Yannis Schumann
| Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_19 |
| git_last_commit: 9a6bbaa |
| git_last_commit_date: 2024-04-30 11:53:11 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-11 14:41 -0400 (Tue, 11 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4522 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4468 |
| 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 156/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.0.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.0.0 |
| 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_1.0.0.tar.gz |
| StartedAt: 2024-06-09 18:55:19 -0400 (Sun, 09 Jun 2024) |
| EndedAt: 2024-06-09 18:56:41 -0400 (Sun, 09 Jun 2024) |
| EllapsedTime: 81.8 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_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/BERT.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.0.0’
* 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 26.443 1.425 18.96
* 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 4.4.0 (2024-04-24) -- "Puppy Cup"
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")
2024-06-09 18:56:20.678841 INFO::Formatting Data.
2024-06-09 18:56:20.684661 INFO::Replacing NaNs with NAs.
2024-06-09 18:56:20.700385 INFO::Removing potential empty rows and columns
2024-06-09 18:56:20.980918 INFO::Found 0 missing values.
2024-06-09 18:56:20.986009 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 18:56:20.986836 INFO::Done
2024-06-09 18:56:20.987356 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 18:56:21.006099 INFO::Starting hierarchical adjustment
2024-06-09 18:56:21.007362 INFO::Found 3 batches.
2024-06-09 18:56:21.008251 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 18:56:21.009884 INFO::Using default BPPARAM
2024-06-09 18:56:21.010657 INFO::Processing subtree level 1
2024-06-09 18:56:21.163717 INFO::Adjusting the last 1 batches sequentially
2024-06-09 18:56:21.169947 INFO::Done
2024-06-09 18:56:21.171057 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 18:56:21.180271 INFO::ASW Batch was -0.0629908448140925 prior to batch effect correction and is now -0.0629908448140925 .
2024-06-09 18:56:21.182546 INFO::Total function execution time is 0.504341840744019 s and adjustment time is 0.162799835205078 s ( 32.28 )
2024-06-09 18:56:21.205411 INFO::Formatting Data.
2024-06-09 18:56:21.206186 INFO::Replacing NaNs with NAs.
2024-06-09 18:56:21.207118 INFO::Removing potential empty rows and columns
2024-06-09 18:56:21.208184 INFO::Found 0 missing values.
2024-06-09 18:56:21.209089 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.
2024-06-09 18:56:21.219131 INFO::Formatting Data.
2024-06-09 18:56:21.219878 INFO::Replacing NaNs with NAs.
2024-06-09 18:56:21.220709 INFO::Removing potential empty rows and columns
2024-06-09 18:56:21.221654 INFO::Found 0 missing values.
2024-06-09 18:56:21.222504 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.
2024-06-09 18:56:21.239338 INFO::Formatting Data.
2024-06-09 18:56:21.240045 INFO::Replacing NaNs with NAs.
2024-06-09 18:56:21.240828 INFO::Removing potential empty rows and columns
2024-06-09 18:56:21.241835 INFO::Found 0 missing values.
2024-06-09 18:56:21.242711 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.
2024-06-09 18:56:21.24861 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 18:56:21.249445 INFO::Done
2024-06-09 18:56:21.250159 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 18:56:21.252194 INFO::Starting hierarchical adjustment
2024-06-09 18:56:21.252948 INFO::Found 2 batches.
2024-06-09 18:56:21.253648 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 18:56:21.254426 INFO::Using default BPPARAM
2024-06-09 18:56:21.254893 INFO::Adjusting the last 2 batches sequentially
2024-06-09 18:56:21.255722 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-09 18:56:21.285684 INFO::Done
2024-06-09 18:56:21.286357 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 18:56:21.288244 INFO::ASW Batch was 0.0227009507756342 prior to batch effect correction and is now -0.0823781275768336 .
2024-06-09 18:56:21.289019 INFO::Total function execution time is 0.0497148036956787 s and adjustment time is 0.0329229831695557 s ( 66.22 )
2024-06-09 18:56:21.29279 INFO::Formatting Data.
2024-06-09 18:56:21.29369 INFO::Replacing NaNs with NAs.
2024-06-09 18:56:21.306642 INFO::Formatting Data.
2024-06-09 18:56:21.307877 INFO::Replacing NaNs with NAs.
2024-06-09 18:56:21.309419 INFO::Removing potential empty rows and columns
2024-06-09 18:56:21.31097 INFO::Found 0 missing values.
2024-06-09 18:56:21.314654 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 18:56:21.315224 INFO::Done
2024-06-09 18:56:21.316083 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 18:56:21.318729 INFO::Starting hierarchical adjustment
2024-06-09 18:56:21.319461 INFO::Found 2 batches.
2024-06-09 18:56:21.320159 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 18:56:21.321061 INFO::Using default BPPARAM
2024-06-09 18:56:21.321688 INFO::Adjusting the last 2 batches sequentially
2024-06-09 18:56:21.322566 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-09 18:56:21.339952 INFO::Done
2024-06-09 18:56:21.340616 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 18:56:21.342435 INFO::ASW Batch was -0.0879768550138461 prior to batch effect correction and is now -0.115685981803164 .
2024-06-09 18:56:21.343141 INFO::Total function execution time is 0.03666090965271 s and adjustment time is 0.0206019878387451 s ( 56.2 )
2024-06-09 18:56:21.344079 INFO::Formatting Data.
2024-06-09 18:56:21.344595 INFO::Replacing NaNs with NAs.
2024-06-09 18:56:21.345844 INFO::Removing potential empty rows and columns
2024-06-09 18:56:21.347241 INFO::Found 0 missing values.
2024-06-09 18:56:21.351315 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 18:56:21.352145 INFO::Done
2024-06-09 18:56:21.352859 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 18:56:21.355691 INFO::Starting hierarchical adjustment
2024-06-09 18:56:21.356755 INFO::Found 2 batches.
2024-06-09 18:56:21.357494 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 18:56:21.358274 INFO::Using default BPPARAM
2024-06-09 18:56:21.358844 INFO::Adjusting the last 2 batches sequentially
2024-06-09 18:56:21.35987 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-09 18:56:21.379687 INFO::Done
2024-06-09 18:56:21.380338 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 18:56:21.383056 INFO::ASW Batch was -0.0879768550138461 prior to batch effect correction and is now -0.115685981803164 .
2024-06-09 18:56:21.384152 INFO::Total function execution time is 0.0399808883666992 s and adjustment time is 0.0231478214263916 s ( 57.9 )
2024-06-09 18:56:23.861434 INFO::Formatting Data.
2024-06-09 18:56:23.86213 INFO::Recognized SummarizedExperiment
2024-06-09 18:56:23.862576 INFO::Typecasting input to dataframe.
2024-06-09 18:56:24.69061 INFO::Replacing NaNs with NAs.
2024-06-09 18:56:24.691641 INFO::Removing potential empty rows and columns
2024-06-09 18:56:24.694923 INFO::Found 0 missing values.
2024-06-09 18:56:24.702682 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 18:56:24.703542 INFO::Done
2024-06-09 18:56:24.704212 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 18:56:24.707539 INFO::Starting hierarchical adjustment
2024-06-09 18:56:24.708345 INFO::Found 2 batches.
2024-06-09 18:56:24.708907 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 18:56:24.709949 INFO::Using default BPPARAM
2024-06-09 18:56:24.710357 INFO::Adjusting the last 2 batches sequentially
2024-06-09 18:56:24.711177 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-09 18:56:24.758489 INFO::Done
2024-06-09 18:56:24.759102 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 18:56:24.762022 INFO::ASW Batch was 0.033581417821755 prior to batch effect correction and is now -0.0995820621303877 .
2024-06-09 18:56:24.762792 INFO::Total function execution time is 0.901731967926025 s and adjustment time is 0.0502920150756836 s ( 5.58 )
2024-06-09 18:56:24.783976 INFO::Formatting Data.
2024-06-09 18:56:24.784976 INFO::Recognized SummarizedExperiment
2024-06-09 18:56:24.785695 INFO::Typecasting input to dataframe.
2024-06-09 18:56:24.796781 INFO::Replacing NaNs with NAs.
2024-06-09 18:56:24.798385 INFO::Removing potential empty rows and columns
2024-06-09 18:56:24.80297 INFO::Found 0 missing values.
2024-06-09 18:56:24.811858 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 18:56:24.81274 INFO::Done
2024-06-09 18:56:24.81346 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 18:56:24.817584 INFO::Starting hierarchical adjustment
2024-06-09 18:56:24.818396 INFO::Found 2 batches.
2024-06-09 18:56:24.819048 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 18:56:24.819744 INFO::Using default BPPARAM
2024-06-09 18:56:24.820349 INFO::Adjusting the last 2 batches sequentially
2024-06-09 18:56:24.821602 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-09 18:56:24.84702 INFO::Done
2024-06-09 18:56:24.847887 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 18:56:24.852393 INFO::ASW Batch was 0.00411683515646182 prior to batch effect correction and is now 0.00411683515646182 .
2024-06-09 18:56:24.85351 INFO::Total function execution time is 0.0695159435272217 s and adjustment time is 0.0288031101226807 s ( 41.43 )
2024-06-09 18:56:24.878583 INFO::Formatting Data.
2024-06-09 18:56:24.879571 INFO::Replacing NaNs with NAs.
2024-06-09 18:56:24.880686 INFO::Removing potential empty rows and columns
2024-06-09 18:56:24.881921 INFO::Found 0 missing values.
2024-06-09 18:56:24.885585 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 18:56:24.88632 INFO::Done
2024-06-09 18:56:24.886838 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 18:56:24.888623 INFO::Starting hierarchical adjustment
2024-06-09 18:56:24.889293 INFO::Found 3 batches.
2024-06-09 18:56:24.889707 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 18:56:24.8904 INFO::Using default BPPARAM
2024-06-09 18:56:24.891018 INFO::Processing subtree level 1
2024-06-09 18:56:25.150387 INFO::Adjusting the last 1 batches sequentially
2024-06-09 18:56:25.160777 INFO::Done
2024-06-09 18:56:25.162718 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 18:56:25.175193 INFO::ASW Batch was -0.130278267796609 prior to batch effect correction and is now -0.161326107490433 .
2024-06-09 18:56:25.179262 INFO::Total function execution time is 0.299611806869507 s and adjustment time is 0.271350145339966 s ( 90.57 )
2024-06-09 18:56:25.203306 INFO::Skipping initial DF formatting
2024-06-09 18:56:25.204328 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 18:56:25.211422 INFO::Starting hierarchical adjustment
2024-06-09 18:56:25.212737 INFO::Found 5 batches.
2024-06-09 18:56:25.213615 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 18:56:25.214531 INFO::Using default BPPARAM
2024-06-09 18:56:25.217319 INFO::Processing subtree level 1
2024-06-09 18:56:25.398647 INFO::Adjusting the last 2 batches sequentially
2024-06-09 18:56:25.409088 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-09 18:56:25.462339 INFO::Done
2024-06-09 18:56:25.463394 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 18:56:25.470045 INFO::ASW Batch was 0.535124903603926 prior to batch effect correction and is now 0.535124903603926 .
2024-06-09 18:56:25.471175 INFO::ASW Label was 0.364112364090705 prior to batch effect correction and is now 0.364112364090705 .
2024-06-09 18:56:25.47262 INFO::Total function execution time is 0.269363880157471 s and adjustment time is 0.249855041503906 s ( 92.76 )
2024-06-09 18:56:25.502582 INFO::Formatting Data.
2024-06-09 18:56:25.503688 INFO::Replacing NaNs with NAs.
2024-06-09 18:56:25.504879 INFO::Removing potential empty rows and columns
2024-06-09 18:56:25.506657 INFO::Found 0 missing values.
2024-06-09 18:56:25.512853 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 18:56:25.51381 INFO::Done
2024-06-09 18:56:25.514562 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 18:56:25.517307 INFO::Starting hierarchical adjustment
2024-06-09 18:56:25.51799 INFO::Found 5 batches.
2024-06-09 18:56:25.518465 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 18:56:25.519005 INFO::Using default BPPARAM
2024-06-09 18:56:25.519944 INFO::Processing subtree level 1
2024-06-09 18:56:25.661824 INFO::Adjusting the last 2 batches sequentially
2024-06-09 18:56:25.678241 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-09 18:56:25.717331 INFO::Done
2024-06-09 18:56:25.718142 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 18:56:25.724678 INFO::ASW Batch was 0.466674965916518 prior to batch effect correction and is now -0.0868225413313597 .
2024-06-09 18:56:25.725689 INFO::ASW Label was 0.334519613787346 prior to batch effect correction and is now 0.781025512518879 .
2024-06-09 18:56:25.727863 INFO::Total function execution time is 0.225322961807251 s and adjustment time is 0.199448108673096 s ( 88.52 )
2024-06-09 18:56:25.728806 INFO::Formatting Data.
2024-06-09 18:56:25.729381 INFO::Replacing NaNs with NAs.
2024-06-09 18:56:25.730595 INFO::Removing potential empty rows and columns
2024-06-09 18:56:25.732236 INFO::Found 0 missing values.
2024-06-09 18:56:25.737514 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 18:56:25.738351 INFO::Done
2024-06-09 18:56:25.739041 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 18:56:25.743542 INFO::Starting hierarchical adjustment
2024-06-09 18:56:25.744745 INFO::Found 5 batches.
2024-06-09 18:56:25.745581 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 18:56:25.74646 INFO::Using default BPPARAM
2024-06-09 18:56:25.747244 INFO::Processing subtree level 1
2024-06-09 18:56:25.887926 INFO::Adjusting the last 2 batches sequentially
2024-06-09 18:56:25.911697 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-09 18:56:25.95502 INFO::Done
2024-06-09 18:56:25.956345 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 18:56:25.962686 INFO::ASW Batch was 0.466674965916518 prior to batch effect correction and is now -0.0868225413313597 .
2024-06-09 18:56:25.963629 INFO::ASW Label was 0.334519613787346 prior to batch effect correction and is now 0.781025512518879 .
2024-06-09 18:56:25.96558 INFO::Total function execution time is 0.236555099487305 s and adjustment time is 0.210453987121582 s ( 88.97 )
2024-06-09 18:56:25.986923 INFO::Formatting Data.
2024-06-09 18:56:25.987773 INFO::Replacing NaNs with NAs.
2024-06-09 18:56:25.98874 INFO::Removing potential empty rows and columns
2024-06-09 18:56:25.989708 INFO::Found 0 missing values.
2024-06-09 18:56:25.994915 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 18:56:25.995788 INFO::Done
2024-06-09 18:56:25.996521 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 18:56:26.001772 INFO::Starting hierarchical adjustment
2024-06-09 18:56:26.002856 INFO::Found 5 batches.
2024-06-09 18:56:26.003443 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 18:56:26.004324 INFO::Using default BPPARAM
2024-06-09 18:56:26.005076 INFO::Processing subtree level 1
2024-06-09 18:56:26.144407 INFO::Adjusting the last 2 batches sequentially
2024-06-09 18:56:26.155716 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-09 18:56:26.187338 INFO::Done
2024-06-09 18:56:26.188325 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 18:56:26.194059 INFO::ASW Batch was 0.561766931426363 prior to batch effect correction and is now -0.0730125117520372 .
2024-06-09 18:56:26.19502 INFO::ASW Label was 0.200332083936438 prior to batch effect correction and is now 0.760808417713784 .
2024-06-09 18:56:26.197114 INFO::Total function execution time is 0.210180997848511 s and adjustment time is 0.184605121612549 s ( 87.83 )
2024-06-09 18:56:26.198523 INFO::Formatting Data.
2024-06-09 18:56:26.199199 INFO::Replacing NaNs with NAs.
2024-06-09 18:56:26.200256 INFO::Removing potential empty rows and columns
2024-06-09 18:56:26.201827 INFO::Found 0 missing values.
2024-06-09 18:56:26.20822 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 18:56:26.209127 INFO::Done
2024-06-09 18:56:26.209896 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 18:56:26.213582 INFO::Starting hierarchical adjustment
2024-06-09 18:56:26.214331 INFO::Found 5 batches.
2024-06-09 18:56:26.215135 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 18:56:26.216147 INFO::Using default BPPARAM
2024-06-09 18:56:26.216854 INFO::Processing subtree level 1
2024-06-09 18:56:26.343116 INFO::Adjusting the last 2 batches sequentially
2024-06-09 18:56:26.36455 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-09 18:56:26.40903 INFO::Done
2024-06-09 18:56:26.40983 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 18:56:26.413172 INFO::ASW Batch was 0.561766931426363 prior to batch effect correction and is now -0.0730125117520372 .
2024-06-09 18:56:26.41379 INFO::ASW Label was 0.200332083936438 prior to batch effect correction and is now 0.760808417713784 .
2024-06-09 18:56:26.414847 INFO::Total function execution time is 0.216459035873413 s and adjustment time is 0.194819927215576 s ( 90 )
2024-06-09 18:56:26.435122 INFO::Formatting Data.
2024-06-09 18:56:26.436197 INFO::Replacing NaNs with NAs.
2024-06-09 18:56:26.437201 INFO::Removing potential empty rows and columns
2024-06-09 18:56:26.438318 INFO::Found 0 missing values.
2024-06-09 18:56:26.442539 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 18:56:26.44344 INFO::Done
2024-06-09 18:56:26.444221 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 18:56:26.448729 INFO::Starting hierarchical adjustment
2024-06-09 18:56:26.44993 INFO::Found 2 batches.
2024-06-09 18:56:26.450734 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 18:56:26.451728 INFO::Using default BPPARAM
2024-06-09 18:56:26.45246 INFO::Adjusting the last 2 batches sequentially
2024-06-09 18:56:26.453886 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-09 18:56:26.474378 INFO::Done
2024-06-09 18:56:26.475313 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 18:56:26.478093 INFO::ASW Batch was 0.701663419449352 prior to batch effect correction and is now 0.0473716443863698 .
2024-06-09 18:56:26.478639 INFO::ASW Label was 0.390250119516021 prior to batch effect correction and is now 0.858269793324794 .
2024-06-09 18:56:26.479623 INFO::Total function execution time is 0.0446109771728516 s and adjustment time is 0.0247030258178711 s ( 55.37 )
2024-06-09 18:56:26.480417 INFO::Formatting Data.
2024-06-09 18:56:26.481249 INFO::Replacing NaNs with NAs.
2024-06-09 18:56:26.482066 INFO::Removing potential empty rows and columns
2024-06-09 18:56:26.482926 INFO::Found 0 missing values.
2024-06-09 18:56:26.485465 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 18:56:26.486209 INFO::Done
2024-06-09 18:56:26.48691 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 18:56:26.490609 INFO::Starting hierarchical adjustment
2024-06-09 18:56:26.491291 INFO::Found 2 batches.
2024-06-09 18:56:26.491837 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 18:56:26.492663 INFO::Using default BPPARAM
2024-06-09 18:56:26.493524 INFO::Adjusting the last 2 batches sequentially
2024-06-09 18:56:26.49496 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-09 18:56:26.515581 INFO::Done
2024-06-09 18:56:26.516509 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 18:56:26.519333 INFO::ASW Batch was 0.701663419449352 prior to batch effect correction and is now 0.0473716443863698 .
2024-06-09 18:56:26.519892 INFO::ASW Label was 0.390250119516021 prior to batch effect correction and is now 0.858269793324794 .
2024-06-09 18:56:26.520594 INFO::Total function execution time is 0.0402162075042725 s and adjustment time is 0.0243380069732666 s ( 60.52 )
2024-06-09 18:56:26.537204 INFO::Formatting Data.
2024-06-09 18:56:26.537944 INFO::Replacing NaNs with NAs.
2024-06-09 18:56:26.538769 INFO::Removing potential empty rows and columns
2024-06-09 18:56:26.539567 INFO::Found 0 missing values.
2024-06-09 18:56:26.541687 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 18:56:26.542376 INFO::Done
2024-06-09 18:56:26.543068 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 18:56:26.545934 INFO::Starting hierarchical adjustment
2024-06-09 18:56:26.546953 INFO::Found 2 batches.
2024-06-09 18:56:26.547647 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 18:56:26.548577 INFO::Using default BPPARAM
2024-06-09 18:56:26.550183 INFO::Adjusting the last 2 batches sequentially
2024-06-09 18:56:26.551545 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-09 18:56:26.581066 INFO::Done
2024-06-09 18:56:26.581717 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 18:56:26.583572 INFO::ASW Batch was 0.0361633163411657 prior to batch effect correction and is now -0.123096369351205 .
2024-06-09 18:56:26.584326 INFO::Total function execution time is 0.0472161769866943 s and adjustment time is 0.0343430042266846 s ( 72.74 )
2024-06-09 18:56:26.601237 INFO::Formatting Data.
2024-06-09 18:56:26.602093 INFO::Replacing NaNs with NAs.
2024-06-09 18:56:26.602957 INFO::Removing potential empty rows and columns
2024-06-09 18:56:26.604026 INFO::Found 0 missing values.
2024-06-09 18:56:26.605581 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.
2024-06-09 18:56:26.611148 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 18:56:26.611966 INFO::Done
2024-06-09 18:56:26.612791 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 18:56:26.617705 INFO::Starting hierarchical adjustment
2024-06-09 18:56:26.618458 INFO::Found 2 batches.
2024-06-09 18:56:26.618954 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 18:56:26.619746 INFO::Using default BPPARAM
2024-06-09 18:56:26.620236 INFO::Adjusting the last 2 batches sequentially
2024-06-09 18:56:26.621107 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-09 18:56:26.641636 INFO::Done
2024-06-09 18:56:26.642619 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 18:56:26.645654 INFO::ASW Batch was 0.483827463057532 prior to batch effect correction and is now -0.00128646192973203 .
2024-06-09 18:56:26.646246 INFO::ASW Label was 0.614867420146162 prior to batch effect correction and is now 0.926000333677834 .
2024-06-09 18:56:26.646996 INFO::Total function execution time is 0.0458610057830811 s and adjustment time is 0.0232710838317871 s ( 50.74 )
2024-06-09 18:56:26.647707 INFO::Formatting Data.
2024-06-09 18:56:26.64853 INFO::Replacing NaNs with NAs.
2024-06-09 18:56:26.649769 INFO::Removing potential empty rows and columns
2024-06-09 18:56:26.650735 INFO::Found 0 missing values.
2024-06-09 18:56:26.651568 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.
2024-06-09 18:56:26.657103 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 18:56:26.657789 INFO::Done
2024-06-09 18:56:26.658259 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 18:56:26.661519 INFO::Starting hierarchical adjustment
2024-06-09 18:56:26.662369 INFO::Found 2 batches.
2024-06-09 18:56:26.663068 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 18:56:26.663871 INFO::Using default BPPARAM
2024-06-09 18:56:26.664473 INFO::Adjusting the last 2 batches sequentially
2024-06-09 18:56:26.665336 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-09 18:56:26.688194 INFO::Done
2024-06-09 18:56:26.689063 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 18:56:26.692168 INFO::ASW Batch was 0.483827463057532 prior to batch effect correction and is now -0.00128646192973203 .
2024-06-09 18:56:26.692721 INFO::ASW Label was 0.614867420146162 prior to batch effect correction and is now 0.926000333677834 .
2024-06-09 18:56:26.693423 INFO::Total function execution time is 0.0457580089569092 s and adjustment time is 0.026015043258667 s ( 56.85 )
2024-06-09 18:56:26.907108 INFO::Formatting Data.
2024-06-09 18:56:26.907884 INFO::Replacing NaNs with NAs.
2024-06-09 18:56:26.908712 INFO::Removing potential empty rows and columns
2024-06-09 18:56:26.909999 INFO::Found 0 missing values.
2024-06-09 18:56:26.914295 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 18:56:26.915173 INFO::Done
2024-06-09 18:56:26.915936 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 18:56:26.918762 INFO::Starting hierarchical adjustment
2024-06-09 18:56:26.920036 INFO::Found 3 batches.
2024-06-09 18:56:26.920573 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 18:56:26.921345 INFO::Using default BPPARAM
2024-06-09 18:56:26.922031 INFO::Processing subtree level 1
2024-06-09 18:56:27.04575 INFO::Adjusting the last 1 batches sequentially
2024-06-09 18:56:27.054882 INFO::Done
2024-06-09 18:56:27.057118 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 18:56:27.068245 INFO::ASW Batch was -0.0914259353002658 prior to batch effect correction and is now -0.0914259353002658 .
2024-06-09 18:56:27.070437 INFO::Total function execution time is 0.163051843643188 s and adjustment time is 0.134986162185669 s ( 82.79 )
2024-06-09 18:56:27.07332 INFO::Formatting Data.
2024-06-09 18:56:27.075602 INFO::Typecasting input to dataframe.
2024-06-09 18:56:27.077272 INFO::Replacing NaNs with NAs.
2024-06-09 18:56:27.078238 INFO::Removing potential empty rows and columns
2024-06-09 18:56:27.079539 INFO::Found 0 missing values.
2024-06-09 18:56:27.082183 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 18:56:27.082661 INFO::Done
2024-06-09 18:56:27.083129 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 18:56:27.084904 INFO::Starting hierarchical adjustment
2024-06-09 18:56:27.085946 INFO::Found 3 batches.
2024-06-09 18:56:27.086426 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 18:56:27.086982 INFO::Using default BPPARAM
2024-06-09 18:56:27.087814 INFO::Processing subtree level 1
2024-06-09 18:56:27.211476 INFO::Adjusting the last 1 batches sequentially
2024-06-09 18:56:27.223752 INFO::Done
2024-06-09 18:56:27.225936 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 18:56:27.239054 INFO::ASW Batch was -0.0914259353002658 prior to batch effect correction and is now -0.0914259353002658 .
2024-06-09 18:56:27.24194 INFO::Total function execution time is 0.168560028076172 s and adjustment time is 0.137842893600464 s ( 81.78 )
2024-06-09 18:56:27.271336 INFO::Formatting Data.
2024-06-09 18:56:27.272621 INFO::Typecasting input to dataframe.
2024-06-09 18:56:27.274412 INFO::Replacing NaNs with NAs.
2024-06-09 18:56:27.276031 INFO::Removing potential empty rows and columns
2024-06-09 18:56:27.277512 INFO::Found 0 missing values.
2024-06-09 18:56:27.281525 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 18:56:27.282318 INFO::Done
2024-06-09 18:56:27.283195 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 18:56:27.29069 INFO::Starting hierarchical adjustment
2024-06-09 18:56:27.291841 INFO::Found 3 batches.
2024-06-09 18:56:27.292638 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 18:56:27.298523 INFO::Using default BPPARAM
2024-06-09 18:56:27.299377 INFO::Processing subtree level 1
2024-06-09 18:56:27.419542 INFO::Adjusting the last 1 batches sequentially
2024-06-09 18:56:27.427265 INFO::Done
2024-06-09 18:56:27.428882 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 18:56:27.444129 INFO::ASW Batch was 0.0453905729487303 prior to batch effect correction and is now 0.0453905729487303 .
2024-06-09 18:56:27.446615 INFO::Total function execution time is 0.174707174301147 s and adjustment time is 0.135640144348145 s ( 77.64 )
2024-06-09 18:56:27.677405 INFO::Formatting Data.
2024-06-09 18:56:27.678275 INFO::Replacing NaNs with NAs.
2024-06-09 18:56:27.679376 INFO::Removing potential empty rows and columns
2024-06-09 18:56:27.684984 INFO::Found 1000 missing values.
2024-06-09 18:56:27.711204 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 18:56:27.712219 INFO::Done
2024-06-09 18:56:27.713091 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 18:56:27.720622 INFO::Starting hierarchical adjustment
2024-06-09 18:56:27.722318 INFO::Found 10 batches.
2024-06-09 18:56:27.723121 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 18:56:27.723976 INFO::Using default BPPARAM
2024-06-09 18:56:27.724695 INFO::Processing subtree level 1
2024-06-09 18:56:27.893998 INFO::Processing subtree level 2
2024-06-09 18:56:28.115801 INFO::Adjusting the last 1 batches sequentially
2024-06-09 18:56:28.13092 INFO::Done
2024-06-09 18:56:28.133326 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 18:56:28.1506 INFO::ASW Batch was 0.507516903588246 prior to batch effect correction and is now 0.507516903588246 .
2024-06-09 18:56:28.151589 INFO::ASW Label was 0.326916555885677 prior to batch effect correction and is now 0.326916555885677 .
2024-06-09 18:56:28.155037 INFO::Total function execution time is 0.476382970809937 s and adjustment time is 0.408813953399658 s ( 85.82 )
2024-06-09 18:56:28.157288 INFO::Formatting Data.
2024-06-09 18:56:28.158444 INFO::Replacing NaNs with NAs.
2024-06-09 18:56:28.161353 INFO::Removing potential empty rows and columns
2024-06-09 18:56:28.166256 INFO::Found 1000 missing values.
2024-06-09 18:56:28.192401 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 18:56:28.193445 INFO::Done
2024-06-09 18:56:28.195738 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 18:56:28.201108 INFO::Starting hierarchical adjustment
2024-06-09 18:56:28.201928 INFO::Found 10 batches.
2024-06-09 18:56:29.229636 INFO::Set up parallel execution backend with 2 workers
2024-06-09 18:56:29.230632 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-06-09 18:56:30.611634 INFO::Adjusting the last 2 batches sequentially
2024-06-09 18:56:30.612864 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-09 18:56:30.63035 INFO::Done
2024-06-09 18:56:30.630981 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 18:56:30.638867 INFO::ASW Batch was 0.507516903588246 prior to batch effect correction and is now 0.507516903588246 .
2024-06-09 18:56:30.640048 INFO::ASW Label was 0.326916555885677 prior to batch effect correction and is now 0.326916555885677 .
2024-06-09 18:56:30.641391 INFO::Total function execution time is 2.48419404029846 s and adjustment time is 2.42856097221375 s ( 97.76 )
2024-06-09 18:56:30.867802 INFO::Formatting Data.
2024-06-09 18:56:30.870102 INFO::Replacing NaNs with NAs.
2024-06-09 18:56:30.872175 INFO::Removing potential empty rows and columns
2024-06-09 18:56:30.873399 INFO::Found 0 missing values.
2024-06-09 18:56:30.878146 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 18:56:30.879133 INFO::Done
2024-06-09 18:56:30.880166 INFO::Acquiring quality metrics before batch effect correction.
2024-06-09 18:56:30.883347 INFO::Starting hierarchical adjustment
2024-06-09 18:56:30.884113 INFO::Found 3 batches.
2024-06-09 18:56:30.884608 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-09 18:56:30.885251 INFO::Using default BPPARAM
2024-06-09 18:56:30.886002 INFO::Processing subtree level 1
2024-06-09 18:56:31.05245 INFO::Adjusting the last 1 batches sequentially
2024-06-09 18:56:31.063175 INFO::Done
2024-06-09 18:56:31.065712 INFO::Acquiring quality metrics after batch effect correction.
2024-06-09 18:56:31.077665 INFO::ASW Batch was 0.17970051668636 prior to batch effect correction and is now -0.158982114696831 .
2024-06-09 18:56:31.078834 INFO::ASW Label was -0.190527435033266 prior to batch effect correction and is now -0.0783980310223563 .
2024-06-09 18:56:31.081971 INFO::Total function execution time is 0.213535070419312 s and adjustment time is 0.179173946380615 s ( 83.91 )
2024-06-09 18:56:31.271758 INFO::Formatting Data.
2024-06-09 18:56:31.272743 INFO::Replacing NaNs with NAs.
2024-06-09 18:56:31.273666 INFO::Removing potential empty rows and columns
2024-06-09 18:56:31.275067 INFO::Found 2 missing values.
2024-06-09 18:56:31.278109 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-06-09 18:56:31.278637 INFO::Done
2024-06-09 18:56:31.324234 INFO::Found NA in Reference column
2024-06-09 18:56:31.339218 INFO::Require at least two references per batch.
2024-06-09 18:56:31.37179 INFO::Formatting Data.
2024-06-09 18:56:31.372952 INFO::Recognized SummarizedExperiment
2024-06-09 18:56:31.37392 INFO::Typecasting input to dataframe.
2024-06-09 18:56:31.386531 INFO::Replacing NaNs with NAs.
2024-06-09 18:56:31.387903 INFO::Removing potential empty rows and columns
2024-06-09 18:56:31.391959 INFO::Found 0 missing values.
2024-06-09 18:56:31.401548 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 18:56:31.4026 INFO::Done
2024-06-09 18:56:31.425357 INFO::Formatting Data.
2024-06-09 18:56:31.426398 INFO::Recognized SummarizedExperiment
2024-06-09 18:56:31.427232 INFO::Typecasting input to dataframe.
2024-06-09 18:56:31.448215 INFO::Replacing NaNs with NAs.
2024-06-09 18:56:31.450047 INFO::Removing potential empty rows and columns
2024-06-09 18:56:31.455415 INFO::Found 0 missing values.
2024-06-09 18:56:31.471921 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 18:56:31.473028 INFO::Done
2024-06-09 18:56:31.491519 INFO::Formatting Data.
2024-06-09 18:56:31.492317 INFO::Recognized SummarizedExperiment
2024-06-09 18:56:31.49282 INFO::Typecasting input to dataframe.
2024-06-09 18:56:31.508758 INFO::Replacing NaNs with NAs.
2024-06-09 18:56:31.509791 INFO::Removing potential empty rows and columns
2024-06-09 18:56:31.510773 INFO::Found 0 missing values.
2024-06-09 18:56:31.511652 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.
2024-06-09 18:56:31.515708 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 18:56:31.516324 INFO::Done
2024-06-09 18:56:31.533016 INFO::Formatting Data.
2024-06-09 18:56:31.534033 INFO::Replacing NaNs with NAs.
2024-06-09 18:56:31.535029 INFO::Removing potential empty rows and columns
2024-06-09 18:56:31.536035 INFO::Found 0 missing values.
2024-06-09 18:56:31.538911 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 18:56:31.539669 INFO::Done
2024-06-09 18:56:31.556033 INFO::Formatting Data.
2024-06-09 18:56:31.556827 INFO::Replacing NaNs with NAs.
2024-06-09 18:56:31.55768 INFO::Removing potential empty rows and columns
2024-06-09 18:56:31.558587 INFO::Found 0 missing values.
2024-06-09 18:56:31.561156 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 18:56:31.561632 INFO::Done
2024-06-09 18:56:31.601324 INFO::Formatting Data.
2024-06-09 18:56:31.602481 INFO::Replacing NaNs with NAs.
2024-06-09 18:56:31.603719 INFO::Removing potential empty rows and columns
2024-06-09 18:56:31.604803 INFO::Found 1 missing values.
2024-06-09 18:56:31.607434 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 18:56:31.608054 INFO::Done
2024-06-09 18:56:31.635815 INFO::Formatting Data.
2024-06-09 18:56:31.636613 INFO::Replacing NaNs with NAs.
2024-06-09 18:56:31.637475 INFO::Removing potential empty rows and columns
2024-06-09 18:56:31.638376 INFO::Found 2 missing values.
2024-06-09 18:56:31.639258 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.
2024-06-09 18:56:31.641378 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-06-09 18:56:31.641902 INFO::Done
2024-06-09 18:56:31.657667 INFO::Formatting Data.
2024-06-09 18:56:31.658946 INFO::Replacing NaNs with NAs.
2024-06-09 18:56:31.660343 INFO::Removing potential empty rows and columns
2024-06-09 18:56:31.661814 INFO::Found 2 missing values.
2024-06-09 18:56:31.664315 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 18:56:31.665149 INFO::Done
2024-06-09 18:56:31.681175 INFO::Formatting Data.
2024-06-09 18:56:31.682025 INFO::Typecasting input to dataframe.
2024-06-09 18:56:31.682857 INFO::Replacing NaNs with NAs.
2024-06-09 18:56:31.683753 INFO::Removing potential empty rows and columns
2024-06-09 18:56:31.684716 INFO::Found 0 missing values.
2024-06-09 18:56:31.688458 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-09 18:56:31.688944 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
20.159 3.858 24.490
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 26.443 | 1.425 | 18.960 | |
| compute_asw | 0.028 | 0.001 | 0.031 | |
| count_existing | 0.011 | 0.000 | 0.012 | |
| generate_data_covariables | 0.011 | 0.001 | 0.011 | |
| generate_dataset | 0.010 | 0.001 | 0.011 | |