Yannis Schumann
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_20 |
| git_last_commit: 9764e3f |
| git_last_commit_date: 2024-10-29 11:26:04 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 159/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.2.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.2.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.2.0.tar.gz |
| StartedAt: 2024-12-20 00:06:03 -0500 (Fri, 20 Dec 2024) |
| EndedAt: 2024-12-20 00:08:26 -0500 (Fri, 20 Dec 2024) |
| EllapsedTime: 143.4 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_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 44.7 2.559 36.38
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘BERT’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2024-12-20 00:07:51.663777 INFO::Formatting Data.
2024-12-20 00:07:51.670487 INFO::Replacing NaNs with NAs.
2024-12-20 00:07:51.705285 INFO::Removing potential empty rows and columns
2024-12-20 00:07:52.427786 INFO::Found 0 missing values.
2024-12-20 00:07:52.437532 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 00:07:52.43898 INFO::Done
2024-12-20 00:07:52.440286 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 00:07:52.468291 INFO::Starting hierarchical adjustment
2024-12-20 00:07:52.470336 INFO::Found 3 batches.
2024-12-20 00:07:52.471739 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 00:07:52.474318 INFO::Using default BPPARAM
2024-12-20 00:07:52.475868 INFO::Processing subtree level 1
2024-12-20 00:07:52.755929 INFO::Adjusting the last 1 batches sequentially
2024-12-20 00:07:52.761933 INFO::Done
2024-12-20 00:07:52.764898 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 00:07:52.771676 INFO::ASW Batch was -0.0510372405220661 prior to batch effect correction and is now -0.0510372405220661 .
2024-12-20 00:07:52.775882 INFO::Total function execution time is 1.11225485801697 s and adjustment time is 0.291953086853027 s ( 26.25 )
2024-12-20 00:07:52.817329 INFO::Formatting Data.
2024-12-20 00:07:52.819108 INFO::Replacing NaNs with NAs.
2024-12-20 00:07:52.821848 INFO::Removing potential empty rows and columns
2024-12-20 00:07:52.82504 INFO::Found 0 missing values.
2024-12-20 00:07:52.827596 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.
2024-12-20 00:07:52.856243 INFO::Formatting Data.
2024-12-20 00:07:52.857783 INFO::Replacing NaNs with NAs.
2024-12-20 00:07:52.859786 INFO::Removing potential empty rows and columns
2024-12-20 00:07:52.86253 INFO::Found 0 missing values.
2024-12-20 00:07:52.865303 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.
2024-12-20 00:07:52.912613 INFO::Formatting Data.
2024-12-20 00:07:52.914272 INFO::Replacing NaNs with NAs.
2024-12-20 00:07:52.916372 INFO::Removing potential empty rows and columns
2024-12-20 00:07:52.919925 INFO::Found 0 missing values.
2024-12-20 00:07:52.922388 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.
2024-12-20 00:07:52.935494 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 00:07:52.936977 INFO::Done
2024-12-20 00:07:52.938967 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 00:07:52.943548 INFO::Starting hierarchical adjustment
2024-12-20 00:07:52.945286 INFO::Found 2 batches.
2024-12-20 00:07:52.946503 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 00:07:52.948085 INFO::Using default BPPARAM
2024-12-20 00:07:52.949473 INFO::Adjusting the last 2 batches sequentially
2024-12-20 00:07:52.951781 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-20 00:07:53.009334 INFO::Done
2024-12-20 00:07:53.011495 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 00:07:53.018071 INFO::ASW Batch was 0.0888600268310752 prior to batch effect correction and is now -0.0822632528839346 .
2024-12-20 00:07:53.021122 INFO::Total function execution time is 0.108561992645264 s and adjustment time is 0.0643110275268555 s ( 59.24 )
2024-12-20 00:07:53.030793 INFO::Formatting Data.
2024-12-20 00:07:53.032453 INFO::Replacing NaNs with NAs.
2024-12-20 00:07:53.056222 INFO::Formatting Data.
2024-12-20 00:07:53.05785 INFO::Replacing NaNs with NAs.
2024-12-20 00:07:53.059943 INFO::Removing potential empty rows and columns
2024-12-20 00:07:53.062564 INFO::Found 0 missing values.
2024-12-20 00:07:53.070385 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 00:07:53.072457 INFO::Done
2024-12-20 00:07:53.073939 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 00:07:53.078842 INFO::Starting hierarchical adjustment
2024-12-20 00:07:53.080836 INFO::Found 2 batches.
2024-12-20 00:07:53.082547 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 00:07:53.084256 INFO::Using default BPPARAM
2024-12-20 00:07:53.085767 INFO::Adjusting the last 2 batches sequentially
2024-12-20 00:07:53.088076 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-20 00:07:53.130983 INFO::Done
2024-12-20 00:07:53.13245 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 00:07:53.137465 INFO::ASW Batch was 0.00167707468141092 prior to batch effect correction and is now -0.11273055250867 .
2024-12-20 00:07:53.139385 INFO::Total function execution time is 0.0832412242889404 s and adjustment time is 0.0505480766296387 s ( 60.72 )
2024-12-20 00:07:53.141927 INFO::Formatting Data.
2024-12-20 00:07:53.143362 INFO::Replacing NaNs with NAs.
2024-12-20 00:07:53.145864 INFO::Removing potential empty rows and columns
2024-12-20 00:07:53.148573 INFO::Found 0 missing values.
2024-12-20 00:07:53.156854 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 00:07:53.158154 INFO::Done
2024-12-20 00:07:53.159605 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 00:07:53.164249 INFO::Starting hierarchical adjustment
2024-12-20 00:07:53.16607 INFO::Found 2 batches.
2024-12-20 00:07:53.168023 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 00:07:53.169517 INFO::Using default BPPARAM
2024-12-20 00:07:53.170792 INFO::Adjusting the last 2 batches sequentially
2024-12-20 00:07:53.172995 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-20 00:07:53.212751 INFO::Done
2024-12-20 00:07:53.2142 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 00:07:53.219002 INFO::ASW Batch was 0.00167707468141092 prior to batch effect correction and is now -0.11273055250867 .
2024-12-20 00:07:53.220902 INFO::Total function execution time is 0.0789988040924072 s and adjustment time is 0.0470058917999268 s ( 59.5 )
2024-12-20 00:07:59.344078 INFO::Formatting Data.
2024-12-20 00:07:59.345345 INFO::Recognized SummarizedExperiment
2024-12-20 00:07:59.346429 INFO::Typecasting input to dataframe.
2024-12-20 00:07:59.411517 INFO::Replacing NaNs with NAs.
2024-12-20 00:07:59.413788 INFO::Removing potential empty rows and columns
2024-12-20 00:07:59.422881 INFO::Found 0 missing values.
2024-12-20 00:07:59.440913 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 00:07:59.442114 INFO::Done
2024-12-20 00:07:59.443147 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 00:07:59.450946 INFO::Starting hierarchical adjustment
2024-12-20 00:07:59.452452 INFO::Found 2 batches.
2024-12-20 00:07:59.453515 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 00:07:59.45551 INFO::Using default BPPARAM
2024-12-20 00:07:59.456595 INFO::Adjusting the last 2 batches sequentially
2024-12-20 00:07:59.458688 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-20 00:07:59.59289 INFO::Done
2024-12-20 00:07:59.594199 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 00:07:59.60342 INFO::ASW Batch was 0.0472603904277994 prior to batch effect correction and is now -0.0897224244723401 .
2024-12-20 00:07:59.605322 INFO::Total function execution time is 0.261893033981323 s and adjustment time is 0.140704870223999 s ( 53.73 )
2024-12-20 00:07:59.653357 INFO::Formatting Data.
2024-12-20 00:07:59.654984 INFO::Recognized SummarizedExperiment
2024-12-20 00:07:59.656348 INFO::Typecasting input to dataframe.
2024-12-20 00:07:59.681934 INFO::Replacing NaNs with NAs.
2024-12-20 00:07:59.684521 INFO::Removing potential empty rows and columns
2024-12-20 00:07:59.695899 INFO::Found 0 missing values.
2024-12-20 00:07:59.721924 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 00:07:59.72339 INFO::Done
2024-12-20 00:07:59.728074 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 00:07:59.748573 INFO::Starting hierarchical adjustment
2024-12-20 00:07:59.753177 INFO::Found 2 batches.
2024-12-20 00:07:59.755235 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 00:07:59.756934 INFO::Using default BPPARAM
2024-12-20 00:07:59.757965 INFO::Adjusting the last 2 batches sequentially
2024-12-20 00:07:59.75996 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-20 00:07:59.851132 INFO::Done
2024-12-20 00:07:59.852629 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 00:07:59.861926 INFO::ASW Batch was -5.62357711450755e-05 prior to batch effect correction and is now -5.62357711450755e-05 .
2024-12-20 00:07:59.863969 INFO::Total function execution time is 0.210546016693115 s and adjustment time is 0.098459005355835 s ( 46.76 )
2024-12-20 00:07:59.911277 INFO::Formatting Data.
2024-12-20 00:07:59.912986 INFO::Replacing NaNs with NAs.
2024-12-20 00:07:59.915211 INFO::Removing potential empty rows and columns
2024-12-20 00:07:59.917824 INFO::Found 0 missing values.
2024-12-20 00:07:59.925612 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 00:07:59.92704 INFO::Done
2024-12-20 00:07:59.928327 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 00:07:59.933041 INFO::Starting hierarchical adjustment
2024-12-20 00:07:59.935052 INFO::Found 3 batches.
2024-12-20 00:07:59.936481 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 00:07:59.937963 INFO::Using default BPPARAM
2024-12-20 00:07:59.939346 INFO::Processing subtree level 1
2024-12-20 00:08:00.313075 INFO::Adjusting the last 1 batches sequentially
2024-12-20 00:08:00.324443 INFO::Done
2024-12-20 00:08:00.326547 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 00:08:00.336091 INFO::ASW Batch was -0.135859909464641 prior to batch effect correction and is now -0.20368105484018 .
2024-12-20 00:08:00.339226 INFO::Total function execution time is 0.427963972091675 s and adjustment time is 0.389766216278076 s ( 91.07 )
2024-12-20 00:08:00.383768 INFO::Skipping initial DF formatting
2024-12-20 00:08:00.38522 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 00:08:00.394826 INFO::Starting hierarchical adjustment
2024-12-20 00:08:00.396718 INFO::Found 5 batches.
2024-12-20 00:08:00.39801 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 00:08:00.399597 INFO::Using default BPPARAM
2024-12-20 00:08:00.400881 INFO::Processing subtree level 1
2024-12-20 00:08:00.71961 INFO::Adjusting the last 2 batches sequentially
2024-12-20 00:08:00.729499 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-20 00:08:00.802994 INFO::Done
2024-12-20 00:08:00.80525 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 00:08:00.818733 INFO::ASW Batch was 0.511130117602635 prior to batch effect correction and is now 0.511130117602635 .
2024-12-20 00:08:00.820323 INFO::ASW Label was 0.415342550377364 prior to batch effect correction and is now 0.415342550377364 .
2024-12-20 00:08:00.823554 INFO::Total function execution time is 0.439351081848145 s and adjustment time is 0.406630992889404 s ( 92.55 )
2024-12-20 00:08:00.87525 INFO::Formatting Data.
2024-12-20 00:08:00.876916 INFO::Replacing NaNs with NAs.
2024-12-20 00:08:00.879049 INFO::Removing potential empty rows and columns
2024-12-20 00:08:00.881491 INFO::Found 0 missing values.
2024-12-20 00:08:00.892994 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 00:08:00.895449 INFO::Done
2024-12-20 00:08:00.896895 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 00:08:00.904041 INFO::Starting hierarchical adjustment
2024-12-20 00:08:00.906364 INFO::Found 5 batches.
2024-12-20 00:08:00.907767 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 00:08:00.909304 INFO::Using default BPPARAM
2024-12-20 00:08:00.910623 INFO::Processing subtree level 1
2024-12-20 00:08:01.178003 INFO::Adjusting the last 2 batches sequentially
2024-12-20 00:08:01.188069 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-20 00:08:01.238672 INFO::Done
2024-12-20 00:08:01.240215 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 00:08:01.249219 INFO::ASW Batch was 0.245293883727055 prior to batch effect correction and is now -0.0815109372899346 .
2024-12-20 00:08:01.250819 INFO::ASW Label was 0.531531603071328 prior to batch effect correction and is now 0.845042780779388 .
2024-12-20 00:08:01.254215 INFO::Total function execution time is 0.378917932510376 s and adjustment time is 0.332765102386475 s ( 87.82 )
2024-12-20 00:08:01.256583 INFO::Formatting Data.
2024-12-20 00:08:01.258196 INFO::Replacing NaNs with NAs.
2024-12-20 00:08:01.260343 INFO::Removing potential empty rows and columns
2024-12-20 00:08:01.263363 INFO::Found 0 missing values.
2024-12-20 00:08:01.274411 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 00:08:01.275898 INFO::Done
2024-12-20 00:08:01.277243 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 00:08:01.284293 INFO::Starting hierarchical adjustment
2024-12-20 00:08:01.286665 INFO::Found 5 batches.
2024-12-20 00:08:01.288175 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 00:08:01.289749 INFO::Using default BPPARAM
2024-12-20 00:08:01.291635 INFO::Processing subtree level 1
2024-12-20 00:08:01.566427 INFO::Adjusting the last 2 batches sequentially
2024-12-20 00:08:01.577025 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-20 00:08:01.631517 INFO::Done
2024-12-20 00:08:01.632932 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 00:08:01.642503 INFO::ASW Batch was 0.245293883727055 prior to batch effect correction and is now -0.0815109372899346 .
2024-12-20 00:08:01.644033 INFO::ASW Label was 0.531531603071328 prior to batch effect correction and is now 0.845042780779388 .
2024-12-20 00:08:01.647057 INFO::Total function execution time is 0.390455961227417 s and adjustment time is 0.345721006393433 s ( 88.54 )
2024-12-20 00:08:01.688793 INFO::Formatting Data.
2024-12-20 00:08:01.690518 INFO::Replacing NaNs with NAs.
2024-12-20 00:08:01.692818 INFO::Removing potential empty rows and columns
2024-12-20 00:08:01.695407 INFO::Found 0 missing values.
2024-12-20 00:08:01.706232 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 00:08:01.707677 INFO::Done
2024-12-20 00:08:01.708944 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 00:08:01.715972 INFO::Starting hierarchical adjustment
2024-12-20 00:08:01.719235 INFO::Found 5 batches.
2024-12-20 00:08:01.720775 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 00:08:01.722276 INFO::Using default BPPARAM
2024-12-20 00:08:01.723561 INFO::Processing subtree level 1
2024-12-20 00:08:01.99645 INFO::Adjusting the last 2 batches sequentially
2024-12-20 00:08:02.009945 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-20 00:08:02.058266 INFO::Done
2024-12-20 00:08:02.059785 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 00:08:02.070583 INFO::ASW Batch was 0.573652121099425 prior to batch effect correction and is now -0.00321164694040062 .
2024-12-20 00:08:02.072087 INFO::ASW Label was 0.25070501810831 prior to batch effect correction and is now 0.691008486667698 .
2024-12-20 00:08:02.075199 INFO::Total function execution time is 0.38641619682312 s and adjustment time is 0.34076189994812 s ( 88.19 )
2024-12-20 00:08:02.077365 INFO::Formatting Data.
2024-12-20 00:08:02.078935 INFO::Replacing NaNs with NAs.
2024-12-20 00:08:02.081073 INFO::Removing potential empty rows and columns
2024-12-20 00:08:02.083578 INFO::Found 0 missing values.
2024-12-20 00:08:02.095354 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 00:08:02.096865 INFO::Done
2024-12-20 00:08:02.098183 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 00:08:02.105643 INFO::Starting hierarchical adjustment
2024-12-20 00:08:02.108322 INFO::Found 5 batches.
2024-12-20 00:08:02.109874 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 00:08:02.111455 INFO::Using default BPPARAM
2024-12-20 00:08:02.112835 INFO::Processing subtree level 1
2024-12-20 00:08:02.387094 INFO::Adjusting the last 2 batches sequentially
2024-12-20 00:08:02.396685 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-20 00:08:02.447784 INFO::Done
2024-12-20 00:08:02.449329 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 00:08:02.457686 INFO::ASW Batch was 0.573652121099425 prior to batch effect correction and is now -0.00321164694040062 .
2024-12-20 00:08:02.45926 INFO::ASW Label was 0.25070501810831 prior to batch effect correction and is now 0.691008486667698 .
2024-12-20 00:08:02.462537 INFO::Total function execution time is 0.385094881057739 s and adjustment time is 0.340517997741699 s ( 88.42 )
2024-12-20 00:08:02.504849 INFO::Formatting Data.
2024-12-20 00:08:02.506677 INFO::Replacing NaNs with NAs.
2024-12-20 00:08:02.509114 INFO::Removing potential empty rows and columns
2024-12-20 00:08:02.511872 INFO::Found 0 missing values.
2024-12-20 00:08:02.519712 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 00:08:02.521234 INFO::Done
2024-12-20 00:08:02.522617 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 00:08:02.530002 INFO::Starting hierarchical adjustment
2024-12-20 00:08:02.531948 INFO::Found 2 batches.
2024-12-20 00:08:02.533322 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 00:08:02.534923 INFO::Using default BPPARAM
2024-12-20 00:08:02.536327 INFO::Adjusting the last 2 batches sequentially
2024-12-20 00:08:02.538595 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-20 00:08:02.574501 INFO::Done
2024-12-20 00:08:02.575914 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 00:08:02.582751 INFO::ASW Batch was 0.468064317541006 prior to batch effect correction and is now 0.0577121325109141 .
2024-12-20 00:08:02.584222 INFO::ASW Label was 0.598420508429108 prior to batch effect correction and is now 0.864591350529918 .
2024-12-20 00:08:02.58605 INFO::Total function execution time is 0.0813608169555664 s and adjustment time is 0.0429677963256836 s ( 52.81 )
2024-12-20 00:08:02.587965 INFO::Formatting Data.
2024-12-20 00:08:02.589498 INFO::Replacing NaNs with NAs.
2024-12-20 00:08:02.59156 INFO::Removing potential empty rows and columns
2024-12-20 00:08:02.593985 INFO::Found 0 missing values.
2024-12-20 00:08:02.601747 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 00:08:02.603203 INFO::Done
2024-12-20 00:08:02.604561 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 00:08:02.611617 INFO::Starting hierarchical adjustment
2024-12-20 00:08:02.613618 INFO::Found 2 batches.
2024-12-20 00:08:02.615186 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 00:08:02.61685 INFO::Using default BPPARAM
2024-12-20 00:08:02.618241 INFO::Adjusting the last 2 batches sequentially
2024-12-20 00:08:02.620332 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-20 00:08:02.655976 INFO::Done
2024-12-20 00:08:02.657435 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 00:08:02.664934 INFO::ASW Batch was 0.468064317541006 prior to batch effect correction and is now 0.0577121325109141 .
2024-12-20 00:08:02.66649 INFO::ASW Label was 0.598420508429108 prior to batch effect correction and is now 0.864591350529918 .
2024-12-20 00:08:02.668481 INFO::Total function execution time is 0.0805628299713135 s and adjustment time is 0.0428931713104248 s ( 53.24 )
2024-12-20 00:08:02.699757 INFO::Formatting Data.
2024-12-20 00:08:02.70137 INFO::Replacing NaNs with NAs.
2024-12-20 00:08:02.703388 INFO::Removing potential empty rows and columns
2024-12-20 00:08:02.705765 INFO::Found 0 missing values.
2024-12-20 00:08:02.711099 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 00:08:02.712538 INFO::Done
2024-12-20 00:08:02.713788 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 00:08:02.718299 INFO::Starting hierarchical adjustment
2024-12-20 00:08:02.720114 INFO::Found 2 batches.
2024-12-20 00:08:02.72178 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 00:08:02.72345 INFO::Using default BPPARAM
2024-12-20 00:08:02.724909 INFO::Adjusting the last 2 batches sequentially
2024-12-20 00:08:02.727498 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-20 00:08:02.815036 INFO::Done
2024-12-20 00:08:02.816565 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 00:08:02.821337 INFO::ASW Batch was -0.0814815148419477 prior to batch effect correction and is now -0.165598262399023 .
2024-12-20 00:08:02.823378 INFO::Total function execution time is 0.12369704246521 s and adjustment time is 0.0952680110931396 s ( 77.02 )
2024-12-20 00:08:02.856785 INFO::Formatting Data.
2024-12-20 00:08:02.858576 INFO::Replacing NaNs with NAs.
2024-12-20 00:08:02.861083 INFO::Removing potential empty rows and columns
2024-12-20 00:08:02.863619 INFO::Found 0 missing values.
2024-12-20 00:08:02.866398 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.
2024-12-20 00:08:02.878704 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 00:08:02.880023 INFO::Done
2024-12-20 00:08:02.881277 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 00:08:02.888454 INFO::Starting hierarchical adjustment
2024-12-20 00:08:02.890467 INFO::Found 2 batches.
2024-12-20 00:08:02.891795 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 00:08:02.893205 INFO::Using default BPPARAM
2024-12-20 00:08:02.894483 INFO::Adjusting the last 2 batches sequentially
2024-12-20 00:08:02.896855 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-20 00:08:02.937412 INFO::Done
2024-12-20 00:08:02.938905 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 00:08:02.945616 INFO::ASW Batch was 0.524871826238533 prior to batch effect correction and is now 0.0986528416182751 .
2024-12-20 00:08:02.947178 INFO::ASW Label was 0.564223667769306 prior to batch effect correction and is now 0.8914437084765 .
2024-12-20 00:08:02.949008 INFO::Total function execution time is 0.0924060344696045 s and adjustment time is 0.0473599433898926 s ( 51.25 )
2024-12-20 00:08:02.950931 INFO::Formatting Data.
2024-12-20 00:08:02.952469 INFO::Replacing NaNs with NAs.
2024-12-20 00:08:02.954621 INFO::Removing potential empty rows and columns
2024-12-20 00:08:02.957136 INFO::Found 0 missing values.
2024-12-20 00:08:02.959432 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.
2024-12-20 00:08:02.971332 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 00:08:02.972652 INFO::Done
2024-12-20 00:08:02.973877 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 00:08:02.98034 INFO::Starting hierarchical adjustment
2024-12-20 00:08:02.982145 INFO::Found 2 batches.
2024-12-20 00:08:02.983394 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 00:08:02.985092 INFO::Using default BPPARAM
2024-12-20 00:08:02.986492 INFO::Adjusting the last 2 batches sequentially
2024-12-20 00:08:02.988836 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-20 00:08:03.030305 INFO::Done
2024-12-20 00:08:03.03177 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 00:08:03.038904 INFO::ASW Batch was 0.524871826238533 prior to batch effect correction and is now 0.0986528416182751 .
2024-12-20 00:08:03.040413 INFO::ASW Label was 0.564223667769306 prior to batch effect correction and is now 0.8914437084765 .
2024-12-20 00:08:03.042311 INFO::Total function execution time is 0.091454029083252 s and adjustment time is 0.0485050678253174 s ( 53.04 )
2024-12-20 00:08:03.607112 INFO::Formatting Data.
2024-12-20 00:08:03.608685 INFO::Replacing NaNs with NAs.
2024-12-20 00:08:03.610713 INFO::Removing potential empty rows and columns
2024-12-20 00:08:03.613177 INFO::Found 0 missing values.
2024-12-20 00:08:03.620843 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 00:08:03.622268 INFO::Done
2024-12-20 00:08:03.623566 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 00:08:03.628253 INFO::Starting hierarchical adjustment
2024-12-20 00:08:03.630025 INFO::Found 3 batches.
2024-12-20 00:08:03.631263 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 00:08:03.632711 INFO::Using default BPPARAM
2024-12-20 00:08:03.633964 INFO::Processing subtree level 1
2024-12-20 00:08:03.857711 INFO::Adjusting the last 1 batches sequentially
2024-12-20 00:08:03.867212 INFO::Done
2024-12-20 00:08:03.869351 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 00:08:03.880568 INFO::ASW Batch was -0.0792804591790131 prior to batch effect correction and is now -0.0792804591790131 .
2024-12-20 00:08:03.884744 INFO::Total function execution time is 0.27763295173645 s and adjustment time is 0.237547159194946 s ( 85.56 )
2024-12-20 00:08:03.887841 INFO::Formatting Data.
2024-12-20 00:08:03.889479 INFO::Typecasting input to dataframe.
2024-12-20 00:08:03.89128 INFO::Replacing NaNs with NAs.
2024-12-20 00:08:03.893387 INFO::Removing potential empty rows and columns
2024-12-20 00:08:03.896428 INFO::Found 0 missing values.
2024-12-20 00:08:03.904623 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 00:08:03.906053 INFO::Done
2024-12-20 00:08:03.907398 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 00:08:03.912203 INFO::Starting hierarchical adjustment
2024-12-20 00:08:03.914737 INFO::Found 3 batches.
2024-12-20 00:08:03.916228 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 00:08:03.917727 INFO::Using default BPPARAM
2024-12-20 00:08:03.919026 INFO::Processing subtree level 1
2024-12-20 00:08:04.171164 INFO::Adjusting the last 1 batches sequentially
2024-12-20 00:08:04.180866 INFO::Done
2024-12-20 00:08:04.18237 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 00:08:04.197184 INFO::ASW Batch was -0.0792804591790131 prior to batch effect correction and is now -0.0792804591790131 .
2024-12-20 00:08:04.202502 INFO::Total function execution time is 0.314082145690918 s and adjustment time is 0.267138004302979 s ( 85.05 )
2024-12-20 00:08:04.269267 INFO::Formatting Data.
2024-12-20 00:08:04.271092 INFO::Typecasting input to dataframe.
2024-12-20 00:08:04.273308 INFO::Replacing NaNs with NAs.
2024-12-20 00:08:04.276076 INFO::Removing potential empty rows and columns
2024-12-20 00:08:04.279217 INFO::Found 0 missing values.
2024-12-20 00:08:04.288 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 00:08:04.289547 INFO::Done
2024-12-20 00:08:04.290981 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 00:08:04.296371 INFO::Starting hierarchical adjustment
2024-12-20 00:08:04.299127 INFO::Found 3 batches.
2024-12-20 00:08:04.30071 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 00:08:04.302438 INFO::Using default BPPARAM
2024-12-20 00:08:04.304012 INFO::Processing subtree level 1
2024-12-20 00:08:04.786221 INFO::Adjusting the last 1 batches sequentially
2024-12-20 00:08:04.807684 INFO::Done
2024-12-20 00:08:04.811752 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 00:08:04.833372 INFO::ASW Batch was -0.0630317199761625 prior to batch effect correction and is now -0.0630317199761625 .
2024-12-20 00:08:04.8419 INFO::Total function execution time is 0.571679830551147 s and adjustment time is 0.508979082107544 s ( 89.03 )
2024-12-20 00:08:05.473773 INFO::Formatting Data.
2024-12-20 00:08:05.475645 INFO::Replacing NaNs with NAs.
2024-12-20 00:08:05.479041 INFO::Removing potential empty rows and columns
2024-12-20 00:08:05.487876 INFO::Found 1000 missing values.
2024-12-20 00:08:05.556854 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 00:08:05.558366 INFO::Done
2024-12-20 00:08:05.559645 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 00:08:05.572027 INFO::Starting hierarchical adjustment
2024-12-20 00:08:05.573991 INFO::Found 10 batches.
2024-12-20 00:08:05.575341 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 00:08:05.576836 INFO::Using default BPPARAM
2024-12-20 00:08:05.578119 INFO::Processing subtree level 1
2024-12-20 00:08:05.996849 INFO::Processing subtree level 2
2024-12-20 00:08:06.565353 INFO::Adjusting the last 1 batches sequentially
2024-12-20 00:08:06.584034 INFO::Done
2024-12-20 00:08:06.586538 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 00:08:06.608693 INFO::ASW Batch was 0.517933819926668 prior to batch effect correction and is now 0.517933819926668 .
2024-12-20 00:08:06.610924 INFO::ASW Label was 0.307640413143098 prior to batch effect correction and is now 0.307640413143098 .
2024-12-20 00:08:06.614397 INFO::Total function execution time is 1.14030003547668 s and adjustment time is 1.01041293144226 s ( 88.61 )
2024-12-20 00:08:06.617695 INFO::Formatting Data.
2024-12-20 00:08:06.620928 INFO::Replacing NaNs with NAs.
2024-12-20 00:08:06.624996 INFO::Removing potential empty rows and columns
2024-12-20 00:08:06.634258 INFO::Found 1000 missing values.
2024-12-20 00:08:06.704272 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 00:08:06.705805 INFO::Done
2024-12-20 00:08:06.707196 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 00:08:06.720559 INFO::Starting hierarchical adjustment
2024-12-20 00:08:06.72255 INFO::Found 10 batches.
2024-12-20 00:08:08.055118 INFO::Set up parallel execution backend with 2 workers
2024-12-20 00:08:08.056471 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-12-20 00:08:09.866428 INFO::Adjusting the last 2 batches sequentially
2024-12-20 00:08:09.869168 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-20 00:08:09.918183 INFO::Done
2024-12-20 00:08:09.91954 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 00:08:09.933276 INFO::ASW Batch was 0.517933819926668 prior to batch effect correction and is now 0.517933819926668 .
2024-12-20 00:08:09.934571 INFO::ASW Label was 0.307640413143098 prior to batch effect correction and is now 0.307640413143098 .
2024-12-20 00:08:09.936131 INFO::Total function execution time is 3.31871485710144 s and adjustment time is 3.19607186317444 s ( 96.3 )
2024-12-20 00:08:10.360218 INFO::Formatting Data.
2024-12-20 00:08:10.362662 INFO::Replacing NaNs with NAs.
2024-12-20 00:08:10.365364 INFO::Removing potential empty rows and columns
2024-12-20 00:08:10.36894 INFO::Found 0 missing values.
2024-12-20 00:08:10.380949 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 00:08:10.382436 INFO::Done
2024-12-20 00:08:10.383816 INFO::Acquiring quality metrics before batch effect correction.
2024-12-20 00:08:10.39079 INFO::Starting hierarchical adjustment
2024-12-20 00:08:10.392654 INFO::Found 3 batches.
2024-12-20 00:08:10.393983 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-20 00:08:10.395466 INFO::Using default BPPARAM
2024-12-20 00:08:10.396754 INFO::Processing subtree level 1
2024-12-20 00:08:10.720538 INFO::Adjusting the last 1 batches sequentially
2024-12-20 00:08:10.732284 INFO::Done
2024-12-20 00:08:10.736125 INFO::Acquiring quality metrics after batch effect correction.
2024-12-20 00:08:10.755091 INFO::ASW Batch was 0.166804516720491 prior to batch effect correction and is now -0.149226350904071 .
2024-12-20 00:08:10.756636 INFO::ASW Label was -0.150057941568486 prior to batch effect correction and is now 0.0599916771539184 .
2024-12-20 00:08:10.760189 INFO::Total function execution time is 0.399671077728271 s and adjustment time is 0.339995861053467 s ( 85.07 )
2024-12-20 00:08:11.101587 INFO::Formatting Data.
2024-12-20 00:08:11.103327 INFO::Replacing NaNs with NAs.
2024-12-20 00:08:11.105528 INFO::Removing potential empty rows and columns
2024-12-20 00:08:11.108214 INFO::Found 2 missing values.
2024-12-20 00:08:11.116698 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-12-20 00:08:11.118259 INFO::Done
2024-12-20 00:08:11.199387 INFO::Found NA in Reference column
2024-12-20 00:08:11.225783 INFO::Require at least two references per batch.
2024-12-20 00:08:11.281299 INFO::Formatting Data.
2024-12-20 00:08:11.282905 INFO::Recognized SummarizedExperiment
2024-12-20 00:08:11.284218 INFO::Typecasting input to dataframe.
2024-12-20 00:08:11.310338 INFO::Replacing NaNs with NAs.
2024-12-20 00:08:11.313096 INFO::Removing potential empty rows and columns
2024-12-20 00:08:11.32464 INFO::Found 0 missing values.
2024-12-20 00:08:11.344895 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 00:08:11.346289 INFO::Done
2024-12-20 00:08:11.385428 INFO::Formatting Data.
2024-12-20 00:08:11.387234 INFO::Recognized SummarizedExperiment
2024-12-20 00:08:11.388602 INFO::Typecasting input to dataframe.
2024-12-20 00:08:11.438495 INFO::Replacing NaNs with NAs.
2024-12-20 00:08:11.441295 INFO::Removing potential empty rows and columns
2024-12-20 00:08:11.4529 INFO::Found 0 missing values.
2024-12-20 00:08:11.493393 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 00:08:11.494954 INFO::Done
2024-12-20 00:08:11.537353 INFO::Formatting Data.
2024-12-20 00:08:11.538947 INFO::Recognized SummarizedExperiment
2024-12-20 00:08:11.540335 INFO::Typecasting input to dataframe.
2024-12-20 00:08:11.586423 INFO::Replacing NaNs with NAs.
2024-12-20 00:08:11.588659 INFO::Removing potential empty rows and columns
2024-12-20 00:08:11.591489 INFO::Found 0 missing values.
2024-12-20 00:08:11.593934 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.
2024-12-20 00:08:11.606799 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 00:08:11.608222 INFO::Done
2024-12-20 00:08:11.636217 INFO::Formatting Data.
2024-12-20 00:08:11.638228 INFO::Replacing NaNs with NAs.
2024-12-20 00:08:11.640483 INFO::Removing potential empty rows and columns
2024-12-20 00:08:11.64305 INFO::Found 0 missing values.
2024-12-20 00:08:11.651324 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 00:08:11.652907 INFO::Done
2024-12-20 00:08:11.68396 INFO::Formatting Data.
2024-12-20 00:08:11.685725 INFO::Replacing NaNs with NAs.
2024-12-20 00:08:11.687831 INFO::Removing potential empty rows and columns
2024-12-20 00:08:11.690291 INFO::Found 0 missing values.
2024-12-20 00:08:11.698213 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 00:08:11.699646 INFO::Done
2024-12-20 00:08:11.782881 INFO::Formatting Data.
2024-12-20 00:08:11.784634 INFO::Replacing NaNs with NAs.
2024-12-20 00:08:11.787188 INFO::Removing potential empty rows and columns
2024-12-20 00:08:11.790524 INFO::Found 1 missing values.
2024-12-20 00:08:11.800113 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 00:08:11.801642 INFO::Done
2024-12-20 00:08:11.853614 INFO::Formatting Data.
2024-12-20 00:08:11.855349 INFO::Replacing NaNs with NAs.
2024-12-20 00:08:11.857432 INFO::Removing potential empty rows and columns
2024-12-20 00:08:11.860318 INFO::Found 2 missing values.
2024-12-20 00:08:11.863161 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.
2024-12-20 00:08:11.869417 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-12-20 00:08:11.870839 INFO::Done
2024-12-20 00:08:11.898973 INFO::Formatting Data.
2024-12-20 00:08:11.900616 INFO::Replacing NaNs with NAs.
2024-12-20 00:08:11.902582 INFO::Removing potential empty rows and columns
2024-12-20 00:08:11.906597 INFO::Found 2 missing values.
2024-12-20 00:08:11.911633 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 00:08:11.913237 INFO::Done
2024-12-20 00:08:11.943798 INFO::Formatting Data.
2024-12-20 00:08:11.945792 INFO::Typecasting input to dataframe.
2024-12-20 00:08:11.947888 INFO::Replacing NaNs with NAs.
2024-12-20 00:08:11.950076 INFO::Removing potential empty rows and columns
2024-12-20 00:08:11.952806 INFO::Found 0 missing values.
2024-12-20 00:08:11.960992 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-20 00:08:11.962445 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
35.657 6.659 43.814
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 44.700 | 2.559 | 36.380 | |
| compute_asw | 0.057 | 0.003 | 0.061 | |
| count_existing | 0.028 | 0.002 | 0.031 | |
| generate_data_covariables | 0.026 | 0.002 | 0.029 | |
| generate_dataset | 0.025 | 0.002 | 0.029 | |