Yannis Schumann
| Snapshot Date: 2024-12-30 13:00 -0500 (Mon, 30 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 2025-01-02 12:04 -0500 (Thu, 02 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 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: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BERT_1.2.0.tar.gz |
| StartedAt: 2024-12-30 23:04:38 -0500 (Mon, 30 Dec 2024) |
| EndedAt: 2024-12-30 23:06:56 -0500 (Mon, 30 Dec 2024) |
| EllapsedTime: 137.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BERT_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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 9.23 0.54 18.66
* 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: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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")
2024-12-30 23:05:42.766746 INFO::Formatting Data.
2024-12-30 23:05:42.769657 INFO::Replacing NaNs with NAs.
2024-12-30 23:05:42.78422 INFO::Removing potential empty rows and columns
2024-12-30 23:05:43.105629 INFO::Found 0 missing values.
2024-12-30 23:05:43.11062 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-30 23:05:43.112008 INFO::Done
2024-12-30 23:05:43.113212 INFO::Acquiring quality metrics before batch effect correction.
2024-12-30 23:05:43.132622 INFO::Starting hierarchical adjustment
2024-12-30 23:05:43.13421 INFO::Found 3 batches.
2024-12-30 23:05:43.135424 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-30 23:05:43.137351 INFO::Using default BPPARAM
2024-12-30 23:05:43.138501 INFO::Processing subtree level 1
2024-12-30 23:05:45.825435 INFO::Adjusting the last 1 batches sequentially
2024-12-30 23:05:45.827687 INFO::Done
2024-12-30 23:05:45.828906 INFO::Acquiring quality metrics after batch effect correction.
2024-12-30 23:05:45.832172 INFO::ASW Batch was -0.112665329727364 prior to batch effect correction and is now -0.112665329727364 .
2024-12-30 23:05:45.833783 INFO::Total function execution time is 3.06769895553589 s and adjustment time is 2.69373393058777 s ( 87.81 )
2024-12-30 23:05:45.855394 INFO::Formatting Data.
2024-12-30 23:05:45.856969 INFO::Replacing NaNs with NAs.
2024-12-30 23:05:45.858678 INFO::Removing potential empty rows and columns
2024-12-30 23:05:45.860434 INFO::Found 0 missing values.
2024-12-30 23:05:45.862005 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.
2024-12-30 23:05:45.874256 INFO::Formatting Data.
2024-12-30 23:05:45.875653 INFO::Replacing NaNs with NAs.
2024-12-30 23:05:45.877263 INFO::Removing potential empty rows and columns
2024-12-30 23:05:45.878965 INFO::Found 0 missing values.
2024-12-30 23:05:45.880533 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.
2024-12-30 23:05:45.902687 INFO::Formatting Data.
2024-12-30 23:05:45.90415 INFO::Replacing NaNs with NAs.
2024-12-30 23:05:45.905773 INFO::Removing potential empty rows and columns
2024-12-30 23:05:45.907543 INFO::Found 0 missing values.
2024-12-30 23:05:45.90919 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.
2024-12-30 23:05:45.914889 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-30 23:05:45.916074 INFO::Done
2024-12-30 23:05:45.91723 INFO::Acquiring quality metrics before batch effect correction.
2024-12-30 23:05:45.920342 INFO::Starting hierarchical adjustment
2024-12-30 23:05:45.9217 INFO::Found 2 batches.
2024-12-30 23:05:45.922928 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-30 23:05:45.924156 INFO::Using default BPPARAM
2024-12-30 23:05:45.925283 INFO::Adjusting the last 2 batches sequentially
2024-12-30 23:05:45.926959 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-30 23:05:45.950772 INFO::Done
2024-12-30 23:05:45.952049 INFO::Acquiring quality metrics after batch effect correction.
2024-12-30 23:05:45.955089 INFO::ASW Batch was -0.0287250621540556 prior to batch effect correction and is now -0.115490994133866 .
2024-12-30 23:05:45.956559 INFO::Total function execution time is 0.0539789199829102 s and adjustment time is 0.0292351245880127 s ( 54.16 )
2024-12-30 23:05:45.960658 INFO::Formatting Data.
2024-12-30 23:05:45.961922 INFO::Replacing NaNs with NAs.
2024-12-30 23:05:45.972507 INFO::Formatting Data.
2024-12-30 23:05:45.973859 INFO::Replacing NaNs with NAs.
2024-12-30 23:05:45.975456 INFO::Removing potential empty rows and columns
2024-12-30 23:05:45.977164 INFO::Found 0 missing values.
2024-12-30 23:05:45.981009 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-30 23:05:45.982138 INFO::Done
2024-12-30 23:05:45.983238 INFO::Acquiring quality metrics before batch effect correction.
2024-12-30 23:05:45.986299 INFO::Starting hierarchical adjustment
2024-12-30 23:05:45.987641 INFO::Found 2 batches.
2024-12-30 23:05:45.988738 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-30 23:05:45.989912 INFO::Using default BPPARAM
2024-12-30 23:05:45.990972 INFO::Adjusting the last 2 batches sequentially
2024-12-30 23:05:45.992553 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-30 23:05:46.010146 INFO::Done
2024-12-30 23:05:46.01141 INFO::Acquiring quality metrics after batch effect correction.
2024-12-30 23:05:46.014436 INFO::ASW Batch was -0.0214273936498818 prior to batch effect correction and is now -0.120528379037581 .
2024-12-30 23:05:46.01596 INFO::Total function execution time is 0.0435068607330322 s and adjustment time is 0.022676944732666 s ( 52.12 )
2024-12-30 23:05:46.017772 INFO::Formatting Data.
2024-12-30 23:05:46.018985 INFO::Replacing NaNs with NAs.
2024-12-30 23:05:46.020516 INFO::Removing potential empty rows and columns
2024-12-30 23:05:46.022189 INFO::Found 0 missing values.
2024-12-30 23:05:46.026054 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-30 23:05:46.027183 INFO::Done
2024-12-30 23:05:46.028303 INFO::Acquiring quality metrics before batch effect correction.
2024-12-30 23:05:46.031375 INFO::Starting hierarchical adjustment
2024-12-30 23:05:46.032715 INFO::Found 2 batches.
2024-12-30 23:05:46.033813 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-30 23:05:46.03501 INFO::Using default BPPARAM
2024-12-30 23:05:46.036104 INFO::Adjusting the last 2 batches sequentially
2024-12-30 23:05:46.03776 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-30 23:05:46.055811 INFO::Done
2024-12-30 23:05:46.057086 INFO::Acquiring quality metrics after batch effect correction.
2024-12-30 23:05:46.060109 INFO::ASW Batch was -0.0214273936498818 prior to batch effect correction and is now -0.120528379037581 .
2024-12-30 23:05:46.061543 INFO::Total function execution time is 0.0437779426574707 s and adjustment time is 0.0232729911804199 s ( 53.16 )
2024-12-30 23:05:48.705386 INFO::Formatting Data.
2024-12-30 23:05:48.706695 INFO::Recognized SummarizedExperiment
2024-12-30 23:05:48.707826 INFO::Typecasting input to dataframe.
2024-12-30 23:05:48.759568 INFO::Replacing NaNs with NAs.
2024-12-30 23:05:48.762057 INFO::Removing potential empty rows and columns
2024-12-30 23:05:48.768282 INFO::Found 0 missing values.
2024-12-30 23:05:48.77831 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-30 23:05:48.779676 INFO::Done
2024-12-30 23:05:48.780836 INFO::Acquiring quality metrics before batch effect correction.
2024-12-30 23:05:48.786554 INFO::Starting hierarchical adjustment
2024-12-30 23:05:48.787898 INFO::Found 2 batches.
2024-12-30 23:05:48.788992 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-30 23:05:48.790762 INFO::Using default BPPARAM
2024-12-30 23:05:48.791838 INFO::Adjusting the last 2 batches sequentially
2024-12-30 23:05:48.793608 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-30 23:05:48.864685 INFO::Done
2024-12-30 23:05:48.866078 INFO::Acquiring quality metrics after batch effect correction.
2024-12-30 23:05:48.872411 INFO::ASW Batch was 0.00244381290815018 prior to batch effect correction and is now -0.0855678403078083 .
2024-12-30 23:05:48.874092 INFO::Total function execution time is 0.169079065322876 s and adjustment time is 0.0769288539886475 s ( 45.5 )
2024-12-30 23:05:49.555688 INFO::Formatting Data.
2024-12-30 23:05:49.556637 INFO::Recognized SummarizedExperiment
2024-12-30 23:05:49.557354 INFO::Typecasting input to dataframe.
2024-12-30 23:05:49.565143 INFO::Replacing NaNs with NAs.
2024-12-30 23:05:49.566365 INFO::Removing potential empty rows and columns
2024-12-30 23:05:49.569094 INFO::Found 0 missing values.
2024-12-30 23:05:49.574001 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-30 23:05:49.574726 INFO::Done
2024-12-30 23:05:49.575425 INFO::Acquiring quality metrics before batch effect correction.
2024-12-30 23:05:49.578998 INFO::Starting hierarchical adjustment
2024-12-30 23:05:49.579851 INFO::Found 2 batches.
2024-12-30 23:05:49.58053 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-30 23:05:49.581273 INFO::Using default BPPARAM
2024-12-30 23:05:49.58195 INFO::Adjusting the last 2 batches sequentially
2024-12-30 23:05:49.583072 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-30 23:05:49.600695 INFO::Done
2024-12-30 23:05:49.601598 INFO::Acquiring quality metrics after batch effect correction.
2024-12-30 23:05:49.605291 INFO::ASW Batch was -0.00793932596909886 prior to batch effect correction and is now -0.00793932596909886 .
2024-12-30 23:05:49.606311 INFO::Total function execution time is 0.0506138801574707 s and adjustment time is 0.0209321975708008 s ( 41.36 )
2024-12-30 23:05:49.625413 INFO::Formatting Data.
2024-12-30 23:05:49.626334 INFO::Replacing NaNs with NAs.
2024-12-30 23:05:49.627358 INFO::Removing potential empty rows and columns
2024-12-30 23:05:49.628446 INFO::Found 0 missing values.
2024-12-30 23:05:49.630993 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-30 23:05:49.631696 INFO::Done
2024-12-30 23:05:49.632375 INFO::Acquiring quality metrics before batch effect correction.
2024-12-30 23:05:49.634413 INFO::Starting hierarchical adjustment
2024-12-30 23:05:49.635293 INFO::Found 3 batches.
2024-12-30 23:05:49.635982 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-30 23:05:49.636741 INFO::Using default BPPARAM
2024-12-30 23:05:49.637424 INFO::Processing subtree level 1
2024-12-30 23:05:59.877677 INFO::Adjusting the last 1 batches sequentially
2024-12-30 23:05:59.879808 INFO::Done
2024-12-30 23:05:59.881091 INFO::Acquiring quality metrics after batch effect correction.
2024-12-30 23:05:59.884336 INFO::ASW Batch was -0.0956152920015678 prior to batch effect correction and is now -0.177998170084274 .
2024-12-30 23:05:59.885771 INFO::Total function execution time is 10.260351896286 s and adjustment time is 10.2445950508118 s ( 99.85 )
2024-12-30 23:05:59.908256 INFO::Skipping initial DF formatting
2024-12-30 23:05:59.909607 INFO::Acquiring quality metrics before batch effect correction.
2024-12-30 23:05:59.91566 INFO::Starting hierarchical adjustment
2024-12-30 23:05:59.917033 INFO::Found 5 batches.
2024-12-30 23:05:59.918088 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-30 23:05:59.919203 INFO::Using default BPPARAM
2024-12-30 23:05:59.920224 INFO::Processing subtree level 1
2024-12-30 23:06:02.963767 INFO::Adjusting the last 2 batches sequentially
2024-12-30 23:06:02.965917 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-30 23:06:02.985362 INFO::Done
2024-12-30 23:06:02.986252 INFO::Acquiring quality metrics after batch effect correction.
2024-12-30 23:06:02.990495 INFO::ASW Batch was 0.495107698294015 prior to batch effect correction and is now 0.495107698294015 .
2024-12-30 23:06:02.991306 INFO::ASW Label was 0.388670471586503 prior to batch effect correction and is now 0.388670471586503 .
2024-12-30 23:06:02.99224 INFO::Total function execution time is 3.08418321609497 s and adjustment time is 3.06854486465454 s ( 99.49 )
2024-12-30 23:06:03.016749 INFO::Formatting Data.
2024-12-30 23:06:03.018248 INFO::Replacing NaNs with NAs.
2024-12-30 23:06:03.020036 INFO::Removing potential empty rows and columns
2024-12-30 23:06:03.021849 INFO::Found 0 missing values.
2024-12-30 23:06:03.027609 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-30 23:06:03.028935 INFO::Done
2024-12-30 23:06:03.030125 INFO::Acquiring quality metrics before batch effect correction.
2024-12-30 23:06:03.034823 INFO::Starting hierarchical adjustment
2024-12-30 23:06:03.036264 INFO::Found 5 batches.
2024-12-30 23:06:03.037434 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-30 23:06:03.038713 INFO::Using default BPPARAM
2024-12-30 23:06:03.039864 INFO::Processing subtree level 1
2024-12-30 23:06:06.121448 INFO::Adjusting the last 2 batches sequentially
2024-12-30 23:06:06.123451 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-30 23:06:06.142143 INFO::Done
2024-12-30 23:06:06.143414 INFO::Acquiring quality metrics after batch effect correction.
2024-12-30 23:06:06.14784 INFO::ASW Batch was 0.574882449515811 prior to batch effect correction and is now -0.0166363034617196 .
2024-12-30 23:06:06.149042 INFO::ASW Label was 0.247892821638981 prior to batch effect correction and is now 0.710413433417944 .
2024-12-30 23:06:06.150461 INFO::Total function execution time is 3.13381505012512 s and adjustment time is 3.10604596138 s ( 99.11 )
2024-12-30 23:06:06.151451 INFO::Formatting Data.
2024-12-30 23:06:06.152209 INFO::Replacing NaNs with NAs.
2024-12-30 23:06:06.153274 INFO::Removing potential empty rows and columns
2024-12-30 23:06:06.154322 INFO::Found 0 missing values.
2024-12-30 23:06:06.15783 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-30 23:06:06.158547 INFO::Done
2024-12-30 23:06:06.159276 INFO::Acquiring quality metrics before batch effect correction.
2024-12-30 23:06:06.162272 INFO::Starting hierarchical adjustment
2024-12-30 23:06:06.163127 INFO::Found 5 batches.
2024-12-30 23:06:06.163805 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-30 23:06:06.164583 INFO::Using default BPPARAM
2024-12-30 23:06:06.165264 INFO::Processing subtree level 1
2024-12-30 23:06:09.324397 INFO::Adjusting the last 2 batches sequentially
2024-12-30 23:06:09.326486 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-30 23:06:09.346854 INFO::Done
2024-12-30 23:06:09.348221 INFO::Acquiring quality metrics after batch effect correction.
2024-12-30 23:06:09.352916 INFO::ASW Batch was 0.574882449515811 prior to batch effect correction and is now -0.0166363034617196 .
2024-12-30 23:06:09.354176 INFO::ASW Label was 0.247892821638981 prior to batch effect correction and is now 0.710413433417944 .
2024-12-30 23:06:09.355691 INFO::Total function execution time is 3.20415902137756 s and adjustment time is 3.18376398086548 s ( 99.36 )
2024-12-30 23:06:09.378332 INFO::Formatting Data.
2024-12-30 23:06:09.37996 INFO::Replacing NaNs with NAs.
2024-12-30 23:06:09.381735 INFO::Removing potential empty rows and columns
2024-12-30 23:06:09.383532 INFO::Found 0 missing values.
2024-12-30 23:06:09.389758 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-30 23:06:09.391077 INFO::Done
2024-12-30 23:06:09.392308 INFO::Acquiring quality metrics before batch effect correction.
2024-12-30 23:06:09.397224 INFO::Starting hierarchical adjustment
2024-12-30 23:06:09.398742 INFO::Found 5 batches.
2024-12-30 23:06:09.399965 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-30 23:06:09.401246 INFO::Using default BPPARAM
2024-12-30 23:06:09.402431 INFO::Processing subtree level 1
2024-12-30 23:06:12.532878 INFO::Adjusting the last 2 batches sequentially
2024-12-30 23:06:12.53495 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-30 23:06:12.553545 INFO::Done
2024-12-30 23:06:12.554893 INFO::Acquiring quality metrics after batch effect correction.
2024-12-30 23:06:12.559523 INFO::ASW Batch was 0.308028319416682 prior to batch effect correction and is now -0.0619509139416678 .
2024-12-30 23:06:12.5608 INFO::ASW Label was 0.477703131793659 prior to batch effect correction and is now 0.801027912069673 .
2024-12-30 23:06:12.562317 INFO::Total function execution time is 3.18408489227295 s and adjustment time is 3.15502285957336 s ( 99.09 )
2024-12-30 23:06:12.563816 INFO::Formatting Data.
2024-12-30 23:06:12.565021 INFO::Replacing NaNs with NAs.
2024-12-30 23:06:12.566618 INFO::Removing potential empty rows and columns
2024-12-30 23:06:12.567785 INFO::Found 0 missing values.
2024-12-30 23:06:12.571172 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-30 23:06:12.571878 INFO::Done
2024-12-30 23:06:12.572555 INFO::Acquiring quality metrics before batch effect correction.
2024-12-30 23:06:12.57556 INFO::Starting hierarchical adjustment
2024-12-30 23:06:12.576417 INFO::Found 5 batches.
2024-12-30 23:06:12.577091 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-30 23:06:12.577823 INFO::Using default BPPARAM
2024-12-30 23:06:12.578492 INFO::Processing subtree level 1
2024-12-30 23:06:15.6774 INFO::Adjusting the last 2 batches sequentially
2024-12-30 23:06:15.679433 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-30 23:06:15.698694 INFO::Done
2024-12-30 23:06:15.699992 INFO::Acquiring quality metrics after batch effect correction.
2024-12-30 23:06:15.704483 INFO::ASW Batch was 0.308028319416682 prior to batch effect correction and is now -0.0619509139416678 .
2024-12-30 23:06:15.70567 INFO::ASW Label was 0.477703131793659 prior to batch effect correction and is now 0.801027912069673 .
2024-12-30 23:06:15.707094 INFO::Total function execution time is 3.14329314231873 s and adjustment time is 3.12233209609985 s ( 99.33 )
2024-12-30 23:06:15.728189 INFO::Formatting Data.
2024-12-30 23:06:15.729671 INFO::Replacing NaNs with NAs.
2024-12-30 23:06:15.731378 INFO::Removing potential empty rows and columns
2024-12-30 23:06:15.733111 INFO::Found 0 missing values.
2024-12-30 23:06:15.736986 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-30 23:06:15.738153 INFO::Done
2024-12-30 23:06:15.739264 INFO::Acquiring quality metrics before batch effect correction.
2024-12-30 23:06:15.743702 INFO::Starting hierarchical adjustment
2024-12-30 23:06:15.745065 INFO::Found 2 batches.
2024-12-30 23:06:15.746193 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-30 23:06:15.747401 INFO::Using default BPPARAM
2024-12-30 23:06:15.748502 INFO::Adjusting the last 2 batches sequentially
2024-12-30 23:06:15.750173 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-30 23:06:15.769141 INFO::Done
2024-12-30 23:06:15.770529 INFO::Acquiring quality metrics after batch effect correction.
2024-12-30 23:06:15.775208 INFO::ASW Batch was 0.621625375693711 prior to batch effect correction and is now -0.00680331479194089 .
2024-12-30 23:06:15.776318 INFO::ASW Label was 0.448920757572533 prior to batch effect correction and is now 0.887227381475156 .
2024-12-30 23:06:15.777668 INFO::Total function execution time is 0.0496208667755127 s and adjustment time is 0.0242469310760498 s ( 48.86 )
2024-12-30 23:06:15.779006 INFO::Formatting Data.
2024-12-30 23:06:15.780221 INFO::Replacing NaNs with NAs.
2024-12-30 23:06:15.781872 INFO::Removing potential empty rows and columns
2024-12-30 23:06:15.78361 INFO::Found 0 missing values.
2024-12-30 23:06:15.787338 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-30 23:06:15.788326 INFO::Done
2024-12-30 23:06:15.789304 INFO::Acquiring quality metrics before batch effect correction.
2024-12-30 23:06:15.79375 INFO::Starting hierarchical adjustment
2024-12-30 23:06:15.795154 INFO::Found 2 batches.
2024-12-30 23:06:15.796315 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-30 23:06:15.797632 INFO::Using default BPPARAM
2024-12-30 23:06:15.798853 INFO::Adjusting the last 2 batches sequentially
2024-12-30 23:06:15.800681 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-30 23:06:15.820428 INFO::Done
2024-12-30 23:06:15.821756 INFO::Acquiring quality metrics after batch effect correction.
2024-12-30 23:06:15.826095 INFO::ASW Batch was 0.621625375693711 prior to batch effect correction and is now -0.00680331479194089 .
2024-12-30 23:06:15.827269 INFO::ASW Label was 0.448920757572533 prior to batch effect correction and is now 0.887227381475156 .
2024-12-30 23:06:15.828662 INFO::Total function execution time is 0.0496630668640137 s and adjustment time is 0.0254309177398682 s ( 51.21 )
2024-12-30 23:06:15.847752 INFO::Formatting Data.
2024-12-30 23:06:15.849143 INFO::Replacing NaNs with NAs.
2024-12-30 23:06:15.850691 INFO::Removing potential empty rows and columns
2024-12-30 23:06:15.85223 INFO::Found 0 missing values.
2024-12-30 23:06:15.855318 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-30 23:06:15.856374 INFO::Done
2024-12-30 23:06:15.857465 INFO::Acquiring quality metrics before batch effect correction.
2024-12-30 23:06:15.860441 INFO::Starting hierarchical adjustment
2024-12-30 23:06:15.861744 INFO::Found 2 batches.
2024-12-30 23:06:15.862795 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-30 23:06:15.863939 INFO::Using default BPPARAM
2024-12-30 23:06:15.86499 INFO::Adjusting the last 2 batches sequentially
2024-12-30 23:06:15.866549 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-30 23:06:15.903595 INFO::Done
2024-12-30 23:06:15.904842 INFO::Acquiring quality metrics after batch effect correction.
2024-12-30 23:06:15.907873 INFO::ASW Batch was -0.157066861582569 prior to batch effect correction and is now -0.157774579390649 .
2024-12-30 23:06:15.909294 INFO::Total function execution time is 0.0616359710693359 s and adjustment time is 0.0420141220092773 s ( 68.16 )
2024-12-30 23:06:15.928683 INFO::Formatting Data.
2024-12-30 23:06:15.929803 INFO::Replacing NaNs with NAs.
2024-12-30 23:06:15.930956 INFO::Removing potential empty rows and columns
2024-12-30 23:06:15.93213 INFO::Found 0 missing values.
2024-12-30 23:06:15.933438 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.
2024-12-30 23:06:15.937916 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-30 23:06:15.938684 INFO::Done
2024-12-30 23:06:15.939394 INFO::Acquiring quality metrics before batch effect correction.
2024-12-30 23:06:15.942465 INFO::Starting hierarchical adjustment
2024-12-30 23:06:15.943374 INFO::Found 2 batches.
2024-12-30 23:06:15.944076 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-30 23:06:15.944851 INFO::Using default BPPARAM
2024-12-30 23:06:15.945558 INFO::Adjusting the last 2 batches sequentially
2024-12-30 23:06:15.946662 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-30 23:06:15.969331 INFO::Done
2024-12-30 23:06:15.970786 INFO::Acquiring quality metrics after batch effect correction.
2024-12-30 23:06:15.975807 INFO::ASW Batch was 0.467846270397397 prior to batch effect correction and is now 0.0251153552807936 .
2024-12-30 23:06:15.977107 INFO::ASW Label was 0.599822961106936 prior to batch effect correction and is now 0.890776446905471 .
2024-12-30 23:06:15.978741 INFO::Total function execution time is 0.0501351356506348 s and adjustment time is 0.0259940624237061 s ( 51.85 )
2024-12-30 23:06:15.980303 INFO::Formatting Data.
2024-12-30 23:06:15.981627 INFO::Replacing NaNs with NAs.
2024-12-30 23:06:15.983392 INFO::Removing potential empty rows and columns
2024-12-30 23:06:15.985253 INFO::Found 0 missing values.
2024-12-30 23:06:15.98702 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.
2024-12-30 23:06:15.993975 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-30 23:06:15.995312 INFO::Done
2024-12-30 23:06:15.996537 INFO::Acquiring quality metrics before batch effect correction.
2024-12-30 23:06:16.001553 INFO::Starting hierarchical adjustment
2024-12-30 23:06:16.003063 INFO::Found 2 batches.
2024-12-30 23:06:16.004324 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-30 23:06:16.005628 INFO::Using default BPPARAM
2024-12-30 23:06:16.006864 INFO::Adjusting the last 2 batches sequentially
2024-12-30 23:06:16.00875 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-30 23:06:16.033977 INFO::Done
2024-12-30 23:06:16.03556 INFO::Acquiring quality metrics after batch effect correction.
2024-12-30 23:06:16.041351 INFO::ASW Batch was 0.467846270397397 prior to batch effect correction and is now 0.0251153552807936 .
2024-12-30 23:06:16.042828 INFO::ASW Label was 0.599822961106936 prior to batch effect correction and is now 0.890776446905471 .
2024-12-30 23:06:16.044631 INFO::Total function execution time is 0.0642921924591064 s and adjustment time is 0.0310819149017334 s ( 48.34 )
2024-12-30 23:06:16.325946 INFO::Formatting Data.
2024-12-30 23:06:16.327023 INFO::Replacing NaNs with NAs.
2024-12-30 23:06:16.32825 INFO::Removing potential empty rows and columns
2024-12-30 23:06:16.329548 INFO::Found 0 missing values.
2024-12-30 23:06:16.332791 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-30 23:06:16.333616 INFO::Done
2024-12-30 23:06:16.334392 INFO::Acquiring quality metrics before batch effect correction.
2024-12-30 23:06:16.336734 INFO::Starting hierarchical adjustment
2024-12-30 23:06:16.337673 INFO::Found 3 batches.
2024-12-30 23:06:16.338526 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-30 23:06:16.339896 INFO::Using default BPPARAM
2024-12-30 23:06:16.341199 INFO::Processing subtree level 1
2024-12-30 23:06:19.242367 INFO::Adjusting the last 1 batches sequentially
2024-12-30 23:06:19.244671 INFO::Done
2024-12-30 23:06:19.245919 INFO::Acquiring quality metrics after batch effect correction.
2024-12-30 23:06:19.249122 INFO::ASW Batch was -0.0935225545641988 prior to batch effect correction and is now -0.0935225545641988 .
2024-12-30 23:06:19.250681 INFO::Total function execution time is 2.92476797103882 s and adjustment time is 2.90707492828369 s ( 99.4 )
2024-12-30 23:06:19.252297 INFO::Formatting Data.
2024-12-30 23:06:19.253535 INFO::Typecasting input to dataframe.
2024-12-30 23:06:19.254897 INFO::Replacing NaNs with NAs.
2024-12-30 23:06:19.256398 INFO::Removing potential empty rows and columns
2024-12-30 23:06:19.258014 INFO::Found 0 missing values.
2024-12-30 23:06:19.262081 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-30 23:06:19.263194 INFO::Done
2024-12-30 23:06:19.264292 INFO::Acquiring quality metrics before batch effect correction.
2024-12-30 23:06:19.267466 INFO::Starting hierarchical adjustment
2024-12-30 23:06:19.268819 INFO::Found 3 batches.
2024-12-30 23:06:19.269936 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-30 23:06:19.271149 INFO::Using default BPPARAM
2024-12-30 23:06:19.272236 INFO::Processing subtree level 1
2024-12-30 23:06:22.342545 INFO::Adjusting the last 1 batches sequentially
2024-12-30 23:06:22.344793 INFO::Done
2024-12-30 23:06:22.346144 INFO::Acquiring quality metrics after batch effect correction.
2024-12-30 23:06:22.349437 INFO::ASW Batch was -0.0935225545641988 prior to batch effect correction and is now -0.0935225545641988 .
2024-12-30 23:06:22.3506 INFO::Total function execution time is 3.09837603569031 s and adjustment time is 3.07614517211914 s ( 99.28 )
2024-12-30 23:06:22.370961 INFO::Formatting Data.
2024-12-30 23:06:22.372687 INFO::Typecasting input to dataframe.
2024-12-30 23:06:22.374136 INFO::Replacing NaNs with NAs.
2024-12-30 23:06:22.375676 INFO::Removing potential empty rows and columns
2024-12-30 23:06:22.37741 INFO::Found 0 missing values.
2024-12-30 23:06:22.381462 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-30 23:06:22.38276 INFO::Done
2024-12-30 23:06:22.383925 INFO::Acquiring quality metrics before batch effect correction.
2024-12-30 23:06:22.387305 INFO::Starting hierarchical adjustment
2024-12-30 23:06:22.388728 INFO::Found 3 batches.
2024-12-30 23:06:22.389712 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-30 23:06:22.390734 INFO::Using default BPPARAM
2024-12-30 23:06:22.39161 INFO::Processing subtree level 1
2024-12-30 23:06:25.396754 INFO::Adjusting the last 1 batches sequentially
2024-12-30 23:06:25.399076 INFO::Done
2024-12-30 23:06:25.400403 INFO::Acquiring quality metrics after batch effect correction.
2024-12-30 23:06:25.403806 INFO::ASW Batch was 0.105227332472697 prior to batch effect correction and is now 0.105227332472697 .
2024-12-30 23:06:25.405372 INFO::Total function execution time is 3.03458714485168 s and adjustment time is 3.01056098937988 s ( 99.21 )
2024-12-30 23:06:28.530443 INFO::Formatting Data.
2024-12-30 23:06:28.531423 INFO::Replacing NaNs with NAs.
2024-12-30 23:06:28.532655 INFO::Removing potential empty rows and columns
2024-12-30 23:06:28.534954 INFO::Found 1000 missing values.
2024-12-30 23:06:28.548461 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-30 23:06:28.549378 INFO::Done
2024-12-30 23:06:28.550131 INFO::Acquiring quality metrics before batch effect correction.
2024-12-30 23:06:28.556293 INFO::Starting hierarchical adjustment
2024-12-30 23:06:28.557336 INFO::Found 10 batches.
2024-12-30 23:06:28.558072 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-30 23:06:28.558831 INFO::Using default BPPARAM
2024-12-30 23:06:28.559598 INFO::Processing subtree level 1
2024-12-30 23:06:31.766821 INFO::Processing subtree level 2
2024-12-30 23:06:34.967833 INFO::Adjusting the last 1 batches sequentially
2024-12-30 23:06:34.97033 INFO::Done
2024-12-30 23:06:34.971561 INFO::Acquiring quality metrics after batch effect correction.
2024-12-30 23:06:34.98048 INFO::ASW Batch was 0.526153166825184 prior to batch effect correction and is now 0.526153166825184 .
2024-12-30 23:06:34.981818 INFO::ASW Label was 0.296176854187615 prior to batch effect correction and is now 0.296176854187615 .
2024-12-30 23:06:34.983415 INFO::Total function execution time is 6.45297598838806 s and adjustment time is 6.41312098503113 s ( 99.38 )
2024-12-30 23:06:34.984856 INFO::Formatting Data.
2024-12-30 23:06:34.986098 INFO::Replacing NaNs with NAs.
2024-12-30 23:06:34.987948 INFO::Removing potential empty rows and columns
2024-12-30 23:06:34.99155 INFO::Found 1000 missing values.
2024-12-30 23:06:35.012297 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-30 23:06:35.013474 INFO::Done
2024-12-30 23:06:35.014223 INFO::Acquiring quality metrics before batch effect correction.
2024-12-30 23:06:35.022921 INFO::Starting hierarchical adjustment
2024-12-30 23:06:35.024758 INFO::Found 10 batches.
2024-12-30 23:06:35.784027 INFO::Set up parallel execution backend with 2 workers
2024-12-30 23:06:35.784985 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-12-30 23:06:38.710334 INFO::Adjusting the last 2 batches sequentially
2024-12-30 23:06:38.711898 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-30 23:06:38.726512 INFO::Done
2024-12-30 23:06:38.7277 INFO::Acquiring quality metrics after batch effect correction.
2024-12-30 23:06:38.734601 INFO::ASW Batch was 0.526153166825184 prior to batch effect correction and is now 0.526153166825184 .
2024-12-30 23:06:38.735474 INFO::ASW Label was 0.296176854187615 prior to batch effect correction and is now 0.296176854187615 .
2024-12-30 23:06:38.736548 INFO::Total function execution time is 3.75173616409302 s and adjustment time is 3.70209789276123 s ( 98.68 )
2024-12-30 23:06:41.709972 INFO::Formatting Data.
2024-12-30 23:06:41.710976 INFO::Replacing NaNs with NAs.
2024-12-30 23:06:41.712154 INFO::Removing potential empty rows and columns
2024-12-30 23:06:41.713311 INFO::Found 0 missing values.
2024-12-30 23:06:41.716593 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-30 23:06:41.717548 INFO::Done
2024-12-30 23:06:41.718419 INFO::Acquiring quality metrics before batch effect correction.
2024-12-30 23:06:41.721306 INFO::Starting hierarchical adjustment
2024-12-30 23:06:41.722188 INFO::Found 3 batches.
2024-12-30 23:06:41.722869 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-30 23:06:41.723606 INFO::Using default BPPARAM
2024-12-30 23:06:41.724279 INFO::Processing subtree level 1
2024-12-30 23:06:45.080293 INFO::Adjusting the last 1 batches sequentially
2024-12-30 23:06:45.082621 INFO::Done
2024-12-30 23:06:45.083892 INFO::Acquiring quality metrics after batch effect correction.
2024-12-30 23:06:45.088122 INFO::ASW Batch was 0.241818775501253 prior to batch effect correction and is now -0.175437778513584 .
2024-12-30 23:06:45.089294 INFO::ASW Label was -0.187558370455088 prior to batch effect correction and is now -0.0582442205503604 .
2024-12-30 23:06:45.090699 INFO::Total function execution time is 3.38075685501099 s and adjustment time is 3.36050796508789 s ( 99.4 )
2024-12-30 23:06:45.249307 INFO::Formatting Data.
2024-12-30 23:06:45.250319 INFO::Replacing NaNs with NAs.
2024-12-30 23:06:45.251351 INFO::Removing potential empty rows and columns
2024-12-30 23:06:45.252443 INFO::Found 2 missing values.
2024-12-30 23:06:45.256066 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-12-30 23:06:45.257272 INFO::Done
2024-12-30 23:06:45.296878 INFO::Found NA in Reference column
2024-12-30 23:06:45.309111 INFO::Require at least two references per batch.
2024-12-30 23:06:45.339679 INFO::Formatting Data.
2024-12-30 23:06:45.341117 INFO::Recognized SummarizedExperiment
2024-12-30 23:06:45.342319 INFO::Typecasting input to dataframe.
2024-12-30 23:06:45.355276 INFO::Replacing NaNs with NAs.
2024-12-30 23:06:45.357269 INFO::Removing potential empty rows and columns
2024-12-30 23:06:45.361963 INFO::Found 0 missing values.
2024-12-30 23:06:45.370584 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-30 23:06:45.371899 INFO::Done
2024-12-30 23:06:45.39448 INFO::Formatting Data.
2024-12-30 23:06:45.396006 INFO::Recognized SummarizedExperiment
2024-12-30 23:06:45.397254 INFO::Typecasting input to dataframe.
2024-12-30 23:06:45.421795 INFO::Replacing NaNs with NAs.
2024-12-30 23:06:45.423884 INFO::Removing potential empty rows and columns
2024-12-30 23:06:45.428684 INFO::Found 0 missing values.
2024-12-30 23:06:45.442383 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-30 23:06:45.443771 INFO::Done
2024-12-30 23:06:45.46606 INFO::Formatting Data.
2024-12-30 23:06:45.467468 INFO::Recognized SummarizedExperiment
2024-12-30 23:06:45.468625 INFO::Typecasting input to dataframe.
2024-12-30 23:06:45.489695 INFO::Replacing NaNs with NAs.
2024-12-30 23:06:45.491495 INFO::Removing potential empty rows and columns
2024-12-30 23:06:45.493364 INFO::Found 0 missing values.
2024-12-30 23:06:45.495003 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.
2024-12-30 23:06:45.501072 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-30 23:06:45.502207 INFO::Done
2024-12-30 23:06:45.521298 INFO::Formatting Data.
2024-12-30 23:06:45.522743 INFO::Replacing NaNs with NAs.
2024-12-30 23:06:45.524411 INFO::Removing potential empty rows and columns
2024-12-30 23:06:45.526247 INFO::Found 0 missing values.
2024-12-30 23:06:45.530487 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-30 23:06:45.531644 INFO::Done
2024-12-30 23:06:45.552231 INFO::Formatting Data.
2024-12-30 23:06:45.553784 INFO::Replacing NaNs with NAs.
2024-12-30 23:06:45.555507 INFO::Removing potential empty rows and columns
2024-12-30 23:06:45.557344 INFO::Found 0 missing values.
2024-12-30 23:06:45.561988 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-30 23:06:45.563158 INFO::Done
2024-12-30 23:06:45.60517 INFO::Formatting Data.
2024-12-30 23:06:45.60624 INFO::Replacing NaNs with NAs.
2024-12-30 23:06:45.607543 INFO::Removing potential empty rows and columns
2024-12-30 23:06:45.608876 INFO::Found 1 missing values.
2024-12-30 23:06:45.61128 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-30 23:06:45.611984 INFO::Done
2024-12-30 23:06:45.635798 INFO::Formatting Data.
2024-12-30 23:06:45.6368 INFO::Replacing NaNs with NAs.
2024-12-30 23:06:45.637841 INFO::Removing potential empty rows and columns
2024-12-30 23:06:45.638898 INFO::Found 2 missing values.
2024-12-30 23:06:45.639959 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.
2024-12-30 23:06:45.642081 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-12-30 23:06:45.642783 INFO::Done
2024-12-30 23:06:45.656661 INFO::Formatting Data.
2024-12-30 23:06:45.657671 INFO::Replacing NaNs with NAs.
2024-12-30 23:06:45.658725 INFO::Removing potential empty rows and columns
2024-12-30 23:06:45.659795 INFO::Found 2 missing values.
2024-12-30 23:06:45.661506 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-30 23:06:45.662207 INFO::Done
2024-12-30 23:06:45.679746 INFO::Formatting Data.
2024-12-30 23:06:45.681361 INFO::Typecasting input to dataframe.
2024-12-30 23:06:45.683138 INFO::Replacing NaNs with NAs.
2024-12-30 23:06:45.684881 INFO::Removing potential empty rows and columns
2024-12-30 23:06:45.686714 INFO::Found 0 missing values.
2024-12-30 23:06:45.689948 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-30 23:06:45.690967 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
30.81 1.34 78.45
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 9.23 | 0.54 | 18.66 | |
| compute_asw | 0.05 | 0.00 | 0.05 | |
| count_existing | 0.03 | 0.00 | 0.03 | |
| generate_data_covariables | 0.01 | 0.00 | 0.02 | |
| generate_dataset | 0.04 | 0.00 | 0.03 | |