Yannis Schumann
| Snapshot Date: 2024-05-30 18:57:37 -0400 (Thu, 30 May 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: 17da2e9 |
| git_last_commit_date: 2024-04-30 11:53:11 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-05-31 19:28:40 -0400 (Fri, 31 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4669 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4404 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4431 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4384 |
| 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 154/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.1.0 (landing page) Yannis Schumann
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | 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: 1.1.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BERT_1.1.0.tar.gz |
| StartedAt: 2024-05-31 01:43:45 -0400 (Fri, 31 May 2024) |
| EndedAt: 2024-05-31 01:45:11 -0400 (Fri, 31 May 2024) |
| EllapsedTime: 86.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BERT.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BERT_1.1.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* 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 ‘1.1.0’
* 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 24.541 1.219 17.575
* 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-3.20-bioc/R/bin/R CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-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 RC (2024-04-16 r86468) -- "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")
2024-05-31 01:44:36.611657 INFO::Formatting Data.
2024-05-31 01:44:36.613048 INFO::Replacing NaNs with NAs.
2024-05-31 01:44:36.623365 INFO::Removing potential empty rows and columns
2024-05-31 01:44:36.860898 INFO::Found 0 missing values.
2024-05-31 01:44:36.863997 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:44:36.864591 INFO::Done
2024-05-31 01:44:36.865085 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:44:36.87604 INFO::Starting hierarchical adjustment
2024-05-31 01:44:36.876813 INFO::Found 3 batches.
2024-05-31 01:44:36.877303 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:44:36.878308 INFO::Using default BPPARAM
2024-05-31 01:44:36.878867 INFO::Processing subtree level 1
2024-05-31 01:44:36.97417 INFO::Adjusting the last 1 batches sequentially
2024-05-31 01:44:36.976148 INFO::Done
2024-05-31 01:44:36.976816 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:44:36.97933 INFO::ASW Batch was -0.0715861511332763 prior to batch effect correction and is now -0.0715861511332763 .
2024-05-31 01:44:36.9804 INFO::Total function execution time is 0.369566917419434 s and adjustment time is 0.0994710922241211 s ( 26.92 )
2024-05-31 01:44:36.995406 INFO::Formatting Data.
2024-05-31 01:44:36.99624 INFO::Replacing NaNs with NAs.
2024-05-31 01:44:36.997227 INFO::Removing potential empty rows and columns
2024-05-31 01:44:36.998377 INFO::Found 0 missing values.
2024-05-31 01:44:36.99933 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.
2024-05-31 01:44:37.011243 INFO::Formatting Data.
2024-05-31 01:44:37.012054 INFO::Replacing NaNs with NAs.
2024-05-31 01:44:37.013098 INFO::Removing potential empty rows and columns
2024-05-31 01:44:37.014239 INFO::Found 0 missing values.
2024-05-31 01:44:37.015217 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.
2024-05-31 01:44:37.03149 INFO::Formatting Data.
2024-05-31 01:44:37.032207 INFO::Replacing NaNs with NAs.
2024-05-31 01:44:37.033036 INFO::Removing potential empty rows and columns
2024-05-31 01:44:37.034049 INFO::Found 0 missing values.
2024-05-31 01:44:37.034899 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.
2024-05-31 01:44:37.039019 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:44:37.039529 INFO::Done
2024-05-31 01:44:37.040015 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:44:37.041937 INFO::Starting hierarchical adjustment
2024-05-31 01:44:37.042583 INFO::Found 2 batches.
2024-05-31 01:44:37.043065 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:44:37.043648 INFO::Using default BPPARAM
2024-05-31 01:44:37.044136 INFO::Adjusting the last 2 batches sequentially
2024-05-31 01:44:37.045014 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 01:44:37.066654 INFO::Done
2024-05-31 01:44:37.067301 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:44:37.069274 INFO::ASW Batch was -0.0299789291577497 prior to batch effect correction and is now -0.124403880896755 .
2024-05-31 01:44:37.070029 INFO::Total function execution time is 0.0386121273040771 s and adjustment time is 0.0241568088531494 s ( 62.56 )
2024-05-31 01:44:37.07275 INFO::Formatting Data.
2024-05-31 01:44:37.07335 INFO::Replacing NaNs with NAs.
2024-05-31 01:44:37.081846 INFO::Formatting Data.
2024-05-31 01:44:37.082539 INFO::Replacing NaNs with NAs.
2024-05-31 01:44:37.083384 INFO::Removing potential empty rows and columns
2024-05-31 01:44:37.084355 INFO::Found 0 missing values.
2024-05-31 01:44:37.087047 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:44:37.087529 INFO::Done
2024-05-31 01:44:37.088013 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:44:37.089893 INFO::Starting hierarchical adjustment
2024-05-31 01:44:37.090545 INFO::Found 2 batches.
2024-05-31 01:44:37.091023 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:44:37.091583 INFO::Using default BPPARAM
2024-05-31 01:44:37.092068 INFO::Adjusting the last 2 batches sequentially
2024-05-31 01:44:37.09294 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 01:44:37.107332 INFO::Done
2024-05-31 01:44:37.107958 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:44:37.10987 INFO::ASW Batch was 0.020698813523875 prior to batch effect correction and is now -0.106139088739572 .
2024-05-31 01:44:37.110594 INFO::Total function execution time is 0.0288040637969971 s and adjustment time is 0.0169017314910889 s ( 58.68 )
2024-05-31 01:44:37.111637 INFO::Formatting Data.
2024-05-31 01:44:37.112205 INFO::Replacing NaNs with NAs.
2024-05-31 01:44:37.113024 INFO::Removing potential empty rows and columns
2024-05-31 01:44:37.113991 INFO::Found 0 missing values.
2024-05-31 01:44:37.116682 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:44:37.117178 INFO::Done
2024-05-31 01:44:37.117643 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:44:37.119516 INFO::Starting hierarchical adjustment
2024-05-31 01:44:37.120153 INFO::Found 2 batches.
2024-05-31 01:44:37.120672 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:44:37.121217 INFO::Using default BPPARAM
2024-05-31 01:44:37.121698 INFO::Adjusting the last 2 batches sequentially
2024-05-31 01:44:37.122532 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 01:44:37.136759 INFO::Done
2024-05-31 01:44:37.137378 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:44:37.139248 INFO::ASW Batch was 0.020698813523875 prior to batch effect correction and is now -0.106139088739572 .
2024-05-31 01:44:37.139979 INFO::Total function execution time is 0.0283381938934326 s and adjustment time is 0.0167269706726074 s ( 59.03 )
2024-05-31 01:44:39.231442 INFO::Formatting Data.
2024-05-31 01:44:39.23216 INFO::Recognized SummarizedExperiment
2024-05-31 01:44:39.235525 INFO::Typecasting input to dataframe.
2024-05-31 01:44:39.266721 INFO::Replacing NaNs with NAs.
2024-05-31 01:44:39.267857 INFO::Removing potential empty rows and columns
2024-05-31 01:44:39.271279 INFO::Found 0 missing values.
2024-05-31 01:44:39.277892 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:44:39.278422 INFO::Done
2024-05-31 01:44:39.278884 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:44:39.282404 INFO::Starting hierarchical adjustment
2024-05-31 01:44:39.283047 INFO::Found 2 batches.
2024-05-31 01:44:39.283507 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:44:39.284564 INFO::Using default BPPARAM
2024-05-31 01:44:39.28507 INFO::Adjusting the last 2 batches sequentially
2024-05-31 01:44:39.285955 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 01:44:39.369046 INFO::Done
2024-05-31 01:44:39.369622 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:44:39.373182 INFO::ASW Batch was 0.0107702166649332 prior to batch effect correction and is now -0.0913921518853305 .
2024-05-31 01:44:39.373871 INFO::Total function execution time is 0.142767429351807 s and adjustment time is 0.086122989654541 s ( 60.32 )
2024-05-31 01:44:39.388238 INFO::Formatting Data.
2024-05-31 01:44:39.388814 INFO::Recognized SummarizedExperiment
2024-05-31 01:44:39.389236 INFO::Typecasting input to dataframe.
2024-05-31 01:44:39.396576 INFO::Replacing NaNs with NAs.
2024-05-31 01:44:39.397515 INFO::Removing potential empty rows and columns
2024-05-31 01:44:39.400247 INFO::Found 0 missing values.
2024-05-31 01:44:39.405579 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:44:39.406052 INFO::Done
2024-05-31 01:44:39.406479 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:44:39.409267 INFO::Starting hierarchical adjustment
2024-05-31 01:44:39.409858 INFO::Found 2 batches.
2024-05-31 01:44:39.410297 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:44:39.410775 INFO::Using default BPPARAM
2024-05-31 01:44:39.411202 INFO::Adjusting the last 2 batches sequentially
2024-05-31 01:44:39.412033 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 01:44:39.43134 INFO::Done
2024-05-31 01:44:39.431922 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:44:39.434942 INFO::ASW Batch was -0.0169678172322407 prior to batch effect correction and is now -0.0169678172322407 .
2024-05-31 01:44:39.435647 INFO::Total function execution time is 0.0473885536193848 s and adjustment time is 0.0215859413146973 s ( 45.55 )
2024-05-31 01:44:39.450791 INFO::Formatting Data.
2024-05-31 01:44:39.451559 INFO::Replacing NaNs with NAs.
2024-05-31 01:44:39.452416 INFO::Removing potential empty rows and columns
2024-05-31 01:44:39.453292 INFO::Found 0 missing values.
2024-05-31 01:44:39.455609 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:44:39.45604 INFO::Done
2024-05-31 01:44:39.456453 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:44:39.458106 INFO::Starting hierarchical adjustment
2024-05-31 01:44:39.458676 INFO::Found 3 batches.
2024-05-31 01:44:39.459093 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:44:39.459576 INFO::Using default BPPARAM
2024-05-31 01:44:39.45999 INFO::Processing subtree level 1
2024-05-31 01:44:39.608784 INFO::Adjusting the last 1 batches sequentially
2024-05-31 01:44:39.610375 INFO::Done
2024-05-31 01:44:39.610924 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:44:39.613173 INFO::ASW Batch was -0.116622385398177 prior to batch effect correction and is now -0.176257165978781 .
2024-05-31 01:44:39.614042 INFO::Total function execution time is 0.163320302963257 s and adjustment time is 0.151804208755493 s ( 92.95 )
2024-05-31 01:44:39.627775 INFO::Skipping initial DF formatting
2024-05-31 01:44:39.628385 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:44:39.632195 INFO::Starting hierarchical adjustment
2024-05-31 01:44:39.632904 INFO::Found 5 batches.
2024-05-31 01:44:39.633381 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:44:39.633949 INFO::Using default BPPARAM
2024-05-31 01:44:39.634438 INFO::Processing subtree level 1
2024-05-31 01:44:39.769118 INFO::Adjusting the last 2 batches sequentially
2024-05-31 01:44:39.770604 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 01:44:39.790324 INFO::Done
2024-05-31 01:44:39.790956 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:44:39.798107 INFO::ASW Batch was 0.492621328885238 prior to batch effect correction and is now 0.492621328885238 .
2024-05-31 01:44:39.799219 INFO::ASW Label was 0.394076755938086 prior to batch effect correction and is now 0.394076755938086 .
2024-05-31 01:44:39.800307 INFO::Total function execution time is 0.172557353973389 s and adjustment time is 0.157544374465942 s ( 91.3 )
2024-05-31 01:44:39.818277 INFO::Formatting Data.
2024-05-31 01:44:39.818961 INFO::Replacing NaNs with NAs.
2024-05-31 01:44:39.819801 INFO::Removing potential empty rows and columns
2024-05-31 01:44:39.820764 INFO::Found 0 missing values.
2024-05-31 01:44:39.824484 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:44:39.82498 INFO::Done
2024-05-31 01:44:39.82545 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:44:39.828227 INFO::Starting hierarchical adjustment
2024-05-31 01:44:39.828911 INFO::Found 5 batches.
2024-05-31 01:44:39.829385 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:44:39.829988 INFO::Using default BPPARAM
2024-05-31 01:44:39.830482 INFO::Processing subtree level 1
2024-05-31 01:44:39.944037 INFO::Adjusting the last 2 batches sequentially
2024-05-31 01:44:39.945519 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 01:44:39.960961 INFO::Done
2024-05-31 01:44:39.961596 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:44:39.964478 INFO::ASW Batch was 0.537489074485098 prior to batch effect correction and is now -0.0964071283606733 .
2024-05-31 01:44:39.96502 INFO::ASW Label was 0.301858480510243 prior to batch effect correction and is now 0.773012621449759 .
2024-05-31 01:44:39.96573 INFO::Total function execution time is 0.147519111633301 s and adjustment time is 0.132178068161011 s ( 89.6 )
2024-05-31 01:44:39.966468 INFO::Formatting Data.
2024-05-31 01:44:39.967011 INFO::Replacing NaNs with NAs.
2024-05-31 01:44:39.967788 INFO::Removing potential empty rows and columns
2024-05-31 01:44:39.968657 INFO::Found 0 missing values.
2024-05-31 01:44:39.972316 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:44:39.972843 INFO::Done
2024-05-31 01:44:39.973315 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:44:39.976044 INFO::Starting hierarchical adjustment
2024-05-31 01:44:39.976691 INFO::Found 5 batches.
2024-05-31 01:44:39.977194 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:44:39.977778 INFO::Using default BPPARAM
2024-05-31 01:44:39.978274 INFO::Processing subtree level 1
2024-05-31 01:44:40.105073 INFO::Adjusting the last 2 batches sequentially
2024-05-31 01:44:40.108427 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 01:44:40.126308 INFO::Done
2024-05-31 01:44:40.127084 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:44:40.130587 INFO::ASW Batch was 0.537489074485098 prior to batch effect correction and is now -0.0964071283606733 .
2024-05-31 01:44:40.131216 INFO::ASW Label was 0.301858480510243 prior to batch effect correction and is now 0.773012621449759 .
2024-05-31 01:44:40.132097 INFO::Total function execution time is 0.165586948394775 s and adjustment time is 0.14970588684082 s ( 90.41 )
2024-05-31 01:44:40.145791 INFO::Formatting Data.
2024-05-31 01:44:40.146554 INFO::Replacing NaNs with NAs.
2024-05-31 01:44:40.14748 INFO::Removing potential empty rows and columns
2024-05-31 01:44:40.148497 INFO::Found 0 missing values.
2024-05-31 01:44:40.15263 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:44:40.153189 INFO::Done
2024-05-31 01:44:40.153714 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:44:40.156746 INFO::Starting hierarchical adjustment
2024-05-31 01:44:40.157454 INFO::Found 5 batches.
2024-05-31 01:44:40.157964 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:44:40.158567 INFO::Using default BPPARAM
2024-05-31 01:44:40.159084 INFO::Processing subtree level 1
2024-05-31 01:44:40.284466 INFO::Adjusting the last 2 batches sequentially
2024-05-31 01:44:40.286381 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 01:44:40.302484 INFO::Done
2024-05-31 01:44:40.303188 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:44:40.306365 INFO::ASW Batch was 0.299824359814122 prior to batch effect correction and is now -0.0307351149271069 .
2024-05-31 01:44:40.306976 INFO::ASW Label was 0.293967546980364 prior to batch effect correction and is now 0.797530254555893 .
2024-05-31 01:44:40.307791 INFO::Total function execution time is 0.162051916122437 s and adjustment time is 0.1451575756073 s ( 89.57 )
2024-05-31 01:44:40.308629 INFO::Formatting Data.
2024-05-31 01:44:40.309277 INFO::Replacing NaNs with NAs.
2024-05-31 01:44:40.310129 INFO::Removing potential empty rows and columns
2024-05-31 01:44:40.311273 INFO::Found 0 missing values.
2024-05-31 01:44:40.315248 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:44:40.315766 INFO::Done
2024-05-31 01:44:40.316265 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:44:40.31911 INFO::Starting hierarchical adjustment
2024-05-31 01:44:40.31979 INFO::Found 5 batches.
2024-05-31 01:44:40.320297 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:44:40.32089 INFO::Using default BPPARAM
2024-05-31 01:44:40.321385 INFO::Processing subtree level 1
2024-05-31 01:44:40.440116 INFO::Adjusting the last 2 batches sequentially
2024-05-31 01:44:40.44175 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 01:44:40.461385 INFO::Done
2024-05-31 01:44:40.462474 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:44:40.466161 INFO::ASW Batch was 0.299824359814122 prior to batch effect correction and is now -0.0307351149271069 .
2024-05-31 01:44:40.466745 INFO::ASW Label was 0.293967546980364 prior to batch effect correction and is now 0.797530254555893 .
2024-05-31 01:44:40.467637 INFO::Total function execution time is 0.158987760543823 s and adjustment time is 0.141564130783081 s ( 89.04 )
2024-05-31 01:44:40.481629 INFO::Formatting Data.
2024-05-31 01:44:40.482328 INFO::Replacing NaNs with NAs.
2024-05-31 01:44:40.483226 INFO::Removing potential empty rows and columns
2024-05-31 01:44:40.484274 INFO::Found 0 missing values.
2024-05-31 01:44:40.486923 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:44:40.487442 INFO::Done
2024-05-31 01:44:40.487946 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:44:40.490849 INFO::Starting hierarchical adjustment
2024-05-31 01:44:40.491529 INFO::Found 2 batches.
2024-05-31 01:44:40.492043 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:44:40.492676 INFO::Using default BPPARAM
2024-05-31 01:44:40.493201 INFO::Adjusting the last 2 batches sequentially
2024-05-31 01:44:40.494108 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 01:44:40.509915 INFO::Done
2024-05-31 01:44:40.510524 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:44:40.513323 INFO::ASW Batch was 0.506971258400923 prior to batch effect correction and is now 0.0697496998537131 .
2024-05-31 01:44:40.513891 INFO::ASW Label was 0.577038321756667 prior to batch effect correction and is now 0.88893053019343 .
2024-05-31 01:44:40.51462 INFO::Total function execution time is 0.0330545902252197 s and adjustment time is 0.0185239315032959 s ( 56.04 )
2024-05-31 01:44:40.515337 INFO::Formatting Data.
2024-05-31 01:44:40.515913 INFO::Replacing NaNs with NAs.
2024-05-31 01:44:40.516716 INFO::Removing potential empty rows and columns
2024-05-31 01:44:40.517635 INFO::Found 0 missing values.
2024-05-31 01:44:40.52017 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:44:40.520674 INFO::Done
2024-05-31 01:44:40.521157 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:44:40.523957 INFO::Starting hierarchical adjustment
2024-05-31 01:44:40.524637 INFO::Found 2 batches.
2024-05-31 01:44:40.525126 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:44:40.525728 INFO::Using default BPPARAM
2024-05-31 01:44:40.526208 INFO::Adjusting the last 2 batches sequentially
2024-05-31 01:44:40.527037 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 01:44:40.541682 INFO::Done
2024-05-31 01:44:40.54233 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:44:40.545254 INFO::ASW Batch was 0.506971258400923 prior to batch effect correction and is now 0.0697496998537131 .
2024-05-31 01:44:40.545818 INFO::ASW Label was 0.577038321756667 prior to batch effect correction and is now 0.88893053019343 .
2024-05-31 01:44:40.546573 INFO::Total function execution time is 0.0312285423278809 s and adjustment time is 0.0171644687652588 s ( 54.96 )
2024-05-31 01:44:40.55749 INFO::Formatting Data.
2024-05-31 01:44:40.558186 INFO::Replacing NaNs with NAs.
2024-05-31 01:44:40.559032 INFO::Removing potential empty rows and columns
2024-05-31 01:44:40.559932 INFO::Found 0 missing values.
2024-05-31 01:44:40.562018 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:44:40.562551 INFO::Done
2024-05-31 01:44:40.563065 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:44:40.564991 INFO::Starting hierarchical adjustment
2024-05-31 01:44:40.565694 INFO::Found 2 batches.
2024-05-31 01:44:40.566214 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:44:40.566822 INFO::Using default BPPARAM
2024-05-31 01:44:40.567342 INFO::Adjusting the last 2 batches sequentially
2024-05-31 01:44:40.568233 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 01:44:40.601657 INFO::Done
2024-05-31 01:44:40.602338 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:44:40.604263 INFO::ASW Batch was -0.0333690557983583 prior to batch effect correction and is now -0.156734862234567 .
2024-05-31 01:44:40.605081 INFO::Total function execution time is 0.0476393699645996 s and adjustment time is 0.0360727310180664 s ( 75.72 )
2024-05-31 01:44:40.617001 INFO::Formatting Data.
2024-05-31 01:44:40.617717 INFO::Replacing NaNs with NAs.
2024-05-31 01:44:40.618609 INFO::Removing potential empty rows and columns
2024-05-31 01:44:40.619624 INFO::Found 0 missing values.
2024-05-31 01:44:40.620856 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.
2024-05-31 01:44:40.656042 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:44:40.656867 INFO::Done
2024-05-31 01:44:40.657369 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:44:40.66029 INFO::Starting hierarchical adjustment
2024-05-31 01:44:40.661016 INFO::Found 2 batches.
2024-05-31 01:44:40.661521 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:44:40.662084 INFO::Using default BPPARAM
2024-05-31 01:44:40.662592 INFO::Adjusting the last 2 batches sequentially
2024-05-31 01:44:40.663554 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 01:44:40.681026 INFO::Done
2024-05-31 01:44:40.681681 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:44:40.684511 INFO::ASW Batch was 0.693272802492125 prior to batch effect correction and is now 0.132675114335321 .
2024-05-31 01:44:40.685053 INFO::ASW Label was 0.406172680950865 prior to batch effect correction and is now 0.801454863273718 .
2024-05-31 01:44:40.685748 INFO::Total function execution time is 0.068821907043457 s and adjustment time is 0.0201466083526611 s ( 29.27 )
2024-05-31 01:44:40.686444 INFO::Formatting Data.
2024-05-31 01:44:40.687029 INFO::Replacing NaNs with NAs.
2024-05-31 01:44:40.687878 INFO::Removing potential empty rows and columns
2024-05-31 01:44:40.688834 INFO::Found 0 missing values.
2024-05-31 01:44:40.689713 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.
2024-05-31 01:44:40.694451 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:44:40.694965 INFO::Done
2024-05-31 01:44:40.695464 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:44:40.69842 INFO::Starting hierarchical adjustment
2024-05-31 01:44:40.699133 INFO::Found 2 batches.
2024-05-31 01:44:40.699651 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:44:40.700223 INFO::Using default BPPARAM
2024-05-31 01:44:40.700725 INFO::Adjusting the last 2 batches sequentially
2024-05-31 01:44:40.70165 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 01:44:40.719271 INFO::Done
2024-05-31 01:44:40.719897 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:44:40.722802 INFO::ASW Batch was 0.693272802492125 prior to batch effect correction and is now 0.132675114335321 .
2024-05-31 01:44:40.723361 INFO::ASW Label was 0.406172680950865 prior to batch effect correction and is now 0.801454863273718 .
2024-05-31 01:44:40.724128 INFO::Total function execution time is 0.0376770496368408 s and adjustment time is 0.020282506942749 s ( 53.83 )
2024-05-31 01:44:40.945752 INFO::Formatting Data.
2024-05-31 01:44:40.946898 INFO::Replacing NaNs with NAs.
2024-05-31 01:44:40.947968 INFO::Removing potential empty rows and columns
2024-05-31 01:44:40.949346 INFO::Found 0 missing values.
2024-05-31 01:44:40.953418 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:44:40.954033 INFO::Done
2024-05-31 01:44:40.954655 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:44:40.957166 INFO::Starting hierarchical adjustment
2024-05-31 01:44:40.957973 INFO::Found 3 batches.
2024-05-31 01:44:40.958592 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:44:40.959303 INFO::Using default BPPARAM
2024-05-31 01:44:40.959938 INFO::Processing subtree level 1
2024-05-31 01:44:41.068275 INFO::Adjusting the last 1 batches sequentially
2024-05-31 01:44:41.069899 INFO::Done
2024-05-31 01:44:41.070477 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:44:41.072771 INFO::ASW Batch was -0.086465736660797 prior to batch effect correction and is now -0.086465736660797 .
2024-05-31 01:44:41.073662 INFO::Total function execution time is 0.128012418746948 s and adjustment time is 0.112122058868408 s ( 87.59 )
2024-05-31 01:44:41.0747 INFO::Formatting Data.
2024-05-31 01:44:41.075319 INFO::Typecasting input to dataframe.
2024-05-31 01:44:41.07605 INFO::Replacing NaNs with NAs.
2024-05-31 01:44:41.076923 INFO::Removing potential empty rows and columns
2024-05-31 01:44:41.077956 INFO::Found 0 missing values.
2024-05-31 01:44:41.080793 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:44:41.081319 INFO::Done
2024-05-31 01:44:41.082303 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:44:41.084259 INFO::Starting hierarchical adjustment
2024-05-31 01:44:41.084946 INFO::Found 3 batches.
2024-05-31 01:44:41.085437 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:44:41.08601 INFO::Using default BPPARAM
2024-05-31 01:44:41.086531 INFO::Processing subtree level 1
2024-05-31 01:44:41.178911 INFO::Adjusting the last 1 batches sequentially
2024-05-31 01:44:41.1805 INFO::Done
2024-05-31 01:44:41.181099 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:44:41.18341 INFO::ASW Batch was -0.086465736660797 prior to batch effect correction and is now -0.086465736660797 .
2024-05-31 01:44:41.184304 INFO::Total function execution time is 0.109565496444702 s and adjustment time is 0.0956852436065674 s ( 87.33 )
2024-05-31 01:44:41.196594 INFO::Formatting Data.
2024-05-31 01:44:41.197459 INFO::Typecasting input to dataframe.
2024-05-31 01:44:41.198363 INFO::Replacing NaNs with NAs.
2024-05-31 01:44:41.199224 INFO::Removing potential empty rows and columns
2024-05-31 01:44:41.200243 INFO::Found 0 missing values.
2024-05-31 01:44:41.203182 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:44:41.203672 INFO::Done
2024-05-31 01:44:41.204155 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:44:41.205999 INFO::Starting hierarchical adjustment
2024-05-31 01:44:41.206633 INFO::Found 3 batches.
2024-05-31 01:44:41.207108 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:44:41.207645 INFO::Using default BPPARAM
2024-05-31 01:44:41.208109 INFO::Processing subtree level 1
2024-05-31 01:44:41.303196 INFO::Adjusting the last 1 batches sequentially
2024-05-31 01:44:41.304946 INFO::Done
2024-05-31 01:44:41.305548 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:44:41.307966 INFO::ASW Batch was -0.087131631023239 prior to batch effect correction and is now -0.087131631023239 .
2024-05-31 01:44:41.308926 INFO::Total function execution time is 0.112434864044189 s and adjustment time is 0.0984261035919189 s ( 87.54 )
2024-05-31 01:44:41.459726 INFO::Formatting Data.
2024-05-31 01:44:41.460414 INFO::Replacing NaNs with NAs.
2024-05-31 01:44:41.461509 INFO::Removing potential empty rows and columns
2024-05-31 01:44:41.464365 INFO::Found 1000 missing values.
2024-05-31 01:44:41.48322 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:44:41.483921 INFO::Done
2024-05-31 01:44:41.484449 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:44:41.490618 INFO::Starting hierarchical adjustment
2024-05-31 01:44:41.491329 INFO::Found 10 batches.
2024-05-31 01:44:41.491838 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:44:41.49249 INFO::Using default BPPARAM
2024-05-31 01:44:41.493082 INFO::Processing subtree level 1
2024-05-31 01:44:41.656043 INFO::Processing subtree level 2
2024-05-31 01:44:41.851888 INFO::Adjusting the last 1 batches sequentially
2024-05-31 01:44:41.853742 INFO::Done
2024-05-31 01:44:41.854386 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:44:41.860165 INFO::ASW Batch was 0.490126037633862 prior to batch effect correction and is now 0.490126037633862 .
2024-05-31 01:44:41.86079 INFO::ASW Label was 0.34073498709981 prior to batch effect correction and is now 0.34073498709981 .
2024-05-31 01:44:41.861722 INFO::Total function execution time is 0.402017831802368 s and adjustment time is 0.362544536590576 s ( 90.18 )
2024-05-31 01:44:41.862601 INFO::Formatting Data.
2024-05-31 01:44:41.863291 INFO::Replacing NaNs with NAs.
2024-05-31 01:44:41.864516 INFO::Removing potential empty rows and columns
2024-05-31 01:44:41.867583 INFO::Found 1000 missing values.
2024-05-31 01:44:41.888055 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:44:41.888848 INFO::Done
2024-05-31 01:44:41.889444 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:44:41.895377 INFO::Starting hierarchical adjustment
2024-05-31 01:44:41.896194 INFO::Found 10 batches.
2024-05-31 01:44:43.004811 INFO::Set up parallel execution backend with 2 workers
2024-05-31 01:44:43.00745 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-05-31 01:44:43.974857 INFO::Adjusting the last 2 batches sequentially
2024-05-31 01:44:43.976292 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-31 01:44:43.991729 INFO::Done
2024-05-31 01:44:43.99233 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:44:43.996928 INFO::ASW Batch was 0.490126037633862 prior to batch effect correction and is now 0.490126037633862 .
2024-05-31 01:44:43.99746 INFO::ASW Label was 0.34073498709981 prior to batch effect correction and is now 0.34073498709981 .
2024-05-31 01:44:43.998138 INFO::Total function execution time is 2.13558530807495 s and adjustment time is 2.09568738937378 s ( 98.13 )
2024-05-31 01:44:44.134202 INFO::Formatting Data.
2024-05-31 01:44:44.135071 INFO::Replacing NaNs with NAs.
2024-05-31 01:44:44.136078 INFO::Removing potential empty rows and columns
2024-05-31 01:44:44.13715 INFO::Found 0 missing values.
2024-05-31 01:44:44.140793 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:44:44.141302 INFO::Done
2024-05-31 01:44:44.141786 INFO::Acquiring quality metrics before batch effect correction.
2024-05-31 01:44:44.144482 INFO::Starting hierarchical adjustment
2024-05-31 01:44:44.145141 INFO::Found 3 batches.
2024-05-31 01:44:44.145613 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-31 01:44:44.14619 INFO::Using default BPPARAM
2024-05-31 01:44:44.146681 INFO::Processing subtree level 1
2024-05-31 01:44:44.24193 INFO::Adjusting the last 1 batches sequentially
2024-05-31 01:44:44.243565 INFO::Done
2024-05-31 01:44:44.244139 INFO::Acquiring quality metrics after batch effect correction.
2024-05-31 01:44:44.247049 INFO::ASW Batch was 0.175526001351045 prior to batch effect correction and is now -0.143609830498874 .
2024-05-31 01:44:44.247618 INFO::ASW Label was -0.169379072899188 prior to batch effect correction and is now 0.0244429719621173 .
2024-05-31 01:44:44.248493 INFO::Total function execution time is 0.114343404769897 s and adjustment time is 0.0985476970672607 s ( 86.19 )
2024-05-31 01:44:44.35029 INFO::Formatting Data.
2024-05-31 01:44:44.351019 INFO::Replacing NaNs with NAs.
2024-05-31 01:44:44.35181 INFO::Removing potential empty rows and columns
2024-05-31 01:44:44.352749 INFO::Found 2 missing values.
2024-05-31 01:44:44.355242 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:44:44.355705 INFO::Done
2024-05-31 01:44:44.379266 INFO::Found NA in Reference column
2024-05-31 01:44:44.387563 INFO::Require at least two references per batch.
2024-05-31 01:44:44.40555 INFO::Formatting Data.
2024-05-31 01:44:44.406263 INFO::Recognized SummarizedExperiment
2024-05-31 01:44:44.406742 INFO::Typecasting input to dataframe.
2024-05-31 01:44:44.415291 INFO::Replacing NaNs with NAs.
2024-05-31 01:44:44.416322 INFO::Removing potential empty rows and columns
2024-05-31 01:44:44.419428 INFO::Found 0 missing values.
2024-05-31 01:44:44.425356 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:44:44.425866 INFO::Done
2024-05-31 01:44:44.439399 INFO::Formatting Data.
2024-05-31 01:44:44.440037 INFO::Recognized SummarizedExperiment
2024-05-31 01:44:44.440493 INFO::Typecasting input to dataframe.
2024-05-31 01:44:44.45593 INFO::Replacing NaNs with NAs.
2024-05-31 01:44:44.457068 INFO::Removing potential empty rows and columns
2024-05-31 01:44:44.460112 INFO::Found 0 missing values.
2024-05-31 01:44:44.469775 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:44:44.470351 INFO::Done
2024-05-31 01:44:44.483995 INFO::Formatting Data.
2024-05-31 01:44:44.484686 INFO::Recognized SummarizedExperiment
2024-05-31 01:44:44.485175 INFO::Typecasting input to dataframe.
2024-05-31 01:44:44.500135 INFO::Replacing NaNs with NAs.
2024-05-31 01:44:44.501106 INFO::Removing potential empty rows and columns
2024-05-31 01:44:44.502212 INFO::Found 0 missing values.
2024-05-31 01:44:44.503046 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.
2024-05-31 01:44:44.507066 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:44:44.507599 INFO::Done
2024-05-31 01:44:44.516761 INFO::Formatting Data.
2024-05-31 01:44:44.517463 INFO::Replacing NaNs with NAs.
2024-05-31 01:44:44.518245 INFO::Removing potential empty rows and columns
2024-05-31 01:44:44.519203 INFO::Found 0 missing values.
2024-05-31 01:44:44.52187 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:44:44.52233 INFO::Done
2024-05-31 01:44:44.532217 INFO::Formatting Data.
2024-05-31 01:44:44.532948 INFO::Replacing NaNs with NAs.
2024-05-31 01:44:44.533705 INFO::Removing potential empty rows and columns
2024-05-31 01:44:44.53457 INFO::Found 0 missing values.
2024-05-31 01:44:44.537075 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:44:44.537534 INFO::Done
2024-05-31 01:44:44.562143 INFO::Formatting Data.
2024-05-31 01:44:44.562846 INFO::Replacing NaNs with NAs.
2024-05-31 01:44:44.563751 INFO::Removing potential empty rows and columns
2024-05-31 01:44:44.564766 INFO::Found 1 missing values.
2024-05-31 01:44:44.567023 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:44:44.567532 INFO::Done
2024-05-31 01:44:44.589038 INFO::Formatting Data.
2024-05-31 01:44:44.589908 INFO::Replacing NaNs with NAs.
2024-05-31 01:44:44.590812 INFO::Removing potential empty rows and columns
2024-05-31 01:44:44.59182 INFO::Found 2 missing values.
2024-05-31 01:44:44.59285 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.
2024-05-31 01:44:44.595169 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:44:44.595695 INFO::Done
2024-05-31 01:44:44.605744 INFO::Formatting Data.
2024-05-31 01:44:44.606467 INFO::Replacing NaNs with NAs.
2024-05-31 01:44:44.607321 INFO::Removing potential empty rows and columns
2024-05-31 01:44:44.608245 INFO::Found 2 missing values.
2024-05-31 01:44:44.609817 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:44:44.610316 INFO::Done
2024-05-31 01:44:44.620579 INFO::Formatting Data.
2024-05-31 01:44:44.621257 INFO::Typecasting input to dataframe.
2024-05-31 01:44:44.622057 INFO::Replacing NaNs with NAs.
2024-05-31 01:44:44.622919 INFO::Removing potential empty rows and columns
2024-05-31 01:44:44.623866 INFO::Found 0 missing values.
2024-05-31 01:44:44.626787 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-31 01:44:44.627325 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
15.986 3.350 18.999
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 24.541 | 1.219 | 17.575 | |
| compute_asw | 0.025 | 0.000 | 0.024 | |
| count_existing | 0.010 | 0.004 | 0.014 | |
| generate_data_covariables | 0.012 | 0.000 | 0.013 | |
| generate_dataset | 0.008 | 0.004 | 0.012 | |