Yannis Schumann
| Snapshot Date: 2024-06-26 14:00 -0400 (Wed, 26 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 2024-06-28 17:42 -0400 (Fri, 28 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" | 4760 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4362 |
| 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 | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | 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: 2024-06-27 00:55:14 -0400 (Thu, 27 Jun 2024) |
| EndedAt: 2024-06-27 00:57:47 -0400 (Thu, 27 Jun 2024) |
| EllapsedTime: 152.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.0.0.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 12.7.4
* 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 46.333 2.764 38.112
* 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")
2024-06-27 00:57:08.781454 INFO::Formatting Data.
2024-06-27 00:57:08.788008 INFO::Replacing NaNs with NAs.
2024-06-27 00:57:08.825831 INFO::Removing potential empty rows and columns
2024-06-27 00:57:09.620564 INFO::Found 0 missing values.
2024-06-27 00:57:09.629712 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 00:57:09.631281 INFO::Done
2024-06-27 00:57:09.632658 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 00:57:09.663289 INFO::Starting hierarchical adjustment
2024-06-27 00:57:09.665188 INFO::Found 3 batches.
2024-06-27 00:57:09.666738 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 00:57:09.669356 INFO::Using default BPPARAM
2024-06-27 00:57:09.670741 INFO::Processing subtree level 1
2024-06-27 00:57:09.96999 INFO::Adjusting the last 1 batches sequentially
2024-06-27 00:57:09.977081 INFO::Done
2024-06-27 00:57:09.978635 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 00:57:09.985471 INFO::ASW Batch was -0.0741587525879276 prior to batch effect correction and is now -0.0741587525879276 .
2024-06-27 00:57:09.988436 INFO::Total function execution time is 1.20800495147705 s and adjustment time is 0.312283992767334 s ( 25.85 )
2024-06-27 00:57:10.024411 INFO::Formatting Data.
2024-06-27 00:57:10.026075 INFO::Replacing NaNs with NAs.
2024-06-27 00:57:10.028355 INFO::Removing potential empty rows and columns
2024-06-27 00:57:10.031258 INFO::Found 0 missing values.
2024-06-27 00:57:10.033614 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.
2024-06-27 00:57:10.063982 INFO::Formatting Data.
2024-06-27 00:57:10.06563 INFO::Replacing NaNs with NAs.
2024-06-27 00:57:10.067721 INFO::Removing potential empty rows and columns
2024-06-27 00:57:10.070346 INFO::Found 0 missing values.
2024-06-27 00:57:10.072808 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.
2024-06-27 00:57:10.125671 INFO::Formatting Data.
2024-06-27 00:57:10.127344 INFO::Replacing NaNs with NAs.
2024-06-27 00:57:10.133054 INFO::Removing potential empty rows and columns
2024-06-27 00:57:10.135999 INFO::Found 0 missing values.
2024-06-27 00:57:10.138356 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.
2024-06-27 00:57:10.157187 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 00:57:10.158675 INFO::Done
2024-06-27 00:57:10.160002 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 00:57:10.16487 INFO::Starting hierarchical adjustment
2024-06-27 00:57:10.166757 INFO::Found 2 batches.
2024-06-27 00:57:10.168095 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 00:57:10.169695 INFO::Using default BPPARAM
2024-06-27 00:57:10.171035 INFO::Adjusting the last 2 batches sequentially
2024-06-27 00:57:10.173401 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-27 00:57:10.23664 INFO::Done
2024-06-27 00:57:10.238086 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 00:57:10.244753 INFO::ASW Batch was -0.0393408189315704 prior to batch effect correction and is now -0.117440701766406 .
2024-06-27 00:57:10.246723 INFO::Total function execution time is 0.121109008789062 s and adjustment time is 0.0702579021453857 s ( 58.01 )
2024-06-27 00:57:10.254202 INFO::Formatting Data.
2024-06-27 00:57:10.255754 INFO::Replacing NaNs with NAs.
2024-06-27 00:57:10.281149 INFO::Formatting Data.
2024-06-27 00:57:10.282923 INFO::Replacing NaNs with NAs.
2024-06-27 00:57:10.285018 INFO::Removing potential empty rows and columns
2024-06-27 00:57:10.287658 INFO::Found 0 missing values.
2024-06-27 00:57:10.29641 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 00:57:10.297978 INFO::Done
2024-06-27 00:57:10.299266 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 00:57:10.30481 INFO::Starting hierarchical adjustment
2024-06-27 00:57:10.308259 INFO::Found 2 batches.
2024-06-27 00:57:10.31024 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 00:57:10.311886 INFO::Using default BPPARAM
2024-06-27 00:57:10.313235 INFO::Adjusting the last 2 batches sequentially
2024-06-27 00:57:10.315646 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-27 00:57:10.360713 INFO::Done
2024-06-27 00:57:10.362807 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 00:57:10.368175 INFO::ASW Batch was 0.0446951853728515 prior to batch effect correction and is now -0.12032809526816 .
2024-06-27 00:57:10.370096 INFO::Total function execution time is 0.0890758037567139 s and adjustment time is 0.0542871952056885 s ( 60.94 )
2024-06-27 00:57:10.376063 INFO::Formatting Data.
2024-06-27 00:57:10.378223 INFO::Replacing NaNs with NAs.
2024-06-27 00:57:10.381109 INFO::Removing potential empty rows and columns
2024-06-27 00:57:10.384116 INFO::Found 0 missing values.
2024-06-27 00:57:10.395346 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 00:57:10.396818 INFO::Done
2024-06-27 00:57:10.398075 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 00:57:10.403375 INFO::Starting hierarchical adjustment
2024-06-27 00:57:10.405223 INFO::Found 2 batches.
2024-06-27 00:57:10.406504 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 00:57:10.408023 INFO::Using default BPPARAM
2024-06-27 00:57:10.409352 INFO::Adjusting the last 2 batches sequentially
2024-06-27 00:57:10.41263 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-27 00:57:10.461582 INFO::Done
2024-06-27 00:57:10.463045 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 00:57:10.467818 INFO::ASW Batch was 0.0446951853728515 prior to batch effect correction and is now -0.12032809526816 .
2024-06-27 00:57:10.470612 INFO::Total function execution time is 0.0978779792785645 s and adjustment time is 0.0567011833190918 s ( 57.93 )
2024-06-27 00:57:16.422769 INFO::Formatting Data.
2024-06-27 00:57:16.424111 INFO::Recognized SummarizedExperiment
2024-06-27 00:57:16.425166 INFO::Typecasting input to dataframe.
2024-06-27 00:57:17.535095 INFO::Replacing NaNs with NAs.
2024-06-27 00:57:17.537353 INFO::Removing potential empty rows and columns
2024-06-27 00:57:17.547379 INFO::Found 0 missing values.
2024-06-27 00:57:17.567452 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 00:57:17.568794 INFO::Done
2024-06-27 00:57:17.569963 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 00:57:17.581162 INFO::Starting hierarchical adjustment
2024-06-27 00:57:17.582779 INFO::Found 2 batches.
2024-06-27 00:57:17.58402 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 00:57:17.588064 INFO::Using default BPPARAM
2024-06-27 00:57:17.589364 INFO::Adjusting the last 2 batches sequentially
2024-06-27 00:57:17.59156 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-27 00:57:17.741016 INFO::Done
2024-06-27 00:57:17.744399 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 00:57:17.752513 INFO::ASW Batch was 0.00231065786052779 prior to batch effect correction and is now -0.0894241347861032 .
2024-06-27 00:57:17.756696 INFO::Total function execution time is 1.33457493782043 s and adjustment time is 0.158566951751709 s ( 11.88 )
2024-06-27 00:57:17.804241 INFO::Formatting Data.
2024-06-27 00:57:17.805595 INFO::Recognized SummarizedExperiment
2024-06-27 00:57:17.806701 INFO::Typecasting input to dataframe.
2024-06-27 00:57:17.830889 INFO::Replacing NaNs with NAs.
2024-06-27 00:57:17.833144 INFO::Removing potential empty rows and columns
2024-06-27 00:57:17.842074 INFO::Found 0 missing values.
2024-06-27 00:57:17.863039 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 00:57:17.864338 INFO::Done
2024-06-27 00:57:17.865471 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 00:57:17.875889 INFO::Starting hierarchical adjustment
2024-06-27 00:57:17.877856 INFO::Found 2 batches.
2024-06-27 00:57:17.878989 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 00:57:17.881829 INFO::Using default BPPARAM
2024-06-27 00:57:17.883045 INFO::Adjusting the last 2 batches sequentially
2024-06-27 00:57:17.88521 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-27 00:57:17.958319 INFO::Done
2024-06-27 00:57:17.960272 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 00:57:17.968288 INFO::ASW Batch was -0.00800728921826663 prior to batch effect correction and is now -0.00800728921826663 .
2024-06-27 00:57:17.971528 INFO::Total function execution time is 0.166409969329834 s and adjustment time is 0.0808110237121582 s ( 48.56 )
2024-06-27 00:57:18.022272 INFO::Formatting Data.
2024-06-27 00:57:18.023884 INFO::Replacing NaNs with NAs.
2024-06-27 00:57:18.025921 INFO::Removing potential empty rows and columns
2024-06-27 00:57:18.028563 INFO::Found 0 missing values.
2024-06-27 00:57:18.037184 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 00:57:18.03856 INFO::Done
2024-06-27 00:57:18.039785 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 00:57:18.045514 INFO::Starting hierarchical adjustment
2024-06-27 00:57:18.047603 INFO::Found 3 batches.
2024-06-27 00:57:18.048821 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 00:57:18.050157 INFO::Using default BPPARAM
2024-06-27 00:57:18.05137 INFO::Processing subtree level 1
2024-06-27 00:57:18.51209 INFO::Adjusting the last 1 batches sequentially
2024-06-27 00:57:18.521401 INFO::Done
2024-06-27 00:57:18.522961 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 00:57:18.532112 INFO::ASW Batch was -0.0666400020537317 prior to batch effect correction and is now -0.161727605825502 .
2024-06-27 00:57:18.53617 INFO::Total function execution time is 0.5137779712677 s and adjustment time is 0.474195957183838 s ( 92.3 )
2024-06-27 00:57:18.578413 INFO::Skipping initial DF formatting
2024-06-27 00:57:18.579916 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 00:57:18.592955 INFO::Starting hierarchical adjustment
2024-06-27 00:57:18.595007 INFO::Found 5 batches.
2024-06-27 00:57:18.596409 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 00:57:18.598032 INFO::Using default BPPARAM
2024-06-27 00:57:18.59951 INFO::Processing subtree level 1
2024-06-27 00:57:18.961369 INFO::Adjusting the last 2 batches sequentially
2024-06-27 00:57:18.97086 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-27 00:57:19.048289 INFO::Done
2024-06-27 00:57:19.049843 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 00:57:19.060876 INFO::ASW Batch was 0.525271818784544 prior to batch effect correction and is now 0.525271818784544 .
2024-06-27 00:57:19.06241 INFO::ASW Label was 0.373044313345471 prior to batch effect correction and is now 0.373044313345471 .
2024-06-27 00:57:19.064574 INFO::Total function execution time is 0.486213207244873 s and adjustment time is 0.453680992126465 s ( 93.31 )
2024-06-27 00:57:19.116966 INFO::Formatting Data.
2024-06-27 00:57:19.118736 INFO::Replacing NaNs with NAs.
2024-06-27 00:57:19.121148 INFO::Removing potential empty rows and columns
2024-06-27 00:57:19.124408 INFO::Found 0 missing values.
2024-06-27 00:57:19.138237 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 00:57:19.139749 INFO::Done
2024-06-27 00:57:19.141103 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 00:57:19.148979 INFO::Starting hierarchical adjustment
2024-06-27 00:57:19.150936 INFO::Found 5 batches.
2024-06-27 00:57:19.152279 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 00:57:19.153848 INFO::Using default BPPARAM
2024-06-27 00:57:19.155226 INFO::Processing subtree level 1
2024-06-27 00:57:19.423746 INFO::Adjusting the last 2 batches sequentially
2024-06-27 00:57:19.433892 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-27 00:57:19.484969 INFO::Done
2024-06-27 00:57:19.486819 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 00:57:19.495576 INFO::ASW Batch was 0.560509999340745 prior to batch effect correction and is now -0.101228332751422 .
2024-06-27 00:57:19.497205 INFO::ASW Label was 0.181524378292728 prior to batch effect correction and is now 0.846452675434943 .
2024-06-27 00:57:19.499603 INFO::Total function execution time is 0.382710933685303 s and adjustment time is 0.334447145462036 s ( 87.39 )
2024-06-27 00:57:19.50247 INFO::Formatting Data.
2024-06-27 00:57:19.503892 INFO::Replacing NaNs with NAs.
2024-06-27 00:57:19.506318 INFO::Removing potential empty rows and columns
2024-06-27 00:57:19.510953 INFO::Found 0 missing values.
2024-06-27 00:57:19.526157 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 00:57:19.53104 INFO::Done
2024-06-27 00:57:19.532726 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 00:57:19.540293 INFO::Starting hierarchical adjustment
2024-06-27 00:57:19.543659 INFO::Found 5 batches.
2024-06-27 00:57:19.545089 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 00:57:19.546667 INFO::Using default BPPARAM
2024-06-27 00:57:19.548042 INFO::Processing subtree level 1
2024-06-27 00:57:19.825626 INFO::Adjusting the last 2 batches sequentially
2024-06-27 00:57:19.836685 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-27 00:57:19.887076 INFO::Done
2024-06-27 00:57:19.888857 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 00:57:19.897478 INFO::ASW Batch was 0.560509999340745 prior to batch effect correction and is now -0.101228332751422 .
2024-06-27 00:57:19.89903 INFO::ASW Label was 0.181524378292728 prior to batch effect correction and is now 0.846452675434943 .
2024-06-27 00:57:19.901269 INFO::Total function execution time is 0.398779153823853 s and adjustment time is 0.343871116638184 s ( 86.23 )
2024-06-27 00:57:19.944443 INFO::Formatting Data.
2024-06-27 00:57:19.946885 INFO::Replacing NaNs with NAs.
2024-06-27 00:57:19.949117 INFO::Removing potential empty rows and columns
2024-06-27 00:57:19.952369 INFO::Found 0 missing values.
2024-06-27 00:57:19.965169 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 00:57:19.967289 INFO::Done
2024-06-27 00:57:19.968839 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 00:57:19.978196 INFO::Starting hierarchical adjustment
2024-06-27 00:57:19.980277 INFO::Found 5 batches.
2024-06-27 00:57:19.9818 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 00:57:19.98344 INFO::Using default BPPARAM
2024-06-27 00:57:19.984844 INFO::Processing subtree level 1
2024-06-27 00:57:20.258263 INFO::Adjusting the last 2 batches sequentially
2024-06-27 00:57:20.271973 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-27 00:57:20.323174 INFO::Done
2024-06-27 00:57:20.324752 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 00:57:20.33307 INFO::ASW Batch was 0.299369173180618 prior to batch effect correction and is now -0.0650339273563246 .
2024-06-27 00:57:20.334676 INFO::ASW Label was 0.421897354600632 prior to batch effect correction and is now 0.848866115097059 .
2024-06-27 00:57:20.336866 INFO::Total function execution time is 0.392959117889404 s and adjustment time is 0.343353033065796 s ( 87.38 )
2024-06-27 00:57:20.339289 INFO::Formatting Data.
2024-06-27 00:57:20.341485 INFO::Replacing NaNs with NAs.
2024-06-27 00:57:20.344083 INFO::Removing potential empty rows and columns
2024-06-27 00:57:20.346936 INFO::Found 0 missing values.
2024-06-27 00:57:20.358918 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 00:57:20.360583 INFO::Done
2024-06-27 00:57:20.362567 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 00:57:20.370289 INFO::Starting hierarchical adjustment
2024-06-27 00:57:20.372869 INFO::Found 5 batches.
2024-06-27 00:57:20.374456 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 00:57:20.37625 INFO::Using default BPPARAM
2024-06-27 00:57:20.377803 INFO::Processing subtree level 1
2024-06-27 00:57:20.645107 INFO::Adjusting the last 2 batches sequentially
2024-06-27 00:57:20.655353 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-27 00:57:20.708117 INFO::Done
2024-06-27 00:57:20.710172 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 00:57:20.718763 INFO::ASW Batch was 0.299369173180618 prior to batch effect correction and is now -0.0650339273563246 .
2024-06-27 00:57:20.720855 INFO::ASW Label was 0.421897354600632 prior to batch effect correction and is now 0.848866115097059 .
2024-06-27 00:57:20.72359 INFO::Total function execution time is 0.384299039840698 s and adjustment time is 0.335738897323608 s ( 87.36 )
2024-06-27 00:57:20.766019 INFO::Formatting Data.
2024-06-27 00:57:20.768488 INFO::Replacing NaNs with NAs.
2024-06-27 00:57:20.770789 INFO::Removing potential empty rows and columns
2024-06-27 00:57:20.775669 INFO::Found 0 missing values.
2024-06-27 00:57:20.784654 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 00:57:20.786163 INFO::Done
2024-06-27 00:57:20.788576 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 00:57:20.79627 INFO::Starting hierarchical adjustment
2024-06-27 00:57:20.798407 INFO::Found 2 batches.
2024-06-27 00:57:20.799965 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 00:57:20.801695 INFO::Using default BPPARAM
2024-06-27 00:57:20.803216 INFO::Adjusting the last 2 batches sequentially
2024-06-27 00:57:20.805674 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-27 00:57:20.850161 INFO::Done
2024-06-27 00:57:20.85183 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 00:57:20.86021 INFO::ASW Batch was 0.528892190833204 prior to batch effect correction and is now 0.0474366574101878 .
2024-06-27 00:57:20.8626 INFO::ASW Label was 0.60575567818113 prior to batch effect correction and is now 0.897670984187908 .
2024-06-27 00:57:20.86507 INFO::Total function execution time is 0.0991549491882324 s and adjustment time is 0.0521910190582275 s ( 52.64 )
2024-06-27 00:57:20.867636 INFO::Formatting Data.
2024-06-27 00:57:20.869389 INFO::Replacing NaNs with NAs.
2024-06-27 00:57:20.871772 INFO::Removing potential empty rows and columns
2024-06-27 00:57:20.87551 INFO::Found 0 missing values.
2024-06-27 00:57:20.88409 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 00:57:20.885561 INFO::Done
2024-06-27 00:57:20.886873 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 00:57:20.897596 INFO::Starting hierarchical adjustment
2024-06-27 00:57:20.899518 INFO::Found 2 batches.
2024-06-27 00:57:20.902065 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 00:57:20.903593 INFO::Using default BPPARAM
2024-06-27 00:57:20.904851 INFO::Adjusting the last 2 batches sequentially
2024-06-27 00:57:20.90814 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-27 00:57:20.949543 INFO::Done
2024-06-27 00:57:20.95112 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 00:57:20.959286 INFO::ASW Batch was 0.528892190833204 prior to batch effect correction and is now 0.0474366574101878 .
2024-06-27 00:57:20.960706 INFO::ASW Label was 0.60575567818113 prior to batch effect correction and is now 0.897670984187908 .
2024-06-27 00:57:20.962791 INFO::Total function execution time is 0.0951030254364014 s and adjustment time is 0.0504319667816162 s ( 53.03 )
2024-06-27 00:57:21.002569 INFO::Formatting Data.
2024-06-27 00:57:21.005192 INFO::Replacing NaNs with NAs.
2024-06-27 00:57:21.007448 INFO::Removing potential empty rows and columns
2024-06-27 00:57:21.010139 INFO::Found 0 missing values.
2024-06-27 00:57:21.016961 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 00:57:21.018342 INFO::Done
2024-06-27 00:57:21.019562 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 00:57:21.024219 INFO::Starting hierarchical adjustment
2024-06-27 00:57:21.026048 INFO::Found 2 batches.
2024-06-27 00:57:21.028998 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 00:57:21.030452 INFO::Using default BPPARAM
2024-06-27 00:57:21.031781 INFO::Adjusting the last 2 batches sequentially
2024-06-27 00:57:21.033982 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-27 00:57:21.133368 INFO::Done
2024-06-27 00:57:21.134807 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 00:57:21.142482 INFO::ASW Batch was -0.0546945447769418 prior to batch effect correction and is now -0.0938674549804736 .
2024-06-27 00:57:21.144525 INFO::Total function execution time is 0.142105102539062 s and adjustment time is 0.107670068740845 s ( 75.77 )
2024-06-27 00:57:21.181065 INFO::Formatting Data.
2024-06-27 00:57:21.182732 INFO::Replacing NaNs with NAs.
2024-06-27 00:57:21.184831 INFO::Removing potential empty rows and columns
2024-06-27 00:57:21.18918 INFO::Found 0 missing values.
2024-06-27 00:57:21.192001 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.
2024-06-27 00:57:21.206692 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 00:57:21.208478 INFO::Done
2024-06-27 00:57:21.211061 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 00:57:21.218229 INFO::Starting hierarchical adjustment
2024-06-27 00:57:21.220208 INFO::Found 2 batches.
2024-06-27 00:57:21.223136 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 00:57:21.224757 INFO::Using default BPPARAM
2024-06-27 00:57:21.226047 INFO::Adjusting the last 2 batches sequentially
2024-06-27 00:57:21.228366 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-27 00:57:21.281039 INFO::Done
2024-06-27 00:57:21.282632 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 00:57:21.290048 INFO::ASW Batch was 0.634516130480931 prior to batch effect correction and is now -0.0266967638788683 .
2024-06-27 00:57:21.29328 INFO::ASW Label was 0.330719507787469 prior to batch effect correction and is now 0.932174546458035 .
2024-06-27 00:57:21.29527 INFO::Total function execution time is 0.114280939102173 s and adjustment time is 0.0611879825592041 s ( 53.54 )
2024-06-27 00:57:21.297668 INFO::Formatting Data.
2024-06-27 00:57:21.299402 INFO::Replacing NaNs with NAs.
2024-06-27 00:57:21.301684 INFO::Removing potential empty rows and columns
2024-06-27 00:57:21.305252 INFO::Found 0 missing values.
2024-06-27 00:57:21.307699 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.
2024-06-27 00:57:21.322071 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 00:57:21.323631 INFO::Done
2024-06-27 00:57:21.326285 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 00:57:21.334527 INFO::Starting hierarchical adjustment
2024-06-27 00:57:21.33756 INFO::Found 2 batches.
2024-06-27 00:57:21.339072 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 00:57:21.340596 INFO::Using default BPPARAM
2024-06-27 00:57:21.341888 INFO::Adjusting the last 2 batches sequentially
2024-06-27 00:57:21.344677 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-27 00:57:21.395047 INFO::Done
2024-06-27 00:57:21.396553 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 00:57:21.404576 INFO::ASW Batch was 0.634516130480931 prior to batch effect correction and is now -0.0266967638788683 .
2024-06-27 00:57:21.406224 INFO::ASW Label was 0.330719507787469 prior to batch effect correction and is now 0.932174546458035 .
2024-06-27 00:57:21.408305 INFO::Total function execution time is 0.110690116882324 s and adjustment time is 0.0589430332183838 s ( 53.25 )
2024-06-27 00:57:22.074727 INFO::Formatting Data.
2024-06-27 00:57:22.076401 INFO::Replacing NaNs with NAs.
2024-06-27 00:57:22.078837 INFO::Removing potential empty rows and columns
2024-06-27 00:57:22.081536 INFO::Found 0 missing values.
2024-06-27 00:57:22.091677 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 00:57:22.093214 INFO::Done
2024-06-27 00:57:22.09458 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 00:57:22.100501 INFO::Starting hierarchical adjustment
2024-06-27 00:57:22.10238 INFO::Found 3 batches.
2024-06-27 00:57:22.103689 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 00:57:22.105927 INFO::Using default BPPARAM
2024-06-27 00:57:22.107247 INFO::Processing subtree level 1
2024-06-27 00:57:22.348187 INFO::Adjusting the last 1 batches sequentially
2024-06-27 00:57:22.359016 INFO::Done
2024-06-27 00:57:22.361015 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 00:57:22.371168 INFO::ASW Batch was 0.033628399805087 prior to batch effect correction and is now 0.033628399805087 .
2024-06-27 00:57:22.376039 INFO::Total function execution time is 0.301295042037964 s and adjustment time is 0.256969928741455 s ( 85.29 )
2024-06-27 00:57:22.378816 INFO::Formatting Data.
2024-06-27 00:57:22.382766 INFO::Typecasting input to dataframe.
2024-06-27 00:57:22.384702 INFO::Replacing NaNs with NAs.
2024-06-27 00:57:22.386924 INFO::Removing potential empty rows and columns
2024-06-27 00:57:22.390362 INFO::Found 0 missing values.
2024-06-27 00:57:22.399211 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 00:57:22.400743 INFO::Done
2024-06-27 00:57:22.402661 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 00:57:22.408098 INFO::Starting hierarchical adjustment
2024-06-27 00:57:22.410432 INFO::Found 3 batches.
2024-06-27 00:57:22.411842 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 00:57:22.414421 INFO::Using default BPPARAM
2024-06-27 00:57:22.417078 INFO::Processing subtree level 1
2024-06-27 00:57:22.660076 INFO::Adjusting the last 1 batches sequentially
2024-06-27 00:57:22.671625 INFO::Done
2024-06-27 00:57:22.675758 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 00:57:22.686411 INFO::ASW Batch was 0.033628399805087 prior to batch effect correction and is now 0.033628399805087 .
2024-06-27 00:57:22.691558 INFO::Total function execution time is 0.312697887420654 s and adjustment time is 0.261983871459961 s ( 83.78 )
2024-06-27 00:57:22.732405 INFO::Formatting Data.
2024-06-27 00:57:22.734253 INFO::Typecasting input to dataframe.
2024-06-27 00:57:22.736445 INFO::Replacing NaNs with NAs.
2024-06-27 00:57:22.738798 INFO::Removing potential empty rows and columns
2024-06-27 00:57:22.743302 INFO::Found 0 missing values.
2024-06-27 00:57:22.752954 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 00:57:22.754491 INFO::Done
2024-06-27 00:57:22.755869 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 00:57:22.761728 INFO::Starting hierarchical adjustment
2024-06-27 00:57:22.763558 INFO::Found 3 batches.
2024-06-27 00:57:22.764814 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 00:57:22.766266 INFO::Using default BPPARAM
2024-06-27 00:57:22.767512 INFO::Processing subtree level 1
2024-06-27 00:57:23.011977 INFO::Adjusting the last 1 batches sequentially
2024-06-27 00:57:23.022736 INFO::Done
2024-06-27 00:57:23.024985 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 00:57:23.034349 INFO::ASW Batch was -0.116919245354201 prior to batch effect correction and is now -0.116919245354201 .
2024-06-27 00:57:23.039793 INFO::Total function execution time is 0.307420969009399 s and adjustment time is 0.259500980377197 s ( 84.41 )
2024-06-27 00:57:23.460622 INFO::Formatting Data.
2024-06-27 00:57:23.462975 INFO::Replacing NaNs with NAs.
2024-06-27 00:57:23.465813 INFO::Removing potential empty rows and columns
2024-06-27 00:57:23.474121 INFO::Found 1000 missing values.
2024-06-27 00:57:23.552763 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 00:57:23.554345 INFO::Done
2024-06-27 00:57:23.555704 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 00:57:23.568263 INFO::Starting hierarchical adjustment
2024-06-27 00:57:23.570819 INFO::Found 10 batches.
2024-06-27 00:57:23.572366 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 00:57:23.574064 INFO::Using default BPPARAM
2024-06-27 00:57:23.575563 INFO::Processing subtree level 1
2024-06-27 00:57:23.921987 INFO::Processing subtree level 2
2024-06-27 00:57:24.370714 INFO::Adjusting the last 1 batches sequentially
2024-06-27 00:57:24.384211 INFO::Done
2024-06-27 00:57:24.386238 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 00:57:24.403759 INFO::ASW Batch was 0.518518234475252 prior to batch effect correction and is now 0.518518234475252 .
2024-06-27 00:57:24.40535 INFO::ASW Label was 0.319684751204324 prior to batch effect correction and is now 0.319684751204324 .
2024-06-27 00:57:24.410668 INFO::Total function execution time is 0.948515892028809 s and adjustment time is 0.813838005065918 s ( 85.8 )
2024-06-27 00:57:24.413194 INFO::Formatting Data.
2024-06-27 00:57:24.415654 INFO::Replacing NaNs with NAs.
2024-06-27 00:57:24.418905 INFO::Removing potential empty rows and columns
2024-06-27 00:57:24.428818 INFO::Found 1000 missing values.
2024-06-27 00:57:24.496057 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 00:57:24.499071 INFO::Done
2024-06-27 00:57:24.500496 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 00:57:24.520653 INFO::Starting hierarchical adjustment
2024-06-27 00:57:24.523774 INFO::Found 10 batches.
2024-06-27 00:57:25.997618 INFO::Set up parallel execution backend with 2 workers
2024-06-27 00:57:25.999234 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-06-27 00:57:28.020034 INFO::Adjusting the last 2 batches sequentially
2024-06-27 00:57:28.022912 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-27 00:57:28.074943 INFO::Done
2024-06-27 00:57:28.076176 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 00:57:28.090006 INFO::ASW Batch was 0.518518234475252 prior to batch effect correction and is now 0.518518234475252 .
2024-06-27 00:57:28.092778 INFO::ASW Label was 0.319684751204324 prior to batch effect correction and is now 0.319684751204324 .
2024-06-27 00:57:28.094411 INFO::Total function execution time is 3.68141198158264 s and adjustment time is 3.55165386199951 s ( 96.48 )
2024-06-27 00:57:28.563544 INFO::Formatting Data.
2024-06-27 00:57:28.565159 INFO::Replacing NaNs with NAs.
2024-06-27 00:57:28.567263 INFO::Removing potential empty rows and columns
2024-06-27 00:57:28.571168 INFO::Found 0 missing values.
2024-06-27 00:57:28.582497 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 00:57:28.583922 INFO::Done
2024-06-27 00:57:28.585227 INFO::Acquiring quality metrics before batch effect correction.
2024-06-27 00:57:28.592514 INFO::Starting hierarchical adjustment
2024-06-27 00:57:28.594349 INFO::Found 3 batches.
2024-06-27 00:57:28.595594 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-27 00:57:28.597841 INFO::Using default BPPARAM
2024-06-27 00:57:28.599023 INFO::Processing subtree level 1
2024-06-27 00:57:28.926189 INFO::Adjusting the last 1 batches sequentially
2024-06-27 00:57:28.939757 INFO::Done
2024-06-27 00:57:28.941952 INFO::Acquiring quality metrics after batch effect correction.
2024-06-27 00:57:28.954869 INFO::ASW Batch was 0.268161255081075 prior to batch effect correction and is now -0.157035489857012 .
2024-06-27 00:57:28.957907 INFO::ASW Label was -0.159834071616991 prior to batch effect correction and is now 0.0517410555946239 .
2024-06-27 00:57:28.961919 INFO::Total function execution time is 0.398401975631714 s and adjustment time is 0.345727920532227 s ( 86.78 )
2024-06-27 00:57:29.375859 INFO::Formatting Data.
2024-06-27 00:57:29.377685 INFO::Replacing NaNs with NAs.
2024-06-27 00:57:29.379908 INFO::Removing potential empty rows and columns
2024-06-27 00:57:29.383283 INFO::Found 2 missing values.
2024-06-27 00:57:29.392917 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-06-27 00:57:29.395731 INFO::Done
2024-06-27 00:57:29.484518 INFO::Found NA in Reference column
2024-06-27 00:57:29.515757 INFO::Require at least two references per batch.
2024-06-27 00:57:29.582108 INFO::Formatting Data.
2024-06-27 00:57:29.583648 INFO::Recognized SummarizedExperiment
2024-06-27 00:57:29.584962 INFO::Typecasting input to dataframe.
2024-06-27 00:57:29.616498 INFO::Replacing NaNs with NAs.
2024-06-27 00:57:29.619156 INFO::Removing potential empty rows and columns
2024-06-27 00:57:29.631692 INFO::Found 0 missing values.
2024-06-27 00:57:29.658739 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 00:57:29.66031 INFO::Done
2024-06-27 00:57:29.706672 INFO::Formatting Data.
2024-06-27 00:57:29.708372 INFO::Recognized SummarizedExperiment
2024-06-27 00:57:29.709694 INFO::Typecasting input to dataframe.
2024-06-27 00:57:29.763143 INFO::Replacing NaNs with NAs.
2024-06-27 00:57:29.76591 INFO::Removing potential empty rows and columns
2024-06-27 00:57:29.778309 INFO::Found 0 missing values.
2024-06-27 00:57:29.910595 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 00:57:29.912163 INFO::Done
2024-06-27 00:57:29.961344 INFO::Formatting Data.
2024-06-27 00:57:29.96296 INFO::Recognized SummarizedExperiment
2024-06-27 00:57:29.964298 INFO::Typecasting input to dataframe.
2024-06-27 00:57:30.020341 INFO::Replacing NaNs with NAs.
2024-06-27 00:57:30.022626 INFO::Removing potential empty rows and columns
2024-06-27 00:57:30.025429 INFO::Found 0 missing values.
2024-06-27 00:57:30.027797 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.
2024-06-27 00:57:30.043517 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 00:57:30.045105 INFO::Done
2024-06-27 00:57:30.074078 INFO::Formatting Data.
2024-06-27 00:57:30.075792 INFO::Replacing NaNs with NAs.
2024-06-27 00:57:30.077795 INFO::Removing potential empty rows and columns
2024-06-27 00:57:30.0805 INFO::Found 0 missing values.
2024-06-27 00:57:30.089753 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 00:57:30.091266 INFO::Done
2024-06-27 00:57:30.129321 INFO::Formatting Data.
2024-06-27 00:57:30.131684 INFO::Replacing NaNs with NAs.
2024-06-27 00:57:30.134168 INFO::Removing potential empty rows and columns
2024-06-27 00:57:30.137641 INFO::Found 0 missing values.
2024-06-27 00:57:30.147764 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 00:57:30.149306 INFO::Done
2024-06-27 00:57:30.24709 INFO::Formatting Data.
2024-06-27 00:57:30.249421 INFO::Replacing NaNs with NAs.
2024-06-27 00:57:30.254467 INFO::Removing potential empty rows and columns
2024-06-27 00:57:30.257746 INFO::Found 1 missing values.
2024-06-27 00:57:30.267961 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 00:57:30.269804 INFO::Done
2024-06-27 00:57:30.330672 INFO::Formatting Data.
2024-06-27 00:57:30.333399 INFO::Replacing NaNs with NAs.
2024-06-27 00:57:30.335535 INFO::Removing potential empty rows and columns
2024-06-27 00:57:30.337963 INFO::Found 2 missing values.
2024-06-27 00:57:30.340544 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.
2024-06-27 00:57:30.347184 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-06-27 00:57:30.348674 INFO::Done
2024-06-27 00:57:30.380134 INFO::Formatting Data.
2024-06-27 00:57:30.381833 INFO::Replacing NaNs with NAs.
2024-06-27 00:57:30.383921 INFO::Removing potential empty rows and columns
2024-06-27 00:57:30.38613 INFO::Found 2 missing values.
2024-06-27 00:57:30.391766 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 00:57:30.393246 INFO::Done
2024-06-27 00:57:30.426636 INFO::Formatting Data.
2024-06-27 00:57:30.42845 INFO::Typecasting input to dataframe.
2024-06-27 00:57:30.43054 INFO::Replacing NaNs with NAs.
2024-06-27 00:57:30.4335 INFO::Removing potential empty rows and columns
2024-06-27 00:57:30.436897 INFO::Found 0 missing values.
2024-06-27 00:57:30.44601 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-27 00:57:30.447442 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
36.330 6.241 47.842
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 46.333 | 2.764 | 38.112 | |
| compute_asw | 0.060 | 0.001 | 0.064 | |
| count_existing | 0.030 | 0.001 | 0.032 | |
| generate_data_covariables | 0.027 | 0.003 | 0.034 | |
| generate_dataset | 0.026 | 0.003 | 0.035 | |