Yannis Schumann
| Snapshot Date: 2025-01-03 13:40 -0500 (Fri, 03 Jan 2025) |
| 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 2025-01-04 11:46 -0500 (Sat, 04 Jan 2025).
| 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" | 4756 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4475 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4435 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4390 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4383 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 159/2275 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: BERT |
| Version: 1.3.3 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.3.3.tar.gz |
| StartedAt: 2025-01-04 03:50:03 -0000 (Sat, 04 Jan 2025) |
| EndedAt: 2025-01-04 03:51:23 -0000 (Sat, 04 Jan 2025) |
| EllapsedTime: 80.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BERT.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BERT_1.3.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 31.446 1.311 22.416
* 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: 1 WARNING
See
‘/home/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck/00check.log’
for details.
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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")
2025-01-04 03:51:07.159382 INFO::Formatting Data.
2025-01-04 03:51:07.161162 INFO::Replacing NaNs with NAs.
2025-01-04 03:51:07.178055 INFO::Removing potential empty rows and columns
2025-01-04 03:51:07.562506 INFO::Found 0 missing values.
2025-01-04 03:51:07.567106 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-04 03:51:07.567902 INFO::Done
2025-01-04 03:51:07.568683 INFO::Acquiring quality metrics before batch effect correction.
2025-01-04 03:51:07.58366 INFO::Starting hierarchical adjustment
2025-01-04 03:51:07.584793 INFO::Found 3 batches.
2025-01-04 03:51:07.585526 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-04 03:51:07.586964 INFO::Using default BPPARAM
2025-01-04 03:51:07.58772 INFO::Processing subtree level 1
2025-01-04 03:51:07.711426 INFO::Adjusting the last 1 batches sequentially
2025-01-04 03:51:07.713766 INFO::Done
2025-01-04 03:51:07.714694 INFO::Acquiring quality metrics after batch effect correction.
2025-01-04 03:51:07.718387 INFO::ASW Batch was -0.0253975677960599 prior to batch effect correction and is now -0.0253975677960599 .
2025-01-04 03:51:07.719952 INFO::Total function execution time is 0.561365604400635 s and adjustment time is 0.129217147827148 s ( 23.02 )
2025-01-04 03:51:07.738482 INFO::Formatting Data.
2025-01-04 03:51:07.739451 INFO::Replacing NaNs with NAs.
2025-01-04 03:51:07.740662 INFO::Removing potential empty rows and columns
2025-01-04 03:51:07.742221 INFO::Found 0 missing values.
2025-01-04 03:51:07.743478 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.
2025-01-04 03:51:07.758194 INFO::Formatting Data.
2025-01-04 03:51:07.759162 INFO::Replacing NaNs with NAs.
2025-01-04 03:51:07.760322 INFO::Removing potential empty rows and columns
2025-01-04 03:51:07.761775 INFO::Found 0 missing values.
2025-01-04 03:51:07.762992 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.
2025-01-04 03:51:07.784554 INFO::Formatting Data.
2025-01-04 03:51:07.785529 INFO::Replacing NaNs with NAs.
2025-01-04 03:51:07.786681 INFO::Removing potential empty rows and columns
2025-01-04 03:51:07.78807 INFO::Found 0 missing values.
2025-01-04 03:51:07.789352 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.
2025-01-04 03:51:07.795848 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-04 03:51:07.796707 INFO::Done
2025-01-04 03:51:07.797464 INFO::Acquiring quality metrics before batch effect correction.
2025-01-04 03:51:07.800281 INFO::Starting hierarchical adjustment
2025-01-04 03:51:07.801393 INFO::Found 2 batches.
2025-01-04 03:51:07.802237 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-04 03:51:07.803115 INFO::Using default BPPARAM
2025-01-04 03:51:07.803859 INFO::Adjusting the last 2 batches sequentially
2025-01-04 03:51:07.805218 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-04 03:51:07.835046 INFO::Done
2025-01-04 03:51:07.835927 INFO::Acquiring quality metrics after batch effect correction.
2025-01-04 03:51:07.838612 INFO::ASW Batch was 0.0491013353739132 prior to batch effect correction and is now -0.103975881608029 .
2025-01-04 03:51:07.839641 INFO::Total function execution time is 0.0551578998565674 s and adjustment time is 0.0339195728302002 s ( 61.5 )
2025-01-04 03:51:07.843782 INFO::Formatting Data.
2025-01-04 03:51:07.844704 INFO::Replacing NaNs with NAs.
2025-01-04 03:51:07.85659 INFO::Formatting Data.
2025-01-04 03:51:07.857564 INFO::Replacing NaNs with NAs.
2025-01-04 03:51:07.858725 INFO::Removing potential empty rows and columns
2025-01-04 03:51:07.860132 INFO::Found 0 missing values.
2025-01-04 03:51:07.864205 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-04 03:51:07.865041 INFO::Done
2025-01-04 03:51:07.865785 INFO::Acquiring quality metrics before batch effect correction.
2025-01-04 03:51:07.868445 INFO::Starting hierarchical adjustment
2025-01-04 03:51:07.869475 INFO::Found 2 batches.
2025-01-04 03:51:07.904308 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-04 03:51:07.907863 INFO::Using default BPPARAM
2025-01-04 03:51:07.908653 INFO::Adjusting the last 2 batches sequentially
2025-01-04 03:51:07.909966 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-04 03:51:07.930415 INFO::Done
2025-01-04 03:51:07.931279 INFO::Acquiring quality metrics after batch effect correction.
2025-01-04 03:51:07.933896 INFO::ASW Batch was -0.0502929210044688 prior to batch effect correction and is now -0.110210096825933 .
2025-01-04 03:51:07.934912 INFO::Total function execution time is 0.0783798694610596 s and adjustment time is 0.0611302852630615 s ( 77.99 )
2025-01-04 03:51:07.936284 INFO::Formatting Data.
2025-01-04 03:51:07.937093 INFO::Replacing NaNs with NAs.
2025-01-04 03:51:07.93821 INFO::Removing potential empty rows and columns
2025-01-04 03:51:07.939592 INFO::Found 0 missing values.
2025-01-04 03:51:07.943625 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-04 03:51:07.944404 INFO::Done
2025-01-04 03:51:07.945169 INFO::Acquiring quality metrics before batch effect correction.
2025-01-04 03:51:07.947748 INFO::Starting hierarchical adjustment
2025-01-04 03:51:07.948731 INFO::Found 2 batches.
2025-01-04 03:51:07.949479 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-04 03:51:07.950307 INFO::Using default BPPARAM
2025-01-04 03:51:07.951024 INFO::Adjusting the last 2 batches sequentially
2025-01-04 03:51:07.952249 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-04 03:51:07.972463 INFO::Done
2025-01-04 03:51:07.973351 INFO::Acquiring quality metrics after batch effect correction.
2025-01-04 03:51:07.975921 INFO::ASW Batch was -0.0502929210044688 prior to batch effect correction and is now -0.110210096825933 .
2025-01-04 03:51:07.97697 INFO::Total function execution time is 0.0406606197357178 s and adjustment time is 0.0239360332489014 s ( 58.87 )
2025-01-04 03:51:11.773909 INFO::Formatting Data.
2025-01-04 03:51:11.77477 INFO::Recognized SummarizedExperiment
2025-01-04 03:51:11.775393 INFO::Typecasting input to dataframe.
2025-01-04 03:51:11.813761 INFO::Replacing NaNs with NAs.
2025-01-04 03:51:11.81515 INFO::Removing potential empty rows and columns
2025-01-04 03:51:11.819861 INFO::Found 0 missing values.
2025-01-04 03:51:11.829037 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-04 03:51:11.829845 INFO::Done
2025-01-04 03:51:11.830487 INFO::Acquiring quality metrics before batch effect correction.
2025-01-04 03:51:11.834904 INFO::Starting hierarchical adjustment
2025-01-04 03:51:11.835829 INFO::Found 2 batches.
2025-01-04 03:51:11.836469 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-04 03:51:11.837755 INFO::Using default BPPARAM
2025-01-04 03:51:11.838407 INFO::Adjusting the last 2 batches sequentially
2025-01-04 03:51:11.839568 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-04 03:51:11.915208 INFO::Done
2025-01-04 03:51:11.916101 INFO::Acquiring quality metrics after batch effect correction.
2025-01-04 03:51:11.92165 INFO::ASW Batch was -0.00252537417546917 prior to batch effect correction and is now -0.0924994578074401 .
2025-01-04 03:51:11.922904 INFO::Total function execution time is 0.149339437484741 s and adjustment time is 0.0795230865478516 s ( 53.25 )
2025-01-04 03:51:11.946368 INFO::Formatting Data.
2025-01-04 03:51:11.94728 INFO::Recognized SummarizedExperiment
2025-01-04 03:51:11.947976 INFO::Typecasting input to dataframe.
2025-01-04 03:51:11.960328 INFO::Replacing NaNs with NAs.
2025-01-04 03:51:11.961945 INFO::Removing potential empty rows and columns
2025-01-04 03:51:11.967031 INFO::Found 0 missing values.
2025-01-04 03:51:11.97693 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-04 03:51:11.977797 INFO::Done
2025-01-04 03:51:11.978523 INFO::Acquiring quality metrics before batch effect correction.
2025-01-04 03:51:11.983333 INFO::Starting hierarchical adjustment
2025-01-04 03:51:11.984366 INFO::Found 2 batches.
2025-01-04 03:51:11.985154 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-04 03:51:11.985985 INFO::Using default BPPARAM
2025-01-04 03:51:11.986712 INFO::Adjusting the last 2 batches sequentially
2025-01-04 03:51:11.988034 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-04 03:51:12.022778 INFO::Done
2025-01-04 03:51:12.023665 INFO::Acquiring quality metrics after batch effect correction.
2025-01-04 03:51:12.028586 INFO::ASW Batch was -0.00620379377186066 prior to batch effect correction and is now -0.00620379377186066 .
2025-01-04 03:51:12.029843 INFO::Total function execution time is 0.0834157466888428 s and adjustment time is 0.0386049747467041 s ( 46.28 )
2025-01-04 03:51:12.053922 INFO::Formatting Data.
2025-01-04 03:51:12.054885 INFO::Replacing NaNs with NAs.
2025-01-04 03:51:12.056046 INFO::Removing potential empty rows and columns
2025-01-04 03:51:12.05746 INFO::Found 0 missing values.
2025-01-04 03:51:12.061547 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-04 03:51:12.06234 INFO::Done
2025-01-04 03:51:12.063055 INFO::Acquiring quality metrics before batch effect correction.
2025-01-04 03:51:12.065695 INFO::Starting hierarchical adjustment
2025-01-04 03:51:12.066661 INFO::Found 3 batches.
2025-01-04 03:51:12.067361 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-04 03:51:12.068166 INFO::Using default BPPARAM
2025-01-04 03:51:12.068935 INFO::Processing subtree level 1
2025-01-04 03:51:12.239428 INFO::Adjusting the last 1 batches sequentially
2025-01-04 03:51:12.242709 INFO::Done
2025-01-04 03:51:12.24359 INFO::Acquiring quality metrics after batch effect correction.
2025-01-04 03:51:12.247489 INFO::ASW Batch was -0.0279738992162079 prior to batch effect correction and is now -0.165017748163312 .
2025-01-04 03:51:12.248972 INFO::Total function execution time is 0.195008516311646 s and adjustment time is 0.176229000091553 s ( 90.37 )
2025-01-04 03:51:12.269102 INFO::Skipping initial DF formatting
2025-01-04 03:51:12.270027 INFO::Acquiring quality metrics before batch effect correction.
2025-01-04 03:51:12.275391 INFO::Starting hierarchical adjustment
2025-01-04 03:51:12.276544 INFO::Found 5 batches.
2025-01-04 03:51:12.277308 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-04 03:51:12.278271 INFO::Using default BPPARAM
2025-01-04 03:51:12.279113 INFO::Processing subtree level 1
2025-01-04 03:51:12.432244 INFO::Adjusting the last 2 batches sequentially
2025-01-04 03:51:12.434501 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-04 03:51:12.462115 INFO::Done
2025-01-04 03:51:12.463033 INFO::Acquiring quality metrics after batch effect correction.
2025-01-04 03:51:12.468851 INFO::ASW Batch was 0.563637808233967 prior to batch effect correction and is now 0.563637808233967 .
2025-01-04 03:51:12.46978 INFO::ASW Label was 0.338399532594085 prior to batch effect correction and is now 0.338399532594085 .
2025-01-04 03:51:12.470999 INFO::Total function execution time is 0.201943635940552 s and adjustment time is 0.185796499252319 s ( 92 )
2025-01-04 03:51:12.495819 INFO::Formatting Data.
2025-01-04 03:51:12.496906 INFO::Replacing NaNs with NAs.
2025-01-04 03:51:12.49815 INFO::Removing potential empty rows and columns
2025-01-04 03:51:12.49958 INFO::Found 0 missing values.
2025-01-04 03:51:12.505465 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-04 03:51:12.506368 INFO::Done
2025-01-04 03:51:12.507107 INFO::Acquiring quality metrics before batch effect correction.
2025-01-04 03:51:12.511151 INFO::Starting hierarchical adjustment
2025-01-04 03:51:12.512301 INFO::Found 5 batches.
2025-01-04 03:51:12.513147 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-04 03:51:12.514034 INFO::Using default BPPARAM
2025-01-04 03:51:12.514918 INFO::Processing subtree level 1
2025-01-04 03:51:12.647125 INFO::Adjusting the last 2 batches sequentially
2025-01-04 03:51:12.649319 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-04 03:51:12.671334 INFO::Done
2025-01-04 03:51:12.672284 INFO::Acquiring quality metrics after batch effect correction.
2025-01-04 03:51:12.676739 INFO::ASW Batch was 0.274256296479733 prior to batch effect correction and is now -0.0768730803821652 .
2025-01-04 03:51:12.677661 INFO::ASW Label was 0.505710697176585 prior to batch effect correction and is now 0.900705114999851 .
2025-01-04 03:51:12.678766 INFO::Total function execution time is 0.183030843734741 s and adjustment time is 0.159241914749146 s ( 87 )
2025-01-04 03:51:12.679864 INFO::Formatting Data.
2025-01-04 03:51:12.680708 INFO::Replacing NaNs with NAs.
2025-01-04 03:51:12.681942 INFO::Removing potential empty rows and columns
2025-01-04 03:51:12.683307 INFO::Found 0 missing values.
2025-01-04 03:51:12.689076 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-04 03:51:12.689959 INFO::Done
2025-01-04 03:51:12.690679 INFO::Acquiring quality metrics before batch effect correction.
2025-01-04 03:51:12.694629 INFO::Starting hierarchical adjustment
2025-01-04 03:51:12.695712 INFO::Found 5 batches.
2025-01-04 03:51:12.696462 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-04 03:51:12.697343 INFO::Using default BPPARAM
2025-01-04 03:51:12.698055 INFO::Processing subtree level 1
2025-01-04 03:51:12.825968 INFO::Adjusting the last 2 batches sequentially
2025-01-04 03:51:12.828062 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-04 03:51:12.861485 INFO::Done
2025-01-04 03:51:12.862736 INFO::Acquiring quality metrics after batch effect correction.
2025-01-04 03:51:12.867749 INFO::ASW Batch was 0.274256296479733 prior to batch effect correction and is now -0.0768730803821652 .
2025-01-04 03:51:12.868662 INFO::ASW Label was 0.505710697176585 prior to batch effect correction and is now 0.900705114999851 .
2025-01-04 03:51:12.869931 INFO::Total function execution time is 0.18996787071228 s and adjustment time is 0.165799856185913 s ( 87.28 )
2025-01-04 03:51:12.889194 INFO::Formatting Data.
2025-01-04 03:51:12.890201 INFO::Replacing NaNs with NAs.
2025-01-04 03:51:12.891573 INFO::Removing potential empty rows and columns
2025-01-04 03:51:12.893148 INFO::Found 0 missing values.
2025-01-04 03:51:12.898822 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-04 03:51:12.899701 INFO::Done
2025-01-04 03:51:12.90042 INFO::Acquiring quality metrics before batch effect correction.
2025-01-04 03:51:12.90435 INFO::Starting hierarchical adjustment
2025-01-04 03:51:12.905494 INFO::Found 5 batches.
2025-01-04 03:51:12.906235 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-04 03:51:12.907182 INFO::Using default BPPARAM
2025-01-04 03:51:12.907896 INFO::Processing subtree level 1
2025-01-04 03:51:13.044499 INFO::Adjusting the last 2 batches sequentially
2025-01-04 03:51:13.046653 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-04 03:51:13.067513 INFO::Done
2025-01-04 03:51:13.068408 INFO::Acquiring quality metrics after batch effect correction.
2025-01-04 03:51:13.072699 INFO::ASW Batch was 0.550402411715934 prior to batch effect correction and is now -0.061083505157057 .
2025-01-04 03:51:13.073556 INFO::ASW Label was 0.223037482608695 prior to batch effect correction and is now 0.847789415467097 .
2025-01-04 03:51:13.074706 INFO::Total function execution time is 0.18562912940979 s and adjustment time is 0.162217140197754 s ( 87.39 )
2025-01-04 03:51:13.075802 INFO::Formatting Data.
2025-01-04 03:51:13.076628 INFO::Replacing NaNs with NAs.
2025-01-04 03:51:13.077833 INFO::Removing potential empty rows and columns
2025-01-04 03:51:13.079155 INFO::Found 0 missing values.
2025-01-04 03:51:13.084709 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-04 03:51:13.085562 INFO::Done
2025-01-04 03:51:13.086271 INFO::Acquiring quality metrics before batch effect correction.
2025-01-04 03:51:13.090139 INFO::Starting hierarchical adjustment
2025-01-04 03:51:13.09117 INFO::Found 5 batches.
2025-01-04 03:51:13.091906 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-04 03:51:13.092765 INFO::Using default BPPARAM
2025-01-04 03:51:13.093509 INFO::Processing subtree level 1
2025-01-04 03:51:13.221725 INFO::Adjusting the last 2 batches sequentially
2025-01-04 03:51:13.223776 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-04 03:51:13.244765 INFO::Done
2025-01-04 03:51:13.245742 INFO::Acquiring quality metrics after batch effect correction.
2025-01-04 03:51:13.250075 INFO::ASW Batch was 0.550402411715934 prior to batch effect correction and is now -0.061083505157057 .
2025-01-04 03:51:13.250947 INFO::ASW Label was 0.223037482608695 prior to batch effect correction and is now 0.847789415467097 .
2025-01-04 03:51:13.252034 INFO::Total function execution time is 0.176201581954956 s and adjustment time is 0.153769969940186 s ( 87.27 )
2025-01-04 03:51:13.269933 INFO::Formatting Data.
2025-01-04 03:51:13.270914 INFO::Replacing NaNs with NAs.
2025-01-04 03:51:13.272083 INFO::Removing potential empty rows and columns
2025-01-04 03:51:13.273675 INFO::Found 0 missing values.
2025-01-04 03:51:13.277393 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-04 03:51:13.278181 INFO::Done
2025-01-04 03:51:13.278896 INFO::Acquiring quality metrics before batch effect correction.
2025-01-04 03:51:13.282719 INFO::Starting hierarchical adjustment
2025-01-04 03:51:13.283737 INFO::Found 2 batches.
2025-01-04 03:51:13.284468 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-04 03:51:13.285649 INFO::Using default BPPARAM
2025-01-04 03:51:13.286364 INFO::Adjusting the last 2 batches sequentially
2025-01-04 03:51:13.287613 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-04 03:51:13.306754 INFO::Done
2025-01-04 03:51:13.307597 INFO::Acquiring quality metrics after batch effect correction.
2025-01-04 03:51:13.31135 INFO::ASW Batch was 0.685796646695729 prior to batch effect correction and is now -0.00408328621525486 .
2025-01-04 03:51:13.312131 INFO::ASW Label was 0.382559658156552 prior to batch effect correction and is now 0.904112595275382 .
2025-01-04 03:51:13.313192 INFO::Total function execution time is 0.0433406829833984 s and adjustment time is 0.023200511932373 s ( 53.53 )
2025-01-04 03:51:13.314199 INFO::Formatting Data.
2025-01-04 03:51:13.314985 INFO::Replacing NaNs with NAs.
2025-01-04 03:51:13.316128 INFO::Removing potential empty rows and columns
2025-01-04 03:51:13.317478 INFO::Found 0 missing values.
2025-01-04 03:51:13.321187 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-04 03:51:13.321955 INFO::Done
2025-01-04 03:51:13.322652 INFO::Acquiring quality metrics before batch effect correction.
2025-01-04 03:51:13.400704 INFO::Starting hierarchical adjustment
2025-01-04 03:51:13.402071 INFO::Found 2 batches.
2025-01-04 03:51:13.402819 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-04 03:51:13.403677 INFO::Using default BPPARAM
2025-01-04 03:51:13.404395 INFO::Adjusting the last 2 batches sequentially
2025-01-04 03:51:13.405766 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-04 03:51:13.428064 INFO::Done
2025-01-04 03:51:13.429104 INFO::Acquiring quality metrics after batch effect correction.
2025-01-04 03:51:13.433329 INFO::ASW Batch was 0.685796646695729 prior to batch effect correction and is now -0.00408328621525486 .
2025-01-04 03:51:13.434265 INFO::ASW Label was 0.382559658156552 prior to batch effect correction and is now 0.904112595275382 .
2025-01-04 03:51:13.435395 INFO::Total function execution time is 0.121180772781372 s and adjustment time is 0.0262088775634766 s ( 21.63 )
2025-01-04 03:51:13.451627 INFO::Formatting Data.
2025-01-04 03:51:13.452644 INFO::Replacing NaNs with NAs.
2025-01-04 03:51:13.453903 INFO::Removing potential empty rows and columns
2025-01-04 03:51:13.455162 INFO::Found 0 missing values.
2025-01-04 03:51:13.458141 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-04 03:51:13.458875 INFO::Done
2025-01-04 03:51:13.459613 INFO::Acquiring quality metrics before batch effect correction.
2025-01-04 03:51:13.462166 INFO::Starting hierarchical adjustment
2025-01-04 03:51:13.463126 INFO::Found 2 batches.
2025-01-04 03:51:13.46387 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-04 03:51:13.464697 INFO::Using default BPPARAM
2025-01-04 03:51:13.465449 INFO::Adjusting the last 2 batches sequentially
2025-01-04 03:51:13.466707 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-04 03:51:13.511748 INFO::Done
2025-01-04 03:51:13.512621 INFO::Acquiring quality metrics after batch effect correction.
2025-01-04 03:51:13.515184 INFO::ASW Batch was -0.11332839274926 prior to batch effect correction and is now -0.14942221135546 .
2025-01-04 03:51:13.516213 INFO::Total function execution time is 0.0646722316741943 s and adjustment time is 0.0488061904907227 s ( 75.47 )
2025-01-04 03:51:13.542651 INFO::Formatting Data.
2025-01-04 03:51:13.543729 INFO::Replacing NaNs with NAs.
2025-01-04 03:51:13.545028 INFO::Removing potential empty rows and columns
2025-01-04 03:51:13.546619 INFO::Found 0 missing values.
2025-01-04 03:51:13.548352 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.
2025-01-04 03:51:13.555955 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-04 03:51:13.557106 INFO::Done
2025-01-04 03:51:13.558258 INFO::Acquiring quality metrics before batch effect correction.
2025-01-04 03:51:13.562702 INFO::Starting hierarchical adjustment
2025-01-04 03:51:13.563776 INFO::Found 2 batches.
2025-01-04 03:51:13.564571 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-04 03:51:13.565482 INFO::Using default BPPARAM
2025-01-04 03:51:13.566253 INFO::Adjusting the last 2 batches sequentially
2025-01-04 03:51:13.567721 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-04 03:51:13.593264 INFO::Done
2025-01-04 03:51:13.594176 INFO::Acquiring quality metrics after batch effect correction.
2025-01-04 03:51:13.598557 INFO::ASW Batch was 0.455294084930956 prior to batch effect correction and is now 0.0858596986195506 .
2025-01-04 03:51:13.599391 INFO::ASW Label was 0.409629482743072 prior to batch effect correction and is now 0.865009737402123 .
2025-01-04 03:51:13.600686 INFO::Total function execution time is 0.0580906867980957 s and adjustment time is 0.0296914577484131 s ( 51.11 )
2025-01-04 03:51:13.601852 INFO::Formatting Data.
2025-01-04 03:51:13.602781 INFO::Replacing NaNs with NAs.
2025-01-04 03:51:13.604164 INFO::Removing potential empty rows and columns
2025-01-04 03:51:13.605958 INFO::Found 0 missing values.
2025-01-04 03:51:13.607291 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.
2025-01-04 03:51:13.614481 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-04 03:51:13.615464 INFO::Done
2025-01-04 03:51:13.616227 INFO::Acquiring quality metrics before batch effect correction.
2025-01-04 03:51:13.620482 INFO::Starting hierarchical adjustment
2025-01-04 03:51:13.621564 INFO::Found 2 batches.
2025-01-04 03:51:13.62231 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-04 03:51:13.623178 INFO::Using default BPPARAM
2025-01-04 03:51:13.623919 INFO::Adjusting the last 2 batches sequentially
2025-01-04 03:51:13.625287 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-04 03:51:13.650051 INFO::Done
2025-01-04 03:51:13.650957 INFO::Acquiring quality metrics after batch effect correction.
2025-01-04 03:51:13.655287 INFO::ASW Batch was 0.455294084930956 prior to batch effect correction and is now 0.0858596986195506 .
2025-01-04 03:51:13.656131 INFO::ASW Label was 0.409629482743072 prior to batch effect correction and is now 0.865009737402123 .
2025-01-04 03:51:13.657322 INFO::Total function execution time is 0.055457592010498 s and adjustment time is 0.0286908149719238 s ( 51.73 )
2025-01-04 03:51:13.989488 INFO::Formatting Data.
2025-01-04 03:51:13.990527 INFO::Replacing NaNs with NAs.
2025-01-04 03:51:13.991782 INFO::Removing potential empty rows and columns
2025-01-04 03:51:13.993325 INFO::Found 0 missing values.
2025-01-04 03:51:13.997992 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-04 03:51:13.998847 INFO::Done
2025-01-04 03:51:13.999604 INFO::Acquiring quality metrics before batch effect correction.
2025-01-04 03:51:14.002451 INFO::Starting hierarchical adjustment
2025-01-04 03:51:14.003498 INFO::Found 3 batches.
2025-01-04 03:51:14.004282 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-04 03:51:14.005234 INFO::Using default BPPARAM
2025-01-04 03:51:14.006019 INFO::Processing subtree level 1
2025-01-04 03:51:14.138053 INFO::Adjusting the last 1 batches sequentially
2025-01-04 03:51:14.140739 INFO::Done
2025-01-04 03:51:14.141791 INFO::Acquiring quality metrics after batch effect correction.
2025-01-04 03:51:14.145648 INFO::ASW Batch was -0.0932664005747132 prior to batch effect correction and is now -0.0932664005747132 .
2025-01-04 03:51:14.147244 INFO::Total function execution time is 0.157721757888794 s and adjustment time is 0.137415647506714 s ( 87.13 )
2025-01-04 03:51:14.149057 INFO::Formatting Data.
2025-01-04 03:51:14.150156 INFO::Typecasting input to dataframe.
2025-01-04 03:51:14.151374 INFO::Replacing NaNs with NAs.
2025-01-04 03:51:14.152849 INFO::Removing potential empty rows and columns
2025-01-04 03:51:14.154715 INFO::Found 0 missing values.
2025-01-04 03:51:14.159818 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-04 03:51:14.160929 INFO::Done
2025-01-04 03:51:14.161761 INFO::Acquiring quality metrics before batch effect correction.
2025-01-04 03:51:14.164891 INFO::Starting hierarchical adjustment
2025-01-04 03:51:14.166148 INFO::Found 3 batches.
2025-01-04 03:51:14.166975 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-04 03:51:14.167984 INFO::Using default BPPARAM
2025-01-04 03:51:14.168813 INFO::Processing subtree level 1
2025-01-04 03:51:14.310084 INFO::Adjusting the last 1 batches sequentially
2025-01-04 03:51:14.312455 INFO::Done
2025-01-04 03:51:14.313319 INFO::Acquiring quality metrics after batch effect correction.
2025-01-04 03:51:14.316662 INFO::ASW Batch was -0.0932664005747132 prior to batch effect correction and is now -0.0932664005747132 .
2025-01-04 03:51:14.317991 INFO::Total function execution time is 0.168978214263916 s and adjustment time is 0.146582841873169 s ( 86.75 )
2025-01-04 03:51:14.335931 INFO::Formatting Data.
2025-01-04 03:51:14.337032 INFO::Typecasting input to dataframe.
2025-01-04 03:51:14.338212 INFO::Replacing NaNs with NAs.
2025-01-04 03:51:14.339494 INFO::Removing potential empty rows and columns
2025-01-04 03:51:14.341054 INFO::Found 0 missing values.
2025-01-04 03:51:14.345516 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-04 03:51:14.346429 INFO::Done
2025-01-04 03:51:14.34719 INFO::Acquiring quality metrics before batch effect correction.
2025-01-04 03:51:14.350112 INFO::Starting hierarchical adjustment
2025-01-04 03:51:14.351209 INFO::Found 3 batches.
2025-01-04 03:51:14.352003 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-04 03:51:14.352912 INFO::Using default BPPARAM
2025-01-04 03:51:14.353724 INFO::Processing subtree level 1
2025-01-04 03:51:14.486296 INFO::Adjusting the last 1 batches sequentially
2025-01-04 03:51:14.488684 INFO::Done
2025-01-04 03:51:14.489541 INFO::Acquiring quality metrics after batch effect correction.
2025-01-04 03:51:14.492956 INFO::ASW Batch was -0.0444982457798575 prior to batch effect correction and is now -0.0444982457798575 .
2025-01-04 03:51:14.494307 INFO::Total function execution time is 0.158410310745239 s and adjustment time is 0.137692213058472 s ( 86.92 )
2025-01-04 03:51:14.706471 INFO::Formatting Data.
2025-01-04 03:51:14.708357 INFO::Replacing NaNs with NAs.
2025-01-04 03:51:14.710796 INFO::Removing potential empty rows and columns
2025-01-04 03:51:14.715899 INFO::Found 1000 missing values.
2025-01-04 03:51:14.748008 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-04 03:51:14.748984 INFO::Done
2025-01-04 03:51:14.749766 INFO::Acquiring quality metrics before batch effect correction.
2025-01-04 03:51:14.758786 INFO::Starting hierarchical adjustment
2025-01-04 03:51:14.760008 INFO::Found 10 batches.
2025-01-04 03:51:14.76082 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-04 03:51:14.761808 INFO::Using default BPPARAM
2025-01-04 03:51:14.762601 INFO::Processing subtree level 1
2025-01-04 03:51:14.973174 INFO::Processing subtree level 2
2025-01-04 03:51:15.196435 INFO::Adjusting the last 1 batches sequentially
2025-01-04 03:51:15.198968 INFO::Done
2025-01-04 03:51:15.199804 INFO::Acquiring quality metrics after batch effect correction.
2025-01-04 03:51:15.207736 INFO::ASW Batch was 0.515983995615399 prior to batch effect correction and is now 0.515983995615399 .
2025-01-04 03:51:15.208716 INFO::ASW Label was 0.333317963305782 prior to batch effect correction and is now 0.333317963305782 .
2025-01-04 03:51:15.210084 INFO::Total function execution time is 0.513304471969604 s and adjustment time is 0.439247369766235 s ( 85.57 )
2025-01-04 03:51:15.211305 INFO::Formatting Data.
2025-01-04 03:51:15.212217 INFO::Replacing NaNs with NAs.
2025-01-04 03:51:15.214038 INFO::Removing potential empty rows and columns
2025-01-04 03:51:15.21855 INFO::Found 1000 missing values.
2025-01-04 03:51:15.248877 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-04 03:51:15.24983 INFO::Done
2025-01-04 03:51:15.250606 INFO::Acquiring quality metrics before batch effect correction.
2025-01-04 03:51:15.258568 INFO::Starting hierarchical adjustment
2025-01-04 03:51:15.259751 INFO::Found 10 batches.
2025-01-04 03:51:16.657383 INFO::Set up parallel execution backend with 2 workers
2025-01-04 03:51:16.659624 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2025-01-04 03:51:18.092725 INFO::Adjusting the last 2 batches sequentially
2025-01-04 03:51:18.094869 INFO::Adjusting sequential tree level 1 with 2 batches
2025-01-04 03:51:18.120341 INFO::Done
2025-01-04 03:51:18.12123 INFO::Acquiring quality metrics after batch effect correction.
2025-01-04 03:51:18.128132 INFO::ASW Batch was 0.515983995615399 prior to batch effect correction and is now 0.515983995615399 .
2025-01-04 03:51:18.129048 INFO::ASW Label was 0.333317963305782 prior to batch effect correction and is now 0.333317963305782 .
2025-01-04 03:51:18.130138 INFO::Total function execution time is 2.91885018348694 s and adjustment time is 2.86081099510193 s ( 98.01 )
2025-01-04 03:51:18.31691 INFO::Formatting Data.
2025-01-04 03:51:18.317942 INFO::Replacing NaNs with NAs.
2025-01-04 03:51:18.319188 INFO::Removing potential empty rows and columns
2025-01-04 03:51:18.320772 INFO::Found 0 missing values.
2025-01-04 03:51:18.326395 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-04 03:51:18.32723 INFO::Done
2025-01-04 03:51:18.328002 INFO::Acquiring quality metrics before batch effect correction.
2025-01-04 03:51:18.331908 INFO::Starting hierarchical adjustment
2025-01-04 03:51:18.332985 INFO::Found 3 batches.
2025-01-04 03:51:18.333778 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2025-01-04 03:51:18.334669 INFO::Using default BPPARAM
2025-01-04 03:51:18.33544 INFO::Processing subtree level 1
2025-01-04 03:51:18.473049 INFO::Adjusting the last 1 batches sequentially
2025-01-04 03:51:18.475417 INFO::Done
2025-01-04 03:51:18.476263 INFO::Acquiring quality metrics after batch effect correction.
2025-01-04 03:51:18.489068 INFO::ASW Batch was 0.105678843046096 prior to batch effect correction and is now -0.147350810234575 .
2025-01-04 03:51:18.490068 INFO::ASW Label was -0.135635449423496 prior to batch effect correction and is now 0.142863535477561 .
2025-01-04 03:51:18.491372 INFO::Total function execution time is 0.174484729766846 s and adjustment time is 0.142632007598877 s ( 81.74 )
2025-01-04 03:51:18.681983 INFO::Formatting Data.
2025-01-04 03:51:18.683294 INFO::Replacing NaNs with NAs.
2025-01-04 03:51:18.6845 INFO::Removing potential empty rows and columns
2025-01-04 03:51:18.686062 INFO::Found 2 missing values.
2025-01-04 03:51:18.690309 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2025-01-04 03:51:18.69112 INFO::Done
2025-01-04 03:51:18.730678 INFO::Found NA in Reference column
2025-01-04 03:51:18.74448 INFO::Require at least two references per batch.
2025-01-04 03:51:18.773897 INFO::Formatting Data.
2025-01-04 03:51:18.774809 INFO::Recognized SummarizedExperiment
2025-01-04 03:51:18.775512 INFO::Typecasting input to dataframe.
2025-01-04 03:51:18.789576 INFO::Replacing NaNs with NAs.
2025-01-04 03:51:18.791106 INFO::Removing potential empty rows and columns
2025-01-04 03:51:18.796469 INFO::Found 0 missing values.
2025-01-04 03:51:18.807035 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-04 03:51:18.807877 INFO::Done
2025-01-04 03:51:18.828688 INFO::Formatting Data.
2025-01-04 03:51:18.829634 INFO::Recognized SummarizedExperiment
2025-01-04 03:51:18.830344 INFO::Typecasting input to dataframe.
2025-01-04 03:51:18.854908 INFO::Replacing NaNs with NAs.
2025-01-04 03:51:18.856467 INFO::Removing potential empty rows and columns
2025-01-04 03:51:18.861935 INFO::Found 0 missing values.
2025-01-04 03:51:18.879284 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-04 03:51:18.880161 INFO::Done
2025-01-04 03:51:18.901125 INFO::Formatting Data.
2025-01-04 03:51:18.902067 INFO::Recognized SummarizedExperiment
2025-01-04 03:51:18.902784 INFO::Typecasting input to dataframe.
2025-01-04 03:51:18.926204 INFO::Replacing NaNs with NAs.
2025-01-04 03:51:18.927528 INFO::Removing potential empty rows and columns
2025-01-04 03:51:18.929053 INFO::Found 0 missing values.
2025-01-04 03:51:18.930291 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.
2025-01-04 03:51:18.936661 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-04 03:51:18.937528 INFO::Done
2025-01-04 03:51:18.951197 INFO::Formatting Data.
2025-01-04 03:51:18.952183 INFO::Replacing NaNs with NAs.
2025-01-04 03:51:18.953392 INFO::Removing potential empty rows and columns
2025-01-04 03:51:18.95475 INFO::Found 0 missing values.
2025-01-04 03:51:18.958879 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-04 03:51:18.959678 INFO::Done
2025-01-04 03:51:18.975484 INFO::Formatting Data.
2025-01-04 03:51:18.976485 INFO::Replacing NaNs with NAs.
2025-01-04 03:51:18.977695 INFO::Removing potential empty rows and columns
2025-01-04 03:51:18.979062 INFO::Found 0 missing values.
2025-01-04 03:51:18.983239 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-04 03:51:18.984046 INFO::Done
2025-01-04 03:51:19.025862 INFO::Formatting Data.
2025-01-04 03:51:19.026878 INFO::Replacing NaNs with NAs.
2025-01-04 03:51:19.02829 INFO::Removing potential empty rows and columns
2025-01-04 03:51:19.030012 INFO::Found 1 missing values.
2025-01-04 03:51:19.033864 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-04 03:51:19.034701 INFO::Done
2025-01-04 03:51:19.061834 INFO::Formatting Data.
2025-01-04 03:51:19.062839 INFO::Replacing NaNs with NAs.
2025-01-04 03:51:19.064073 INFO::Removing potential empty rows and columns
2025-01-04 03:51:19.065461 INFO::Found 2 missing values.
2025-01-04 03:51:19.066669 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.
2025-01-04 03:51:19.069918 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2025-01-04 03:51:19.070718 INFO::Done
2025-01-04 03:51:19.085734 INFO::Formatting Data.
2025-01-04 03:51:19.086718 INFO::Replacing NaNs with NAs.
2025-01-04 03:51:19.087883 INFO::Removing potential empty rows and columns
2025-01-04 03:51:19.089188 INFO::Found 2 missing values.
2025-01-04 03:51:19.091426 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-04 03:51:19.092149 INFO::Done
2025-01-04 03:51:19.10672 INFO::Formatting Data.
2025-01-04 03:51:19.107722 INFO::Typecasting input to dataframe.
2025-01-04 03:51:19.108808 INFO::Replacing NaNs with NAs.
2025-01-04 03:51:19.109989 INFO::Removing potential empty rows and columns
2025-01-04 03:51:19.111435 INFO::Found 0 missing values.
2025-01-04 03:51:19.115582 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2025-01-04 03:51:19.116393 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 138 ]
>
> proc.time()
user system elapsed
22.451 4.380 26.564
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 31.446 | 1.311 | 22.416 | |
| compute_asw | 0.036 | 0.000 | 0.036 | |
| count_existing | 0.019 | 0.000 | 0.019 | |
| generate_data_covariables | 0.017 | 0.000 | 0.016 | |
| generate_dataset | 0.015 | 0.000 | 0.016 | |