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 11:44 -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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.3.3.tar.gz |
| StartedAt: 2024-12-23 18:17:00 -0500 (Mon, 23 Dec 2024) |
| EndedAt: 2024-12-23 18:17:30 -0500 (Mon, 23 Dec 2024) |
| EllapsedTime: 30.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BERT.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BERT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BERT_1.3.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* 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 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 9.916 0.381 7.11
* 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
‘/Users/biocbuild/bbs-3.21-bioc/meat/BERT.Rcheck/00check.log’
for details.
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘BERT’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2024-12-23 18:17:23.698261 INFO::Formatting Data.
2024-12-23 18:17:23.700088 INFO::Replacing NaNs with NAs.
2024-12-23 18:17:23.704642 INFO::Removing potential empty rows and columns
2024-12-23 18:17:23.813085 INFO::Found 0 missing values.
2024-12-23 18:17:23.814426 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 18:17:23.814653 INFO::Done
2024-12-23 18:17:23.814854 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 18:17:23.820547 INFO::Starting hierarchical adjustment
2024-12-23 18:17:23.821189 INFO::Found 3 batches.
2024-12-23 18:17:23.821355 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 18:17:23.821762 INFO::Using default BPPARAM
2024-12-23 18:17:23.821928 INFO::Processing subtree level 1
2024-12-23 18:17:23.876054 INFO::Adjusting the last 1 batches sequentially
2024-12-23 18:17:23.877665 INFO::Done
2024-12-23 18:17:23.87811 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 18:17:23.880337 INFO::ASW Batch was -0.0493452648347228 prior to batch effect correction and is now -0.0493452648347228 .
2024-12-23 18:17:23.881367 INFO::Total function execution time is 0.183397054672241 s and adjustment time is 0.0564990043640137 s ( 30.81 )
2024-12-23 18:17:23.890702 INFO::Formatting Data.
2024-12-23 18:17:23.891008 INFO::Replacing NaNs with NAs.
2024-12-23 18:17:23.891359 INFO::Removing potential empty rows and columns
2024-12-23 18:17:23.891962 INFO::Found 0 missing values.
2024-12-23 18:17:23.892345 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 18:17:23.897173 INFO::Formatting Data.
2024-12-23 18:17:23.897439 INFO::Replacing NaNs with NAs.
2024-12-23 18:17:23.897764 INFO::Removing potential empty rows and columns
2024-12-23 18:17:23.898148 INFO::Found 0 missing values.
2024-12-23 18:17:23.898471 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 18:17:23.904824 INFO::Formatting Data.
2024-12-23 18:17:23.905068 INFO::Replacing NaNs with NAs.
2024-12-23 18:17:23.905372 INFO::Removing potential empty rows and columns
2024-12-23 18:17:23.905713 INFO::Found 0 missing values.
2024-12-23 18:17:23.906001 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 18:17:23.907475 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 18:17:23.907651 INFO::Done
2024-12-23 18:17:23.907847 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 18:17:23.908555 INFO::Starting hierarchical adjustment
2024-12-23 18:17:23.908781 INFO::Found 2 batches.
2024-12-23 18:17:23.908948 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 18:17:23.909195 INFO::Using default BPPARAM
2024-12-23 18:17:23.909373 INFO::Adjusting the last 2 batches sequentially
2024-12-23 18:17:23.909687 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-23 18:17:23.920399 INFO::Done
2024-12-23 18:17:23.920633 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 18:17:23.921289 INFO::ASW Batch was 0.0209786317131389 prior to batch effect correction and is now -0.0882660967493702 .
2024-12-23 18:17:23.921533 INFO::Total function execution time is 0.0167388916015625 s and adjustment time is 0.0116448402404785 s ( 69.57 )
2024-12-23 18:17:23.92256 INFO::Formatting Data.
2024-12-23 18:17:23.922758 INFO::Replacing NaNs with NAs.
2024-12-23 18:17:23.925815 INFO::Formatting Data.
2024-12-23 18:17:23.92612 INFO::Replacing NaNs with NAs.
2024-12-23 18:17:23.926387 INFO::Removing potential empty rows and columns
2024-12-23 18:17:23.926759 INFO::Found 0 missing values.
2024-12-23 18:17:23.927727 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 18:17:23.927906 INFO::Done
2024-12-23 18:17:23.928077 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 18:17:23.928833 INFO::Starting hierarchical adjustment
2024-12-23 18:17:23.950982 INFO::Found 2 batches.
2024-12-23 18:17:23.951968 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 18:17:23.952177 INFO::Using default BPPARAM
2024-12-23 18:17:23.95235 INFO::Adjusting the last 2 batches sequentially
2024-12-23 18:17:23.952684 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-23 18:17:23.957791 INFO::Done
2024-12-23 18:17:23.958007 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 18:17:23.958643 INFO::ASW Batch was 0.015320912521815 prior to batch effect correction and is now -0.119087546184924 .
2024-12-23 18:17:23.958889 INFO::Total function execution time is 0.0330967903137207 s and adjustment time is 0.0287151336669922 s ( 86.76 )
2024-12-23 18:17:23.959211 INFO::Formatting Data.
2024-12-23 18:17:23.959385 INFO::Replacing NaNs with NAs.
2024-12-23 18:17:23.959653 INFO::Removing potential empty rows and columns
2024-12-23 18:17:23.959957 INFO::Found 0 missing values.
2024-12-23 18:17:23.960811 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 18:17:23.960963 INFO::Done
2024-12-23 18:17:23.961108 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 18:17:23.961657 INFO::Starting hierarchical adjustment
2024-12-23 18:17:23.961854 INFO::Found 2 batches.
2024-12-23 18:17:23.962003 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 18:17:23.962177 INFO::Using default BPPARAM
2024-12-23 18:17:23.962304 INFO::Adjusting the last 2 batches sequentially
2024-12-23 18:17:23.962548 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-23 18:17:23.967036 INFO::Done
2024-12-23 18:17:23.967231 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 18:17:23.967828 INFO::ASW Batch was 0.015320912521815 prior to batch effect correction and is now -0.119087546184924 .
2024-12-23 18:17:23.968061 INFO::Total function execution time is 0.00884389877319336 s and adjustment time is 0.00521993637084961 s ( 59.02 )
2024-12-23 18:17:25.063306 INFO::Formatting Data.
2024-12-23 18:17:25.063554 INFO::Recognized SummarizedExperiment
2024-12-23 18:17:25.063698 INFO::Typecasting input to dataframe.
2024-12-23 18:17:25.073528 INFO::Replacing NaNs with NAs.
2024-12-23 18:17:25.073891 INFO::Removing potential empty rows and columns
2024-12-23 18:17:25.074911 INFO::Found 0 missing values.
2024-12-23 18:17:25.076822 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 18:17:25.076973 INFO::Done
2024-12-23 18:17:25.077109 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 18:17:25.07835 INFO::Starting hierarchical adjustment
2024-12-23 18:17:25.078547 INFO::Found 2 batches.
2024-12-23 18:17:25.078686 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 18:17:25.078989 INFO::Using default BPPARAM
2024-12-23 18:17:25.079125 INFO::Adjusting the last 2 batches sequentially
2024-12-23 18:17:25.079395 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-23 18:17:25.095816 INFO::Done
2024-12-23 18:17:25.096017 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 18:17:25.097146 INFO::ASW Batch was 0.0184424475264686 prior to batch effect correction and is now -0.0927549805804117 .
2024-12-23 18:17:25.09738 INFO::Total function execution time is 0.0341649055480957 s and adjustment time is 0.0173060894012451 s ( 50.65 )
2024-12-23 18:17:25.102908 INFO::Formatting Data.
2024-12-23 18:17:25.103114 INFO::Recognized SummarizedExperiment
2024-12-23 18:17:25.103262 INFO::Typecasting input to dataframe.
2024-12-23 18:17:25.106022 INFO::Replacing NaNs with NAs.
2024-12-23 18:17:25.106349 INFO::Removing potential empty rows and columns
2024-12-23 18:17:25.107448 INFO::Found 0 missing values.
2024-12-23 18:17:25.109476 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 18:17:25.109643 INFO::Done
2024-12-23 18:17:25.109792 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 18:17:25.110955 INFO::Starting hierarchical adjustment
2024-12-23 18:17:25.111162 INFO::Found 2 batches.
2024-12-23 18:17:25.111308 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 18:17:25.11148 INFO::Using default BPPARAM
2024-12-23 18:17:25.111622 INFO::Adjusting the last 2 batches sequentially
2024-12-23 18:17:25.111896 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-23 18:17:25.119576 INFO::Done
2024-12-23 18:17:25.119773 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 18:17:25.120894 INFO::ASW Batch was 0.00997240152439409 prior to batch effect correction and is now 0.00997240152439409 .
2024-12-23 18:17:25.121143 INFO::Total function execution time is 0.0182299613952637 s and adjustment time is 0.0084531307220459 s ( 46.37 )
2024-12-23 18:17:25.127218 INFO::Formatting Data.
2024-12-23 18:17:25.127419 INFO::Replacing NaNs with NAs.
2024-12-23 18:17:25.127661 INFO::Removing potential empty rows and columns
2024-12-23 18:17:25.12795 INFO::Found 0 missing values.
2024-12-23 18:17:25.128754 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 18:17:25.128904 INFO::Done
2024-12-23 18:17:25.129046 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 18:17:25.129589 INFO::Starting hierarchical adjustment
2024-12-23 18:17:25.12977 INFO::Found 3 batches.
2024-12-23 18:17:25.129908 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 18:17:25.130082 INFO::Using default BPPARAM
2024-12-23 18:17:25.130214 INFO::Processing subtree level 1
2024-12-23 18:17:25.184615 INFO::Adjusting the last 1 batches sequentially
2024-12-23 18:17:25.185936 INFO::Done
2024-12-23 18:17:25.186321 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 18:17:25.187682 INFO::ASW Batch was -0.117096177876961 prior to batch effect correction and is now -0.163969000019682 .
2024-12-23 18:17:25.188167 INFO::Total function execution time is 0.0609300136566162 s and adjustment time is 0.0561881065368652 s ( 92.22 )
2024-12-23 18:17:25.194665 INFO::Skipping initial DF formatting
2024-12-23 18:17:25.194875 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 18:17:25.196133 INFO::Starting hierarchical adjustment
2024-12-23 18:17:25.196362 INFO::Found 5 batches.
2024-12-23 18:17:25.196518 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 18:17:25.196727 INFO::Using default BPPARAM
2024-12-23 18:17:25.196876 INFO::Processing subtree level 1
2024-12-23 18:17:25.237496 INFO::Adjusting the last 2 batches sequentially
2024-12-23 18:17:25.239794 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-23 18:17:25.247138 INFO::Done
2024-12-23 18:17:25.247467 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 18:17:25.249509 INFO::ASW Batch was 0.4919506543538 prior to batch effect correction and is now 0.4919506543538 .
2024-12-23 18:17:25.249699 INFO::ASW Label was 0.36628031385579 prior to batch effect correction and is now 0.36628031385579 .
2024-12-23 18:17:25.25035 INFO::Total function execution time is 0.0556809902191162 s and adjustment time is 0.0508241653442383 s ( 91.28 )
2024-12-23 18:17:25.257471 INFO::Formatting Data.
2024-12-23 18:17:25.257705 INFO::Replacing NaNs with NAs.
2024-12-23 18:17:25.258 INFO::Removing potential empty rows and columns
2024-12-23 18:17:25.258337 INFO::Found 0 missing values.
2024-12-23 18:17:25.259491 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 18:17:25.259657 INFO::Done
2024-12-23 18:17:25.259932 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 18:17:25.260799 INFO::Starting hierarchical adjustment
2024-12-23 18:17:25.261017 INFO::Found 5 batches.
2024-12-23 18:17:25.261166 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 18:17:25.261374 INFO::Using default BPPARAM
2024-12-23 18:17:25.261576 INFO::Processing subtree level 1
2024-12-23 18:17:25.30319 INFO::Adjusting the last 2 batches sequentially
2024-12-23 18:17:25.305643 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-23 18:17:25.315603 INFO::Done
2024-12-23 18:17:25.315842 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 18:17:25.317475 INFO::ASW Batch was 0.589900280801751 prior to batch effect correction and is now -0.0633934556545198 .
2024-12-23 18:17:25.317781 INFO::ASW Label was 0.164014717905799 prior to batch effect correction and is now 0.728807054258505 .
2024-12-23 18:17:25.318411 INFO::Total function execution time is 0.0607659816741943 s and adjustment time is 0.054624080657959 s ( 89.89 )
2024-12-23 18:17:25.318708 INFO::Formatting Data.
2024-12-23 18:17:25.318886 INFO::Replacing NaNs with NAs.
2024-12-23 18:17:25.319163 INFO::Removing potential empty rows and columns
2024-12-23 18:17:25.3195 INFO::Found 0 missing values.
2024-12-23 18:17:25.320754 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 18:17:25.321027 INFO::Done
2024-12-23 18:17:25.321175 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 18:17:25.322044 INFO::Starting hierarchical adjustment
2024-12-23 18:17:25.322254 INFO::Found 5 batches.
2024-12-23 18:17:25.322409 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 18:17:25.322634 INFO::Using default BPPARAM
2024-12-23 18:17:25.322826 INFO::Processing subtree level 1
2024-12-23 18:17:25.365464 INFO::Adjusting the last 2 batches sequentially
2024-12-23 18:17:25.367641 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-23 18:17:25.376163 INFO::Done
2024-12-23 18:17:25.376443 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 18:17:25.378033 INFO::ASW Batch was 0.589900280801751 prior to batch effect correction and is now -0.0633934556545198 .
2024-12-23 18:17:25.378338 INFO::ASW Label was 0.164014717905799 prior to batch effect correction and is now 0.728807054258505 .
2024-12-23 18:17:25.37874 INFO::Total function execution time is 0.0599989891052246 s and adjustment time is 0.0539381504058838 s ( 89.9 )
2024-12-23 18:17:25.38514 INFO::Formatting Data.
2024-12-23 18:17:25.385376 INFO::Replacing NaNs with NAs.
2024-12-23 18:17:25.38567 INFO::Removing potential empty rows and columns
2024-12-23 18:17:25.386045 INFO::Found 0 missing values.
2024-12-23 18:17:25.387189 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 18:17:25.387354 INFO::Done
2024-12-23 18:17:25.387529 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 18:17:25.388439 INFO::Starting hierarchical adjustment
2024-12-23 18:17:25.38868 INFO::Found 5 batches.
2024-12-23 18:17:25.388954 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 18:17:25.389161 INFO::Using default BPPARAM
2024-12-23 18:17:25.389371 INFO::Processing subtree level 1
2024-12-23 18:17:25.43297 INFO::Adjusting the last 2 batches sequentially
2024-12-23 18:17:25.435781 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-23 18:17:25.445638 INFO::Done
2024-12-23 18:17:25.445903 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 18:17:25.447588 INFO::ASW Batch was 0.377911827028741 prior to batch effect correction and is now -0.0551499188897552 .
2024-12-23 18:17:25.447981 INFO::ASW Label was 0.315443557629374 prior to batch effect correction and is now 0.857317183383767 .
2024-12-23 18:17:25.44861 INFO::Total function execution time is 0.0633101463317871 s and adjustment time is 0.0569961071014404 s ( 90.03 )
2024-12-23 18:17:25.448991 INFO::Formatting Data.
2024-12-23 18:17:25.44917 INFO::Replacing NaNs with NAs.
2024-12-23 18:17:25.449666 INFO::Removing potential empty rows and columns
2024-12-23 18:17:25.450035 INFO::Found 0 missing values.
2024-12-23 18:17:25.451199 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 18:17:25.451361 INFO::Done
2024-12-23 18:17:25.451512 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 18:17:25.452388 INFO::Starting hierarchical adjustment
2024-12-23 18:17:25.452801 INFO::Found 5 batches.
2024-12-23 18:17:25.452967 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 18:17:25.453197 INFO::Using default BPPARAM
2024-12-23 18:17:25.453442 INFO::Processing subtree level 1
2024-12-23 18:17:25.497531 INFO::Adjusting the last 2 batches sequentially
2024-12-23 18:17:25.500539 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-23 18:17:25.509626 INFO::Done
2024-12-23 18:17:25.509916 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 18:17:25.511725 INFO::ASW Batch was 0.377911827028741 prior to batch effect correction and is now -0.0551499188897552 .
2024-12-23 18:17:25.511936 INFO::ASW Label was 0.315443557629374 prior to batch effect correction and is now 0.857317183383767 .
2024-12-23 18:17:25.512365 INFO::Total function execution time is 0.0633480548858643 s and adjustment time is 0.0568528175354004 s ( 89.75 )
2024-12-23 18:17:25.518923 INFO::Formatting Data.
2024-12-23 18:17:25.519161 INFO::Replacing NaNs with NAs.
2024-12-23 18:17:25.51948 INFO::Removing potential empty rows and columns
2024-12-23 18:17:25.519843 INFO::Found 0 missing values.
2024-12-23 18:17:25.52067 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 18:17:25.520829 INFO::Done
2024-12-23 18:17:25.520981 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 18:17:25.521931 INFO::Starting hierarchical adjustment
2024-12-23 18:17:25.52231 INFO::Found 2 batches.
2024-12-23 18:17:25.522477 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 18:17:25.522686 INFO::Using default BPPARAM
2024-12-23 18:17:25.522963 INFO::Adjusting the last 2 batches sequentially
2024-12-23 18:17:25.523223 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-23 18:17:25.528201 INFO::Done
2024-12-23 18:17:25.528424 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 18:17:25.529317 INFO::ASW Batch was 0.555154718909645 prior to batch effect correction and is now -0.0268058098486937 .
2024-12-23 18:17:25.529512 INFO::ASW Label was 0.528707219793697 prior to batch effect correction and is now 0.927440885839946 .
2024-12-23 18:17:25.529758 INFO::Total function execution time is 0.010883092880249 s and adjustment time is 0.0059361457824707 s ( 54.54 )
2024-12-23 18:17:25.529984 INFO::Formatting Data.
2024-12-23 18:17:25.530146 INFO::Replacing NaNs with NAs.
2024-12-23 18:17:25.530388 INFO::Removing potential empty rows and columns
2024-12-23 18:17:25.530685 INFO::Found 0 missing values.
2024-12-23 18:17:25.571619 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 18:17:25.571906 INFO::Done
2024-12-23 18:17:25.572083 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 18:17:25.573118 INFO::Starting hierarchical adjustment
2024-12-23 18:17:25.573358 INFO::Found 2 batches.
2024-12-23 18:17:25.573519 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 18:17:25.573705 INFO::Using default BPPARAM
2024-12-23 18:17:25.573851 INFO::Adjusting the last 2 batches sequentially
2024-12-23 18:17:25.574129 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-23 18:17:25.57975 INFO::Done
2024-12-23 18:17:25.579964 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 18:17:25.580987 INFO::ASW Batch was 0.555154718909645 prior to batch effect correction and is now -0.0268058098486937 .
2024-12-23 18:17:25.581166 INFO::ASW Label was 0.528707219793697 prior to batch effect correction and is now 0.927440885839946 .
2024-12-23 18:17:25.581418 INFO::Total function execution time is 0.0514159202575684 s and adjustment time is 0.00642013549804688 s ( 12.49 )
2024-12-23 18:17:25.585891 INFO::Formatting Data.
2024-12-23 18:17:25.586106 INFO::Replacing NaNs with NAs.
2024-12-23 18:17:25.586355 INFO::Removing potential empty rows and columns
2024-12-23 18:17:25.586611 INFO::Found 0 missing values.
2024-12-23 18:17:25.58722 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 18:17:25.587362 INFO::Done
2024-12-23 18:17:25.587507 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 18:17:25.588025 INFO::Starting hierarchical adjustment
2024-12-23 18:17:25.588224 INFO::Found 2 batches.
2024-12-23 18:17:25.588368 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 18:17:25.588541 INFO::Using default BPPARAM
2024-12-23 18:17:25.588684 INFO::Adjusting the last 2 batches sequentially
2024-12-23 18:17:25.588918 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-23 18:17:25.599454 INFO::Done
2024-12-23 18:17:25.599675 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 18:17:25.600277 INFO::ASW Batch was 0.0556647076790151 prior to batch effect correction and is now -0.0593657081169292 .
2024-12-23 18:17:25.60052 INFO::Total function execution time is 0.0146431922912598 s and adjustment time is 0.0112571716308594 s ( 76.88 )
2024-12-23 18:17:25.60496 INFO::Formatting Data.
2024-12-23 18:17:25.605185 INFO::Replacing NaNs with NAs.
2024-12-23 18:17:25.605442 INFO::Removing potential empty rows and columns
2024-12-23 18:17:25.605744 INFO::Found 0 missing values.
2024-12-23 18:17:25.606162 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 18:17:25.607531 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 18:17:25.607707 INFO::Done
2024-12-23 18:17:25.607868 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 18:17:25.608807 INFO::Starting hierarchical adjustment
2024-12-23 18:17:25.608999 INFO::Found 2 batches.
2024-12-23 18:17:25.60915 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 18:17:25.609335 INFO::Using default BPPARAM
2024-12-23 18:17:25.609491 INFO::Adjusting the last 2 batches sequentially
2024-12-23 18:17:25.609749 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-23 18:17:25.615237 INFO::Done
2024-12-23 18:17:25.615468 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 18:17:25.61634 INFO::ASW Batch was 0.499905428121124 prior to batch effect correction and is now 0.116499511547309 .
2024-12-23 18:17:25.616566 INFO::ASW Label was 0.632695730407114 prior to batch effect correction and is now 0.864877323656102 .
2024-12-23 18:17:25.616892 INFO::Total function execution time is 0.0119400024414062 s and adjustment time is 0.00625205039978027 s ( 52.36 )
2024-12-23 18:17:25.617143 INFO::Formatting Data.
2024-12-23 18:17:25.617339 INFO::Replacing NaNs with NAs.
2024-12-23 18:17:25.617617 INFO::Removing potential empty rows and columns
2024-12-23 18:17:25.617928 INFO::Found 0 missing values.
2024-12-23 18:17:25.618213 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 18:17:25.619451 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 18:17:25.61963 INFO::Done
2024-12-23 18:17:25.619785 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 18:17:25.62063 INFO::Starting hierarchical adjustment
2024-12-23 18:17:25.620833 INFO::Found 2 batches.
2024-12-23 18:17:25.62099 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 18:17:25.621171 INFO::Using default BPPARAM
2024-12-23 18:17:25.62131 INFO::Adjusting the last 2 batches sequentially
2024-12-23 18:17:25.621556 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-23 18:17:25.627236 INFO::Done
2024-12-23 18:17:25.627476 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 18:17:25.628416 INFO::ASW Batch was 0.499905428121124 prior to batch effect correction and is now 0.116499511547309 .
2024-12-23 18:17:25.628654 INFO::ASW Label was 0.632695730407114 prior to batch effect correction and is now 0.864877323656102 .
2024-12-23 18:17:25.628896 INFO::Total function execution time is 0.0117428302764893 s and adjustment time is 0.00643706321716309 s ( 54.82 )
2024-12-23 18:17:25.704412 INFO::Formatting Data.
2024-12-23 18:17:25.704678 INFO::Replacing NaNs with NAs.
2024-12-23 18:17:25.704971 INFO::Removing potential empty rows and columns
2024-12-23 18:17:25.705293 INFO::Found 0 missing values.
2024-12-23 18:17:25.706173 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 18:17:25.706338 INFO::Done
2024-12-23 18:17:25.706486 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 18:17:25.707157 INFO::Starting hierarchical adjustment
2024-12-23 18:17:25.70737 INFO::Found 3 batches.
2024-12-23 18:17:25.707535 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 18:17:25.707726 INFO::Using default BPPARAM
2024-12-23 18:17:25.70788 INFO::Processing subtree level 1
2024-12-23 18:17:25.754958 INFO::Adjusting the last 1 batches sequentially
2024-12-23 18:17:25.756437 INFO::Done
2024-12-23 18:17:25.756663 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 18:17:25.758631 INFO::ASW Batch was -0.00828950226442872 prior to batch effect correction and is now -0.00828950226442872 .
2024-12-23 18:17:25.759352 INFO::Total function execution time is 0.0548300743103027 s and adjustment time is 0.0491011142730713 s ( 89.55 )
2024-12-23 18:17:25.759886 INFO::Formatting Data.
2024-12-23 18:17:25.760327 INFO::Typecasting input to dataframe.
2024-12-23 18:17:25.760641 INFO::Replacing NaNs with NAs.
2024-12-23 18:17:25.761167 INFO::Removing potential empty rows and columns
2024-12-23 18:17:25.761595 INFO::Found 0 missing values.
2024-12-23 18:17:25.762672 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 18:17:25.76286 INFO::Done
2024-12-23 18:17:25.763047 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 18:17:25.763739 INFO::Starting hierarchical adjustment
2024-12-23 18:17:25.763984 INFO::Found 3 batches.
2024-12-23 18:17:25.764167 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 18:17:25.764387 INFO::Using default BPPARAM
2024-12-23 18:17:25.764562 INFO::Processing subtree level 1
2024-12-23 18:17:25.80606 INFO::Adjusting the last 1 batches sequentially
2024-12-23 18:17:25.808161 INFO::Done
2024-12-23 18:17:25.808596 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 18:17:25.811048 INFO::ASW Batch was -0.00828950226442872 prior to batch effect correction and is now -0.00828950226442872 .
2024-12-23 18:17:25.811652 INFO::Total function execution time is 0.0517652034759521 s and adjustment time is 0.0442130565643311 s ( 85.41 )
2024-12-23 18:17:25.818185 INFO::Formatting Data.
2024-12-23 18:17:25.818435 INFO::Typecasting input to dataframe.
2024-12-23 18:17:25.818711 INFO::Replacing NaNs with NAs.
2024-12-23 18:17:25.819037 INFO::Removing potential empty rows and columns
2024-12-23 18:17:25.819497 INFO::Found 0 missing values.
2024-12-23 18:17:25.82072 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 18:17:25.820902 INFO::Done
2024-12-23 18:17:25.821075 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 18:17:25.822029 INFO::Starting hierarchical adjustment
2024-12-23 18:17:25.822266 INFO::Found 3 batches.
2024-12-23 18:17:25.822439 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 18:17:25.82268 INFO::Using default BPPARAM
2024-12-23 18:17:25.822859 INFO::Processing subtree level 1
2024-12-23 18:17:25.869559 INFO::Adjusting the last 1 batches sequentially
2024-12-23 18:17:25.87127 INFO::Done
2024-12-23 18:17:25.871724 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 18:17:25.873404 INFO::ASW Batch was -0.0318054490468961 prior to batch effect correction and is now -0.0318054490468961 .
2024-12-23 18:17:25.874083 INFO::Total function execution time is 0.0558979511260986 s and adjustment time is 0.0490539073944092 s ( 87.76 )
2024-12-23 18:17:25.946345 INFO::Formatting Data.
2024-12-23 18:17:25.946638 INFO::Replacing NaNs with NAs.
2024-12-23 18:17:25.947055 INFO::Removing potential empty rows and columns
2024-12-23 18:17:25.948359 INFO::Found 1000 missing values.
2024-12-23 18:17:25.956383 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 18:17:25.956697 INFO::Done
2024-12-23 18:17:25.956912 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 18:17:25.959357 INFO::Starting hierarchical adjustment
2024-12-23 18:17:25.959654 INFO::Found 10 batches.
2024-12-23 18:17:25.959854 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 18:17:25.960114 INFO::Using default BPPARAM
2024-12-23 18:17:25.960307 INFO::Processing subtree level 1
2024-12-23 18:17:26.028614 INFO::Processing subtree level 2
2024-12-23 18:17:26.092722 INFO::Adjusting the last 1 batches sequentially
2024-12-23 18:17:26.094388 INFO::Done
2024-12-23 18:17:26.09462 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 18:17:26.097433 INFO::ASW Batch was 0.430838456112433 prior to batch effect correction and is now 0.430838456112433 .
2024-12-23 18:17:26.097655 INFO::ASW Label was 0.386888784808189 prior to batch effect correction and is now 0.386888784808189 .
2024-12-23 18:17:26.098172 INFO::Total function execution time is 0.151834964752197 s and adjustment time is 0.134784936904907 s ( 88.77 )
2024-12-23 18:17:26.098473 INFO::Formatting Data.
2024-12-23 18:17:26.098665 INFO::Replacing NaNs with NAs.
2024-12-23 18:17:26.099222 INFO::Removing potential empty rows and columns
2024-12-23 18:17:26.10044 INFO::Found 1000 missing values.
2024-12-23 18:17:26.106506 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 18:17:26.106698 INFO::Done
2024-12-23 18:17:26.106869 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 18:17:26.108794 INFO::Starting hierarchical adjustment
2024-12-23 18:17:26.109272 INFO::Found 10 batches.
2024-12-23 18:17:26.52222 INFO::Set up parallel execution backend with 2 workers
2024-12-23 18:17:26.52251 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-12-23 18:17:26.987539 INFO::Adjusting the last 2 batches sequentially
2024-12-23 18:17:26.98806 INFO::Adjusting sequential tree level 1 with 2 batches
2024-12-23 18:17:26.993299 INFO::Done
2024-12-23 18:17:26.993493 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 18:17:26.995259 INFO::ASW Batch was 0.430838456112433 prior to batch effect correction and is now 0.430838456112433 .
2024-12-23 18:17:26.995431 INFO::ASW Label was 0.386888784808189 prior to batch effect correction and is now 0.386888784808189 .
2024-12-23 18:17:26.99564 INFO::Total function execution time is 0.89717698097229 s and adjustment time is 0.884109020233154 s ( 98.54 )
2024-12-23 18:17:27.062887 INFO::Formatting Data.
2024-12-23 18:17:27.063264 INFO::Replacing NaNs with NAs.
2024-12-23 18:17:27.063699 INFO::Removing potential empty rows and columns
2024-12-23 18:17:27.06414 INFO::Found 0 missing values.
2024-12-23 18:17:27.065453 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 18:17:27.065636 INFO::Done
2024-12-23 18:17:27.065813 INFO::Acquiring quality metrics before batch effect correction.
2024-12-23 18:17:27.066783 INFO::Starting hierarchical adjustment
2024-12-23 18:17:27.067018 INFO::Found 3 batches.
2024-12-23 18:17:27.067183 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-12-23 18:17:27.067419 INFO::Using default BPPARAM
2024-12-23 18:17:27.067591 INFO::Processing subtree level 1
2024-12-23 18:17:27.122201 INFO::Adjusting the last 1 batches sequentially
2024-12-23 18:17:27.123549 INFO::Done
2024-12-23 18:17:27.123757 INFO::Acquiring quality metrics after batch effect correction.
2024-12-23 18:17:27.125457 INFO::ASW Batch was 0.127817003264256 prior to batch effect correction and is now -0.121595804051541 .
2024-12-23 18:17:27.12568 INFO::ASW Label was -0.154928296584551 prior to batch effect correction and is now 0.0172718240539312 .
2024-12-23 18:17:27.126218 INFO::Total function execution time is 0.0633299350738525 s and adjustment time is 0.0565710067749023 s ( 89.33 )
2024-12-23 18:17:27.17364 INFO::Formatting Data.
2024-12-23 18:17:27.173976 INFO::Replacing NaNs with NAs.
2024-12-23 18:17:27.174325 INFO::Removing potential empty rows and columns
2024-12-23 18:17:27.174747 INFO::Found 2 missing values.
2024-12-23 18:17:27.175809 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-12-23 18:17:27.175998 INFO::Done
2024-12-23 18:17:27.187347 INFO::Found NA in Reference column
2024-12-23 18:17:27.190813 INFO::Require at least two references per batch.
2024-12-23 18:17:27.198838 INFO::Formatting Data.
2024-12-23 18:17:27.199105 INFO::Recognized SummarizedExperiment
2024-12-23 18:17:27.199293 INFO::Typecasting input to dataframe.
2024-12-23 18:17:27.203404 INFO::Replacing NaNs with NAs.
2024-12-23 18:17:27.203827 INFO::Removing potential empty rows and columns
2024-12-23 18:17:27.205089 INFO::Found 0 missing values.
2024-12-23 18:17:27.207491 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 18:17:27.207688 INFO::Done
2024-12-23 18:17:27.213434 INFO::Formatting Data.
2024-12-23 18:17:27.213687 INFO::Recognized SummarizedExperiment
2024-12-23 18:17:27.213863 INFO::Typecasting input to dataframe.
2024-12-23 18:17:27.219733 INFO::Replacing NaNs with NAs.
2024-12-23 18:17:27.220165 INFO::Removing potential empty rows and columns
2024-12-23 18:17:27.221521 INFO::Found 0 missing values.
2024-12-23 18:17:27.225839 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 18:17:27.226103 INFO::Done
2024-12-23 18:17:27.232482 INFO::Formatting Data.
2024-12-23 18:17:27.232799 INFO::Recognized SummarizedExperiment
2024-12-23 18:17:27.232985 INFO::Typecasting input to dataframe.
2024-12-23 18:17:27.238582 INFO::Replacing NaNs with NAs.
2024-12-23 18:17:27.238956 INFO::Removing potential empty rows and columns
2024-12-23 18:17:27.239343 INFO::Found 0 missing values.
2024-12-23 18:17:27.23966 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 18:17:27.24106 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 18:17:27.241249 INFO::Done
2024-12-23 18:17:27.245271 INFO::Formatting Data.
2024-12-23 18:17:27.245519 INFO::Replacing NaNs with NAs.
2024-12-23 18:17:27.24578 INFO::Removing potential empty rows and columns
2024-12-23 18:17:27.246075 INFO::Found 0 missing values.
2024-12-23 18:17:27.246916 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 18:17:27.247069 INFO::Done
2024-12-23 18:17:27.251529 INFO::Formatting Data.
2024-12-23 18:17:27.251768 INFO::Replacing NaNs with NAs.
2024-12-23 18:17:27.252022 INFO::Removing potential empty rows and columns
2024-12-23 18:17:27.252309 INFO::Found 0 missing values.
2024-12-23 18:17:27.253135 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 18:17:27.253289 INFO::Done
2024-12-23 18:17:27.264589 INFO::Formatting Data.
2024-12-23 18:17:27.264868 INFO::Replacing NaNs with NAs.
2024-12-23 18:17:27.26518 INFO::Removing potential empty rows and columns
2024-12-23 18:17:27.265611 INFO::Found 1 missing values.
2024-12-23 18:17:27.266446 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 18:17:27.266613 INFO::Done
2024-12-23 18:17:27.274037 INFO::Formatting Data.
2024-12-23 18:17:27.274292 INFO::Replacing NaNs with NAs.
2024-12-23 18:17:27.274557 INFO::Removing potential empty rows and columns
2024-12-23 18:17:27.274952 INFO::Found 2 missing values.
2024-12-23 18:17:27.275229 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 18:17:27.27595 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-12-23 18:17:27.276112 INFO::Done
2024-12-23 18:17:27.280157 INFO::Formatting Data.
2024-12-23 18:17:27.28042 INFO::Replacing NaNs with NAs.
2024-12-23 18:17:27.280687 INFO::Removing potential empty rows and columns
2024-12-23 18:17:27.28095 INFO::Found 2 missing values.
2024-12-23 18:17:27.281441 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 18:17:27.281589 INFO::Done
2024-12-23 18:17:27.285314 INFO::Formatting Data.
2024-12-23 18:17:27.285541 INFO::Typecasting input to dataframe.
2024-12-23 18:17:27.285778 INFO::Replacing NaNs with NAs.
2024-12-23 18:17:27.286041 INFO::Removing potential empty rows and columns
2024-12-23 18:17:27.286388 INFO::Found 0 missing values.
2024-12-23 18:17:27.28724 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-12-23 18:17:27.287411 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 138 ]
>
> proc.time()
user system elapsed
6.603 1.445 8.203
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 9.916 | 0.381 | 7.110 | |
| compute_asw | 0.01 | 0.00 | 0.01 | |
| count_existing | 0.005 | 0.001 | 0.006 | |
| generate_data_covariables | 0.005 | 0.000 | 0.005 | |
| generate_dataset | 0.004 | 0.001 | 0.005 | |