Yannis Schumann
| Snapshot Date: 2024-07-25 14:00 -0400 (Thu, 25 Jul 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: aaedecb |
| git_last_commit_date: 2024-07-22 10:00:51 -0400 (Mon, 22 Jul 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-26 11:39 -0400 (Fri, 26 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4690 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4384 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4457 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4406 |
| 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 157/2248 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.1.2 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.1.2 |
| 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_1.1.2.tar.gz |
| StartedAt: 2024-07-25 22:50:57 -0400 (Thu, 25 Jul 2024) |
| EndedAt: 2024-07-25 22:53:10 -0400 (Thu, 25 Jul 2024) |
| EllapsedTime: 132.9 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_1.1.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* 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 '1.1.2'
* 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 8.18 0.59 18.22
* 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 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
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")
2024-07-25 22:52:00.045381 INFO::Formatting Data.
2024-07-25 22:52:00.048634 INFO::Replacing NaNs with NAs.
2024-07-25 22:52:00.064443 INFO::Removing potential empty rows and columns
2024-07-25 22:52:00.360892 INFO::Found 0 missing values.
2024-07-25 22:52:00.366023 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 22:52:00.367426 INFO::Done
2024-07-25 22:52:00.368707 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 22:52:00.389441 INFO::Starting hierarchical adjustment
2024-07-25 22:52:00.39119 INFO::Found 3 batches.
2024-07-25 22:52:00.392497 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 22:52:00.394502 INFO::Using default BPPARAM
2024-07-25 22:52:00.39576 INFO::Processing subtree level 1
2024-07-25 22:52:03.304773 INFO::Adjusting the last 1 batches sequentially
2024-07-25 22:52:03.307165 INFO::Done
2024-07-25 22:52:03.308137 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 22:52:03.310244 INFO::ASW Batch was -0.0983141365353644 prior to batch effect correction and is now -0.0983141365353644 .
2024-07-25 22:52:03.311335 INFO::Total function execution time is 3.26683282852173 s and adjustment time is 2.91624402999878 s ( 89.27 )
2024-07-25 22:52:03.330996 INFO::Formatting Data.
2024-07-25 22:52:03.332587 INFO::Replacing NaNs with NAs.
2024-07-25 22:52:03.33437 INFO::Removing potential empty rows and columns
2024-07-25 22:52:03.336294 INFO::Found 0 missing values.
2024-07-25 22:52:03.338031 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.
2024-07-25 22:52:03.352188 INFO::Formatting Data.
2024-07-25 22:52:03.353733 INFO::Replacing NaNs with NAs.
2024-07-25 22:52:03.355516 INFO::Removing potential empty rows and columns
2024-07-25 22:52:03.35738 INFO::Found 0 missing values.
2024-07-25 22:52:03.359125 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.
2024-07-25 22:52:03.380262 INFO::Formatting Data.
2024-07-25 22:52:03.381653 INFO::Replacing NaNs with NAs.
2024-07-25 22:52:03.383199 INFO::Removing potential empty rows and columns
2024-07-25 22:52:03.384827 INFO::Found 0 missing values.
2024-07-25 22:52:03.386362 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.
2024-07-25 22:52:03.391358 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 22:52:03.392097 INFO::Done
2024-07-25 22:52:03.392796 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 22:52:03.394851 INFO::Starting hierarchical adjustment
2024-07-25 22:52:03.39579 INFO::Found 2 batches.
2024-07-25 22:52:03.396603 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 22:52:03.397392 INFO::Using default BPPARAM
2024-07-25 22:52:03.398088 INFO::Adjusting the last 2 batches sequentially
2024-07-25 22:52:03.399176 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 22:52:03.414885 INFO::Done
2024-07-25 22:52:03.415747 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 22:52:03.417795 INFO::ASW Batch was -0.0156097092412499 prior to batch effect correction and is now -0.131045292308166 .
2024-07-25 22:52:03.418746 INFO::Total function execution time is 0.0386631488800049 s and adjustment time is 0.0192680358886719 s ( 49.84 )
2024-07-25 22:52:03.421491 INFO::Formatting Data.
2024-07-25 22:52:03.422286 INFO::Replacing NaNs with NAs.
2024-07-25 22:52:03.42896 INFO::Formatting Data.
2024-07-25 22:52:03.429855 INFO::Replacing NaNs with NAs.
2024-07-25 22:52:03.430874 INFO::Removing potential empty rows and columns
2024-07-25 22:52:03.431977 INFO::Found 0 missing values.
2024-07-25 22:52:03.434371 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 22:52:03.435081 INFO::Done
2024-07-25 22:52:03.435773 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 22:52:03.437787 INFO::Starting hierarchical adjustment
2024-07-25 22:52:03.438652 INFO::Found 2 batches.
2024-07-25 22:52:03.439352 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 22:52:03.440118 INFO::Using default BPPARAM
2024-07-25 22:52:03.440823 INFO::Adjusting the last 2 batches sequentially
2024-07-25 22:52:03.441861 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 22:52:03.453508 INFO::Done
2024-07-25 22:52:03.454337 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 22:52:03.456374 INFO::ASW Batch was -0.0120114617441934 prior to batch effect correction and is now -0.118216290417296 .
2024-07-25 22:52:03.457348 INFO::Total function execution time is 0.0284039974212646 s and adjustment time is 0.01497483253479 s ( 52.72 )
2024-07-25 22:52:03.458501 INFO::Formatting Data.
2024-07-25 22:52:03.459271 INFO::Replacing NaNs with NAs.
2024-07-25 22:52:03.460266 INFO::Removing potential empty rows and columns
2024-07-25 22:52:03.461399 INFO::Found 0 missing values.
2024-07-25 22:52:03.463816 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 22:52:03.464527 INFO::Done
2024-07-25 22:52:03.465219 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 22:52:03.467225 INFO::Starting hierarchical adjustment
2024-07-25 22:52:03.468086 INFO::Found 2 batches.
2024-07-25 22:52:03.468787 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 22:52:03.469554 INFO::Using default BPPARAM
2024-07-25 22:52:03.470249 INFO::Adjusting the last 2 batches sequentially
2024-07-25 22:52:03.4713 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 22:52:03.483192 INFO::Done
2024-07-25 22:52:03.484052 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 22:52:03.486128 INFO::ASW Batch was -0.0120114617441934 prior to batch effect correction and is now -0.118216290417296 .
2024-07-25 22:52:03.487091 INFO::Total function execution time is 0.0285739898681641 s and adjustment time is 0.0152099132537842 s ( 53.23 )
2024-07-25 22:52:06.022257 INFO::Formatting Data.
2024-07-25 22:52:06.023208 INFO::Recognized SummarizedExperiment
2024-07-25 22:52:06.023948 INFO::Typecasting input to dataframe.
2024-07-25 22:52:06.052352 INFO::Replacing NaNs with NAs.
2024-07-25 22:52:06.053764 INFO::Removing potential empty rows and columns
2024-07-25 22:52:06.056718 INFO::Found 0 missing values.
2024-07-25 22:52:06.062057 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 22:52:06.062919 INFO::Done
2024-07-25 22:52:06.063667 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 22:52:06.067373 INFO::Starting hierarchical adjustment
2024-07-25 22:52:06.068279 INFO::Found 2 batches.
2024-07-25 22:52:06.06903 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 22:52:06.070271 INFO::Using default BPPARAM
2024-07-25 22:52:06.071027 INFO::Adjusting the last 2 batches sequentially
2024-07-25 22:52:06.072419 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 22:52:06.116887 INFO::Done
2024-07-25 22:52:06.117837 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 22:52:06.12216 INFO::ASW Batch was -0.0062465944480173 prior to batch effect correction and is now -0.0928620439274918 .
2024-07-25 22:52:06.124023 INFO::Total function execution time is 0.101937055587769 s and adjustment time is 0.0487000942230225 s ( 47.77 )
2024-07-25 22:52:06.155537 INFO::Formatting Data.
2024-07-25 22:52:06.157243 INFO::Recognized SummarizedExperiment
2024-07-25 22:52:06.15871 INFO::Typecasting input to dataframe.
2024-07-25 22:52:06.174381 INFO::Replacing NaNs with NAs.
2024-07-25 22:52:06.176947 INFO::Removing potential empty rows and columns
2024-07-25 22:52:06.181098 INFO::Found 0 missing values.
2024-07-25 22:52:06.188286 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 22:52:06.189239 INFO::Done
2024-07-25 22:52:06.190108 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 22:52:06.194536 INFO::Starting hierarchical adjustment
2024-07-25 22:52:06.195597 INFO::Found 2 batches.
2024-07-25 22:52:06.196475 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 22:52:06.197392 INFO::Using default BPPARAM
2024-07-25 22:52:06.198197 INFO::Adjusting the last 2 batches sequentially
2024-07-25 22:52:06.199527 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 22:52:06.235179 INFO::Done
2024-07-25 22:52:06.23617 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 22:52:06.240633 INFO::ASW Batch was -0.00069931488085015 prior to batch effect correction and is now -0.00069931488085015 .
2024-07-25 22:52:06.241802 INFO::Total function execution time is 0.0863180160522461 s and adjustment time is 0.0397160053253174 s ( 46.01 )
2024-07-25 22:52:06.265348 INFO::Formatting Data.
2024-07-25 22:52:06.26643 INFO::Replacing NaNs with NAs.
2024-07-25 22:52:06.267633 INFO::Removing potential empty rows and columns
2024-07-25 22:52:06.268921 INFO::Found 0 missing values.
2024-07-25 22:52:06.272064 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 22:52:06.272854 INFO::Done
2024-07-25 22:52:06.273636 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 22:52:06.27607 INFO::Starting hierarchical adjustment
2024-07-25 22:52:06.2771 INFO::Found 3 batches.
2024-07-25 22:52:06.277942 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 22:52:06.278888 INFO::Using default BPPARAM
2024-07-25 22:52:06.279733 INFO::Processing subtree level 1
2024-07-25 22:52:15.962621 INFO::Adjusting the last 1 batches sequentially
2024-07-25 22:52:15.964959 INFO::Done
2024-07-25 22:52:15.966337 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 22:52:15.969523 INFO::ASW Batch was -0.0124587842042165 prior to batch effect correction and is now -0.167048508808856 .
2024-07-25 22:52:15.971058 INFO::Total function execution time is 9.70574402809143 s and adjustment time is 9.68795084953308 s ( 99.82 )
2024-07-25 22:52:15.993999 INFO::Skipping initial DF formatting
2024-07-25 22:52:15.995306 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 22:52:16.001387 INFO::Starting hierarchical adjustment
2024-07-25 22:52:16.002803 INFO::Found 5 batches.
2024-07-25 22:52:16.003902 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 22:52:16.005067 INFO::Using default BPPARAM
2024-07-25 22:52:16.006118 INFO::Processing subtree level 1
2024-07-25 22:52:18.891711 INFO::Adjusting the last 2 batches sequentially
2024-07-25 22:52:18.893917 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 22:52:18.917055 INFO::Done
2024-07-25 22:52:18.91849 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 22:52:18.925112 INFO::ASW Batch was 0.498113222886499 prior to batch effect correction and is now 0.498113222886499 .
2024-07-25 22:52:18.926485 INFO::ASW Label was 0.392153401113209 prior to batch effect correction and is now 0.392153401113209 .
2024-07-25 22:52:18.928054 INFO::Total function execution time is 2.93414807319641 s and adjustment time is 2.91442108154297 s ( 99.33 )
2024-07-25 22:52:18.956669 INFO::Formatting Data.
2024-07-25 22:52:18.958219 INFO::Replacing NaNs with NAs.
2024-07-25 22:52:18.959971 INFO::Removing potential empty rows and columns
2024-07-25 22:52:18.961759 INFO::Found 0 missing values.
2024-07-25 22:52:18.967546 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 22:52:18.968829 INFO::Done
2024-07-25 22:52:18.970052 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 22:52:18.974818 INFO::Starting hierarchical adjustment
2024-07-25 22:52:18.976303 INFO::Found 5 batches.
2024-07-25 22:52:18.977495 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 22:52:18.978782 INFO::Using default BPPARAM
2024-07-25 22:52:18.980111 INFO::Processing subtree level 1
2024-07-25 22:52:22.028048 INFO::Adjusting the last 2 batches sequentially
2024-07-25 22:52:22.03006 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 22:52:22.047031 INFO::Done
2024-07-25 22:52:22.048294 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 22:52:22.052606 INFO::ASW Batch was 0.546355554153342 prior to batch effect correction and is now -0.0622425621627885 .
2024-07-25 22:52:22.053735 INFO::ASW Label was 0.255298637160966 prior to batch effect correction and is now 0.7251319278247 .
2024-07-25 22:52:22.055292 INFO::Total function execution time is 3.09874415397644 s and adjustment time is 3.07090902328491 s ( 99.1 )
2024-07-25 22:52:22.0568 INFO::Formatting Data.
2024-07-25 22:52:22.058033 INFO::Replacing NaNs with NAs.
2024-07-25 22:52:22.059703 INFO::Removing potential empty rows and columns
2024-07-25 22:52:22.06155 INFO::Found 0 missing values.
2024-07-25 22:52:22.067339 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 22:52:22.068705 INFO::Done
2024-07-25 22:52:22.070002 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 22:52:22.074921 INFO::Starting hierarchical adjustment
2024-07-25 22:52:22.076484 INFO::Found 5 batches.
2024-07-25 22:52:22.077756 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 22:52:22.079146 INFO::Using default BPPARAM
2024-07-25 22:52:22.080396 INFO::Processing subtree level 1
2024-07-25 22:52:25.087998 INFO::Adjusting the last 2 batches sequentially
2024-07-25 22:52:25.089961 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 22:52:25.101973 INFO::Done
2024-07-25 22:52:25.102928 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 22:52:25.105961 INFO::ASW Batch was 0.546355554153342 prior to batch effect correction and is now -0.0622425621627885 .
2024-07-25 22:52:25.106806 INFO::ASW Label was 0.255298637160966 prior to batch effect correction and is now 0.7251319278247 .
2024-07-25 22:52:25.10782 INFO::Total function execution time is 3.05110788345337 s and adjustment time is 3.02572512626648 s ( 99.17 )
2024-07-25 22:52:25.124019 INFO::Formatting Data.
2024-07-25 22:52:25.125207 INFO::Replacing NaNs with NAs.
2024-07-25 22:52:25.126351 INFO::Removing potential empty rows and columns
2024-07-25 22:52:25.127453 INFO::Found 0 missing values.
2024-07-25 22:52:25.130788 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 22:52:25.131991 INFO::Done
2024-07-25 22:52:25.133058 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 22:52:25.137454 INFO::Starting hierarchical adjustment
2024-07-25 22:52:25.138894 INFO::Found 5 batches.
2024-07-25 22:52:25.140065 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 22:52:25.141329 INFO::Using default BPPARAM
2024-07-25 22:52:25.14251 INFO::Processing subtree level 1
2024-07-25 22:52:28.090305 INFO::Adjusting the last 2 batches sequentially
2024-07-25 22:52:28.09248 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 22:52:28.110497 INFO::Done
2024-07-25 22:52:28.111928 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 22:52:28.116449 INFO::ASW Batch was 0.107805231562113 prior to batch effect correction and is now -0.03147722525432 .
2024-07-25 22:52:28.117883 INFO::ASW Label was 0.690675133409336 prior to batch effect correction and is now 0.805539834177838 .
2024-07-25 22:52:28.119426 INFO::Total function execution time is 2.99543905258179 s and adjustment time is 2.97175002098083 s ( 99.21 )
2024-07-25 22:52:28.12094 INFO::Formatting Data.
2024-07-25 22:52:28.122329 INFO::Replacing NaNs with NAs.
2024-07-25 22:52:28.123848 INFO::Removing potential empty rows and columns
2024-07-25 22:52:28.124964 INFO::Found 0 missing values.
2024-07-25 22:52:28.128365 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 22:52:28.129135 INFO::Done
2024-07-25 22:52:28.129867 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 22:52:28.132832 INFO::Starting hierarchical adjustment
2024-07-25 22:52:28.133749 INFO::Found 5 batches.
2024-07-25 22:52:28.134491 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 22:52:28.135279 INFO::Using default BPPARAM
2024-07-25 22:52:28.135982 INFO::Processing subtree level 1
2024-07-25 22:52:31.336186 INFO::Adjusting the last 2 batches sequentially
2024-07-25 22:52:31.338345 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 22:52:31.356134 INFO::Done
2024-07-25 22:52:31.35754 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 22:52:31.362225 INFO::ASW Batch was 0.107805231562113 prior to batch effect correction and is now -0.03147722525432 .
2024-07-25 22:52:31.36353 INFO::ASW Label was 0.690675133409336 prior to batch effect correction and is now 0.805539834177838 .
2024-07-25 22:52:31.365023 INFO::Total function execution time is 3.24407601356506 s and adjustment time is 3.22245407104492 s ( 99.33 )
2024-07-25 22:52:31.388043 INFO::Formatting Data.
2024-07-25 22:52:31.389462 INFO::Replacing NaNs with NAs.
2024-07-25 22:52:31.391049 INFO::Removing potential empty rows and columns
2024-07-25 22:52:31.392663 INFO::Found 0 missing values.
2024-07-25 22:52:31.396253 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 22:52:31.397294 INFO::Done
2024-07-25 22:52:31.398316 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 22:52:31.40248 INFO::Starting hierarchical adjustment
2024-07-25 22:52:31.403732 INFO::Found 2 batches.
2024-07-25 22:52:31.404759 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 22:52:31.405885 INFO::Using default BPPARAM
2024-07-25 22:52:31.406921 INFO::Adjusting the last 2 batches sequentially
2024-07-25 22:52:31.408469 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 22:52:31.426127 INFO::Done
2024-07-25 22:52:31.427415 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 22:52:31.431791 INFO::ASW Batch was 0.714977164667923 prior to batch effect correction and is now 0.167007792148717 .
2024-07-25 22:52:31.432956 INFO::ASW Label was 0.348116338243835 prior to batch effect correction and is now 0.731982701416436 .
2024-07-25 22:52:31.434334 INFO::Total function execution time is 0.046450138092041 s and adjustment time is 0.0225520133972168 s ( 48.55 )
2024-07-25 22:52:31.435698 INFO::Formatting Data.
2024-07-25 22:52:31.43687 INFO::Replacing NaNs with NAs.
2024-07-25 22:52:31.438372 INFO::Removing potential empty rows and columns
2024-07-25 22:52:31.439981 INFO::Found 0 missing values.
2024-07-25 22:52:31.443163 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 22:52:31.444062 INFO::Done
2024-07-25 22:52:31.444856 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 22:52:31.448215 INFO::Starting hierarchical adjustment
2024-07-25 22:52:31.44908 INFO::Found 2 batches.
2024-07-25 22:52:31.449825 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 22:52:31.450636 INFO::Using default BPPARAM
2024-07-25 22:52:31.451342 INFO::Adjusting the last 2 batches sequentially
2024-07-25 22:52:31.452448 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 22:52:31.464534 INFO::Done
2024-07-25 22:52:31.465374 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 22:52:31.468288 INFO::ASW Batch was 0.714977164667923 prior to batch effect correction and is now 0.167007792148717 .
2024-07-25 22:52:31.469045 INFO::ASW Label was 0.348116338243835 prior to batch effect correction and is now 0.731982701416436 .
2024-07-25 22:52:31.469964 INFO::Total function execution time is 0.0343630313873291 s and adjustment time is 0.0155699253082275 s ( 45.31 )
2024-07-25 22:52:31.484992 INFO::Formatting Data.
2024-07-25 22:52:31.485956 INFO::Replacing NaNs with NAs.
2024-07-25 22:52:31.487002 INFO::Removing potential empty rows and columns
2024-07-25 22:52:31.488081 INFO::Found 0 missing values.
2024-07-25 22:52:31.490229 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 22:52:31.491021 INFO::Done
2024-07-25 22:52:31.491715 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 22:52:31.494592 INFO::Starting hierarchical adjustment
2024-07-25 22:52:31.495539 INFO::Found 2 batches.
2024-07-25 22:52:31.496261 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 22:52:31.497107 INFO::Using default BPPARAM
2024-07-25 22:52:31.497902 INFO::Adjusting the last 2 batches sequentially
2024-07-25 22:52:31.498948 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 22:52:31.52524 INFO::Done
2024-07-25 22:52:31.526198 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 22:52:31.528327 INFO::ASW Batch was -0.0220831398198096 prior to batch effect correction and is now -0.1159650707193 .
2024-07-25 22:52:31.529365 INFO::Total function execution time is 0.0444481372833252 s and adjustment time is 0.0297989845275879 s ( 67.04 )
2024-07-25 22:52:31.54452 INFO::Formatting Data.
2024-07-25 22:52:31.5455 INFO::Replacing NaNs with NAs.
2024-07-25 22:52:31.54656 INFO::Removing potential empty rows and columns
2024-07-25 22:52:31.547799 INFO::Found 0 missing values.
2024-07-25 22:52:31.549116 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.
2024-07-25 22:52:31.553189 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 22:52:31.553963 INFO::Done
2024-07-25 22:52:31.554711 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 22:52:31.557877 INFO::Starting hierarchical adjustment
2024-07-25 22:52:31.558774 INFO::Found 2 batches.
2024-07-25 22:52:31.559479 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 22:52:31.560318 INFO::Using default BPPARAM
2024-07-25 22:52:31.561064 INFO::Adjusting the last 2 batches sequentially
2024-07-25 22:52:31.562131 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 22:52:31.575433 INFO::Done
2024-07-25 22:52:31.576304 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 22:52:31.579431 INFO::ASW Batch was 0.766277309822421 prior to batch effect correction and is now -0.0157641312356768 .
2024-07-25 22:52:31.58022 INFO::ASW Label was 0.266900375810245 prior to batch effect correction and is now 0.888473253479142 .
2024-07-25 22:52:31.581169 INFO::Total function execution time is 0.0367329120635986 s and adjustment time is 0.0167689323425293 s ( 45.65 )
2024-07-25 22:52:31.582187 INFO::Formatting Data.
2024-07-25 22:52:31.583045 INFO::Replacing NaNs with NAs.
2024-07-25 22:52:31.584141 INFO::Removing potential empty rows and columns
2024-07-25 22:52:31.585313 INFO::Found 0 missing values.
2024-07-25 22:52:31.586366 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.
2024-07-25 22:52:31.590371 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 22:52:31.591138 INFO::Done
2024-07-25 22:52:31.591924 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 22:52:31.595101 INFO::Starting hierarchical adjustment
2024-07-25 22:52:31.595967 INFO::Found 2 batches.
2024-07-25 22:52:31.596775 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 22:52:31.597678 INFO::Using default BPPARAM
2024-07-25 22:52:31.598396 INFO::Adjusting the last 2 batches sequentially
2024-07-25 22:52:31.5995 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 22:52:31.613575 INFO::Done
2024-07-25 22:52:31.614436 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 22:52:31.617342 INFO::ASW Batch was 0.766277309822421 prior to batch effect correction and is now -0.0157641312356768 .
2024-07-25 22:52:31.618108 INFO::ASW Label was 0.266900375810245 prior to batch effect correction and is now 0.888473253479142 .
2024-07-25 22:52:31.619076 INFO::Total function execution time is 0.0369298458099365 s and adjustment time is 0.0177202224731445 s ( 47.98 )
2024-07-25 22:52:31.866793 INFO::Formatting Data.
2024-07-25 22:52:31.868453 INFO::Replacing NaNs with NAs.
2024-07-25 22:52:31.870357 INFO::Removing potential empty rows and columns
2024-07-25 22:52:31.872452 INFO::Found 0 missing values.
2024-07-25 22:52:31.877507 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 22:52:31.878839 INFO::Done
2024-07-25 22:52:31.880033 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 22:52:31.883503 INFO::Starting hierarchical adjustment
2024-07-25 22:52:31.884995 INFO::Found 3 batches.
2024-07-25 22:52:31.886263 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 22:52:31.887606 INFO::Using default BPPARAM
2024-07-25 22:52:31.888878 INFO::Processing subtree level 1
2024-07-25 22:52:34.761761 INFO::Adjusting the last 1 batches sequentially
2024-07-25 22:52:34.764021 INFO::Done
2024-07-25 22:52:34.765322 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 22:52:34.768349 INFO::ASW Batch was -0.108237180916918 prior to batch effect correction and is now -0.108237180916918 .
2024-07-25 22:52:34.769849 INFO::Total function execution time is 2.90319395065308 s and adjustment time is 2.87922406196594 s ( 99.17 )
2024-07-25 22:52:34.771495 INFO::Formatting Data.
2024-07-25 22:52:34.772715 INFO::Typecasting input to dataframe.
2024-07-25 22:52:34.774094 INFO::Replacing NaNs with NAs.
2024-07-25 22:52:34.775664 INFO::Removing potential empty rows and columns
2024-07-25 22:52:34.777322 INFO::Found 0 missing values.
2024-07-25 22:52:34.781069 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 22:52:34.781794 INFO::Done
2024-07-25 22:52:34.782487 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 22:52:34.784553 INFO::Starting hierarchical adjustment
2024-07-25 22:52:34.78543 INFO::Found 3 batches.
2024-07-25 22:52:34.786146 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 22:52:34.786986 INFO::Using default BPPARAM
2024-07-25 22:52:34.787765 INFO::Processing subtree level 1
2024-07-25 22:52:37.528964 INFO::Adjusting the last 1 batches sequentially
2024-07-25 22:52:37.530767 INFO::Done
2024-07-25 22:52:37.532104 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 22:52:37.535304 INFO::ASW Batch was -0.108237180916918 prior to batch effect correction and is now -0.108237180916918 .
2024-07-25 22:52:37.536567 INFO::Total function execution time is 2.7651219367981 s and adjustment time is 2.74539804458618 s ( 99.29 )
2024-07-25 22:52:37.557116 INFO::Formatting Data.
2024-07-25 22:52:37.558636 INFO::Typecasting input to dataframe.
2024-07-25 22:52:37.560361 INFO::Replacing NaNs with NAs.
2024-07-25 22:52:37.561794 INFO::Removing potential empty rows and columns
2024-07-25 22:52:37.563707 INFO::Found 0 missing values.
2024-07-25 22:52:37.567631 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 22:52:37.5689 INFO::Done
2024-07-25 22:52:37.570083 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 22:52:37.573126 INFO::Starting hierarchical adjustment
2024-07-25 22:52:37.574568 INFO::Found 3 batches.
2024-07-25 22:52:37.575762 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 22:52:37.577023 INFO::Using default BPPARAM
2024-07-25 22:52:37.578185 INFO::Processing subtree level 1
2024-07-25 22:52:40.289273 INFO::Adjusting the last 1 batches sequentially
2024-07-25 22:52:40.291255 INFO::Done
2024-07-25 22:52:40.292629 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 22:52:40.296063 INFO::ASW Batch was -0.0809372928993525 prior to batch effect correction and is now -0.0809372928993525 .
2024-07-25 22:52:40.297702 INFO::Total function execution time is 2.74065589904785 s and adjustment time is 2.71684503555298 s ( 99.13 )
2024-07-25 22:52:43.265466 INFO::Formatting Data.
2024-07-25 22:52:43.267051 INFO::Replacing NaNs with NAs.
2024-07-25 22:52:43.268674 INFO::Removing potential empty rows and columns
2024-07-25 22:52:43.271017 INFO::Found 1000 missing values.
2024-07-25 22:52:43.28494 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 22:52:43.286007 INFO::Done
2024-07-25 22:52:43.286802 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 22:52:43.296043 INFO::Starting hierarchical adjustment
2024-07-25 22:52:43.297803 INFO::Found 10 batches.
2024-07-25 22:52:43.299112 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 22:52:43.300485 INFO::Using default BPPARAM
2024-07-25 22:52:43.301728 INFO::Processing subtree level 1
2024-07-25 22:52:46.400772 INFO::Processing subtree level 2
2024-07-25 22:52:49.417887 INFO::Adjusting the last 1 batches sequentially
2024-07-25 22:52:49.420192 INFO::Done
2024-07-25 22:52:49.421546 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 22:52:49.430833 INFO::ASW Batch was 0.47375447335861 prior to batch effect correction and is now 0.47375447335861 .
2024-07-25 22:52:49.432267 INFO::ASW Label was 0.345050349143912 prior to batch effect correction and is now 0.345050349143912 .
2024-07-25 22:52:49.433995 INFO::Total function execution time is 6.16863179206848 s and adjustment time is 6.12268495559692 s ( 99.26 )
2024-07-25 22:52:49.435524 INFO::Formatting Data.
2024-07-25 22:52:49.436877 INFO::Replacing NaNs with NAs.
2024-07-25 22:52:49.438797 INFO::Removing potential empty rows and columns
2024-07-25 22:52:49.442432 INFO::Found 1000 missing values.
2024-07-25 22:52:49.464737 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 22:52:49.466191 INFO::Done
2024-07-25 22:52:49.46747 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 22:52:49.477191 INFO::Starting hierarchical adjustment
2024-07-25 22:52:49.478867 INFO::Found 10 batches.
2024-07-25 22:52:50.215925 INFO::Set up parallel execution backend with 2 workers
2024-07-25 22:52:50.217475 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-07-25 22:52:53.439876 INFO::Adjusting the last 2 batches sequentially
2024-07-25 22:52:53.441392 INFO::Adjusting sequential tree level 1 with 2 batches
2024-07-25 22:52:53.455869 INFO::Done
2024-07-25 22:52:53.456768 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 22:52:53.462874 INFO::ASW Batch was 0.47375447335861 prior to batch effect correction and is now 0.47375447335861 .
2024-07-25 22:52:53.463807 INFO::ASW Label was 0.345050349143912 prior to batch effect correction and is now 0.345050349143912 .
2024-07-25 22:52:53.465086 INFO::Total function execution time is 4.02956986427307 s and adjustment time is 3.97726917266846 s ( 98.7 )
2024-07-25 22:52:56.513829 INFO::Formatting Data.
2024-07-25 22:52:56.514826 INFO::Replacing NaNs with NAs.
2024-07-25 22:52:56.515915 INFO::Removing potential empty rows and columns
2024-07-25 22:52:56.517044 INFO::Found 0 missing values.
2024-07-25 22:52:56.520232 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 22:52:56.520979 INFO::Done
2024-07-25 22:52:56.52168 INFO::Acquiring quality metrics before batch effect correction.
2024-07-25 22:52:56.524378 INFO::Starting hierarchical adjustment
2024-07-25 22:52:56.525254 INFO::Found 3 batches.
2024-07-25 22:52:56.526005 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-07-25 22:52:56.526782 INFO::Using default BPPARAM
2024-07-25 22:52:56.527472 INFO::Processing subtree level 1
2024-07-25 22:52:59.480922 INFO::Adjusting the last 1 batches sequentially
2024-07-25 22:52:59.483348 INFO::Done
2024-07-25 22:52:59.484784 INFO::Acquiring quality metrics after batch effect correction.
2024-07-25 22:52:59.489089 INFO::ASW Batch was 0.249200174377029 prior to batch effect correction and is now -0.139393609946634 .
2024-07-25 22:52:59.49043 INFO::ASW Label was -0.204466993150933 prior to batch effect correction and is now -0.0967696902439281 .
2024-07-25 22:52:59.491944 INFO::Total function execution time is 2.97812700271606 s and adjustment time is 2.95812702178955 s ( 99.33 )
2024-07-25 22:52:59.656655 INFO::Formatting Data.
2024-07-25 22:52:59.658203 INFO::Replacing NaNs with NAs.
2024-07-25 22:52:59.659858 INFO::Removing potential empty rows and columns
2024-07-25 22:52:59.661639 INFO::Found 2 missing values.
2024-07-25 22:52:59.6655 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-07-25 22:52:59.666726 INFO::Done
2024-07-25 22:52:59.712893 INFO::Found NA in Reference column
2024-07-25 22:52:59.726926 INFO::Require at least two references per batch.
2024-07-25 22:52:59.760214 INFO::Formatting Data.
2024-07-25 22:52:59.761719 INFO::Recognized SummarizedExperiment
2024-07-25 22:52:59.763007 INFO::Typecasting input to dataframe.
2024-07-25 22:52:59.775998 INFO::Replacing NaNs with NAs.
2024-07-25 22:52:59.778286 INFO::Removing potential empty rows and columns
2024-07-25 22:52:59.783152 INFO::Found 0 missing values.
2024-07-25 22:52:59.791845 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 22:52:59.793265 INFO::Done
2024-07-25 22:52:59.81642 INFO::Formatting Data.
2024-07-25 22:52:59.817908 INFO::Recognized SummarizedExperiment
2024-07-25 22:52:59.819207 INFO::Typecasting input to dataframe.
2024-07-25 22:52:59.844737 INFO::Replacing NaNs with NAs.
2024-07-25 22:52:59.847127 INFO::Removing potential empty rows and columns
2024-07-25 22:52:59.852274 INFO::Found 0 missing values.
2024-07-25 22:52:59.866479 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 22:52:59.867945 INFO::Done
2024-07-25 22:52:59.887636 INFO::Formatting Data.
2024-07-25 22:52:59.889071 INFO::Recognized SummarizedExperiment
2024-07-25 22:52:59.890328 INFO::Typecasting input to dataframe.
2024-07-25 22:52:59.912194 INFO::Replacing NaNs with NAs.
2024-07-25 22:52:59.914126 INFO::Removing potential empty rows and columns
2024-07-25 22:52:59.916117 INFO::Found 0 missing values.
2024-07-25 22:52:59.917983 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.
2024-07-25 22:52:59.924607 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 22:52:59.925995 INFO::Done
2024-07-25 22:52:59.947283 INFO::Formatting Data.
2024-07-25 22:52:59.948865 INFO::Replacing NaNs with NAs.
2024-07-25 22:52:59.950673 INFO::Removing potential empty rows and columns
2024-07-25 22:52:59.952597 INFO::Found 0 missing values.
2024-07-25 22:52:59.957146 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 22:52:59.958425 INFO::Done
2024-07-25 22:52:59.981758 INFO::Formatting Data.
2024-07-25 22:52:59.983359 INFO::Replacing NaNs with NAs.
2024-07-25 22:52:59.98516 INFO::Removing potential empty rows and columns
2024-07-25 22:52:59.987021 INFO::Found 0 missing values.
2024-07-25 22:52:59.991403 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 22:52:59.992614 INFO::Done
2024-07-25 22:53:00.042445 INFO::Formatting Data.
2024-07-25 22:53:00.043462 INFO::Replacing NaNs with NAs.
2024-07-25 22:53:00.044669 INFO::Removing potential empty rows and columns
2024-07-25 22:53:00.045942 INFO::Found 1 missing values.
2024-07-25 22:53:00.048325 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 22:53:00.049056 INFO::Done
2024-07-25 22:53:00.074431 INFO::Formatting Data.
2024-07-25 22:53:00.075452 INFO::Replacing NaNs with NAs.
2024-07-25 22:53:00.076522 INFO::Removing potential empty rows and columns
2024-07-25 22:53:00.077609 INFO::Found 2 missing values.
2024-07-25 22:53:00.078678 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.
2024-07-25 22:53:00.080813 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-07-25 22:53:00.081544 INFO::Done
2024-07-25 22:53:00.095693 INFO::Formatting Data.
2024-07-25 22:53:00.096685 INFO::Replacing NaNs with NAs.
2024-07-25 22:53:00.097744 INFO::Removing potential empty rows and columns
2024-07-25 22:53:00.09879 INFO::Found 2 missing values.
2024-07-25 22:53:00.100466 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 22:53:00.101198 INFO::Done
2024-07-25 22:53:00.115796 INFO::Formatting Data.
2024-07-25 22:53:00.116803 INFO::Typecasting input to dataframe.
2024-07-25 22:53:00.117815 INFO::Replacing NaNs with NAs.
2024-07-25 22:53:00.118897 INFO::Removing potential empty rows and columns
2024-07-25 22:53:00.120013 INFO::Found 0 missing values.
2024-07-25 22:53:00.122598 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-07-25 22:53:00.123327 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
29.39 1.43 75.45
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 8.18 | 0.59 | 18.22 | |
| compute_asw | 0.04 | 0.00 | 0.04 | |
| count_existing | 0.01 | 0.00 | 0.01 | |
| generate_data_covariables | 0.02 | 0.00 | 0.02 | |
| generate_dataset | 0.02 | 0.00 | 0.01 | |