
2025-01-14 00:01:23.064617 INFO::Removing potential empty rows and columns
2025-01-14 00:01:23.067689 INFO::Found 0 missing values.
2025-01-14 00:01:23.079644 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 00:01:23.08124 INFO::Done
2025-01-14 00:01:23.083505 INFO::Acquiring quality metrics before batch effect correction.
2025-01-14 00:01:23.090686 INFO::Starting hierarchical adjustment
2025-01-14 00:01:23.092698 INFO::Found 3 batches.
2025-01-14 00:01:23.0942 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-14 00:01:23.0958 INFO::Using default BPPARAM
2025-01-14 00:01:23.097192 INFO::Processing subtree level 1
2025-01-14 00:01:23.434822 INFO::Adjusting the last 1 batches sequentially
2025-01-14 00:01:23.454514 INFO::Done
2025-01-14 00:01:23.4565 INFO::Acquiring quality metrics after batch effect correction.
2025-01-14 00:01:23.47704 INFO::ASW Batch was 0.220520380041761 prior to batch effect correction and is now -0.144452127179201 .
2025-01-14 00:01:23.479136 INFO::ASW Label was -0.173338329607498 prior to batch effect correction and is now -0.0290523516092353 .
2025-01-14 00:01:23.482516 INFO::Total function execution time is 0.421991109848022 s and adjustment time is 0.362149000167847 s ( 85.82 )
2025-01-14 00:01:23.830951 INFO::Formatting Data.
2025-01-14 00:01:23.832799 INFO::Replacing NaNs with NAs.
2025-01-14 00:01:23.83523 INFO::Removing potential empty rows and columns
2025-01-14 00:01:23.838621 INFO::Found 2 missing values.
2025-01-14 00:01:23.847829 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-01-14 00:01:23.849603 INFO::Done
2025-01-14 00:01:23.93366 INFO::Found NA in Reference column
2025-01-14 00:01:23.963677 INFO::Require at least two references per batch.
2025-01-14 00:01:24.020549 INFO::Formatting Data.
2025-01-14 00:01:24.022211 INFO::Recognized SummarizedExperiment
2025-01-14 00:01:24.023521 INFO::Typecasting input to dataframe.
2025-01-14 00:01:24.049734 INFO::Replacing NaNs with NAs.
2025-01-14 00:01:24.052598 INFO::Removing potential empty rows and columns
2025-01-14 00:01:24.065848 INFO::Found 0 missing values.
2025-01-14 00:01:24.090931 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 00:01:24.092485 INFO::Done
2025-01-14 00:01:24.133161 INFO::Formatting Data.
2025-01-14 00:01:24.134757 INFO::Recognized SummarizedExperiment
2025-01-14 00:01:24.136108 INFO::Typecasting input to dataframe.
2025-01-14 00:01:24.188176 INFO::Replacing NaNs with NAs.
2025-01-14 00:01:24.191223 INFO::Removing potential empty rows and columns
2025-01-14 00:01:24.202911 INFO::Found 0 missing values.
2025-01-14 00:01:24.245931 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 00:01:24.247809 INFO::Done
2025-01-14 00:01:24.293614 INFO::Formatting Data.
2025-01-14 00:01:24.295424 INFO::Recognized SummarizedExperiment
2025-01-14 00:01:24.296998 INFO::Typecasting input to dataframe.
2025-01-14 00:01:24.346371 INFO::Replacing NaNs with NAs.
2025-01-14 00:01:24.348748 INFO::Removing potential empty rows and columns
2025-01-14 00:01:24.351749 INFO::Found 0 missing values.
2025-01-14 00:01:24.3543 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.
2025-01-14 00:01:24.367745 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 00:01:24.36935 INFO::Done
2025-01-14 00:01:24.397366 INFO::Formatting Data.
2025-01-14 00:01:24.399174 INFO::Replacing NaNs with NAs.
2025-01-14 00:01:24.402136 INFO::Removing potential empty rows and columns
2025-01-14 00:01:24.40477 INFO::Found 0 missing values.
2025-01-14 00:01:24.41374 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 00:01:24.415275 INFO::Done
2025-01-14 00:01:24.444999 INFO::Formatting Data.
2025-01-14 00:01:24.446754 INFO::Replacing NaNs with NAs.
2025-01-14 00:01:24.449102 INFO::Removing potential empty rows and columns
2025-01-14 00:01:24.451813 INFO::Found 0 missing values.
2025-01-14 00:01:24.460267 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 00:01:24.461831 INFO::Done
2025-01-14 00:01:24.546892 INFO::Formatting Data.
2025-01-14 00:01:24.54868 INFO::Replacing NaNs with NAs.
2025-01-14 00:01:24.551668 INFO::Removing potential empty rows and columns
2025-01-14 00:01:24.554918 INFO::Found 1 missing values.
2025-01-14 00:01:24.562272 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 00:01:24.563708 INFO::Done
2025-01-14 00:01:24.616339 INFO::Formatting Data.
2025-01-14 00:01:24.618091 INFO::Replacing NaNs with NAs.
2025-01-14 00:01:24.620086 INFO::Removing potential empty rows and columns
2025-01-14 00:01:24.623674 INFO::Found 2 missing values.
2025-01-14 00:01:24.626062 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.
2025-01-14 00:01:24.632016 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-01-14 00:01:24.633362 INFO::Done
2025-01-14 00:01:24.660291 INFO::Formatting Data.
2025-01-14 00:01:24.662187 INFO::Replacing NaNs with NAs.
2025-01-14 00:01:24.664403 INFO::Removing potential empty rows and columns
2025-01-14 00:01:24.666906 INFO::Found 2 missing values.
2025-01-14 00:01:24.671169 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 00:01:24.672529 INFO::Done
2025-01-14 00:01:24.702634 INFO::Formatting Data.
2025-01-14 00:01:24.704519 INFO::Typecasting input to dataframe.
2025-01-14 00:01:24.706857 INFO::Replacing NaNs with NAs.
2025-01-14 00:01:24.709318 INFO::Removing potential empty rows and columns
2025-01-14 00:01:24.71212 INFO::Found 0 missing values.
2025-01-14 00:01:24.720633 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-14 00:01:24.722201 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
35.536 7.114 44.704
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 45.192 | 2.673 | 36.446 | |
| compute_asw | 0.057 | 0.003 | 0.067 | |
| count_existing | 0.027 | 0.002 | 0.032 | |
| generate_data_covariables | 0.026 | 0.002 | 0.033 | |
| generate_dataset | 0.023 | 0.002 | 0.028 | |