Yannis Schumann
| Snapshot Date: 2024-06-19 14:00 -0400 (Wed, 19 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: RELEASE_3_19 |
| git_last_commit: 9a6bbaa |
| git_last_commit_date: 2024-04-30 11:53:11 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-21 17:38 -0400 (Fri, 21 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4758 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4492 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4506 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
| 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 156/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.0.0 (landing page) Yannis Schumann
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.0.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BERT_1.0.0.tar.gz |
| StartedAt: 2024-06-19 20:52:31 -0400 (Wed, 19 Jun 2024) |
| EndedAt: 2024-06-19 20:53:56 -0400 (Wed, 19 Jun 2024) |
| EllapsedTime: 85.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BERT_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/BERT.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘BERT/DESCRIPTION’ ... OK
* this is package ‘BERT’ version ‘1.0.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking 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 ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BERT 23.518 1.45 17.151
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘BERT’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BERT)
BERT.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(BERT)
>
> test_check("BERT")
2024-06-19 20:53:21.859497 INFO::Formatting Data.
2024-06-19 20:53:21.860929 INFO::Replacing NaNs with NAs.
2024-06-19 20:53:21.871327 INFO::Removing potential empty rows and columns
2024-06-19 20:53:22.120024 INFO::Found 0 missing values.
2024-06-19 20:53:22.123468 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-19 20:53:22.124117 INFO::Done
2024-06-19 20:53:22.124634 INFO::Acquiring quality metrics before batch effect correction.
2024-06-19 20:53:22.136985 INFO::Starting hierarchical adjustment
2024-06-19 20:53:22.137838 INFO::Found 3 batches.
2024-06-19 20:53:22.138353 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-19 20:53:22.139461 INFO::Using default BPPARAM
2024-06-19 20:53:22.139986 INFO::Processing subtree level 1
2024-06-19 20:53:22.231229 INFO::Adjusting the last 1 batches sequentially
2024-06-19 20:53:22.232922 INFO::Done
2024-06-19 20:53:22.233581 INFO::Acquiring quality metrics after batch effect correction.
2024-06-19 20:53:22.236042 INFO::ASW Batch was -0.155483680962165 prior to batch effect correction and is now -0.155483680962165 .
2024-06-19 20:53:22.237097 INFO::Total function execution time is 0.378416538238525 s and adjustment time is 0.0952627658843994 s ( 25.17 )
2024-06-19 20:53:22.251542 INFO::Formatting Data.
2024-06-19 20:53:22.252325 INFO::Replacing NaNs with NAs.
2024-06-19 20:53:22.253215 INFO::Removing potential empty rows and columns
2024-06-19 20:53:22.254307 INFO::Found 0 missing values.
2024-06-19 20:53:22.255283 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.
2024-06-19 20:53:22.266542 INFO::Formatting Data.
2024-06-19 20:53:22.267428 INFO::Replacing NaNs with NAs.
2024-06-19 20:53:22.268365 INFO::Removing potential empty rows and columns
2024-06-19 20:53:22.269474 INFO::Found 0 missing values.
2024-06-19 20:53:22.270407 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.
2024-06-19 20:53:22.286223 INFO::Formatting Data.
2024-06-19 20:53:22.286961 INFO::Replacing NaNs with NAs.
2024-06-19 20:53:22.287794 INFO::Removing potential empty rows and columns
2024-06-19 20:53:22.288768 INFO::Found 0 missing values.
2024-06-19 20:53:22.289612 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.
2024-06-19 20:53:22.293799 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-19 20:53:22.294335 INFO::Done
2024-06-19 20:53:22.294857 INFO::Acquiring quality metrics before batch effect correction.
2024-06-19 20:53:22.29673 INFO::Starting hierarchical adjustment
2024-06-19 20:53:22.297397 INFO::Found 2 batches.
2024-06-19 20:53:22.297889 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-19 20:53:22.298487 INFO::Using default BPPARAM
2024-06-19 20:53:22.299006 INFO::Adjusting the last 2 batches sequentially
2024-06-19 20:53:22.299888 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-19 20:53:22.321125 INFO::Done
2024-06-19 20:53:22.321792 INFO::Acquiring quality metrics after batch effect correction.
2024-06-19 20:53:22.323711 INFO::ASW Batch was 0.0423338369658966 prior to batch effect correction and is now -0.119315750110404 .
2024-06-19 20:53:22.324468 INFO::Total function execution time is 0.0383017063140869 s and adjustment time is 0.0238337516784668 s ( 62.23 )
2024-06-19 20:53:22.327111 INFO::Formatting Data.
2024-06-19 20:53:22.327724 INFO::Replacing NaNs with NAs.
2024-06-19 20:53:22.336179 INFO::Formatting Data.
2024-06-19 20:53:22.3369 INFO::Replacing NaNs with NAs.
2024-06-19 20:53:22.337748 INFO::Removing potential empty rows and columns
2024-06-19 20:53:22.338746 INFO::Found 0 missing values.
2024-06-19 20:53:22.341474 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-19 20:53:22.341991 INFO::Done
2024-06-19 20:53:22.34249 INFO::Acquiring quality metrics before batch effect correction.
2024-06-19 20:53:22.344406 INFO::Starting hierarchical adjustment
2024-06-19 20:53:22.345082 INFO::Found 2 batches.
2024-06-19 20:53:22.345587 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-19 20:53:22.346169 INFO::Using default BPPARAM
2024-06-19 20:53:22.346696 INFO::Adjusting the last 2 batches sequentially
2024-06-19 20:53:22.34757 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-19 20:53:22.361784 INFO::Done
2024-06-19 20:53:22.362425 INFO::Acquiring quality metrics after batch effect correction.
2024-06-19 20:53:22.364321 INFO::ASW Batch was -0.0324334071096038 prior to batch effect correction and is now -0.122886234210351 .
2024-06-19 20:53:22.365049 INFO::Total function execution time is 0.0289230346679688 s and adjustment time is 0.0168156623840332 s ( 58.14 )
2024-06-19 20:53:22.366076 INFO::Formatting Data.
2024-06-19 20:53:22.366665 INFO::Replacing NaNs with NAs.
2024-06-19 20:53:22.367489 INFO::Removing potential empty rows and columns
2024-06-19 20:53:22.368465 INFO::Found 0 missing values.
2024-06-19 20:53:22.371174 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-19 20:53:22.371673 INFO::Done
2024-06-19 20:53:22.372166 INFO::Acquiring quality metrics before batch effect correction.
2024-06-19 20:53:22.374035 INFO::Starting hierarchical adjustment
2024-06-19 20:53:22.374705 INFO::Found 2 batches.
2024-06-19 20:53:22.375213 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-19 20:53:22.375778 INFO::Using default BPPARAM
2024-06-19 20:53:22.376283 INFO::Adjusting the last 2 batches sequentially
2024-06-19 20:53:22.377132 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-19 20:53:22.391428 INFO::Done
2024-06-19 20:53:22.392072 INFO::Acquiring quality metrics after batch effect correction.
2024-06-19 20:53:22.393963 INFO::ASW Batch was -0.0324334071096038 prior to batch effect correction and is now -0.122886234210351 .
2024-06-19 20:53:22.394705 INFO::Total function execution time is 0.0286257266998291 s and adjustment time is 0.016848087310791 s ( 58.86 )
2024-06-19 20:53:24.538868 INFO::Formatting Data.
2024-06-19 20:53:24.539628 INFO::Recognized SummarizedExperiment
2024-06-19 20:53:24.540128 INFO::Typecasting input to dataframe.
2024-06-19 20:53:24.570633 INFO::Replacing NaNs with NAs.
2024-06-19 20:53:24.571752 INFO::Removing potential empty rows and columns
2024-06-19 20:53:24.575022 INFO::Found 0 missing values.
2024-06-19 20:53:24.581001 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-19 20:53:24.581506 INFO::Done
2024-06-19 20:53:24.581978 INFO::Acquiring quality metrics before batch effect correction.
2024-06-19 20:53:24.585315 INFO::Starting hierarchical adjustment
2024-06-19 20:53:24.58594 INFO::Found 2 batches.
2024-06-19 20:53:24.586401 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-19 20:53:24.58743 INFO::Using default BPPARAM
2024-06-19 20:53:24.587921 INFO::Adjusting the last 2 batches sequentially
2024-06-19 20:53:24.588801 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-19 20:53:24.670101 INFO::Done
2024-06-19 20:53:24.670821 INFO::Acquiring quality metrics after batch effect correction.
2024-06-19 20:53:24.673761 INFO::ASW Batch was -0.000961022364527974 prior to batch effect correction and is now -0.0911611033259906 .
2024-06-19 20:53:24.674513 INFO::Total function execution time is 0.136007308959961 s and adjustment time is 0.0842511653900146 s ( 61.95 )
2024-06-19 20:53:24.68904 INFO::Formatting Data.
2024-06-19 20:53:24.689699 INFO::Recognized SummarizedExperiment
2024-06-19 20:53:24.690152 INFO::Typecasting input to dataframe.
2024-06-19 20:53:24.697604 INFO::Replacing NaNs with NAs.
2024-06-19 20:53:24.698621 INFO::Removing potential empty rows and columns
2024-06-19 20:53:24.701406 INFO::Found 0 missing values.
2024-06-19 20:53:24.706684 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-19 20:53:24.70716 INFO::Done
2024-06-19 20:53:24.70759 INFO::Acquiring quality metrics before batch effect correction.
2024-06-19 20:53:24.710351 INFO::Starting hierarchical adjustment
2024-06-19 20:53:24.710995 INFO::Found 2 batches.
2024-06-19 20:53:24.711439 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-19 20:53:24.711937 INFO::Using default BPPARAM
2024-06-19 20:53:24.712384 INFO::Adjusting the last 2 batches sequentially
2024-06-19 20:53:24.713205 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-19 20:53:24.732135 INFO::Done
2024-06-19 20:53:24.732673 INFO::Acquiring quality metrics after batch effect correction.
2024-06-19 20:53:24.735466 INFO::ASW Batch was -0.00331414529430172 prior to batch effect correction and is now -0.00331414529430172 .
2024-06-19 20:53:24.736152 INFO::Total function execution time is 0.0471000671386719 s and adjustment time is 0.0212633609771729 s ( 45.15 )
2024-06-19 20:53:24.750249 INFO::Formatting Data.
2024-06-19 20:53:24.750869 INFO::Replacing NaNs with NAs.
2024-06-19 20:53:24.751598 INFO::Removing potential empty rows and columns
2024-06-19 20:53:24.752423 INFO::Found 0 missing values.
2024-06-19 20:53:24.754741 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-19 20:53:24.755189 INFO::Done
2024-06-19 20:53:24.755622 INFO::Acquiring quality metrics before batch effect correction.
2024-06-19 20:53:24.757243 INFO::Starting hierarchical adjustment
2024-06-19 20:53:24.757818 INFO::Found 3 batches.
2024-06-19 20:53:24.758251 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-19 20:53:24.758777 INFO::Using default BPPARAM
2024-06-19 20:53:24.759215 INFO::Processing subtree level 1
2024-06-19 20:53:24.90902 INFO::Adjusting the last 1 batches sequentially
2024-06-19 20:53:24.910652 INFO::Done
2024-06-19 20:53:24.911232 INFO::Acquiring quality metrics after batch effect correction.
2024-06-19 20:53:24.913549 INFO::ASW Batch was -0.146296460108486 prior to batch effect correction and is now -0.170784589722826 .
2024-06-19 20:53:24.914438 INFO::Total function execution time is 0.164155960083008 s and adjustment time is 0.152916193008423 s ( 93.15 )
2024-06-19 20:53:24.92856 INFO::Skipping initial DF formatting
2024-06-19 20:53:24.929233 INFO::Acquiring quality metrics before batch effect correction.
2024-06-19 20:53:24.933184 INFO::Starting hierarchical adjustment
2024-06-19 20:53:24.933946 INFO::Found 5 batches.
2024-06-19 20:53:24.934463 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-19 20:53:24.935107 INFO::Using default BPPARAM
2024-06-19 20:53:24.935632 INFO::Processing subtree level 1
2024-06-19 20:53:25.090133 INFO::Adjusting the last 2 batches sequentially
2024-06-19 20:53:25.092098 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-19 20:53:25.117085 INFO::Done
2024-06-19 20:53:25.117874 INFO::Acquiring quality metrics after batch effect correction.
2024-06-19 20:53:25.122729 INFO::ASW Batch was 0.536614543887618 prior to batch effect correction and is now 0.536614543887618 .
2024-06-19 20:53:25.123535 INFO::ASW Label was 0.376291063691046 prior to batch effect correction and is now 0.376291063691046 .
2024-06-19 20:53:25.124843 INFO::Total function execution time is 0.196300745010376 s and adjustment time is 0.183260679244995 s ( 93.36 )
2024-06-19 20:53:25.144241 INFO::Formatting Data.
2024-06-19 20:53:25.145019 INFO::Replacing NaNs with NAs.
2024-06-19 20:53:25.14593 INFO::Removing potential empty rows and columns
2024-06-19 20:53:25.14695 INFO::Found 0 missing values.
2024-06-19 20:53:25.150986 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-19 20:53:25.151526 INFO::Done
2024-06-19 20:53:25.15207 INFO::Acquiring quality metrics before batch effect correction.
2024-06-19 20:53:25.155139 INFO::Starting hierarchical adjustment
2024-06-19 20:53:25.155881 INFO::Found 5 batches.
2024-06-19 20:53:25.156423 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-19 20:53:25.157076 INFO::Using default BPPARAM
2024-06-19 20:53:25.157643 INFO::Processing subtree level 1
2024-06-19 20:53:25.280527 INFO::Adjusting the last 2 batches sequentially
2024-06-19 20:53:25.282379 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-19 20:53:25.299027 INFO::Done
2024-06-19 20:53:25.299861 INFO::Acquiring quality metrics after batch effect correction.
2024-06-19 20:53:25.303351 INFO::ASW Batch was 0.278298783784937 prior to batch effect correction and is now -0.0333165947968927 .
2024-06-19 20:53:25.304029 INFO::ASW Label was 0.465453626554492 prior to batch effect correction and is now 0.851543106272999 .
2024-06-19 20:53:25.304913 INFO::Total function execution time is 0.160707235336304 s and adjustment time is 0.14326286315918 s ( 89.15 )
2024-06-19 20:53:25.305836 INFO::Formatting Data.
2024-06-19 20:53:25.306478 INFO::Replacing NaNs with NAs.
2024-06-19 20:53:25.307441 INFO::Removing potential empty rows and columns
2024-06-19 20:53:25.308422 INFO::Found 0 missing values.
2024-06-19 20:53:25.312415 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-19 20:53:25.312968 INFO::Done
2024-06-19 20:53:25.313473 INFO::Acquiring quality metrics before batch effect correction.
2024-06-19 20:53:25.316573 INFO::Starting hierarchical adjustment
2024-06-19 20:53:25.317306 INFO::Found 5 batches.
2024-06-19 20:53:25.317832 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-19 20:53:25.318469 INFO::Using default BPPARAM
2024-06-19 20:53:25.31901 INFO::Processing subtree level 1
2024-06-19 20:53:25.450436 INFO::Adjusting the last 2 batches sequentially
2024-06-19 20:53:25.45274 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-19 20:53:25.475821 INFO::Done
2024-06-19 20:53:25.476859 INFO::Acquiring quality metrics after batch effect correction.
2024-06-19 20:53:25.481804 INFO::ASW Batch was 0.278298783784937 prior to batch effect correction and is now -0.0333165947968927 .
2024-06-19 20:53:25.482729 INFO::ASW Label was 0.465453626554492 prior to batch effect correction and is now 0.851543106272999 .
2024-06-19 20:53:25.484003 INFO::Total function execution time is 0.17812705039978 s and adjustment time is 0.1586012840271 s ( 89.04 )
2024-06-19 20:53:25.504569 INFO::Formatting Data.
2024-06-19 20:53:25.505668 INFO::Replacing NaNs with NAs.
2024-06-19 20:53:25.507046 INFO::Removing potential empty rows and columns
2024-06-19 20:53:25.508648 INFO::Found 0 missing values.
2024-06-19 20:53:25.515976 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-19 20:53:25.516941 INFO::Done
2024-06-19 20:53:25.517841 INFO::Acquiring quality metrics before batch effect correction.
2024-06-19 20:53:25.522797 INFO::Starting hierarchical adjustment
2024-06-19 20:53:25.523903 INFO::Found 5 batches.
2024-06-19 20:53:25.524742 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-19 20:53:25.52575 INFO::Using default BPPARAM
2024-06-19 20:53:25.526595 INFO::Processing subtree level 1
2024-06-19 20:53:25.667638 INFO::Adjusting the last 2 batches sequentially
2024-06-19 20:53:25.669369 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-19 20:53:25.685596 INFO::Done
2024-06-19 20:53:25.686394 INFO::Acquiring quality metrics after batch effect correction.
2024-06-19 20:53:25.689795 INFO::ASW Batch was 0.339765495562671 prior to batch effect correction and is now -0.105042721186485 .
2024-06-19 20:53:25.690441 INFO::ASW Label was 0.388370957443249 prior to batch effect correction and is now 0.805368035788588 .
2024-06-19 20:53:25.691304 INFO::Total function execution time is 0.186910390853882 s and adjustment time is 0.16194224357605 s ( 86.64 )
2024-06-19 20:53:25.692173 INFO::Formatting Data.
2024-06-19 20:53:25.69283 INFO::Replacing NaNs with NAs.
2024-06-19 20:53:25.693724 INFO::Removing potential empty rows and columns
2024-06-19 20:53:25.694845 INFO::Found 0 missing values.
2024-06-19 20:53:25.698862 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-19 20:53:25.69939 INFO::Done
2024-06-19 20:53:25.699895 INFO::Acquiring quality metrics before batch effect correction.
2024-06-19 20:53:25.702843 INFO::Starting hierarchical adjustment
2024-06-19 20:53:25.703577 INFO::Found 5 batches.
2024-06-19 20:53:25.704074 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-19 20:53:25.704683 INFO::Using default BPPARAM
2024-06-19 20:53:25.705207 INFO::Processing subtree level 1
2024-06-19 20:53:25.825083 INFO::Adjusting the last 2 batches sequentially
2024-06-19 20:53:25.827404 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-19 20:53:25.851597 INFO::Done
2024-06-19 20:53:25.85265 INFO::Acquiring quality metrics after batch effect correction.
2024-06-19 20:53:25.857712 INFO::ASW Batch was 0.339765495562671 prior to batch effect correction and is now -0.105042721186485 .
2024-06-19 20:53:25.858639 INFO::ASW Label was 0.388370957443249 prior to batch effect correction and is now 0.805368035788588 .
2024-06-19 20:53:25.859884 INFO::Total function execution time is 0.167618751525879 s and adjustment time is 0.148061752319336 s ( 88.33 )
2024-06-19 20:53:25.880275 INFO::Formatting Data.
2024-06-19 20:53:25.881455 INFO::Replacing NaNs with NAs.
2024-06-19 20:53:25.882916 INFO::Removing potential empty rows and columns
2024-06-19 20:53:25.884484 INFO::Found 0 missing values.
2024-06-19 20:53:25.888853 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-19 20:53:25.889682 INFO::Done
2024-06-19 20:53:25.890496 INFO::Acquiring quality metrics before batch effect correction.
2024-06-19 20:53:25.895163 INFO::Starting hierarchical adjustment
2024-06-19 20:53:25.89626 INFO::Found 2 batches.
2024-06-19 20:53:25.897093 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-19 20:53:25.898058 INFO::Using default BPPARAM
2024-06-19 20:53:25.898919 INFO::Adjusting the last 2 batches sequentially
2024-06-19 20:53:25.900318 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-19 20:53:25.930498 INFO::Done
2024-06-19 20:53:25.93177 INFO::Acquiring quality metrics after batch effect correction.
2024-06-19 20:53:25.936703 INFO::ASW Batch was 0.352285804433305 prior to batch effect correction and is now 0.0358342251879359 .
2024-06-19 20:53:25.937554 INFO::ASW Label was 0.703698229586275 prior to batch effect correction and is now 0.906431467737857 .
2024-06-19 20:53:25.938698 INFO::Total function execution time is 0.0584983825683594 s and adjustment time is 0.0343785285949707 s ( 58.77 )
2024-06-19 20:53:25.939979 INFO::Formatting Data.
2024-06-19 20:53:25.940917 INFO::Replacing NaNs with NAs.
2024-06-19 20:53:25.94213 INFO::Removing potential empty rows and columns
2024-06-19 20:53:25.943456 INFO::Found 0 missing values.
2024-06-19 20:53:25.946232 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-19 20:53:25.946818 INFO::Done
2024-06-19 20:53:25.947345 INFO::Acquiring quality metrics before batch effect correction.
2024-06-19 20:53:25.950274 INFO::Starting hierarchical adjustment
2024-06-19 20:53:25.95097 INFO::Found 2 batches.
2024-06-19 20:53:25.951472 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-19 20:53:25.952092 INFO::Using default BPPARAM
2024-06-19 20:53:25.952631 INFO::Adjusting the last 2 batches sequentially
2024-06-19 20:53:25.953515 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-19 20:53:25.96816 INFO::Done
2024-06-19 20:53:25.968816 INFO::Acquiring quality metrics after batch effect correction.
2024-06-19 20:53:25.971647 INFO::ASW Batch was 0.352285804433305 prior to batch effect correction and is now 0.0358342251879359 .
2024-06-19 20:53:25.972196 INFO::ASW Label was 0.703698229586275 prior to batch effect correction and is now 0.906431467737857 .
2024-06-19 20:53:25.972946 INFO::Total function execution time is 0.0330872535705566 s and adjustment time is 0.0173354148864746 s ( 52.39 )
2024-06-19 20:53:25.983673 INFO::Formatting Data.
2024-06-19 20:53:25.984392 INFO::Replacing NaNs with NAs.
2024-06-19 20:53:25.985242 INFO::Removing potential empty rows and columns
2024-06-19 20:53:25.986084 INFO::Found 0 missing values.
2024-06-19 20:53:25.988082 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-19 20:53:25.988614 INFO::Done
2024-06-19 20:53:25.989138 INFO::Acquiring quality metrics before batch effect correction.
2024-06-19 20:53:25.991009 INFO::Starting hierarchical adjustment
2024-06-19 20:53:25.991711 INFO::Found 2 batches.
2024-06-19 20:53:25.992233 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-19 20:53:25.992837 INFO::Using default BPPARAM
2024-06-19 20:53:25.993335 INFO::Adjusting the last 2 batches sequentially
2024-06-19 20:53:25.994238 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-19 20:53:26.026366 INFO::Done
2024-06-19 20:53:26.027074 INFO::Acquiring quality metrics after batch effect correction.
2024-06-19 20:53:26.029008 INFO::ASW Batch was -0.0576077267001269 prior to batch effect correction and is now -0.12845704998678 .
2024-06-19 20:53:26.029775 INFO::Total function execution time is 0.0461735725402832 s and adjustment time is 0.0347750186920166 s ( 75.31 )
2024-06-19 20:53:26.041436 INFO::Formatting Data.
2024-06-19 20:53:26.042216 INFO::Replacing NaNs with NAs.
2024-06-19 20:53:26.043104 INFO::Removing potential empty rows and columns
2024-06-19 20:53:26.044066 INFO::Found 0 missing values.
2024-06-19 20:53:26.04525 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.
2024-06-19 20:53:26.071806 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-19 20:53:26.072504 INFO::Done
2024-06-19 20:53:26.073078 INFO::Acquiring quality metrics before batch effect correction.
2024-06-19 20:53:26.076071 INFO::Starting hierarchical adjustment
2024-06-19 20:53:26.076798 INFO::Found 2 batches.
2024-06-19 20:53:26.077332 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-19 20:53:26.077919 INFO::Using default BPPARAM
2024-06-19 20:53:26.078436 INFO::Adjusting the last 2 batches sequentially
2024-06-19 20:53:26.079422 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-19 20:53:26.096909 INFO::Done
2024-06-19 20:53:26.097569 INFO::Acquiring quality metrics after batch effect correction.
2024-06-19 20:53:26.100538 INFO::ASW Batch was 0.307095009169851 prior to batch effect correction and is now 0.109097417639093 .
2024-06-19 20:53:26.101093 INFO::ASW Label was 0.767816773481594 prior to batch effect correction and is now 0.857578808783255 .
2024-06-19 20:53:26.101807 INFO::Total function execution time is 0.0604524612426758 s and adjustment time is 0.0202474594116211 s ( 33.49 )
2024-06-19 20:53:26.102581 INFO::Formatting Data.
2024-06-19 20:53:26.10319 INFO::Replacing NaNs with NAs.
2024-06-19 20:53:26.104109 INFO::Removing potential empty rows and columns
2024-06-19 20:53:26.105067 INFO::Found 0 missing values.
2024-06-19 20:53:26.10596 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.
2024-06-19 20:53:26.110805 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-19 20:53:26.111359 INFO::Done
2024-06-19 20:53:26.11188 INFO::Acquiring quality metrics before batch effect correction.
2024-06-19 20:53:26.114934 INFO::Starting hierarchical adjustment
2024-06-19 20:53:26.115633 INFO::Found 2 batches.
2024-06-19 20:53:26.116181 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-19 20:53:26.116808 INFO::Using default BPPARAM
2024-06-19 20:53:26.117335 INFO::Adjusting the last 2 batches sequentially
2024-06-19 20:53:26.118282 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-19 20:53:26.135834 INFO::Done
2024-06-19 20:53:26.136505 INFO::Acquiring quality metrics after batch effect correction.
2024-06-19 20:53:26.139525 INFO::ASW Batch was 0.307095009169851 prior to batch effect correction and is now 0.109097417639093 .
2024-06-19 20:53:26.140145 INFO::ASW Label was 0.767816773481594 prior to batch effect correction and is now 0.857578808783255 .
2024-06-19 20:53:26.140935 INFO::Total function execution time is 0.038358211517334 s and adjustment time is 0.0203342437744141 s ( 53.01 )
2024-06-19 20:53:26.345145 INFO::Formatting Data.
2024-06-19 20:53:26.345926 INFO::Replacing NaNs with NAs.
2024-06-19 20:53:26.346818 INFO::Removing potential empty rows and columns
2024-06-19 20:53:26.347857 INFO::Found 0 missing values.
2024-06-19 20:53:26.350891 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-19 20:53:26.351424 INFO::Done
2024-06-19 20:53:26.351937 INFO::Acquiring quality metrics before batch effect correction.
2024-06-19 20:53:26.353969 INFO::Starting hierarchical adjustment
2024-06-19 20:53:26.354694 INFO::Found 3 batches.
2024-06-19 20:53:26.355215 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-19 20:53:26.355807 INFO::Using default BPPARAM
2024-06-19 20:53:26.356339 INFO::Processing subtree level 1
2024-06-19 20:53:26.452747 INFO::Adjusting the last 1 batches sequentially
2024-06-19 20:53:26.454589 INFO::Done
2024-06-19 20:53:26.455244 INFO::Acquiring quality metrics after batch effect correction.
2024-06-19 20:53:26.457745 INFO::ASW Batch was -0.0490950755347141 prior to batch effect correction and is now -0.0490950755347141 .
2024-06-19 20:53:26.460924 INFO::Total function execution time is 0.113586187362671 s and adjustment time is 0.100042581558228 s ( 88.08 )
2024-06-19 20:53:26.462559 INFO::Formatting Data.
2024-06-19 20:53:26.463453 INFO::Typecasting input to dataframe.
2024-06-19 20:53:26.464435 INFO::Replacing NaNs with NAs.
2024-06-19 20:53:26.46572 INFO::Removing potential empty rows and columns
2024-06-19 20:53:26.467191 INFO::Found 0 missing values.
2024-06-19 20:53:26.470799 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-19 20:53:26.471405 INFO::Done
2024-06-19 20:53:26.472044 INFO::Acquiring quality metrics before batch effect correction.
2024-06-19 20:53:26.474283 INFO::Starting hierarchical adjustment
2024-06-19 20:53:26.475108 INFO::Found 3 batches.
2024-06-19 20:53:26.475687 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-19 20:53:26.476398 INFO::Using default BPPARAM
2024-06-19 20:53:26.477061 INFO::Processing subtree level 1
2024-06-19 20:53:26.576017 INFO::Adjusting the last 1 batches sequentially
2024-06-19 20:53:26.577897 INFO::Done
2024-06-19 20:53:26.578567 INFO::Acquiring quality metrics after batch effect correction.
2024-06-19 20:53:26.581167 INFO::ASW Batch was -0.0490950755347141 prior to batch effect correction and is now -0.0490950755347141 .
2024-06-19 20:53:26.582147 INFO::Total function execution time is 0.119665861129761 s and adjustment time is 0.102937459945679 s ( 86.02 )
2024-06-19 20:53:26.597697 INFO::Formatting Data.
2024-06-19 20:53:26.598794 INFO::Typecasting input to dataframe.
2024-06-19 20:53:26.599874 INFO::Replacing NaNs with NAs.
2024-06-19 20:53:26.600967 INFO::Removing potential empty rows and columns
2024-06-19 20:53:26.602427 INFO::Found 0 missing values.
2024-06-19 20:53:26.606748 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-19 20:53:26.607455 INFO::Done
2024-06-19 20:53:26.608122 INFO::Acquiring quality metrics before batch effect correction.
2024-06-19 20:53:26.610668 INFO::Starting hierarchical adjustment
2024-06-19 20:53:26.611531 INFO::Found 3 batches.
2024-06-19 20:53:26.612172 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-19 20:53:26.61293 INFO::Using default BPPARAM
2024-06-19 20:53:26.613546 INFO::Processing subtree level 1
2024-06-19 20:53:26.705217 INFO::Adjusting the last 1 batches sequentially
2024-06-19 20:53:26.707008 INFO::Done
2024-06-19 20:53:26.707649 INFO::Acquiring quality metrics after batch effect correction.
2024-06-19 20:53:26.710097 INFO::ASW Batch was -0.00627787467701339 prior to batch effect correction and is now -0.00627787467701339 .
2024-06-19 20:53:26.71106 INFO::Total function execution time is 0.113523960113525 s and adjustment time is 0.0956659317016602 s ( 84.27 )
2024-06-19 20:53:26.846095 INFO::Formatting Data.
2024-06-19 20:53:26.846848 INFO::Replacing NaNs with NAs.
2024-06-19 20:53:26.847876 INFO::Removing potential empty rows and columns
2024-06-19 20:53:26.850417 INFO::Found 1000 missing values.
2024-06-19 20:53:26.868119 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-19 20:53:26.86879 INFO::Done
2024-06-19 20:53:26.869333 INFO::Acquiring quality metrics before batch effect correction.
2024-06-19 20:53:26.875021 INFO::Starting hierarchical adjustment
2024-06-19 20:53:26.875714 INFO::Found 10 batches.
2024-06-19 20:53:26.876203 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-19 20:53:26.8768 INFO::Using default BPPARAM
2024-06-19 20:53:26.877298 INFO::Processing subtree level 1
2024-06-19 20:53:27.013104 INFO::Processing subtree level 2
2024-06-19 20:53:27.210527 INFO::Adjusting the last 1 batches sequentially
2024-06-19 20:53:27.212504 INFO::Done
2024-06-19 20:53:27.213162 INFO::Acquiring quality metrics after batch effect correction.
2024-06-19 20:53:27.218982 INFO::ASW Batch was 0.477926254573785 prior to batch effect correction and is now 0.477926254573785 .
2024-06-19 20:53:27.219699 INFO::ASW Label was 0.349322365302249 prior to batch effect correction and is now 0.349322365302249 .
2024-06-19 20:53:27.220608 INFO::Total function execution time is 0.37455940246582 s and adjustment time is 0.336910963058472 s ( 89.95 )
2024-06-19 20:53:27.221473 INFO::Formatting Data.
2024-06-19 20:53:27.222137 INFO::Replacing NaNs with NAs.
2024-06-19 20:53:27.223359 INFO::Removing potential empty rows and columns
2024-06-19 20:53:27.226272 INFO::Found 1000 missing values.
2024-06-19 20:53:27.248577 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-19 20:53:27.249688 INFO::Done
2024-06-19 20:53:27.25029 INFO::Acquiring quality metrics before batch effect correction.
2024-06-19 20:53:27.256948 INFO::Starting hierarchical adjustment
2024-06-19 20:53:27.257812 INFO::Found 10 batches.
2024-06-19 20:53:28.285613 INFO::Set up parallel execution backend with 2 workers
2024-06-19 20:53:28.286936 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-06-19 20:53:29.294236 INFO::Adjusting the last 2 batches sequentially
2024-06-19 20:53:29.295547 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-19 20:53:29.310385 INFO::Done
2024-06-19 20:53:29.310981 INFO::Acquiring quality metrics after batch effect correction.
2024-06-19 20:53:29.315329 INFO::ASW Batch was 0.477926254573785 prior to batch effect correction and is now 0.477926254573785 .
2024-06-19 20:53:29.315822 INFO::ASW Label was 0.349322365302249 prior to batch effect correction and is now 0.349322365302249 .
2024-06-19 20:53:29.316505 INFO::Total function execution time is 2.09506845474243 s and adjustment time is 2.05276370048523 s ( 97.98 )
2024-06-19 20:53:29.441962 INFO::Formatting Data.
2024-06-19 20:53:29.442754 INFO::Replacing NaNs with NAs.
2024-06-19 20:53:29.44361 INFO::Removing potential empty rows and columns
2024-06-19 20:53:29.444582 INFO::Found 0 missing values.
2024-06-19 20:53:29.447966 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-19 20:53:29.448482 INFO::Done
2024-06-19 20:53:29.448954 INFO::Acquiring quality metrics before batch effect correction.
2024-06-19 20:53:29.451488 INFO::Starting hierarchical adjustment
2024-06-19 20:53:29.452124 INFO::Found 3 batches.
2024-06-19 20:53:29.45259 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-19 20:53:29.453144 INFO::Using default BPPARAM
2024-06-19 20:53:29.453629 INFO::Processing subtree level 1
2024-06-19 20:53:29.546026 INFO::Adjusting the last 1 batches sequentially
2024-06-19 20:53:29.547604 INFO::Done
2024-06-19 20:53:29.548167 INFO::Acquiring quality metrics after batch effect correction.
2024-06-19 20:53:29.550987 INFO::ASW Batch was 0.299433056984321 prior to batch effect correction and is now -0.145387264173663 .
2024-06-19 20:53:29.551555 INFO::ASW Label was -0.229837523764126 prior to batch effect correction and is now -0.0378205583877813 .
2024-06-19 20:53:29.552365 INFO::Total function execution time is 0.110445499420166 s and adjustment time is 0.0955989360809326 s ( 86.56 )
2024-06-19 20:53:29.66237 INFO::Formatting Data.
2024-06-19 20:53:29.663137 INFO::Replacing NaNs with NAs.
2024-06-19 20:53:29.663958 INFO::Removing potential empty rows and columns
2024-06-19 20:53:29.664949 INFO::Found 2 missing values.
2024-06-19 20:53:29.6676 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-06-19 20:53:29.668095 INFO::Done
2024-06-19 20:53:29.70139 INFO::Found NA in Reference column
2024-06-19 20:53:29.715668 INFO::Require at least two references per batch.
2024-06-19 20:53:29.746835 INFO::Formatting Data.
2024-06-19 20:53:29.747943 INFO::Recognized SummarizedExperiment
2024-06-19 20:53:29.748785 INFO::Typecasting input to dataframe.
2024-06-19 20:53:29.763767 INFO::Replacing NaNs with NAs.
2024-06-19 20:53:29.765501 INFO::Removing potential empty rows and columns
2024-06-19 20:53:29.771428 INFO::Found 0 missing values.
2024-06-19 20:53:29.782094 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-19 20:53:29.783098 INFO::Done
2024-06-19 20:53:29.800396 INFO::Formatting Data.
2024-06-19 20:53:29.801051 INFO::Recognized SummarizedExperiment
2024-06-19 20:53:29.801531 INFO::Typecasting input to dataframe.
2024-06-19 20:53:29.817018 INFO::Replacing NaNs with NAs.
2024-06-19 20:53:29.818116 INFO::Removing potential empty rows and columns
2024-06-19 20:53:29.821332 INFO::Found 0 missing values.
2024-06-19 20:53:29.831386 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-19 20:53:29.832021 INFO::Done
2024-06-19 20:53:29.845832 INFO::Formatting Data.
2024-06-19 20:53:29.846493 INFO::Recognized SummarizedExperiment
2024-06-19 20:53:29.84701 INFO::Typecasting input to dataframe.
2024-06-19 20:53:29.862023 INFO::Replacing NaNs with NAs.
2024-06-19 20:53:29.862956 INFO::Removing potential empty rows and columns
2024-06-19 20:53:29.864063 INFO::Found 0 missing values.
2024-06-19 20:53:29.865009 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.
2024-06-19 20:53:29.869131 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-19 20:53:29.869688 INFO::Done
2024-06-19 20:53:29.879189 INFO::Formatting Data.
2024-06-19 20:53:29.879858 INFO::Replacing NaNs with NAs.
2024-06-19 20:53:29.880634 INFO::Removing potential empty rows and columns
2024-06-19 20:53:29.881671 INFO::Found 0 missing values.
2024-06-19 20:53:29.884313 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-19 20:53:29.884784 INFO::Done
2024-06-19 20:53:29.894897 INFO::Formatting Data.
2024-06-19 20:53:29.895605 INFO::Replacing NaNs with NAs.
2024-06-19 20:53:29.896394 INFO::Removing potential empty rows and columns
2024-06-19 20:53:29.897292 INFO::Found 0 missing values.
2024-06-19 20:53:29.899837 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-19 20:53:29.900347 INFO::Done
2024-06-19 20:53:29.925408 INFO::Formatting Data.
2024-06-19 20:53:29.926135 INFO::Replacing NaNs with NAs.
2024-06-19 20:53:29.927086 INFO::Removing potential empty rows and columns
2024-06-19 20:53:29.928095 INFO::Found 1 missing values.
2024-06-19 20:53:29.930404 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-19 20:53:29.930923 INFO::Done
2024-06-19 20:53:29.947286 INFO::Formatting Data.
2024-06-19 20:53:29.948015 INFO::Replacing NaNs with NAs.
2024-06-19 20:53:29.948797 INFO::Removing potential empty rows and columns
2024-06-19 20:53:29.949647 INFO::Found 2 missing values.
2024-06-19 20:53:29.950488 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.
2024-06-19 20:53:29.952602 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-06-19 20:53:29.953113 INFO::Done
2024-06-19 20:53:29.961899 INFO::Formatting Data.
2024-06-19 20:53:29.962552 INFO::Replacing NaNs with NAs.
2024-06-19 20:53:29.963363 INFO::Removing potential empty rows and columns
2024-06-19 20:53:29.96422 INFO::Found 2 missing values.
2024-06-19 20:53:29.965671 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-19 20:53:29.966159 INFO::Done
2024-06-19 20:53:29.975397 INFO::Formatting Data.
2024-06-19 20:53:29.976112 INFO::Typecasting input to dataframe.
2024-06-19 20:53:29.976818 INFO::Replacing NaNs with NAs.
2024-06-19 20:53:29.977611 INFO::Removing potential empty rows and columns
2024-06-19 20:53:29.978515 INFO::Found 0 missing values.
2024-06-19 20:53:29.981223 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-19 20:53:29.981704 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
15.862 3.612 19.161
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 23.518 | 1.450 | 17.151 | |
| compute_asw | 0.024 | 0.000 | 0.025 | |
| count_existing | 0.008 | 0.006 | 0.015 | |
| generate_data_covariables | 0.012 | 0.002 | 0.013 | |
| generate_dataset | 0.004 | 0.008 | 0.012 | |