Yannis Schumann
| Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 10fd252 |
| git_last_commit_date: 2024-11-20 10:26:09 -0500 (Wed, 20 Nov 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:39 -0500 (Tue, 24 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
| 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 158/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.3.3 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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: 1.3.3 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings BERT_1.3.3.tar.gz |
| StartedAt: 2024-12-23 20:00:22 -0500 (Mon, 23 Dec 2024) |
| EndedAt: 2024-12-23 20:01:52 -0500 (Mon, 23 Dec 2024) |
| EllapsedTime: 90.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BERT.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings BERT_1.3.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.3.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BERT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... WARNING
Undocumented code objects:
‘generate_truncated_dataset’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 24.695 1.826 18.077
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING
See
‘/home/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck/00check.log’
for details.
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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 Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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")
2024-12-23 20:01:14.036132 INFO::Formatting Data.
2024-12-23 20:01:14.037455 INFO::Replacing NaNs with NAs.
2024-12-23 20:01:14.048537 INFO::Removing potential empty rows and columns
2024-12-23 20:01:14.304222 INFO::Found 0 missing values.
2024-12-23 20:01:14.307909 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 20:01:14.308548 INFO::Done
2024-12-23 20:01:14.309069 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 20:01:14.320693 INFO::Starting hierarchical adjustment
2024-12-23 20:01:14.321586 INFO::Found 3 batches.
2024-12-23 20:01:14.322121 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 20:01:14.32329 INFO::Using default BPPARAM
2024-12-23 20:01:14.323839 INFO::Processing subtree level 1
2024-12-23 20:01:14.425804 INFO::Adjusting the last 1 batches sequentially
2024-12-23 20:01:14.427722 INFO::Done
2024-12-23 20:01:14.42844 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 20:01:14.431138 INFO::ASW Batch was -0.0582675760609083 prior to batch effect correction and is now -0.0582675760609083 .
2024-12-23 20:01:14.432324 INFO::Total function execution time is 0.396732807159424 s and adjustment time is 0.106289863586426 s ( 26.79 )
2024-12-23 20:01:14.447003 INFO::Formatting Data.
2024-12-23 20:01:14.447828 INFO::Replacing NaNs with NAs.
2024-12-23 20:01:14.448808 INFO::Removing potential empty rows and columns
2024-12-23 20:01:14.44995 INFO::Found 0 missing values.
2024-12-23 20:01:14.450925 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.
2024-12-23 20:01:14.461874 INFO::Formatting Data.
2024-12-23 20:01:14.462593 INFO::Replacing NaNs with NAs.
2024-12-23 20:01:14.463469 INFO::Removing potential empty rows and columns
2024-12-23 20:01:14.464516 INFO::Found 0 missing values.
2024-12-23 20:01:14.465444 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.
2024-12-23 20:01:14.48135 INFO::Formatting Data.
2024-12-23 20:01:14.482125 INFO::Replacing NaNs with NAs.
2024-12-23 20:01:14.483038 INFO::Removing potential empty rows and columns
2024-12-23 20:01:14.484057 INFO::Found 0 missing values.
2024-12-23 20:01:14.48497 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.
2024-12-23 20:01:14.489345 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 20:01:14.489912 INFO::Done
2024-12-23 20:01:14.490431 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 20:01:14.492443 INFO::Starting hierarchical adjustment
2024-12-23 20:01:14.493136 INFO::Found 2 batches.
2024-12-23 20:01:14.493664 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 20:01:14.494336 INFO::Using default BPPARAM
2024-12-23 20:01:14.494871 INFO::Adjusting the last 2 batches sequentially
2024-12-23 20:01:14.495839 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-23 20:01:14.518944 INFO::Done
2024-12-23 20:01:14.519681 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 20:01:14.521746 INFO::ASW Batch was 0.060524326388128 prior to batch effect correction and is now -0.118778368959154 .
2024-12-23 20:01:14.522567 INFO::Total function execution time is 0.0412998199462891 s and adjustment time is 0.0259130001068115 s ( 62.74 )
2024-12-23 20:01:14.525322 INFO::Formatting Data.
2024-12-23 20:01:14.525956 INFO::Replacing NaNs with NAs.
2024-12-23 20:01:14.53474 INFO::Formatting Data.
2024-12-23 20:01:14.535462 INFO::Replacing NaNs with NAs.
2024-12-23 20:01:14.536356 INFO::Removing potential empty rows and columns
2024-12-23 20:01:14.537402 INFO::Found 0 missing values.
2024-12-23 20:01:14.540364 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 20:01:14.540904 INFO::Done
2024-12-23 20:01:14.541436 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 20:01:14.543495 INFO::Starting hierarchical adjustment
2024-12-23 20:01:14.544206 INFO::Found 2 batches.
2024-12-23 20:01:14.572825 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 20:01:14.575458 INFO::Using default BPPARAM
2024-12-23 20:01:14.576028 INFO::Adjusting the last 2 batches sequentially
2024-12-23 20:01:14.576948 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-23 20:01:14.597903 INFO::Done
2024-12-23 20:01:14.598843 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 20:01:14.601378 INFO::ASW Batch was -0.0439666838043079 prior to batch effect correction and is now -0.102795770702617 .
2024-12-23 20:01:14.60233 INFO::Total function execution time is 0.067573070526123 s and adjustment time is 0.0537629127502441 s ( 79.56 )
2024-12-23 20:01:14.603558 INFO::Formatting Data.
2024-12-23 20:01:14.604265 INFO::Replacing NaNs with NAs.
2024-12-23 20:01:14.60527 INFO::Removing potential empty rows and columns
2024-12-23 20:01:14.606431 INFO::Found 0 missing values.
2024-12-23 20:01:14.60945 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 20:01:14.609995 INFO::Done
2024-12-23 20:01:14.610551 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 20:01:14.612593 INFO::Starting hierarchical adjustment
2024-12-23 20:01:14.61336 INFO::Found 2 batches.
2024-12-23 20:01:14.613898 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 20:01:14.614544 INFO::Using default BPPARAM
2024-12-23 20:01:14.615086 INFO::Adjusting the last 2 batches sequentially
2024-12-23 20:01:14.616008 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-23 20:01:14.632322 INFO::Done
2024-12-23 20:01:14.633062 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 20:01:14.635144 INFO::ASW Batch was -0.0439666838043079 prior to batch effect correction and is now -0.102795770702617 .
2024-12-23 20:01:14.635983 INFO::Total function execution time is 0.0324382781982422 s and adjustment time is 0.0191164016723633 s ( 58.93 )
2024-12-23 20:01:17.519943 INFO::Formatting Data.
2024-12-23 20:01:17.520616 INFO::Recognized SummarizedExperiment
2024-12-23 20:01:17.521105 INFO::Typecasting input to dataframe.
2024-12-23 20:01:17.547793 INFO::Replacing NaNs with NAs.
2024-12-23 20:01:17.54889 INFO::Removing potential empty rows and columns
2024-12-23 20:01:17.551917 INFO::Found 0 missing values.
2024-12-23 20:01:17.557605 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 20:01:17.558092 INFO::Done
2024-12-23 20:01:17.558556 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 20:01:17.561595 INFO::Starting hierarchical adjustment
2024-12-23 20:01:17.562212 INFO::Found 2 batches.
2024-12-23 20:01:17.562658 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 20:01:17.563569 INFO::Using default BPPARAM
2024-12-23 20:01:17.564031 INFO::Adjusting the last 2 batches sequentially
2024-12-23 20:01:17.564869 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-23 20:01:17.619052 INFO::Done
2024-12-23 20:01:17.619761 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 20:01:17.623289 INFO::ASW Batch was -0.00278109149420539 prior to batch effect correction and is now -0.0888401214447596 .
2024-12-23 20:01:17.624117 INFO::Total function execution time is 0.104416847229004 s and adjustment time is 0.0569384098052979 s ( 54.53 )
2024-12-23 20:01:17.641568 INFO::Formatting Data.
2024-12-23 20:01:17.64232 INFO::Recognized SummarizedExperiment
2024-12-23 20:01:17.642886 INFO::Typecasting input to dataframe.
2024-12-23 20:01:17.652019 INFO::Replacing NaNs with NAs.
2024-12-23 20:01:17.653204 INFO::Removing potential empty rows and columns
2024-12-23 20:01:17.656987 INFO::Found 0 missing values.
2024-12-23 20:01:17.664297 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 20:01:17.664931 INFO::Done
2024-12-23 20:01:17.665474 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 20:01:17.669038 INFO::Starting hierarchical adjustment
2024-12-23 20:01:17.669809 INFO::Found 2 batches.
2024-12-23 20:01:17.670322 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 20:01:17.670925 INFO::Using default BPPARAM
2024-12-23 20:01:17.671455 INFO::Adjusting the last 2 batches sequentially
2024-12-23 20:01:17.672433 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-23 20:01:17.697651 INFO::Done
2024-12-23 20:01:17.698388 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 20:01:17.70198 INFO::ASW Batch was -0.00235047920260137 prior to batch effect correction and is now -0.00235047920260137 .
2024-12-23 20:01:17.702836 INFO::Total function execution time is 0.0612540245056152 s and adjustment time is 0.027972936630249 s ( 45.67 )
2024-12-23 20:01:17.720937 INFO::Formatting Data.
2024-12-23 20:01:17.721698 INFO::Replacing NaNs with NAs.
2024-12-23 20:01:17.722602 INFO::Removing potential empty rows and columns
2024-12-23 20:01:17.723654 INFO::Found 0 missing values.
2024-12-23 20:01:17.726678 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 20:01:17.727215 INFO::Done
2024-12-23 20:01:17.727726 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 20:01:17.729746 INFO::Starting hierarchical adjustment
2024-12-23 20:01:17.730446 INFO::Found 3 batches.
2024-12-23 20:01:17.730959 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 20:01:17.731596 INFO::Using default BPPARAM
2024-12-23 20:01:17.732114 INFO::Processing subtree level 1
2024-12-23 20:01:17.863178 INFO::Adjusting the last 1 batches sequentially
2024-12-23 20:01:17.865046 INFO::Done
2024-12-23 20:01:17.865738 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 20:01:17.868276 INFO::ASW Batch was -0.0792348734693018 prior to batch effect correction and is now -0.165088018371738 .
2024-12-23 20:01:17.869232 INFO::Total function execution time is 0.148324728012085 s and adjustment time is 0.134729146957397 s ( 90.83 )
2024-12-23 20:01:17.883569 INFO::Skipping initial DF formatting
2024-12-23 20:01:17.884318 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 20:01:17.888328 INFO::Starting hierarchical adjustment
2024-12-23 20:01:17.889119 INFO::Found 5 batches.
2024-12-23 20:01:17.889663 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 20:01:17.890318 INFO::Using default BPPARAM
2024-12-23 20:01:17.890858 INFO::Processing subtree level 1
2024-12-23 20:01:18.012369 INFO::Adjusting the last 2 batches sequentially
2024-12-23 20:01:18.014365 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-23 20:01:18.035869 INFO::Done
2024-12-23 20:01:18.036667 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 20:01:18.041099 INFO::ASW Batch was 0.544966715095364 prior to batch effect correction and is now 0.544966715095364 .
2024-12-23 20:01:18.041837 INFO::ASW Label was 0.387931871404755 prior to batch effect correction and is now 0.387931871404755 .
2024-12-23 20:01:18.042771 INFO::Total function execution time is 0.159288167953491 s and adjustment time is 0.146877765655518 s ( 92.21 )
2024-12-23 20:01:18.061617 INFO::Formatting Data.
2024-12-23 20:01:18.062491 INFO::Replacing NaNs with NAs.
2024-12-23 20:01:18.0635 INFO::Removing potential empty rows and columns
2024-12-23 20:01:18.064593 INFO::Found 0 missing values.
2024-12-23 20:01:18.06891 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 20:01:18.06949 INFO::Done
2024-12-23 20:01:18.070028 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 20:01:18.073155 INFO::Starting hierarchical adjustment
2024-12-23 20:01:18.073925 INFO::Found 5 batches.
2024-12-23 20:01:18.074473 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 20:01:18.075132 INFO::Using default BPPARAM
2024-12-23 20:01:18.0757 INFO::Processing subtree level 1
2024-12-23 20:01:18.187541 INFO::Adjusting the last 2 batches sequentially
2024-12-23 20:01:18.189551 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-23 20:01:18.207007 INFO::Done
2024-12-23 20:01:18.207802 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 20:01:18.211329 INFO::ASW Batch was 0.621093054437795 prior to batch effect correction and is now -0.0924617558196326 .
2024-12-23 20:01:18.212014 INFO::ASW Label was 0.0793978942585588 prior to batch effect correction and is now 0.756239259442599 .
2024-12-23 20:01:18.21288 INFO::Total function execution time is 0.151370048522949 s and adjustment time is 0.133192539215088 s ( 87.99 )
2024-12-23 20:01:18.213756 INFO::Formatting Data.
2024-12-23 20:01:18.21439 INFO::Replacing NaNs with NAs.
2024-12-23 20:01:18.215327 INFO::Removing potential empty rows and columns
2024-12-23 20:01:18.216354 INFO::Found 0 missing values.
2024-12-23 20:01:18.220578 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 20:01:18.221153 INFO::Done
2024-12-23 20:01:18.221684 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 20:01:18.224834 INFO::Starting hierarchical adjustment
2024-12-23 20:01:18.225797 INFO::Found 5 batches.
2024-12-23 20:01:18.22634 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 20:01:18.226983 INFO::Using default BPPARAM
2024-12-23 20:01:18.227531 INFO::Processing subtree level 1
2024-12-23 20:01:18.340673 INFO::Adjusting the last 2 batches sequentially
2024-12-23 20:01:18.342601 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-23 20:01:18.359249 INFO::Done
2024-12-23 20:01:18.360061 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 20:01:18.363505 INFO::ASW Batch was 0.621093054437795 prior to batch effect correction and is now -0.0924617558196326 .
2024-12-23 20:01:18.364159 INFO::ASW Label was 0.0793978942585588 prior to batch effect correction and is now 0.756239259442599 .
2024-12-23 20:01:18.36501 INFO::Total function execution time is 0.151259422302246 s and adjustment time is 0.133761167526245 s ( 88.43 )
2024-12-23 20:01:18.378484 INFO::Formatting Data.
2024-12-23 20:01:18.379305 INFO::Replacing NaNs with NAs.
2024-12-23 20:01:18.380289 INFO::Removing potential empty rows and columns
2024-12-23 20:01:18.381326 INFO::Found 0 missing values.
2024-12-23 20:01:18.385456 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 20:01:18.386008 INFO::Done
2024-12-23 20:01:18.386547 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 20:01:18.389538 INFO::Starting hierarchical adjustment
2024-12-23 20:01:18.390277 INFO::Found 5 batches.
2024-12-23 20:01:18.390812 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 20:01:18.391469 INFO::Using default BPPARAM
2024-12-23 20:01:18.392 INFO::Processing subtree level 1
2024-12-23 20:01:18.498559 INFO::Adjusting the last 2 batches sequentially
2024-12-23 20:01:18.50037 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-23 20:01:18.517156 INFO::Done
2024-12-23 20:01:18.517934 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 20:01:18.521254 INFO::ASW Batch was 0.542102581288257 prior to batch effect correction and is now -0.0434354487359324 .
2024-12-23 20:01:18.521907 INFO::ASW Label was 0.252618153242712 prior to batch effect correction and is now 0.81923507461769 .
2024-12-23 20:01:18.522751 INFO::Total function execution time is 0.144334554672241 s and adjustment time is 0.12698221206665 s ( 87.98 )
2024-12-23 20:01:18.523614 INFO::Formatting Data.
2024-12-23 20:01:18.524251 INFO::Replacing NaNs with NAs.
2024-12-23 20:01:18.525147 INFO::Removing potential empty rows and columns
2024-12-23 20:01:18.52616 INFO::Found 0 missing values.
2024-12-23 20:01:18.530298 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 20:01:18.530845 INFO::Done
2024-12-23 20:01:18.53136 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 20:01:18.534364 INFO::Starting hierarchical adjustment
2024-12-23 20:01:18.535067 INFO::Found 5 batches.
2024-12-23 20:01:18.535609 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 20:01:18.536255 INFO::Using default BPPARAM
2024-12-23 20:01:18.536783 INFO::Processing subtree level 1
2024-12-23 20:01:18.648671 INFO::Adjusting the last 2 batches sequentially
2024-12-23 20:01:18.650459 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-23 20:01:18.666103 INFO::Done
2024-12-23 20:01:18.666819 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 20:01:18.670022 INFO::ASW Batch was 0.542102581288257 prior to batch effect correction and is now -0.0434354487359324 .
2024-12-23 20:01:18.670669 INFO::ASW Label was 0.252618153242712 prior to batch effect correction and is now 0.81923507461769 .
2024-12-23 20:01:18.671499 INFO::Total function execution time is 0.147884368896484 s and adjustment time is 0.131161689758301 s ( 88.69 )
2024-12-23 20:01:18.685127 INFO::Formatting Data.
2024-12-23 20:01:18.685939 INFO::Replacing NaNs with NAs.
2024-12-23 20:01:18.686889 INFO::Removing potential empty rows and columns
2024-12-23 20:01:18.687901 INFO::Found 0 missing values.
2024-12-23 20:01:18.6907 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 20:01:18.691245 INFO::Done
2024-12-23 20:01:18.691755 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 20:01:18.694635 INFO::Starting hierarchical adjustment
2024-12-23 20:01:18.695355 INFO::Found 2 batches.
2024-12-23 20:01:18.695879 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 20:01:18.696539 INFO::Using default BPPARAM
2024-12-23 20:01:18.697056 INFO::Adjusting the last 2 batches sequentially
2024-12-23 20:01:18.697973 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-23 20:01:18.712756 INFO::Done
2024-12-23 20:01:18.713444 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 20:01:18.71637 INFO::ASW Batch was 0.24536616888078 prior to batch effect correction and is now 0.162182863880624 .
2024-12-23 20:01:18.716975 INFO::ASW Label was 0.837671141784531 prior to batch effect correction and is now 0.82250453946357 .
2024-12-23 20:01:18.717794 INFO::Total function execution time is 0.0327677726745605 s and adjustment time is 0.0175371170043945 s ( 53.52 )
2024-12-23 20:01:18.718593 INFO::Formatting Data.
2024-12-23 20:01:18.719192 INFO::Replacing NaNs with NAs.
2024-12-23 20:01:18.72005 INFO::Removing potential empty rows and columns
2024-12-23 20:01:18.721024 INFO::Found 0 missing values.
2024-12-23 20:01:18.7716 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 20:01:18.773237 INFO::Done
2024-12-23 20:01:18.773795 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 20:01:18.776599 INFO::Starting hierarchical adjustment
2024-12-23 20:01:18.777309 INFO::Found 2 batches.
2024-12-23 20:01:18.777821 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 20:01:18.778404 INFO::Using default BPPARAM
2024-12-23 20:01:18.778927 INFO::Adjusting the last 2 batches sequentially
2024-12-23 20:01:18.779818 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-23 20:01:18.794328 INFO::Done
2024-12-23 20:01:18.794984 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 20:01:18.797917 INFO::ASW Batch was 0.24536616888078 prior to batch effect correction and is now 0.162182863880624 .
2024-12-23 20:01:18.798507 INFO::ASW Label was 0.837671141784531 prior to batch effect correction and is now 0.82250453946357 .
2024-12-23 20:01:18.799331 INFO::Total function execution time is 0.0807266235351562 s and adjustment time is 0.0171639919281006 s ( 21.26 )
2024-12-23 20:01:18.810342 INFO::Formatting Data.
2024-12-23 20:01:18.811082 INFO::Replacing NaNs with NAs.
2024-12-23 20:01:18.811915 INFO::Removing potential empty rows and columns
2024-12-23 20:01:18.812767 INFO::Found 0 missing values.
2024-12-23 20:01:18.814728 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 20:01:18.815278 INFO::Done
2024-12-23 20:01:18.815778 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 20:01:18.817578 INFO::Starting hierarchical adjustment
2024-12-23 20:01:18.818271 INFO::Found 2 batches.
2024-12-23 20:01:18.818753 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 20:01:18.819325 INFO::Using default BPPARAM
2024-12-23 20:01:18.819805 INFO::Adjusting the last 2 batches sequentially
2024-12-23 20:01:18.82071 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-23 20:01:18.850494 INFO::Done
2024-12-23 20:01:18.851148 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 20:01:18.853051 INFO::ASW Batch was -0.0304879199935446 prior to batch effect correction and is now -0.0960218421030614 .
2024-12-23 20:01:18.853829 INFO::Total function execution time is 0.0435807704925537 s and adjustment time is 0.0323548316955566 s ( 74.24 )
2024-12-23 20:01:18.865093 INFO::Formatting Data.
2024-12-23 20:01:18.865854 INFO::Replacing NaNs with NAs.
2024-12-23 20:01:18.866694 INFO::Removing potential empty rows and columns
2024-12-23 20:01:18.86763 INFO::Found 0 missing values.
2024-12-23 20:01:18.868682 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.
2024-12-23 20:01:18.872942 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 20:01:18.8735 INFO::Done
2024-12-23 20:01:18.873992 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 20:01:18.876758 INFO::Starting hierarchical adjustment
2024-12-23 20:01:18.877416 INFO::Found 2 batches.
2024-12-23 20:01:18.877911 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 20:01:18.878489 INFO::Using default BPPARAM
2024-12-23 20:01:18.878974 INFO::Adjusting the last 2 batches sequentially
2024-12-23 20:01:18.879891 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-23 20:01:18.89587 INFO::Done
2024-12-23 20:01:18.896532 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 20:01:18.899433 INFO::ASW Batch was 0.689838983559346 prior to batch effect correction and is now -0.00123226076061741 .
2024-12-23 20:01:18.900006 INFO::ASW Label was 0.381794562607818 prior to batch effect correction and is now 0.888780190311093 .
2024-12-23 20:01:18.900863 INFO::Total function execution time is 0.0358271598815918 s and adjustment time is 0.0185840129852295 s ( 51.87 )
2024-12-23 20:01:18.901723 INFO::Formatting Data.
2024-12-23 20:01:18.902336 INFO::Replacing NaNs with NAs.
2024-12-23 20:01:18.903233 INFO::Removing potential empty rows and columns
2024-12-23 20:01:18.904239 INFO::Found 0 missing values.
2024-12-23 20:01:18.905215 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.
2024-12-23 20:01:18.90955 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 20:01:18.9101 INFO::Done
2024-12-23 20:01:18.910596 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 20:01:18.913383 INFO::Starting hierarchical adjustment
2024-12-23 20:01:18.914049 INFO::Found 2 batches.
2024-12-23 20:01:18.914543 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 20:01:18.915121 INFO::Using default BPPARAM
2024-12-23 20:01:18.915614 INFO::Adjusting the last 2 batches sequentially
2024-12-23 20:01:18.916536 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-23 20:01:18.933223 INFO::Done
2024-12-23 20:01:18.933918 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 20:01:18.936754 INFO::ASW Batch was 0.689838983559346 prior to batch effect correction and is now -0.00123226076061741 .
2024-12-23 20:01:18.937389 INFO::ASW Label was 0.381794562607818 prior to batch effect correction and is now 0.888780190311093 .
2024-12-23 20:01:18.938224 INFO::Total function execution time is 0.0365195274353027 s and adjustment time is 0.0192697048187256 s ( 52.77 )
2024-12-23 20:01:19.156713 INFO::Formatting Data.
2024-12-23 20:01:19.157563 INFO::Replacing NaNs with NAs.
2024-12-23 20:01:19.158509 INFO::Removing potential empty rows and columns
2024-12-23 20:01:19.159576 INFO::Found 0 missing values.
2024-12-23 20:01:19.16269 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 20:01:19.163268 INFO::Done
2024-12-23 20:01:19.163818 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 20:01:19.16607 INFO::Starting hierarchical adjustment
2024-12-23 20:01:19.166855 INFO::Found 3 batches.
2024-12-23 20:01:19.167425 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 20:01:19.168148 INFO::Using default BPPARAM
2024-12-23 20:01:19.168768 INFO::Processing subtree level 1
2024-12-23 20:01:19.270517 INFO::Adjusting the last 1 batches sequentially
2024-12-23 20:01:19.272505 INFO::Done
2024-12-23 20:01:19.273257 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 20:01:19.276246 INFO::ASW Batch was -0.0630562914460052 prior to batch effect correction and is now -0.0630562914460052 .
2024-12-23 20:01:19.277398 INFO::Total function execution time is 0.120695829391479 s and adjustment time is 0.105788230895996 s ( 87.65 )
2024-12-23 20:01:19.278568 INFO::Formatting Data.
2024-12-23 20:01:19.279279 INFO::Typecasting input to dataframe.
2024-12-23 20:01:19.280143 INFO::Replacing NaNs with NAs.
2024-12-23 20:01:19.281215 INFO::Removing potential empty rows and columns
2024-12-23 20:01:19.282405 INFO::Found 0 missing values.
2024-12-23 20:01:19.285772 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 20:01:19.286482 INFO::Done
2024-12-23 20:01:19.287054 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 20:01:19.289271 INFO::Starting hierarchical adjustment
2024-12-23 20:01:19.290026 INFO::Found 3 batches.
2024-12-23 20:01:19.290601 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 20:01:19.291309 INFO::Using default BPPARAM
2024-12-23 20:01:19.291887 INFO::Processing subtree level 1
2024-12-23 20:01:19.386175 INFO::Adjusting the last 1 batches sequentially
2024-12-23 20:01:19.388045 INFO::Done
2024-12-23 20:01:19.388775 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 20:01:19.391359 INFO::ASW Batch was -0.0630562914460052 prior to batch effect correction and is now -0.0630562914460052 .
2024-12-23 20:01:19.392356 INFO::Total function execution time is 0.113768815994263 s and adjustment time is 0.0981495380401611 s ( 86.27 )
2024-12-23 20:01:19.40593 INFO::Formatting Data.
2024-12-23 20:01:19.406839 INFO::Typecasting input to dataframe.
2024-12-23 20:01:19.40776 INFO::Replacing NaNs with NAs.
2024-12-23 20:01:19.408742 INFO::Removing potential empty rows and columns
2024-12-23 20:01:19.409899 INFO::Found 0 missing values.
2024-12-23 20:01:19.41301 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 20:01:19.413595 INFO::Done
2024-12-23 20:01:19.414131 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 20:01:19.416255 INFO::Starting hierarchical adjustment
2024-12-23 20:01:19.417009 INFO::Found 3 batches.
2024-12-23 20:01:19.41756 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 20:01:19.418191 INFO::Using default BPPARAM
2024-12-23 20:01:19.418749 INFO::Processing subtree level 1
2024-12-23 20:01:19.522025 INFO::Adjusting the last 1 batches sequentially
2024-12-23 20:01:19.523984 INFO::Done
2024-12-23 20:01:19.524725 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 20:01:19.527438 INFO::ASW Batch was -0.0549106614877503 prior to batch effect correction and is now -0.0549106614877503 .
2024-12-23 20:01:19.528508 INFO::Total function execution time is 0.122657537460327 s and adjustment time is 0.107081174850464 s ( 87.3 )
2024-12-23 20:01:19.681935 INFO::Formatting Data.
2024-12-23 20:01:19.682768 INFO::Replacing NaNs with NAs.
2024-12-23 20:01:19.68393 INFO::Removing potential empty rows and columns
2024-12-23 20:01:19.686976 INFO::Found 1000 missing values.
2024-12-23 20:01:19.709003 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 20:01:19.709835 INFO::Done
2024-12-23 20:01:19.710471 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 20:01:19.716429 INFO::Starting hierarchical adjustment
2024-12-23 20:01:19.717332 INFO::Found 10 batches.
2024-12-23 20:01:19.717931 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 20:01:19.718647 INFO::Using default BPPARAM
2024-12-23 20:01:19.719215 INFO::Processing subtree level 1
2024-12-23 20:01:19.888393 INFO::Processing subtree level 2
2024-12-23 20:01:20.046265 INFO::Adjusting the last 1 batches sequentially
2024-12-23 20:01:20.04827 INFO::Done
2024-12-23 20:01:20.048947 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 20:01:20.054354 INFO::ASW Batch was 0.447467754045893 prior to batch effect correction and is now 0.447467754045893 .
2024-12-23 20:01:20.055063 INFO::ASW Label was 0.392184006995659 prior to batch effect correction and is now 0.392184006995659 .
2024-12-23 20:01:20.055984 INFO::Total function execution time is 0.374121427536011 s and adjustment time is 0.331114292144775 s ( 88.5 )
2024-12-23 20:01:20.056847 INFO::Formatting Data.
2024-12-23 20:01:20.057516 INFO::Replacing NaNs with NAs.
2024-12-23 20:01:20.058724 INFO::Removing potential empty rows and columns
2024-12-23 20:01:20.061576 INFO::Found 1000 missing values.
2024-12-23 20:01:20.081234 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 20:01:20.082028 INFO::Done
2024-12-23 20:01:20.08265 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 20:01:20.08831 INFO::Starting hierarchical adjustment
2024-12-23 20:01:20.089168 INFO::Found 10 batches.
2024-12-23 20:01:21.098022 INFO::Set up parallel execution backend with 2 workers
2024-12-23 20:01:21.100271 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-12-23 20:01:22.247429 INFO::Adjusting the last 2 batches sequentially
2024-12-23 20:01:22.249461 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-23 20:01:22.268571 INFO::Done
2024-12-23 20:01:22.26939 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 20:01:22.274209 INFO::ASW Batch was 0.447467754045893 prior to batch effect correction and is now 0.447467754045893 .
2024-12-23 20:01:22.27487 INFO::ASW Label was 0.392184006995659 prior to batch effect correction and is now 0.392184006995659 .
2024-12-23 20:01:22.2757 INFO::Total function execution time is 2.21887993812561 s and adjustment time is 2.17952442169189 s ( 98.23 )
2024-12-23 20:01:22.423407 INFO::Formatting Data.
2024-12-23 20:01:22.424259 INFO::Replacing NaNs with NAs.
2024-12-23 20:01:22.425264 INFO::Removing potential empty rows and columns
2024-12-23 20:01:22.42641 INFO::Found 0 missing values.
2024-12-23 20:01:22.430253 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 20:01:22.430871 INFO::Done
2024-12-23 20:01:22.431438 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 20:01:22.434407 INFO::Starting hierarchical adjustment
2024-12-23 20:01:22.435175 INFO::Found 3 batches.
2024-12-23 20:01:22.435754 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 20:01:22.436424 INFO::Using default BPPARAM
2024-12-23 20:01:22.436983 INFO::Processing subtree level 1
2024-12-23 20:01:22.543075 INFO::Adjusting the last 1 batches sequentially
2024-12-23 20:01:22.544845 INFO::Done
2024-12-23 20:01:22.545491 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 20:01:22.548694 INFO::ASW Batch was 0.16191143266308 prior to batch effect correction and is now -0.181524988912245 .
2024-12-23 20:01:22.549345 INFO::ASW Label was -0.155538236551568 prior to batch effect correction and is now 0.0848833626811463 .
2024-12-23 20:01:22.550322 INFO::Total function execution time is 0.126954555511475 s and adjustment time is 0.109829425811768 s ( 86.51 )
2024-12-23 20:01:22.6688 INFO::Formatting Data.
2024-12-23 20:01:22.669816 INFO::Replacing NaNs with NAs.
2024-12-23 20:01:22.670814 INFO::Removing potential empty rows and columns
2024-12-23 20:01:22.67187 INFO::Found 2 missing values.
2024-12-23 20:01:22.674709 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-12-23 20:01:22.67525 INFO::Done
2024-12-23 20:01:22.703499 INFO::Found NA in Reference column
2024-12-23 20:01:22.713745 INFO::Require at least two references per batch.
2024-12-23 20:01:22.733641 INFO::Formatting Data.
2024-12-23 20:01:22.734514 INFO::Recognized SummarizedExperiment
2024-12-23 20:01:22.735091 INFO::Typecasting input to dataframe.
2024-12-23 20:01:22.745223 INFO::Replacing NaNs with NAs.
2024-12-23 20:01:22.746551 INFO::Removing potential empty rows and columns
2024-12-23 20:01:22.750082 INFO::Found 0 missing values.
2024-12-23 20:01:22.757022 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 20:01:22.757739 INFO::Done
2024-12-23 20:01:22.772814 INFO::Formatting Data.
2024-12-23 20:01:22.773618 INFO::Recognized SummarizedExperiment
2024-12-23 20:01:22.774163 INFO::Typecasting input to dataframe.
2024-12-23 20:01:22.792248 INFO::Replacing NaNs with NAs.
2024-12-23 20:01:22.793587 INFO::Removing potential empty rows and columns
2024-12-23 20:01:22.797185 INFO::Found 0 missing values.
2024-12-23 20:01:22.808131 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 20:01:22.808808 INFO::Done
2024-12-23 20:01:22.823956 INFO::Formatting Data.
2024-12-23 20:01:22.824735 INFO::Recognized SummarizedExperiment
2024-12-23 20:01:22.825279 INFO::Typecasting input to dataframe.
2024-12-23 20:01:22.852378 INFO::Replacing NaNs with NAs.
2024-12-23 20:01:22.853909 INFO::Removing potential empty rows and columns
2024-12-23 20:01:22.855256 INFO::Found 0 missing values.
2024-12-23 20:01:22.856429 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.
2024-12-23 20:01:22.861527 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 20:01:22.862143 INFO::Done
2024-12-23 20:01:22.874322 INFO::Formatting Data.
2024-12-23 20:01:22.875342 INFO::Replacing NaNs with NAs.
2024-12-23 20:01:22.876408 INFO::Removing potential empty rows and columns
2024-12-23 20:01:22.877637 INFO::Found 0 missing values.
2024-12-23 20:01:22.880985 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 20:01:22.881605 INFO::Done
2024-12-23 20:01:22.895299 INFO::Formatting Data.
2024-12-23 20:01:22.896179 INFO::Replacing NaNs with NAs.
2024-12-23 20:01:22.897135 INFO::Removing potential empty rows and columns
2024-12-23 20:01:22.898255 INFO::Found 0 missing values.
2024-12-23 20:01:22.901353 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 20:01:22.90196 INFO::Done
2024-12-23 20:01:22.934128 INFO::Formatting Data.
2024-12-23 20:01:22.935071 INFO::Replacing NaNs with NAs.
2024-12-23 20:01:22.936248 INFO::Removing potential empty rows and columns
2024-12-23 20:01:22.937519 INFO::Found 1 missing values.
2024-12-23 20:01:22.940385 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 20:01:22.941022 INFO::Done
2024-12-23 20:01:22.963537 INFO::Formatting Data.
2024-12-23 20:01:22.964645 INFO::Replacing NaNs with NAs.
2024-12-23 20:01:22.965739 INFO::Removing potential empty rows and columns
2024-12-23 20:01:22.96689 INFO::Found 2 missing values.
2024-12-23 20:01:22.967952 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.
2024-12-23 20:01:22.970661 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-12-23 20:01:22.971315 INFO::Done
2024-12-23 20:01:22.982866 INFO::Formatting Data.
2024-12-23 20:01:22.983726 INFO::Replacing NaNs with NAs.
2024-12-23 20:01:22.98472 INFO::Removing potential empty rows and columns
2024-12-23 20:01:22.985736 INFO::Found 2 missing values.
2024-12-23 20:01:22.987522 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 20:01:22.98806 INFO::Done
2024-12-23 20:01:23.000156 INFO::Formatting Data.
2024-12-23 20:01:23.001214 INFO::Typecasting input to dataframe.
2024-12-23 20:01:23.00211 INFO::Replacing NaNs with NAs.
2024-12-23 20:01:23.003056 INFO::Removing potential empty rows and columns
2024-12-23 20:01:23.004177 INFO::Found 0 missing values.
2024-12-23 20:01:23.007175 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 20:01:23.007761 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 138 ]
>
> proc.time()
user system elapsed
17.546 3.349 20.650
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.695 | 1.826 | 18.077 | |
| compute_asw | 0.025 | 0.001 | 0.026 | |
| count_existing | 0.014 | 0.002 | 0.015 | |
| generate_data_covariables | 0.012 | 0.001 | 0.013 | |
| generate_dataset | 0.012 | 0.001 | 0.012 | |