Yannis Schumann
| Snapshot Date: 2024-10-16 14:00 -0400 (Wed, 16 Oct 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 2024-10-18 20:41 -0400 (Fri, 18 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4530 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4480 |
| 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 | | ||||||||
| palomino7 | 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 | | ||||||||
|
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: 2024-10-17 13:29:34 -0400 (Thu, 17 Oct 2024) |
| EndedAt: 2024-10-17 13:31:07 -0400 (Thu, 17 Oct 2024) |
| EllapsedTime: 93.4 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 4.4.1 (2024-06-14)
* using platform: aarch64-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 Ventura 13.6.6
* 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 30.583 1.668 24.032
* 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-arm64/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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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")
2024-10-17 13:30:42.303374 INFO::Formatting Data.
2024-10-17 13:30:42.307846 INFO::Replacing NaNs with NAs.
2024-10-17 13:30:42.31677 INFO::Removing potential empty rows and columns
2024-10-17 13:30:42.624226 INFO::Found 0 missing values.
2024-10-17 13:30:42.711311 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 13:30:42.711997 INFO::Done
2024-10-17 13:30:42.712299 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 13:30:42.73822 INFO::Starting hierarchical adjustment
2024-10-17 13:30:42.74004 INFO::Found 3 batches.
2024-10-17 13:30:42.740725 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 13:30:42.741851 INFO::Using default BPPARAM
2024-10-17 13:30:42.742123 INFO::Processing subtree level 1
2024-10-17 13:30:42.897561 INFO::Adjusting the last 1 batches sequentially
2024-10-17 13:30:42.905943 INFO::Done
2024-10-17 13:30:42.90683 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 13:30:42.913379 INFO::ASW Batch was -0.0371029957883678 prior to batch effect correction and is now -0.0371029957883678 .
2024-10-17 13:30:42.918988 INFO::Total function execution time is 0.61532187461853 s and adjustment time is 0.166146039962769 s ( 27 )
2024-10-17 13:30:42.9394 INFO::Formatting Data.
2024-10-17 13:30:42.940004 INFO::Replacing NaNs with NAs.
2024-10-17 13:30:42.940668 INFO::Removing potential empty rows and columns
2024-10-17 13:30:42.941566 INFO::Found 0 missing values.
2024-10-17 13:30:42.94236 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.
2024-10-17 13:30:42.966253 INFO::Formatting Data.
2024-10-17 13:30:42.966933 INFO::Replacing NaNs with NAs.
2024-10-17 13:30:42.967514 INFO::Removing potential empty rows and columns
2024-10-17 13:30:42.968084 INFO::Found 0 missing values.
2024-10-17 13:30:42.968664 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.
2024-10-17 13:30:42.99609 INFO::Formatting Data.
2024-10-17 13:30:42.997128 INFO::Replacing NaNs with NAs.
2024-10-17 13:30:42.998165 INFO::Removing potential empty rows and columns
2024-10-17 13:30:42.999327 INFO::Found 0 missing values.
2024-10-17 13:30:43.000299 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.
2024-10-17 13:30:43.006014 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 13:30:43.006738 INFO::Done
2024-10-17 13:30:43.007253 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 13:30:43.0098 INFO::Starting hierarchical adjustment
2024-10-17 13:30:43.010635 INFO::Found 2 batches.
2024-10-17 13:30:43.01114 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 13:30:43.012052 INFO::Using default BPPARAM
2024-10-17 13:30:43.012572 INFO::Adjusting the last 2 batches sequentially
2024-10-17 13:30:43.013462 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 13:30:43.055324 INFO::Done
2024-10-17 13:30:43.05612 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 13:30:43.058388 INFO::ASW Batch was 0.0701478895488332 prior to batch effect correction and is now -0.117100208354884 .
2024-10-17 13:30:43.059212 INFO::Total function execution time is 0.0633211135864258 s and adjustment time is 0.0447771549224854 s ( 70.71 )
2024-10-17 13:30:43.066337 INFO::Formatting Data.
2024-10-17 13:30:43.068726 INFO::Replacing NaNs with NAs.
2024-10-17 13:30:43.088093 INFO::Formatting Data.
2024-10-17 13:30:43.089311 INFO::Replacing NaNs with NAs.
2024-10-17 13:30:43.090934 INFO::Removing potential empty rows and columns
2024-10-17 13:30:43.09238 INFO::Found 0 missing values.
2024-10-17 13:30:43.098707 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 13:30:43.099724 INFO::Done
2024-10-17 13:30:43.100587 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 13:30:43.105242 INFO::Starting hierarchical adjustment
2024-10-17 13:30:43.107146 INFO::Found 2 batches.
2024-10-17 13:30:43.108565 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 13:30:43.109669 INFO::Using default BPPARAM
2024-10-17 13:30:43.110213 INFO::Adjusting the last 2 batches sequentially
2024-10-17 13:30:43.112589 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 13:30:43.13033 INFO::Done
2024-10-17 13:30:43.131313 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 13:30:43.134025 INFO::ASW Batch was -0.0699944933020479 prior to batch effect correction and is now -0.115183454608406 .
2024-10-17 13:30:43.135165 INFO::Total function execution time is 0.0487449169158936 s and adjustment time is 0.0239801406860352 s ( 49.2 )
2024-10-17 13:30:43.136632 INFO::Formatting Data.
2024-10-17 13:30:43.137775 INFO::Replacing NaNs with NAs.
2024-10-17 13:30:43.138964 INFO::Removing potential empty rows and columns
2024-10-17 13:30:43.140314 INFO::Found 0 missing values.
2024-10-17 13:30:43.143962 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 13:30:43.144704 INFO::Done
2024-10-17 13:30:43.145185 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 13:30:43.147381 INFO::Starting hierarchical adjustment
2024-10-17 13:30:43.148043 INFO::Found 2 batches.
2024-10-17 13:30:43.153747 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 13:30:43.154534 INFO::Using default BPPARAM
2024-10-17 13:30:43.155106 INFO::Adjusting the last 2 batches sequentially
2024-10-17 13:30:43.156314 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 13:30:43.180127 INFO::Done
2024-10-17 13:30:43.181089 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 13:30:43.183927 INFO::ASW Batch was -0.0699944933020479 prior to batch effect correction and is now -0.115183454608406 .
2024-10-17 13:30:43.185036 INFO::Total function execution time is 0.0484569072723389 s and adjustment time is 0.0321331024169922 s ( 66.31 )
2024-10-17 13:30:46.193469 INFO::Formatting Data.
2024-10-17 13:30:46.19467 INFO::Recognized SummarizedExperiment
2024-10-17 13:30:46.195123 INFO::Typecasting input to dataframe.
2024-10-17 13:30:46.238225 INFO::Replacing NaNs with NAs.
2024-10-17 13:30:46.239576 INFO::Removing potential empty rows and columns
2024-10-17 13:30:46.280215 INFO::Found 0 missing values.
2024-10-17 13:30:46.287376 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 13:30:46.288105 INFO::Done
2024-10-17 13:30:46.288561 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 13:30:46.292082 INFO::Starting hierarchical adjustment
2024-10-17 13:30:46.2927 INFO::Found 2 batches.
2024-10-17 13:30:46.293102 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 13:30:46.294242 INFO::Using default BPPARAM
2024-10-17 13:30:46.294654 INFO::Adjusting the last 2 batches sequentially
2024-10-17 13:30:46.295518 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 13:30:46.350783 INFO::Done
2024-10-17 13:30:46.351514 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 13:30:46.35498 INFO::ASW Batch was -0.00209939510901031 prior to batch effect correction and is now -0.0858293146712028 .
2024-10-17 13:30:46.355741 INFO::Total function execution time is 0.163186073303223 s and adjustment time is 0.0581619739532471 s ( 35.64 )
2024-10-17 13:30:46.378751 INFO::Formatting Data.
2024-10-17 13:30:46.379897 INFO::Recognized SummarizedExperiment
2024-10-17 13:30:46.380474 INFO::Typecasting input to dataframe.
2024-10-17 13:30:46.390399 INFO::Replacing NaNs with NAs.
2024-10-17 13:30:46.392105 INFO::Removing potential empty rows and columns
2024-10-17 13:30:46.39573 INFO::Found 0 missing values.
2024-10-17 13:30:46.401967 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 13:30:46.402625 INFO::Done
2024-10-17 13:30:46.403058 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 13:30:46.406628 INFO::Starting hierarchical adjustment
2024-10-17 13:30:46.407316 INFO::Found 2 batches.
2024-10-17 13:30:46.407732 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 13:30:46.408218 INFO::Using default BPPARAM
2024-10-17 13:30:46.408597 INFO::Adjusting the last 2 batches sequentially
2024-10-17 13:30:46.409426 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 13:30:46.435837 INFO::Done
2024-10-17 13:30:46.437012 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 13:30:46.440985 INFO::ASW Batch was -0.0267759219626453 prior to batch effect correction and is now -0.0267759219626453 .
2024-10-17 13:30:46.441924 INFO::Total function execution time is 0.0633080005645752 s and adjustment time is 0.0284590721130371 s ( 44.95 )
2024-10-17 13:30:46.461651 INFO::Formatting Data.
2024-10-17 13:30:46.462409 INFO::Replacing NaNs with NAs.
2024-10-17 13:30:46.463222 INFO::Removing potential empty rows and columns
2024-10-17 13:30:46.464158 INFO::Found 0 missing values.
2024-10-17 13:30:46.466554 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 13:30:46.46707 INFO::Done
2024-10-17 13:30:46.467487 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 13:30:46.469322 INFO::Starting hierarchical adjustment
2024-10-17 13:30:46.469903 INFO::Found 3 batches.
2024-10-17 13:30:46.470293 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 13:30:46.470774 INFO::Using default BPPARAM
2024-10-17 13:30:46.471178 INFO::Processing subtree level 1
2024-10-17 13:30:46.751933 INFO::Adjusting the last 1 batches sequentially
2024-10-17 13:30:46.758179 INFO::Done
2024-10-17 13:30:46.759755 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 13:30:46.767419 INFO::ASW Batch was 0.172976022694729 prior to batch effect correction and is now -0.146448966874804 .
2024-10-17 13:30:46.770506 INFO::Total function execution time is 0.308722019195557 s and adjustment time is 0.287793874740601 s ( 93.22 )
2024-10-17 13:30:46.804194 INFO::Skipping initial DF formatting
2024-10-17 13:30:46.805412 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 13:30:46.811129 INFO::Starting hierarchical adjustment
2024-10-17 13:30:46.812205 INFO::Found 5 batches.
2024-10-17 13:30:46.812886 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 13:30:46.814167 INFO::Using default BPPARAM
2024-10-17 13:30:46.815903 INFO::Processing subtree level 1
2024-10-17 13:30:47.051049 INFO::Adjusting the last 2 batches sequentially
2024-10-17 13:30:47.056178 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 13:30:47.096759 INFO::Done
2024-10-17 13:30:47.098183 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 13:30:47.107339 INFO::ASW Batch was 0.451980329171413 prior to batch effect correction and is now 0.451980329171413 .
2024-10-17 13:30:47.108349 INFO::ASW Label was 0.402372161307113 prior to batch effect correction and is now 0.402372161307113 .
2024-10-17 13:30:47.110678 INFO::Total function execution time is 0.306490182876587 s and adjustment time is 0.28470516204834 s ( 92.89 )
2024-10-17 13:30:47.141214 INFO::Formatting Data.
2024-10-17 13:30:47.142342 INFO::Replacing NaNs with NAs.
2024-10-17 13:30:47.1439 INFO::Removing potential empty rows and columns
2024-10-17 13:30:47.145253 INFO::Found 0 missing values.
2024-10-17 13:30:47.149898 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 13:30:47.150674 INFO::Done
2024-10-17 13:30:47.151313 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 13:30:47.155479 INFO::Starting hierarchical adjustment
2024-10-17 13:30:47.156652 INFO::Found 5 batches.
2024-10-17 13:30:47.157374 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 13:30:47.158304 INFO::Using default BPPARAM
2024-10-17 13:30:47.158908 INFO::Processing subtree level 1
2024-10-17 13:30:47.377903 INFO::Adjusting the last 2 batches sequentially
2024-10-17 13:30:47.382992 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 13:30:47.419807 INFO::Done
2024-10-17 13:30:47.420967 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 13:30:47.426247 INFO::ASW Batch was 0.552847509636476 prior to batch effect correction and is now 0.00977846261248277 .
2024-10-17 13:30:47.427024 INFO::ASW Label was 0.239596979650202 prior to batch effect correction and is now 0.70089827860449 .
2024-10-17 13:30:47.428625 INFO::Total function execution time is 0.287517070770264 s and adjustment time is 0.263346195220947 s ( 91.59 )
2024-10-17 13:30:47.429791 INFO::Formatting Data.
2024-10-17 13:30:47.430452 INFO::Replacing NaNs with NAs.
2024-10-17 13:30:47.433347 INFO::Removing potential empty rows and columns
2024-10-17 13:30:47.43568 INFO::Found 0 missing values.
2024-10-17 13:30:47.442615 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 13:30:47.447283 INFO::Done
2024-10-17 13:30:47.448016 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 13:30:47.451701 INFO::Starting hierarchical adjustment
2024-10-17 13:30:47.454079 INFO::Found 5 batches.
2024-10-17 13:30:47.454945 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 13:30:47.45584 INFO::Using default BPPARAM
2024-10-17 13:30:47.456453 INFO::Processing subtree level 1
2024-10-17 13:30:47.679345 INFO::Adjusting the last 2 batches sequentially
2024-10-17 13:30:47.684131 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 13:30:47.728516 INFO::Done
2024-10-17 13:30:47.729792 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 13:30:47.736088 INFO::ASW Batch was 0.552847509636476 prior to batch effect correction and is now 0.00977846261248277 .
2024-10-17 13:30:47.737315 INFO::ASW Label was 0.239596979650202 prior to batch effect correction and is now 0.70089827860449 .
2024-10-17 13:30:47.738865 INFO::Total function execution time is 0.308954954147339 s and adjustment time is 0.274863958358765 s ( 88.97 )
2024-10-17 13:30:47.776476 INFO::Formatting Data.
2024-10-17 13:30:47.777511 INFO::Replacing NaNs with NAs.
2024-10-17 13:30:47.7787 INFO::Removing potential empty rows and columns
2024-10-17 13:30:47.779995 INFO::Found 0 missing values.
2024-10-17 13:30:47.78452 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 13:30:47.78524 INFO::Done
2024-10-17 13:30:47.785808 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 13:30:47.792673 INFO::Starting hierarchical adjustment
2024-10-17 13:30:47.794433 INFO::Found 5 batches.
2024-10-17 13:30:47.795298 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 13:30:47.796144 INFO::Using default BPPARAM
2024-10-17 13:30:47.796707 INFO::Processing subtree level 1
2024-10-17 13:30:48.014224 INFO::Adjusting the last 2 batches sequentially
2024-10-17 13:30:48.019987 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 13:30:48.058339 INFO::Done
2024-10-17 13:30:48.059462 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 13:30:48.065749 INFO::ASW Batch was 0.249272466664648 prior to batch effect correction and is now -0.103730384172325 .
2024-10-17 13:30:48.068902 INFO::ASW Label was 0.519990224762453 prior to batch effect correction and is now 0.888464594715373 .
2024-10-17 13:30:48.072148 INFO::Total function execution time is 0.295680999755859 s and adjustment time is 0.264315128326416 s ( 89.39 )
2024-10-17 13:30:48.073444 INFO::Formatting Data.
2024-10-17 13:30:48.074164 INFO::Replacing NaNs with NAs.
2024-10-17 13:30:48.075373 INFO::Removing potential empty rows and columns
2024-10-17 13:30:48.076588 INFO::Found 0 missing values.
2024-10-17 13:30:48.08537 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 13:30:48.086637 INFO::Done
2024-10-17 13:30:48.087276 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 13:30:48.091361 INFO::Starting hierarchical adjustment
2024-10-17 13:30:48.092404 INFO::Found 5 batches.
2024-10-17 13:30:48.093046 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 13:30:48.093881 INFO::Using default BPPARAM
2024-10-17 13:30:48.094442 INFO::Processing subtree level 1
2024-10-17 13:30:48.301356 INFO::Adjusting the last 2 batches sequentially
2024-10-17 13:30:48.307638 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 13:30:48.351858 INFO::Done
2024-10-17 13:30:48.354319 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 13:30:48.363258 INFO::ASW Batch was 0.249272466664648 prior to batch effect correction and is now -0.103730384172325 .
2024-10-17 13:30:48.36585 INFO::ASW Label was 0.519990224762453 prior to batch effect correction and is now 0.888464594715373 .
2024-10-17 13:30:48.36763 INFO::Total function execution time is 0.293959856033325 s and adjustment time is 0.259566068649292 s ( 88.3 )
2024-10-17 13:30:48.393354 INFO::Formatting Data.
2024-10-17 13:30:48.394563 INFO::Replacing NaNs with NAs.
2024-10-17 13:30:48.396916 INFO::Removing potential empty rows and columns
2024-10-17 13:30:48.398908 INFO::Found 0 missing values.
2024-10-17 13:30:48.402414 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 13:30:48.403205 INFO::Done
2024-10-17 13:30:48.403817 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 13:30:48.40765 INFO::Starting hierarchical adjustment
2024-10-17 13:30:48.408757 INFO::Found 2 batches.
2024-10-17 13:30:48.409535 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 13:30:48.410681 INFO::Using default BPPARAM
2024-10-17 13:30:48.411465 INFO::Adjusting the last 2 batches sequentially
2024-10-17 13:30:48.412909 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 13:30:48.434423 INFO::Done
2024-10-17 13:30:48.435413 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 13:30:48.443059 INFO::ASW Batch was 0.484442764835385 prior to batch effect correction and is now -0.0280026223779544 .
2024-10-17 13:30:48.444752 INFO::ASW Label was 0.453499350441086 prior to batch effect correction and is now 0.916114388292659 .
2024-10-17 13:30:48.446089 INFO::Total function execution time is 0.052764892578125 s and adjustment time is 0.0257799625396729 s ( 48.86 )
2024-10-17 13:30:48.447056 INFO::Formatting Data.
2024-10-17 13:30:48.447923 INFO::Replacing NaNs with NAs.
2024-10-17 13:30:48.449122 INFO::Removing potential empty rows and columns
2024-10-17 13:30:48.450641 INFO::Found 0 missing values.
2024-10-17 13:30:48.454262 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 13:30:48.455075 INFO::Done
2024-10-17 13:30:48.455823 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 13:30:48.459641 INFO::Starting hierarchical adjustment
2024-10-17 13:30:48.460768 INFO::Found 2 batches.
2024-10-17 13:30:48.461589 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 13:30:48.462662 INFO::Using default BPPARAM
2024-10-17 13:30:48.463354 INFO::Adjusting the last 2 batches sequentially
2024-10-17 13:30:48.464642 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 13:30:48.489855 INFO::Done
2024-10-17 13:30:48.491323 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 13:30:48.552277 INFO::ASW Batch was 0.484442764835385 prior to batch effect correction and is now -0.0280026223779544 .
2024-10-17 13:30:48.554075 INFO::ASW Label was 0.453499350441086 prior to batch effect correction and is now 0.916114388292659 .
2024-10-17 13:30:48.555627 INFO::Total function execution time is 0.108520984649658 s and adjustment time is 0.0292220115661621 s ( 26.93 )
2024-10-17 13:30:48.584194 INFO::Formatting Data.
2024-10-17 13:30:48.585622 INFO::Replacing NaNs with NAs.
2024-10-17 13:30:48.587182 INFO::Removing potential empty rows and columns
2024-10-17 13:30:48.588713 INFO::Found 0 missing values.
2024-10-17 13:30:48.592062 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 13:30:48.592888 INFO::Done
2024-10-17 13:30:48.593553 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 13:30:48.601074 INFO::Starting hierarchical adjustment
2024-10-17 13:30:48.602583 INFO::Found 2 batches.
2024-10-17 13:30:48.603542 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 13:30:48.604479 INFO::Using default BPPARAM
2024-10-17 13:30:48.605317 INFO::Adjusting the last 2 batches sequentially
2024-10-17 13:30:48.607108 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 13:30:48.68941 INFO::Done
2024-10-17 13:30:48.691182 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 13:30:48.694829 INFO::ASW Batch was 0.0896968550980908 prior to batch effect correction and is now -0.148977454206382 .
2024-10-17 13:30:48.696416 INFO::Total function execution time is 0.112372875213623 s and adjustment time is 0.0869309902191162 s ( 77.36 )
2024-10-17 13:30:48.721958 INFO::Formatting Data.
2024-10-17 13:30:48.723117 INFO::Replacing NaNs with NAs.
2024-10-17 13:30:48.725196 INFO::Removing potential empty rows and columns
2024-10-17 13:30:48.727964 INFO::Found 0 missing values.
2024-10-17 13:30:48.731539 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.
2024-10-17 13:30:48.740284 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 13:30:48.741214 INFO::Done
2024-10-17 13:30:48.742038 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 13:30:48.747328 INFO::Starting hierarchical adjustment
2024-10-17 13:30:48.748396 INFO::Found 2 batches.
2024-10-17 13:30:48.749142 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 13:30:48.7499 INFO::Using default BPPARAM
2024-10-17 13:30:48.750497 INFO::Adjusting the last 2 batches sequentially
2024-10-17 13:30:48.752036 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 13:30:48.783161 INFO::Done
2024-10-17 13:30:48.784653 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 13:30:48.789705 INFO::ASW Batch was 0.406461732107133 prior to batch effect correction and is now -0.036962774741528 .
2024-10-17 13:30:48.790768 INFO::ASW Label was 0.64682149209284 prior to batch effect correction and is now 0.92936771392341 .
2024-10-17 13:30:48.791972 INFO::Total function execution time is 0.0700538158416748 s and adjustment time is 0.0348320007324219 s ( 49.72 )
2024-10-17 13:30:48.793517 INFO::Formatting Data.
2024-10-17 13:30:48.794621 INFO::Replacing NaNs with NAs.
2024-10-17 13:30:48.795908 INFO::Removing potential empty rows and columns
2024-10-17 13:30:48.797354 INFO::Found 0 missing values.
2024-10-17 13:30:48.79856 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.
2024-10-17 13:30:48.804423 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 13:30:48.805071 INFO::Done
2024-10-17 13:30:48.806035 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 13:30:48.809788 INFO::Starting hierarchical adjustment
2024-10-17 13:30:48.810769 INFO::Found 2 batches.
2024-10-17 13:30:48.811315 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 13:30:48.811987 INFO::Using default BPPARAM
2024-10-17 13:30:48.812636 INFO::Adjusting the last 2 batches sequentially
2024-10-17 13:30:48.813774 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 13:30:48.84602 INFO::Done
2024-10-17 13:30:48.84703 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 13:30:48.851449 INFO::ASW Batch was 0.406461732107133 prior to batch effect correction and is now -0.036962774741528 .
2024-10-17 13:30:48.852258 INFO::ASW Label was 0.64682149209284 prior to batch effect correction and is now 0.92936771392341 .
2024-10-17 13:30:48.85323 INFO::Total function execution time is 0.0598461627960205 s and adjustment time is 0.0353519916534424 s ( 59.07 )
2024-10-17 13:30:49.222219 INFO::Formatting Data.
2024-10-17 13:30:49.223248 INFO::Replacing NaNs with NAs.
2024-10-17 13:30:49.224325 INFO::Removing potential empty rows and columns
2024-10-17 13:30:49.225638 INFO::Found 0 missing values.
2024-10-17 13:30:49.229061 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 13:30:49.229659 INFO::Done
2024-10-17 13:30:49.230185 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 13:30:49.23493 INFO::Starting hierarchical adjustment
2024-10-17 13:30:49.23613 INFO::Found 3 batches.
2024-10-17 13:30:49.236788 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 13:30:49.23757 INFO::Using default BPPARAM
2024-10-17 13:30:49.238154 INFO::Processing subtree level 1
2024-10-17 13:30:49.508706 INFO::Adjusting the last 1 batches sequentially
2024-10-17 13:30:49.524849 INFO::Done
2024-10-17 13:30:49.526935 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 13:30:49.536594 INFO::ASW Batch was -0.0535273382468205 prior to batch effect correction and is now -0.0535273382468205 .
2024-10-17 13:30:49.540024 INFO::Total function execution time is 0.317386150360107 s and adjustment time is 0.288793802261353 s ( 90.99 )
2024-10-17 13:30:49.542701 INFO::Formatting Data.
2024-10-17 13:30:49.544273 INFO::Typecasting input to dataframe.
2024-10-17 13:30:49.547661 INFO::Replacing NaNs with NAs.
2024-10-17 13:30:49.550847 INFO::Removing potential empty rows and columns
2024-10-17 13:30:49.552947 INFO::Found 0 missing values.
2024-10-17 13:30:49.557408 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 13:30:49.558212 INFO::Done
2024-10-17 13:30:49.559042 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 13:30:49.563575 INFO::Starting hierarchical adjustment
2024-10-17 13:30:49.565125 INFO::Found 3 batches.
2024-10-17 13:30:49.566046 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 13:30:49.567335 INFO::Using default BPPARAM
2024-10-17 13:30:49.568037 INFO::Processing subtree level 1
2024-10-17 13:30:49.756475 INFO::Adjusting the last 1 batches sequentially
2024-10-17 13:30:49.764004 INFO::Done
2024-10-17 13:30:49.767154 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 13:30:49.772521 INFO::ASW Batch was -0.0535273382468205 prior to batch effect correction and is now -0.0535273382468205 .
2024-10-17 13:30:49.774328 INFO::Total function execution time is 0.231531143188477 s and adjustment time is 0.199105978012085 s ( 86 )
2024-10-17 13:30:49.801402 INFO::Formatting Data.
2024-10-17 13:30:49.802458 INFO::Typecasting input to dataframe.
2024-10-17 13:30:49.803474 INFO::Replacing NaNs with NAs.
2024-10-17 13:30:49.804635 INFO::Removing potential empty rows and columns
2024-10-17 13:30:49.806004 INFO::Found 0 missing values.
2024-10-17 13:30:49.811361 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 13:30:49.813087 INFO::Done
2024-10-17 13:30:49.814731 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 13:30:49.818235 INFO::Starting hierarchical adjustment
2024-10-17 13:30:49.819189 INFO::Found 3 batches.
2024-10-17 13:30:49.819892 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 13:30:49.820758 INFO::Using default BPPARAM
2024-10-17 13:30:49.82145 INFO::Processing subtree level 1
2024-10-17 13:30:50.029573 INFO::Adjusting the last 1 batches sequentially
2024-10-17 13:30:50.03585 INFO::Done
2024-10-17 13:30:50.037399 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 13:30:50.046054 INFO::ASW Batch was 0.0630403788151937 prior to batch effect correction and is now 0.0630403788151937 .
2024-10-17 13:30:50.048578 INFO::Total function execution time is 0.246858835220337 s and adjustment time is 0.2168288230896 s ( 87.84 )
2024-10-17 13:30:50.358227 INFO::Formatting Data.
2024-10-17 13:30:50.35935 INFO::Replacing NaNs with NAs.
2024-10-17 13:30:50.360907 INFO::Removing potential empty rows and columns
2024-10-17 13:30:50.364799 INFO::Found 1000 missing values.
2024-10-17 13:30:50.389914 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 13:30:50.391614 INFO::Done
2024-10-17 13:30:50.392804 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 13:30:50.402412 INFO::Starting hierarchical adjustment
2024-10-17 13:30:50.403767 INFO::Found 10 batches.
2024-10-17 13:30:50.40454 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 13:30:50.405475 INFO::Using default BPPARAM
2024-10-17 13:30:50.406014 INFO::Processing subtree level 1
2024-10-17 13:30:50.915878 INFO::Processing subtree level 2
2024-10-17 13:30:51.297491 INFO::Adjusting the last 1 batches sequentially
2024-10-17 13:30:51.30394 INFO::Done
2024-10-17 13:30:51.307098 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 13:30:51.32153 INFO::ASW Batch was 0.514327056780551 prior to batch effect correction and is now 0.514327056780551 .
2024-10-17 13:30:51.32285 INFO::ASW Label was 0.323134681210297 prior to batch effect correction and is now 0.323134681210297 .
2024-10-17 13:30:51.324555 INFO::Total function execution time is 0.966245889663696 s and adjustment time is 0.900281190872192 s ( 93.17 )
2024-10-17 13:30:51.325864 INFO::Formatting Data.
2024-10-17 13:30:51.326579 INFO::Replacing NaNs with NAs.
2024-10-17 13:30:51.328174 INFO::Removing potential empty rows and columns
2024-10-17 13:30:51.331757 INFO::Found 1000 missing values.
2024-10-17 13:30:51.380074 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 13:30:51.381136 INFO::Done
2024-10-17 13:30:51.381833 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 13:30:51.392266 INFO::Starting hierarchical adjustment
2024-10-17 13:30:51.393927 INFO::Found 10 batches.
2024-10-17 13:30:52.916583 INFO::Set up parallel execution backend with 2 workers
2024-10-17 13:30:52.917496 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-10-17 13:30:54.600212 INFO::Adjusting the last 2 batches sequentially
2024-10-17 13:30:54.601955 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-17 13:30:54.62134 INFO::Done
2024-10-17 13:30:54.622172 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 13:30:54.628451 INFO::ASW Batch was 0.514327056780551 prior to batch effect correction and is now 0.514327056780551 .
2024-10-17 13:30:54.629087 INFO::ASW Label was 0.323134681210297 prior to batch effect correction and is now 0.323134681210297 .
2024-10-17 13:30:54.629813 INFO::Total function execution time is 3.30405497550964 s and adjustment time is 3.22771215438843 s ( 97.69 )
2024-10-17 13:30:54.87971 INFO::Formatting Data.
2024-10-17 13:30:54.880782 INFO::Replacing NaNs with NAs.
2024-10-17 13:30:54.881907 INFO::Removing potential empty rows and columns
2024-10-17 13:30:54.883225 INFO::Found 0 missing values.
2024-10-17 13:30:54.887842 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 13:30:54.888557 INFO::Done
2024-10-17 13:30:54.889156 INFO::Acquiring quality metrics before batch effect correction.
2024-10-17 13:30:54.893703 INFO::Starting hierarchical adjustment
2024-10-17 13:30:54.895025 INFO::Found 3 batches.
2024-10-17 13:30:54.896133 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-17 13:30:54.897116 INFO::Using default BPPARAM
2024-10-17 13:30:54.897706 INFO::Processing subtree level 1
2024-10-17 13:30:55.093922 INFO::Adjusting the last 1 batches sequentially
2024-10-17 13:30:55.100459 INFO::Done
2024-10-17 13:30:55.102194 INFO::Acquiring quality metrics after batch effect correction.
2024-10-17 13:30:55.111235 INFO::ASW Batch was 0.205296969811481 prior to batch effect correction and is now -0.146599870093516 .
2024-10-17 13:30:55.112228 INFO::ASW Label was -0.176128166061192 prior to batch effect correction and is now -0.00544645545593079 .
2024-10-17 13:30:55.114155 INFO::Total function execution time is 0.234078168869019 s and adjustment time is 0.20564079284668 s ( 87.85 )
2024-10-17 13:30:55.310836 INFO::Formatting Data.
2024-10-17 13:30:55.311933 INFO::Replacing NaNs with NAs.
2024-10-17 13:30:55.31301 INFO::Removing potential empty rows and columns
2024-10-17 13:30:55.314322 INFO::Found 2 missing values.
2024-10-17 13:30:55.318232 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-10-17 13:30:55.319231 INFO::Done
2024-10-17 13:30:55.35884 INFO::Found NA in Reference column
2024-10-17 13:30:55.374607 INFO::Require at least two references per batch.
2024-10-17 13:30:55.405162 INFO::Formatting Data.
2024-10-17 13:30:55.406219 INFO::Recognized SummarizedExperiment
2024-10-17 13:30:55.406734 INFO::Typecasting input to dataframe.
2024-10-17 13:30:55.423289 INFO::Replacing NaNs with NAs.
2024-10-17 13:30:55.425085 INFO::Removing potential empty rows and columns
2024-10-17 13:30:55.430428 INFO::Found 0 missing values.
2024-10-17 13:30:55.440882 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 13:30:55.441831 INFO::Done
2024-10-17 13:30:55.46424 INFO::Formatting Data.
2024-10-17 13:30:55.465387 INFO::Recognized SummarizedExperiment
2024-10-17 13:30:55.466147 INFO::Typecasting input to dataframe.
2024-10-17 13:30:55.488718 INFO::Replacing NaNs with NAs.
2024-10-17 13:30:55.490963 INFO::Removing potential empty rows and columns
2024-10-17 13:30:55.495614 INFO::Found 0 missing values.
2024-10-17 13:30:55.512699 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 13:30:55.513773 INFO::Done
2024-10-17 13:30:55.532313 INFO::Formatting Data.
2024-10-17 13:30:55.534226 INFO::Recognized SummarizedExperiment
2024-10-17 13:30:55.535096 INFO::Typecasting input to dataframe.
2024-10-17 13:30:55.560392 INFO::Replacing NaNs with NAs.
2024-10-17 13:30:55.56296 INFO::Removing potential empty rows and columns
2024-10-17 13:30:55.564862 INFO::Found 0 missing values.
2024-10-17 13:30:55.566024 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.
2024-10-17 13:30:55.571578 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 13:30:55.572335 INFO::Done
2024-10-17 13:30:55.587577 INFO::Formatting Data.
2024-10-17 13:30:55.588476 INFO::Replacing NaNs with NAs.
2024-10-17 13:30:55.589376 INFO::Removing potential empty rows and columns
2024-10-17 13:30:55.590448 INFO::Found 0 missing values.
2024-10-17 13:30:55.59423 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 13:30:55.594871 INFO::Done
2024-10-17 13:30:55.612594 INFO::Formatting Data.
2024-10-17 13:30:55.613598 INFO::Replacing NaNs with NAs.
2024-10-17 13:30:55.615011 INFO::Removing potential empty rows and columns
2024-10-17 13:30:55.616119 INFO::Found 0 missing values.
2024-10-17 13:30:55.619501 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 13:30:55.620135 INFO::Done
2024-10-17 13:30:55.663032 INFO::Formatting Data.
2024-10-17 13:30:55.664073 INFO::Replacing NaNs with NAs.
2024-10-17 13:30:55.665285 INFO::Removing potential empty rows and columns
2024-10-17 13:30:55.666589 INFO::Found 1 missing values.
2024-10-17 13:30:55.670476 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 13:30:55.671682 INFO::Done
2024-10-17 13:30:55.697025 INFO::Formatting Data.
2024-10-17 13:30:55.698129 INFO::Replacing NaNs with NAs.
2024-10-17 13:30:55.699223 INFO::Removing potential empty rows and columns
2024-10-17 13:30:55.700335 INFO::Found 2 missing values.
2024-10-17 13:30:55.701486 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.
2024-10-17 13:30:55.705692 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-10-17 13:30:55.707057 INFO::Done
2024-10-17 13:30:55.72166 INFO::Formatting Data.
2024-10-17 13:30:55.722619 INFO::Replacing NaNs with NAs.
2024-10-17 13:30:55.723586 INFO::Removing potential empty rows and columns
2024-10-17 13:30:55.724659 INFO::Found 2 missing values.
2024-10-17 13:30:55.726456 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 13:30:55.727029 INFO::Done
2024-10-17 13:30:55.745324 INFO::Formatting Data.
2024-10-17 13:30:55.746256 INFO::Typecasting input to dataframe.
2024-10-17 13:30:55.748201 INFO::Replacing NaNs with NAs.
2024-10-17 13:30:55.749628 INFO::Removing potential empty rows and columns
2024-10-17 13:30:55.751107 INFO::Found 0 missing values.
2024-10-17 13:30:55.754961 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-17 13:30:55.755611 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
20.276 6.623 28.477
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 30.583 | 1.668 | 24.032 | |
| compute_asw | 0.031 | 0.001 | 0.035 | |
| count_existing | 0.016 | 0.000 | 0.017 | |
| generate_data_covariables | 0.015 | 0.001 | 0.016 | |
| generate_dataset | 0.015 | 0.002 | 0.017 | |