Yannis Schumann
| Snapshot Date: 2024-06-23 14:00 -0400 (Sun, 23 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 2024-06-25 17:40 -0400 (Tue, 25 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" | 4760 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
| 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: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings BERT_1.0.0.tar.gz |
| StartedAt: 2024-06-24 00:42:05 -0400 (Mon, 24 Jun 2024) |
| EndedAt: 2024-06-24 00:49:06 -0400 (Mon, 24 Jun 2024) |
| EllapsedTime: 421.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings BERT_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/BERT.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* 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 whether package 'BERT' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... 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 8.09 4.77 29.71
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
BERT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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")
2024-06-24 00:45:00.982002 INFO::Formatting Data.
2024-06-24 00:45:00.997062 INFO::Replacing NaNs with NAs.
2024-06-24 00:45:01.007637 INFO::Removing potential empty rows and columns
2024-06-24 00:45:01.661758 INFO::Found 0 missing values.
2024-06-24 00:45:01.666528 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 00:45:01.667508 INFO::Done
2024-06-24 00:45:01.66845 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 00:45:01.739745 INFO::Starting hierarchical adjustment
2024-06-24 00:45:01.740974 INFO::Found 3 batches.
2024-06-24 00:45:01.741845 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 00:45:01.743193 INFO::Using default BPPARAM
2024-06-24 00:45:01.743953 INFO::Processing subtree level 1
2024-06-24 00:45:15.056464 INFO::Adjusting the last 1 batches sequentially
2024-06-24 00:45:15.059101 INFO::Done
2024-06-24 00:45:15.060379 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 00:45:15.066583 INFO::ASW Batch was 0.0287054010194563 prior to batch effect correction and is now 0.0287054010194563 .
2024-06-24 00:45:15.073154 INFO::Total function execution time is 14.0914840698242 s and adjustment time is 13.3182618618011 s ( 94.51 )
2024-06-24 00:45:15.097544 INFO::Formatting Data.
2024-06-24 00:45:15.098992 INFO::Replacing NaNs with NAs.
2024-06-24 00:45:15.10066 INFO::Removing potential empty rows and columns
2024-06-24 00:45:15.103292 INFO::Found 0 missing values.
2024-06-24 00:45:15.104999 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.
2024-06-24 00:45:15.118842 INFO::Formatting Data.
2024-06-24 00:45:15.120289 INFO::Replacing NaNs with NAs.
2024-06-24 00:45:15.122087 INFO::Removing potential empty rows and columns
2024-06-24 00:45:15.123865 INFO::Found 0 missing values.
2024-06-24 00:45:15.125525 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.
2024-06-24 00:45:15.151708 INFO::Formatting Data.
2024-06-24 00:45:15.153288 INFO::Replacing NaNs with NAs.
2024-06-24 00:45:15.154942 INFO::Removing potential empty rows and columns
2024-06-24 00:45:15.156711 INFO::Found 0 missing values.
2024-06-24 00:45:15.15842 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.
2024-06-24 00:45:15.16442 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 00:45:15.165627 INFO::Done
2024-06-24 00:45:15.166724 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 00:45:15.169937 INFO::Starting hierarchical adjustment
2024-06-24 00:45:15.171252 INFO::Found 2 batches.
2024-06-24 00:45:15.172424 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 00:45:15.173614 INFO::Using default BPPARAM
2024-06-24 00:45:15.174895 INFO::Adjusting the last 2 batches sequentially
2024-06-24 00:45:15.176552 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-24 00:45:15.203573 INFO::Done
2024-06-24 00:45:15.204885 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 00:45:15.207978 INFO::ASW Batch was 0.0294878129690008 prior to batch effect correction and is now -0.111118283354763 .
2024-06-24 00:45:15.209546 INFO::Total function execution time is 0.0578188896179199 s and adjustment time is 0.0324809551239014 s ( 56.18 )
2024-06-24 00:45:15.213768 INFO::Formatting Data.
2024-06-24 00:45:15.215064 INFO::Replacing NaNs with NAs.
2024-06-24 00:45:15.226513 INFO::Formatting Data.
2024-06-24 00:45:15.227921 INFO::Replacing NaNs with NAs.
2024-06-24 00:45:15.229519 INFO::Removing potential empty rows and columns
2024-06-24 00:45:15.231349 INFO::Found 0 missing values.
2024-06-24 00:45:15.235422 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 00:45:15.236537 INFO::Done
2024-06-24 00:45:15.237631 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 00:45:15.240861 INFO::Starting hierarchical adjustment
2024-06-24 00:45:15.242191 INFO::Found 2 batches.
2024-06-24 00:45:15.243283 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 00:45:15.244477 INFO::Using default BPPARAM
2024-06-24 00:45:15.24558 INFO::Adjusting the last 2 batches sequentially
2024-06-24 00:45:15.247213 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-24 00:45:15.266731 INFO::Done
2024-06-24 00:45:15.268075 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 00:45:15.271634 INFO::ASW Batch was 0.000687327253952501 prior to batch effect correction and is now -0.11433847373576 .
2024-06-24 00:45:15.273116 INFO::Total function execution time is 0.046673059463501 s and adjustment time is 0.0247108936309814 s ( 52.94 )
2024-06-24 00:45:15.27495 INFO::Formatting Data.
2024-06-24 00:45:15.276167 INFO::Replacing NaNs with NAs.
2024-06-24 00:45:15.277713 INFO::Removing potential empty rows and columns
2024-06-24 00:45:15.279481 INFO::Found 0 missing values.
2024-06-24 00:45:15.283633 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 00:45:15.284753 INFO::Done
2024-06-24 00:45:15.285857 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 00:45:15.288968 INFO::Starting hierarchical adjustment
2024-06-24 00:45:15.290298 INFO::Found 2 batches.
2024-06-24 00:45:15.291537 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 00:45:15.292726 INFO::Using default BPPARAM
2024-06-24 00:45:15.293796 INFO::Adjusting the last 2 batches sequentially
2024-06-24 00:45:15.295687 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-24 00:45:15.315073 INFO::Done
2024-06-24 00:45:15.316303 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 00:45:15.319304 INFO::ASW Batch was 0.000687327253952501 prior to batch effect correction and is now -0.11433847373576 .
2024-06-24 00:45:15.320693 INFO::Total function execution time is 0.0457539558410645 s and adjustment time is 0.024960994720459 s ( 54.55 )
2024-06-24 00:45:17.757677 INFO::Formatting Data.
2024-06-24 00:45:17.758721 INFO::Recognized SummarizedExperiment
2024-06-24 00:45:17.759472 INFO::Typecasting input to dataframe.
2024-06-24 00:45:17.808554 INFO::Replacing NaNs with NAs.
2024-06-24 00:45:17.810061 INFO::Removing potential empty rows and columns
2024-06-24 00:45:17.813037 INFO::Found 0 missing values.
2024-06-24 00:45:18.684557 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 00:45:18.686053 INFO::Done
2024-06-24 00:45:18.687439 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 00:45:18.69571 INFO::Starting hierarchical adjustment
2024-06-24 00:45:18.697308 INFO::Found 2 batches.
2024-06-24 00:45:18.698492 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 00:45:18.700363 INFO::Using default BPPARAM
2024-06-24 00:45:18.701506 INFO::Adjusting the last 2 batches sequentially
2024-06-24 00:45:18.70334 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-24 00:45:18.784489 INFO::Done
2024-06-24 00:45:18.78589 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 00:45:18.792289 INFO::ASW Batch was 0.0223625020122773 prior to batch effect correction and is now -0.0906335312196247 .
2024-06-24 00:45:18.793982 INFO::Total function execution time is 1.03649687767029 s and adjustment time is 0.0873908996582031 s ( 8.43 )
2024-06-24 00:45:18.824485 INFO::Formatting Data.
2024-06-24 00:45:18.825929 INFO::Recognized SummarizedExperiment
2024-06-24 00:45:18.827168 INFO::Typecasting input to dataframe.
2024-06-24 00:45:18.840824 INFO::Replacing NaNs with NAs.
2024-06-24 00:45:18.843002 INFO::Removing potential empty rows and columns
2024-06-24 00:45:18.848313 INFO::Found 0 missing values.
2024-06-24 00:45:18.858128 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 00:45:18.859611 INFO::Done
2024-06-24 00:45:18.860872 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 00:45:18.86729 INFO::Starting hierarchical adjustment
2024-06-24 00:45:18.868783 INFO::Found 2 batches.
2024-06-24 00:45:18.870076 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 00:45:18.871349 INFO::Using default BPPARAM
2024-06-24 00:45:18.872512 INFO::Adjusting the last 2 batches sequentially
2024-06-24 00:45:18.874379 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-24 00:45:18.91272 INFO::Done
2024-06-24 00:45:18.914158 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 00:45:18.920595 INFO::ASW Batch was -0.0184933673028156 prior to batch effect correction and is now -0.0184933673028156 .
2024-06-24 00:45:18.922266 INFO::Total function execution time is 0.0977342128753662 s and adjustment time is 0.0441040992736816 s ( 45.13 )
2024-06-24 00:45:18.954594 INFO::Formatting Data.
2024-06-24 00:45:18.956052 INFO::Replacing NaNs with NAs.
2024-06-24 00:45:18.957773 INFO::Removing potential empty rows and columns
2024-06-24 00:45:18.959512 INFO::Found 0 missing values.
2024-06-24 00:45:18.963889 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 00:45:18.965032 INFO::Done
2024-06-24 00:45:18.966164 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 00:45:18.96924 INFO::Starting hierarchical adjustment
2024-06-24 00:45:18.970533 INFO::Found 3 batches.
2024-06-24 00:45:18.971729 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 00:45:18.973409 INFO::Using default BPPARAM
2024-06-24 00:45:18.974531 INFO::Processing subtree level 1
2024-06-24 00:45:42.090999 INFO::Adjusting the last 1 batches sequentially
2024-06-24 00:45:42.093258 INFO::Done
2024-06-24 00:45:42.094551 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 00:45:42.097665 INFO::ASW Batch was -0.0799339214409542 prior to batch effect correction and is now -0.143536573763083 .
2024-06-24 00:45:42.099477 INFO::Total function execution time is 23.1449790000916 s and adjustment time is 23.1228799819946 s ( 99.9 )
2024-06-24 00:45:42.12367 INFO::Skipping initial DF formatting
2024-06-24 00:45:42.124929 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 00:45:42.13128 INFO::Starting hierarchical adjustment
2024-06-24 00:45:42.13273 INFO::Found 5 batches.
2024-06-24 00:45:42.133835 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 00:45:42.134976 INFO::Using default BPPARAM
2024-06-24 00:45:42.136011 INFO::Processing subtree level 1
2024-06-24 00:45:55.774435 INFO::Adjusting the last 2 batches sequentially
2024-06-24 00:45:55.776567 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-24 00:45:55.798267 INFO::Done
2024-06-24 00:45:55.799539 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 00:45:55.806231 INFO::ASW Batch was 0.466756444618795 prior to batch effect correction and is now 0.466756444618795 .
2024-06-24 00:45:55.807452 INFO::ASW Label was 0.380469298512557 prior to batch effect correction and is now 0.380469298512557 .
2024-06-24 00:45:55.808872 INFO::Total function execution time is 13.6852819919586 s and adjustment time is 13.6657209396362 s ( 99.86 )
2024-06-24 00:45:55.833618 INFO::Formatting Data.
2024-06-24 00:45:55.835083 INFO::Replacing NaNs with NAs.
2024-06-24 00:45:55.836769 INFO::Removing potential empty rows and columns
2024-06-24 00:45:55.838523 INFO::Found 0 missing values.
2024-06-24 00:45:55.844374 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 00:45:55.845662 INFO::Done
2024-06-24 00:45:55.846924 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 00:45:55.851711 INFO::Starting hierarchical adjustment
2024-06-24 00:45:55.853141 INFO::Found 5 batches.
2024-06-24 00:45:55.854268 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 00:45:55.855519 INFO::Using default BPPARAM
2024-06-24 00:45:55.856598 INFO::Processing subtree level 1
2024-06-24 00:46:09.7402 INFO::Adjusting the last 2 batches sequentially
2024-06-24 00:46:09.742453 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-24 00:46:09.761174 INFO::Done
2024-06-24 00:46:09.76256 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 00:46:09.7674 INFO::ASW Batch was 0.43689899739404 prior to batch effect correction and is now 0.00101979096745711 .
2024-06-24 00:46:09.768718 INFO::ASW Label was 0.263489619946577 prior to batch effect correction and is now 0.79247781022623 .
2024-06-24 00:46:09.770248 INFO::Total function execution time is 13.9367349147797 s and adjustment time is 13.9082169532776 s ( 99.8 )
2024-06-24 00:46:09.771732 INFO::Formatting Data.
2024-06-24 00:46:09.772917 INFO::Replacing NaNs with NAs.
2024-06-24 00:46:09.77416 INFO::Removing potential empty rows and columns
2024-06-24 00:46:09.77534 INFO::Found 0 missing values.
2024-06-24 00:46:09.778887 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 00:46:09.779617 INFO::Done
2024-06-24 00:46:09.780311 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 00:46:09.783263 INFO::Starting hierarchical adjustment
2024-06-24 00:46:09.784123 INFO::Found 5 batches.
2024-06-24 00:46:09.78482 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 00:46:09.785575 INFO::Using default BPPARAM
2024-06-24 00:46:09.786631 INFO::Processing subtree level 1
2024-06-24 00:46:23.667115 INFO::Adjusting the last 2 batches sequentially
2024-06-24 00:46:23.66861 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-24 00:46:23.686942 INFO::Done
2024-06-24 00:46:23.688381 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 00:46:23.693422 INFO::ASW Batch was 0.43689899739404 prior to batch effect correction and is now 0.00101979096745711 .
2024-06-24 00:46:23.694298 INFO::ASW Label was 0.263489619946577 prior to batch effect correction and is now 0.79247781022623 .
2024-06-24 00:46:23.695316 INFO::Total function execution time is 13.9236259460449 s and adjustment time is 13.9028270244598 s ( 99.85 )
2024-06-24 00:46:23.712405 INFO::Formatting Data.
2024-06-24 00:46:23.713626 INFO::Replacing NaNs with NAs.
2024-06-24 00:46:23.714802 INFO::Removing potential empty rows and columns
2024-06-24 00:46:23.716074 INFO::Found 0 missing values.
2024-06-24 00:46:23.719773 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 00:46:23.720617 INFO::Done
2024-06-24 00:46:23.72154 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 00:46:23.724857 INFO::Starting hierarchical adjustment
2024-06-24 00:46:23.725815 INFO::Found 5 batches.
2024-06-24 00:46:23.726538 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 00:46:23.727411 INFO::Using default BPPARAM
2024-06-24 00:46:23.7282 INFO::Processing subtree level 1
2024-06-24 00:46:37.46277 INFO::Adjusting the last 2 batches sequentially
2024-06-24 00:46:37.464819 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-24 00:46:37.484247 INFO::Done
2024-06-24 00:46:37.485638 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 00:46:37.490326 INFO::ASW Batch was 0.562053872028707 prior to batch effect correction and is now -0.0720634326926468 .
2024-06-24 00:46:37.491626 INFO::ASW Label was 0.102579950159023 prior to batch effect correction and is now 0.780175842973495 .
2024-06-24 00:46:37.493195 INFO::Total function execution time is 13.7807919979095 s and adjustment time is 13.7585091590881 s ( 99.84 )
2024-06-24 00:46:37.494667 INFO::Formatting Data.
2024-06-24 00:46:37.495761 INFO::Replacing NaNs with NAs.
2024-06-24 00:46:37.497168 INFO::Removing potential empty rows and columns
2024-06-24 00:46:37.498701 INFO::Found 0 missing values.
2024-06-24 00:46:37.503683 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 00:46:37.504434 INFO::Done
2024-06-24 00:46:37.505129 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 00:46:37.508213 INFO::Starting hierarchical adjustment
2024-06-24 00:46:37.509366 INFO::Found 5 batches.
2024-06-24 00:46:37.510239 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 00:46:37.511096 INFO::Using default BPPARAM
2024-06-24 00:46:37.511802 INFO::Processing subtree level 1
2024-06-24 00:46:51.11037 INFO::Adjusting the last 2 batches sequentially
2024-06-24 00:46:51.111756 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-24 00:46:51.12384 INFO::Done
2024-06-24 00:46:51.125172 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 00:46:51.128292 INFO::ASW Batch was 0.562053872028707 prior to batch effect correction and is now -0.0720634326926468 .
2024-06-24 00:46:51.129103 INFO::ASW Label was 0.102579950159023 prior to batch effect correction and is now 0.780175842973495 .
2024-06-24 00:46:51.130032 INFO::Total function execution time is 13.6354420185089 s and adjustment time is 13.6146879196167 s ( 99.85 )
2024-06-24 00:46:51.147467 INFO::Formatting Data.
2024-06-24 00:46:51.148479 INFO::Replacing NaNs with NAs.
2024-06-24 00:46:51.149522 INFO::Removing potential empty rows and columns
2024-06-24 00:46:51.15063 INFO::Found 0 missing values.
2024-06-24 00:46:51.153054 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 00:46:51.153778 INFO::Done
2024-06-24 00:46:51.154636 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 00:46:51.157702 INFO::Starting hierarchical adjustment
2024-06-24 00:46:51.158563 INFO::Found 2 batches.
2024-06-24 00:46:51.159292 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 00:46:51.160104 INFO::Using default BPPARAM
2024-06-24 00:46:51.16086 INFO::Adjusting the last 2 batches sequentially
2024-06-24 00:46:51.161899 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-24 00:46:51.17367 INFO::Done
2024-06-24 00:46:51.174592 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 00:46:51.177572 INFO::ASW Batch was 0.632062931668814 prior to batch effect correction and is now 0.0279684870490926 .
2024-06-24 00:46:51.178356 INFO::ASW Label was 0.455544283376787 prior to batch effect correction and is now 0.888290725526864 .
2024-06-24 00:46:51.179316 INFO::Total function execution time is 0.0319359302520752 s and adjustment time is 0.0152199268341064 s ( 47.66 )
2024-06-24 00:46:51.180287 INFO::Formatting Data.
2024-06-24 00:46:51.181103 INFO::Replacing NaNs with NAs.
2024-06-24 00:46:51.18213 INFO::Removing potential empty rows and columns
2024-06-24 00:46:51.183184 INFO::Found 0 missing values.
2024-06-24 00:46:51.185612 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 00:46:51.186321 INFO::Done
2024-06-24 00:46:51.187042 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 00:46:51.190134 INFO::Starting hierarchical adjustment
2024-06-24 00:46:51.190999 INFO::Found 2 batches.
2024-06-24 00:46:51.19169 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 00:46:51.192443 INFO::Using default BPPARAM
2024-06-24 00:46:51.193127 INFO::Adjusting the last 2 batches sequentially
2024-06-24 00:46:51.194279 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-24 00:46:51.206939 INFO::Done
2024-06-24 00:46:51.207811 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 00:46:51.210895 INFO::ASW Batch was 0.632062931668814 prior to batch effect correction and is now 0.0279684870490926 .
2024-06-24 00:46:51.211669 INFO::ASW Label was 0.455544283376787 prior to batch effect correction and is now 0.888290725526864 .
2024-06-24 00:46:51.212604 INFO::Total function execution time is 0.0323309898376465 s and adjustment time is 0.0160348415374756 s ( 49.6 )
2024-06-24 00:46:51.228547 INFO::Formatting Data.
2024-06-24 00:46:51.229486 INFO::Replacing NaNs with NAs.
2024-06-24 00:46:51.230612 INFO::Removing potential empty rows and columns
2024-06-24 00:46:51.231707 INFO::Found 0 missing values.
2024-06-24 00:46:51.233757 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 00:46:51.234465 INFO::Done
2024-06-24 00:46:51.235213 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 00:46:51.238171 INFO::Starting hierarchical adjustment
2024-06-24 00:46:51.23912 INFO::Found 2 batches.
2024-06-24 00:46:51.239843 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 00:46:51.240618 INFO::Using default BPPARAM
2024-06-24 00:46:51.24135 INFO::Adjusting the last 2 batches sequentially
2024-06-24 00:46:51.242443 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-24 00:46:51.268666 INFO::Done
2024-06-24 00:46:51.269841 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 00:46:51.271901 INFO::ASW Batch was -0.0584448129866135 prior to batch effect correction and is now -0.154788224690581 .
2024-06-24 00:46:51.272934 INFO::Total function execution time is 0.0444729328155518 s and adjustment time is 0.0296518802642822 s ( 66.67 )
2024-06-24 00:46:51.288986 INFO::Formatting Data.
2024-06-24 00:46:51.289924 INFO::Replacing NaNs with NAs.
2024-06-24 00:46:51.291011 INFO::Removing potential empty rows and columns
2024-06-24 00:46:51.292148 INFO::Found 0 missing values.
2024-06-24 00:46:51.293435 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.
2024-06-24 00:46:51.297376 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 00:46:51.298099 INFO::Done
2024-06-24 00:46:51.298936 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 00:46:51.301833 INFO::Starting hierarchical adjustment
2024-06-24 00:46:51.302709 INFO::Found 2 batches.
2024-06-24 00:46:51.303475 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 00:46:51.304335 INFO::Using default BPPARAM
2024-06-24 00:46:51.305053 INFO::Adjusting the last 2 batches sequentially
2024-06-24 00:46:51.3061 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-24 00:46:51.32044 INFO::Done
2024-06-24 00:46:51.321614 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 00:46:51.324685 INFO::ASW Batch was 0.588258559524977 prior to batch effect correction and is now 0.14153869377596 .
2024-06-24 00:46:51.325486 INFO::ASW Label was 0.565549080948034 prior to batch effect correction and is now 0.848933235207133 .
2024-06-24 00:46:51.326466 INFO::Total function execution time is 0.037553071975708 s and adjustment time is 0.0178380012512207 s ( 47.5 )
2024-06-24 00:46:51.327533 INFO::Formatting Data.
2024-06-24 00:46:51.328584 INFO::Replacing NaNs with NAs.
2024-06-24 00:46:51.329813 INFO::Removing potential empty rows and columns
2024-06-24 00:46:51.331045 INFO::Found 0 missing values.
2024-06-24 00:46:51.332127 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.
2024-06-24 00:46:51.33627 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 00:46:51.337068 INFO::Done
2024-06-24 00:46:51.339389 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 00:46:51.342443 INFO::Starting hierarchical adjustment
2024-06-24 00:46:51.343384 INFO::Found 2 batches.
2024-06-24 00:46:51.344103 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 00:46:51.344894 INFO::Using default BPPARAM
2024-06-24 00:46:51.345604 INFO::Adjusting the last 2 batches sequentially
2024-06-24 00:46:51.347098 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-24 00:46:51.36143 INFO::Done
2024-06-24 00:46:51.362361 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 00:46:51.365374 INFO::ASW Batch was 0.588258559524977 prior to batch effect correction and is now 0.14153869377596 .
2024-06-24 00:46:51.366218 INFO::ASW Label was 0.565549080948034 prior to batch effect correction and is now 0.848933235207133 .
2024-06-24 00:46:51.367237 INFO::Total function execution time is 0.0397090911865234 s and adjustment time is 0.0181629657745361 s ( 45.74 )
2024-06-24 00:46:51.579243 INFO::Formatting Data.
2024-06-24 00:46:51.580528 INFO::Replacing NaNs with NAs.
2024-06-24 00:46:51.58188 INFO::Removing potential empty rows and columns
2024-06-24 00:46:51.583338 INFO::Found 0 missing values.
2024-06-24 00:46:51.586771 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 00:46:51.5876 INFO::Done
2024-06-24 00:46:51.588398 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 00:46:51.590961 INFO::Starting hierarchical adjustment
2024-06-24 00:46:51.59198 INFO::Found 3 batches.
2024-06-24 00:46:51.592794 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 00:46:51.593748 INFO::Using default BPPARAM
2024-06-24 00:46:51.594523 INFO::Processing subtree level 1
2024-06-24 00:47:04.612028 INFO::Adjusting the last 1 batches sequentially
2024-06-24 00:47:04.613804 INFO::Done
2024-06-24 00:47:04.615042 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 00:47:04.618136 INFO::ASW Batch was -0.0876463312658886 prior to batch effect correction and is now -0.0876463312658886 .
2024-06-24 00:47:04.619692 INFO::Total function execution time is 13.0404798984528 s and adjustment time is 13.0219540596008 s ( 99.86 )
2024-06-24 00:47:04.621424 INFO::Formatting Data.
2024-06-24 00:47:04.622732 INFO::Typecasting input to dataframe.
2024-06-24 00:47:04.62421 INFO::Replacing NaNs with NAs.
2024-06-24 00:47:04.625871 INFO::Removing potential empty rows and columns
2024-06-24 00:47:04.627579 INFO::Found 0 missing values.
2024-06-24 00:47:04.631773 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 00:47:04.632947 INFO::Done
2024-06-24 00:47:04.634108 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 00:47:04.637246 INFO::Starting hierarchical adjustment
2024-06-24 00:47:04.638614 INFO::Found 3 batches.
2024-06-24 00:47:04.639785 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 00:47:04.641038 INFO::Using default BPPARAM
2024-06-24 00:47:04.642262 INFO::Processing subtree level 1
2024-06-24 00:47:17.979936 INFO::Adjusting the last 1 batches sequentially
2024-06-24 00:47:17.982119 INFO::Done
2024-06-24 00:47:17.983351 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 00:47:17.986355 INFO::ASW Batch was -0.0876463312658886 prior to batch effect correction and is now -0.0876463312658886 .
2024-06-24 00:47:17.987835 INFO::Total function execution time is 13.3664259910583 s and adjustment time is 13.3436748981476 s ( 99.83 )
2024-06-24 00:47:18.007221 INFO::Formatting Data.
2024-06-24 00:47:18.008185 INFO::Typecasting input to dataframe.
2024-06-24 00:47:18.009226 INFO::Replacing NaNs with NAs.
2024-06-24 00:47:18.010314 INFO::Removing potential empty rows and columns
2024-06-24 00:47:18.011487 INFO::Found 0 missing values.
2024-06-24 00:47:18.014222 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 00:47:18.015163 INFO::Done
2024-06-24 00:47:18.015884 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 00:47:18.018028 INFO::Starting hierarchical adjustment
2024-06-24 00:47:18.018913 INFO::Found 3 batches.
2024-06-24 00:47:18.019611 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 00:47:18.020365 INFO::Using default BPPARAM
2024-06-24 00:47:18.021126 INFO::Processing subtree level 1
2024-06-24 00:47:31.411902 INFO::Adjusting the last 1 batches sequentially
2024-06-24 00:47:31.414082 INFO::Done
2024-06-24 00:47:31.415378 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 00:47:31.418508 INFO::ASW Batch was -0.0424658153701573 prior to batch effect correction and is now -0.0424658153701573 .
2024-06-24 00:47:31.420005 INFO::Total function execution time is 13.4128019809723 s and adjustment time is 13.3952498435974 s ( 99.87 )
2024-06-24 00:47:44.928531 INFO::Formatting Data.
2024-06-24 00:47:44.93017 INFO::Replacing NaNs with NAs.
2024-06-24 00:47:44.932182 INFO::Removing potential empty rows and columns
2024-06-24 00:47:44.935483 INFO::Found 1000 missing values.
2024-06-24 00:47:44.953463 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 00:47:44.954709 INFO::Done
2024-06-24 00:47:44.955787 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 00:47:44.964798 INFO::Starting hierarchical adjustment
2024-06-24 00:47:44.966357 INFO::Found 10 batches.
2024-06-24 00:47:44.967476 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 00:47:44.968747 INFO::Using default BPPARAM
2024-06-24 00:47:44.969875 INFO::Processing subtree level 1
2024-06-24 00:47:58.45665 INFO::Processing subtree level 2
2024-06-24 00:48:11.697132 INFO::Adjusting the last 1 batches sequentially
2024-06-24 00:48:11.698883 INFO::Done
2024-06-24 00:48:11.699753 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 00:48:11.705854 INFO::ASW Batch was 0.462771247698756 prior to batch effect correction and is now 0.462771247698756 .
2024-06-24 00:48:11.706758 INFO::ASW Label was 0.353153679592662 prior to batch effect correction and is now 0.353153679592662 .
2024-06-24 00:48:11.707807 INFO::Total function execution time is 26.7794458866119 s and adjustment time is 26.7327930927277 s ( 99.83 )
2024-06-24 00:48:11.708858 INFO::Formatting Data.
2024-06-24 00:48:11.70977 INFO::Replacing NaNs with NAs.
2024-06-24 00:48:11.711162 INFO::Removing potential empty rows and columns
2024-06-24 00:48:11.713533 INFO::Found 1000 missing values.
2024-06-24 00:48:11.728101 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 00:48:11.729049 INFO::Done
2024-06-24 00:48:11.72993 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 00:48:11.736164 INFO::Starting hierarchical adjustment
2024-06-24 00:48:11.737155 INFO::Found 10 batches.
2024-06-24 00:48:12.467316 INFO::Set up parallel execution backend with 2 workers
2024-06-24 00:48:12.468797 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-06-24 00:48:20.960169 INFO::Adjusting the last 2 batches sequentially
2024-06-24 00:48:20.96238 INFO::Adjusting sequential tree level 1 with 2 batches
2024-06-24 00:48:20.986143 INFO::Done
2024-06-24 00:48:20.987545 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 00:48:20.996755 INFO::ASW Batch was 0.462771247698756 prior to batch effect correction and is now 0.462771247698756 .
2024-06-24 00:48:20.99819 INFO::ASW Label was 0.353153679592662 prior to batch effect correction and is now 0.353153679592662 .
2024-06-24 00:48:20.999778 INFO::Total function execution time is 9.29085898399353 s and adjustment time is 9.24905300140381 s ( 99.55 )
2024-06-24 00:48:34.860245 INFO::Formatting Data.
2024-06-24 00:48:34.861776 INFO::Replacing NaNs with NAs.
2024-06-24 00:48:34.863512 INFO::Removing potential empty rows and columns
2024-06-24 00:48:34.865415 INFO::Found 0 missing values.
2024-06-24 00:48:34.870788 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 00:48:34.872047 INFO::Done
2024-06-24 00:48:34.873231 INFO::Acquiring quality metrics before batch effect correction.
2024-06-24 00:48:34.877556 INFO::Starting hierarchical adjustment
2024-06-24 00:48:34.878995 INFO::Found 3 batches.
2024-06-24 00:48:34.880161 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-06-24 00:48:34.881467 INFO::Using default BPPARAM
2024-06-24 00:48:34.882631 INFO::Processing subtree level 1
2024-06-24 00:48:48.289916 INFO::Adjusting the last 1 batches sequentially
2024-06-24 00:48:48.29153 INFO::Done
2024-06-24 00:48:48.292361 INFO::Acquiring quality metrics after batch effect correction.
2024-06-24 00:48:48.295164 INFO::ASW Batch was 0.210283578089765 prior to batch effect correction and is now -0.162547878494899 .
2024-06-24 00:48:48.296281 INFO::ASW Label was -0.199727233007924 prior to batch effect correction and is now -0.0652610881726363 .
2024-06-24 00:48:48.297658 INFO::Total function execution time is 13.4375381469727 s and adjustment time is 13.4127650260925 s ( 99.82 )
2024-06-24 00:48:48.502517 INFO::Formatting Data.
2024-06-24 00:48:48.50385 INFO::Replacing NaNs with NAs.
2024-06-24 00:48:48.50533 INFO::Removing potential empty rows and columns
2024-06-24 00:48:48.506954 INFO::Found 2 missing values.
2024-06-24 00:48:48.51072 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-06-24 00:48:48.511729 INFO::Done
2024-06-24 00:48:48.565858 INFO::Found NA in Reference column
2024-06-24 00:48:48.584968 INFO::Require at least two references per batch.
2024-06-24 00:48:48.607896 INFO::Formatting Data.
2024-06-24 00:48:48.608854 INFO::Recognized SummarizedExperiment
2024-06-24 00:48:48.609581 INFO::Typecasting input to dataframe.
2024-06-24 00:48:48.617425 INFO::Replacing NaNs with NAs.
2024-06-24 00:48:48.618748 INFO::Removing potential empty rows and columns
2024-06-24 00:48:48.621388 INFO::Found 0 missing values.
2024-06-24 00:48:48.62665 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 00:48:48.627984 INFO::Done
2024-06-24 00:48:48.650256 INFO::Formatting Data.
2024-06-24 00:48:48.651573 INFO::Recognized SummarizedExperiment
2024-06-24 00:48:48.652665 INFO::Typecasting input to dataframe.
2024-06-24 00:48:48.674469 INFO::Replacing NaNs with NAs.
2024-06-24 00:48:48.676384 INFO::Removing potential empty rows and columns
2024-06-24 00:48:48.681014 INFO::Found 0 missing values.
2024-06-24 00:48:48.691098 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 00:48:48.691977 INFO::Done
2024-06-24 00:48:48.707138 INFO::Formatting Data.
2024-06-24 00:48:48.708168 INFO::Recognized SummarizedExperiment
2024-06-24 00:48:48.708963 INFO::Typecasting input to dataframe.
2024-06-24 00:48:48.723347 INFO::Replacing NaNs with NAs.
2024-06-24 00:48:48.724518 INFO::Removing potential empty rows and columns
2024-06-24 00:48:48.725703 INFO::Found 0 missing values.
2024-06-24 00:48:48.726799 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.
2024-06-24 00:48:48.73046 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 00:48:48.731215 INFO::Done
2024-06-24 00:48:48.745775 INFO::Formatting Data.
2024-06-24 00:48:48.746796 INFO::Replacing NaNs with NAs.
2024-06-24 00:48:48.747843 INFO::Removing potential empty rows and columns
2024-06-24 00:48:48.749014 INFO::Found 0 missing values.
2024-06-24 00:48:48.751782 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 00:48:48.752529 INFO::Done
2024-06-24 00:48:48.767534 INFO::Formatting Data.
2024-06-24 00:48:48.768495 INFO::Replacing NaNs with NAs.
2024-06-24 00:48:48.769583 INFO::Removing potential empty rows and columns
2024-06-24 00:48:48.770703 INFO::Found 0 missing values.
2024-06-24 00:48:48.773438 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 00:48:48.774154 INFO::Done
2024-06-24 00:48:48.814524 INFO::Formatting Data.
2024-06-24 00:48:48.815544 INFO::Replacing NaNs with NAs.
2024-06-24 00:48:48.816822 INFO::Removing potential empty rows and columns
2024-06-24 00:48:48.818074 INFO::Found 1 missing values.
2024-06-24 00:48:48.820526 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 00:48:48.821266 INFO::Done
2024-06-24 00:48:48.847844 INFO::Formatting Data.
2024-06-24 00:48:48.849406 INFO::Replacing NaNs with NAs.
2024-06-24 00:48:48.851045 INFO::Removing potential empty rows and columns
2024-06-24 00:48:48.852493 INFO::Found 2 missing values.
2024-06-24 00:48:48.85359 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.
2024-06-24 00:48:48.855811 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-06-24 00:48:48.8566 INFO::Done
2024-06-24 00:48:48.87102 INFO::Formatting Data.
2024-06-24 00:48:48.871989 INFO::Replacing NaNs with NAs.
2024-06-24 00:48:48.873016 INFO::Removing potential empty rows and columns
2024-06-24 00:48:48.874115 INFO::Found 2 missing values.
2024-06-24 00:48:48.878008 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 00:48:48.879247 INFO::Done
2024-06-24 00:48:48.900176 INFO::Formatting Data.
2024-06-24 00:48:48.901603 INFO::Typecasting input to dataframe.
2024-06-24 00:48:48.903294 INFO::Replacing NaNs with NAs.
2024-06-24 00:48:48.905187 INFO::Removing potential empty rows and columns
2024-06-24 00:48:48.907009 INFO::Found 0 missing values.
2024-06-24 00:48:48.91111 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-06-24 00:48:48.912261 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
27.93 11.60 265.12
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 8.09 | 4.77 | 29.71 | |
| compute_asw | 0.03 | 0.00 | 0.03 | |
| count_existing | 0.01 | 0.00 | 0.01 | |
| generate_data_covariables | 0.00 | 0.01 | 0.02 | |
| generate_dataset | 0.02 | 0.00 | 0.02 | |