Yannis Schumann
| Snapshot Date: 2024-05-21 14:00:15 -0400 (Tue, 21 May 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 2024-05-22 11:35:26 -0400 (Wed, 22 May 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" | 4751 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4485 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 3444 |
| 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 | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 2024-05-21 23:21:08 -0400 (Tue, 21 May 2024) |
| EndedAt: 2024-05-21 23:23:20 -0400 (Tue, 21 May 2024) |
| EllapsedTime: 131.9 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 8.81 0.48 18.52
* 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")
2024-05-21 23:22:09.949774 INFO::Formatting Data.
2024-05-21 23:22:09.952967 INFO::Replacing NaNs with NAs.
2024-05-21 23:22:09.968061 INFO::Removing potential empty rows and columns
2024-05-21 23:22:10.29446 INFO::Found 0 missing values.
2024-05-21 23:22:10.29925 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-21 23:22:10.30059 INFO::Done
2024-05-21 23:22:10.301948 INFO::Acquiring quality metrics before batch effect correction.
2024-05-21 23:22:10.321868 INFO::Starting hierarchical adjustment
2024-05-21 23:22:10.323603 INFO::Found 3 batches.
2024-05-21 23:22:10.324874 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-21 23:22:10.326825 INFO::Using default BPPARAM
2024-05-21 23:22:10.328018 INFO::Processing subtree level 1
2024-05-21 23:22:12.965267 INFO::Adjusting the last 1 batches sequentially
2024-05-21 23:22:12.966733 INFO::Done
2024-05-21 23:22:12.967511 INFO::Acquiring quality metrics after batch effect correction.
2024-05-21 23:22:12.969624 INFO::ASW Batch was 0.0787236672925157 prior to batch effect correction and is now 0.0787236672925157 .
2024-05-21 23:22:12.970709 INFO::Total function execution time is 3.02172517776489 s and adjustment time is 2.6434440612793 s ( 87.48 )
2024-05-21 23:22:12.986831 INFO::Formatting Data.
2024-05-21 23:22:12.987899 INFO::Replacing NaNs with NAs.
2024-05-21 23:22:12.989139 INFO::Removing potential empty rows and columns
2024-05-21 23:22:12.990342 INFO::Found 0 missing values.
2024-05-21 23:22:12.991459 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.
2024-05-21 23:22:12.999902 INFO::Formatting Data.
2024-05-21 23:22:13.000865 INFO::Replacing NaNs with NAs.
2024-05-21 23:22:13.00194 INFO::Removing potential empty rows and columns
2024-05-21 23:22:13.003156 INFO::Found 0 missing values.
2024-05-21 23:22:13.004263 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.
2024-05-21 23:22:13.020784 INFO::Formatting Data.
2024-05-21 23:22:13.021747 INFO::Replacing NaNs with NAs.
2024-05-21 23:22:13.022795 INFO::Removing potential empty rows and columns
2024-05-21 23:22:13.023904 INFO::Found 0 missing values.
2024-05-21 23:22:13.024984 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.
2024-05-21 23:22:13.028632 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-21 23:22:13.02935 INFO::Done
2024-05-21 23:22:13.030051 INFO::Acquiring quality metrics before batch effect correction.
2024-05-21 23:22:13.032144 INFO::Starting hierarchical adjustment
2024-05-21 23:22:13.033011 INFO::Found 2 batches.
2024-05-21 23:22:13.033807 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-21 23:22:13.03461 INFO::Using default BPPARAM
2024-05-21 23:22:13.035321 INFO::Adjusting the last 2 batches sequentially
2024-05-21 23:22:13.036382 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-21 23:22:13.052599 INFO::Done
2024-05-21 23:22:13.053467 INFO::Acquiring quality metrics after batch effect correction.
2024-05-21 23:22:13.055767 INFO::ASW Batch was -0.0563611841953705 prior to batch effect correction and is now -0.131441690107613 .
2024-05-21 23:22:13.057181 INFO::Total function execution time is 0.036423921585083 s and adjustment time is 0.0196750164031982 s ( 54.02 )
2024-05-21 23:22:13.060241 INFO::Formatting Data.
2024-05-21 23:22:13.061274 INFO::Replacing NaNs with NAs.
2024-05-21 23:22:13.068215 INFO::Formatting Data.
2024-05-21 23:22:13.069061 INFO::Replacing NaNs with NAs.
2024-05-21 23:22:13.07008 INFO::Removing potential empty rows and columns
2024-05-21 23:22:13.0712 INFO::Found 0 missing values.
2024-05-21 23:22:13.073637 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-21 23:22:13.074359 INFO::Done
2024-05-21 23:22:13.075056 INFO::Acquiring quality metrics before batch effect correction.
2024-05-21 23:22:13.077129 INFO::Starting hierarchical adjustment
2024-05-21 23:22:13.077999 INFO::Found 2 batches.
2024-05-21 23:22:13.078704 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-21 23:22:13.079476 INFO::Using default BPPARAM
2024-05-21 23:22:13.08018 INFO::Adjusting the last 2 batches sequentially
2024-05-21 23:22:13.081225 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-21 23:22:13.09318 INFO::Done
2024-05-21 23:22:13.093992 INFO::Acquiring quality metrics after batch effect correction.
2024-05-21 23:22:13.096026 INFO::ASW Batch was -0.0314368390840415 prior to batch effect correction and is now -0.111747639356064 .
2024-05-21 23:22:13.096966 INFO::Total function execution time is 0.0287749767303467 s and adjustment time is 0.0153019428253174 s ( 53.18 )
2024-05-21 23:22:13.098142 INFO::Formatting Data.
2024-05-21 23:22:13.098931 INFO::Replacing NaNs with NAs.
2024-05-21 23:22:13.099929 INFO::Removing potential empty rows and columns
2024-05-21 23:22:13.101012 INFO::Found 0 missing values.
2024-05-21 23:22:13.103685 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-21 23:22:13.104422 INFO::Done
2024-05-21 23:22:13.105205 INFO::Acquiring quality metrics before batch effect correction.
2024-05-21 23:22:13.107631 INFO::Starting hierarchical adjustment
2024-05-21 23:22:13.108877 INFO::Found 2 batches.
2024-05-21 23:22:13.109794 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-21 23:22:13.110688 INFO::Using default BPPARAM
2024-05-21 23:22:13.111437 INFO::Adjusting the last 2 batches sequentially
2024-05-21 23:22:13.112522 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-21 23:22:13.124917 INFO::Done
2024-05-21 23:22:13.125763 INFO::Acquiring quality metrics after batch effect correction.
2024-05-21 23:22:13.127869 INFO::ASW Batch was -0.0314368390840415 prior to batch effect correction and is now -0.111747639356064 .
2024-05-21 23:22:13.128836 INFO::Total function execution time is 0.0306839942932129 s and adjustment time is 0.0162239074707031 s ( 52.87 )
2024-05-21 23:22:15.95513 INFO::Formatting Data.
2024-05-21 23:22:15.956082 INFO::Recognized SummarizedExperiment
2024-05-21 23:22:15.956824 INFO::Typecasting input to dataframe.
2024-05-21 23:22:15.985455 INFO::Replacing NaNs with NAs.
2024-05-21 23:22:15.986918 INFO::Removing potential empty rows and columns
2024-05-21 23:22:15.990039 INFO::Found 0 missing values.
2024-05-21 23:22:15.995871 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-21 23:22:15.996761 INFO::Done
2024-05-21 23:22:15.997547 INFO::Acquiring quality metrics before batch effect correction.
2024-05-21 23:22:16.001469 INFO::Starting hierarchical adjustment
2024-05-21 23:22:16.002381 INFO::Found 2 batches.
2024-05-21 23:22:16.003107 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-21 23:22:16.004416 INFO::Using default BPPARAM
2024-05-21 23:22:16.005178 INFO::Adjusting the last 2 batches sequentially
2024-05-21 23:22:16.006422 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-21 23:22:16.052421 INFO::Done
2024-05-21 23:22:16.053342 INFO::Acquiring quality metrics after batch effect correction.
2024-05-21 23:22:16.057342 INFO::ASW Batch was 0.0114381369422939 prior to batch effect correction and is now -0.0899707465159887 .
2024-05-21 23:22:16.058438 INFO::Total function execution time is 0.103597164154053 s and adjustment time is 0.0501542091369629 s ( 48.41 )
2024-05-21 23:22:16.077691 INFO::Formatting Data.
2024-05-21 23:22:16.078661 INFO::Recognized SummarizedExperiment
2024-05-21 23:22:16.079431 INFO::Typecasting input to dataframe.
2024-05-21 23:22:16.087499 INFO::Replacing NaNs with NAs.
2024-05-21 23:22:16.08889 INFO::Removing potential empty rows and columns
2024-05-21 23:22:16.091824 INFO::Found 0 missing values.
2024-05-21 23:22:16.097402 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-21 23:22:16.098198 INFO::Done
2024-05-21 23:22:16.098931 INFO::Acquiring quality metrics before batch effect correction.
2024-05-21 23:22:16.102801 INFO::Starting hierarchical adjustment
2024-05-21 23:22:16.103756 INFO::Found 2 batches.
2024-05-21 23:22:16.104501 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-21 23:22:16.105297 INFO::Using default BPPARAM
2024-05-21 23:22:16.106024 INFO::Adjusting the last 2 batches sequentially
2024-05-21 23:22:16.107225 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-21 23:22:16.12701 INFO::Done
2024-05-21 23:22:16.127912 INFO::Acquiring quality metrics after batch effect correction.
2024-05-21 23:22:16.131749 INFO::ASW Batch was 0.0136720597425404 prior to batch effect correction and is now 0.0136720597425404 .
2024-05-21 23:22:16.132817 INFO::Total function execution time is 0.0551269054412842 s and adjustment time is 0.0233738422393799 s ( 42.4 )
2024-05-21 23:22:16.156406 INFO::Formatting Data.
2024-05-21 23:22:16.157709 INFO::Replacing NaNs with NAs.
2024-05-21 23:22:16.159867 INFO::Removing potential empty rows and columns
2024-05-21 23:22:16.161121 INFO::Found 0 missing values.
2024-05-21 23:22:16.164033 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-21 23:22:16.164794 INFO::Done
2024-05-21 23:22:16.165553 INFO::Acquiring quality metrics before batch effect correction.
2024-05-21 23:22:16.168555 INFO::Starting hierarchical adjustment
2024-05-21 23:22:16.170025 INFO::Found 3 batches.
2024-05-21 23:22:16.171336 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-21 23:22:16.172748 INFO::Using default BPPARAM
2024-05-21 23:22:16.174046 INFO::Processing subtree level 1
2024-05-21 23:22:25.987707 INFO::Adjusting the last 1 batches sequentially
2024-05-21 23:22:25.989953 INFO::Done
2024-05-21 23:22:25.991269 INFO::Acquiring quality metrics after batch effect correction.
2024-05-21 23:22:25.994478 INFO::ASW Batch was -0.151589451040986 prior to batch effect correction and is now -0.170959422797001 .
2024-05-21 23:22:25.996015 INFO::Total function execution time is 9.83963513374329 s and adjustment time is 9.82009792327881 s ( 99.8 )
2024-05-21 23:22:26.017476 INFO::Skipping initial DF formatting
2024-05-21 23:22:26.018905 INFO::Acquiring quality metrics before batch effect correction.
2024-05-21 23:22:26.025738 INFO::Starting hierarchical adjustment
2024-05-21 23:22:26.027333 INFO::Found 5 batches.
2024-05-21 23:22:26.028598 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-21 23:22:26.029895 INFO::Using default BPPARAM
2024-05-21 23:22:26.031052 INFO::Processing subtree level 1
2024-05-21 23:22:29.122453 INFO::Adjusting the last 2 batches sequentially
2024-05-21 23:22:29.123957 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-21 23:22:29.138299 INFO::Done
2024-05-21 23:22:29.139208 INFO::Acquiring quality metrics after batch effect correction.
2024-05-21 23:22:29.143531 INFO::ASW Batch was 0.524745358738237 prior to batch effect correction and is now 0.524745358738237 .
2024-05-21 23:22:29.144359 INFO::ASW Label was 0.354623939025468 prior to batch effect correction and is now 0.354623939025468 .
2024-05-21 23:22:29.145347 INFO::Total function execution time is 3.12806177139282 s and adjustment time is 3.11123895645142 s ( 99.46 )
2024-05-21 23:22:29.164216 INFO::Formatting Data.
2024-05-21 23:22:29.165196 INFO::Replacing NaNs with NAs.
2024-05-21 23:22:29.166272 INFO::Removing potential empty rows and columns
2024-05-21 23:22:29.167376 INFO::Found 0 missing values.
2024-05-21 23:22:29.170849 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-21 23:22:29.171584 INFO::Done
2024-05-21 23:22:29.172312 INFO::Acquiring quality metrics before batch effect correction.
2024-05-21 23:22:29.175436 INFO::Starting hierarchical adjustment
2024-05-21 23:22:29.17633 INFO::Found 5 batches.
2024-05-21 23:22:29.17705 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-21 23:22:29.177833 INFO::Using default BPPARAM
2024-05-21 23:22:29.178607 INFO::Processing subtree level 1
2024-05-21 23:22:32.355778 INFO::Adjusting the last 2 batches sequentially
2024-05-21 23:22:32.357912 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-21 23:22:32.375387 INFO::Done
2024-05-21 23:22:32.376701 INFO::Acquiring quality metrics after batch effect correction.
2024-05-21 23:22:32.381063 INFO::ASW Batch was 0.365993210271013 prior to batch effect correction and is now -0.088261193282514 .
2024-05-21 23:22:32.382302 INFO::ASW Label was 0.390063518693048 prior to batch effect correction and is now 0.782316838297022 .
2024-05-21 23:22:32.383752 INFO::Total function execution time is 3.21961116790771 s and adjustment time is 3.19911599159241 s ( 99.36 )
2024-05-21 23:22:32.384858 INFO::Formatting Data.
2024-05-21 23:22:32.385714 INFO::Replacing NaNs with NAs.
2024-05-21 23:22:32.386884 INFO::Removing potential empty rows and columns
2024-05-21 23:22:32.388098 INFO::Found 0 missing values.
2024-05-21 23:22:32.391814 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-21 23:22:32.392842 INFO::Done
2024-05-21 23:22:32.393892 INFO::Acquiring quality metrics before batch effect correction.
2024-05-21 23:22:32.397968 INFO::Starting hierarchical adjustment
2024-05-21 23:22:32.399215 INFO::Found 5 batches.
2024-05-21 23:22:32.399979 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-21 23:22:32.40102 INFO::Using default BPPARAM
2024-05-21 23:22:32.402175 INFO::Processing subtree level 1
2024-05-21 23:22:35.605465 INFO::Adjusting the last 2 batches sequentially
2024-05-21 23:22:35.607591 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-21 23:22:35.626336 INFO::Done
2024-05-21 23:22:35.627822 INFO::Acquiring quality metrics after batch effect correction.
2024-05-21 23:22:35.632428 INFO::ASW Batch was 0.365993210271013 prior to batch effect correction and is now -0.088261193282514 .
2024-05-21 23:22:35.633756 INFO::ASW Label was 0.390063518693048 prior to batch effect correction and is now 0.782316838297022 .
2024-05-21 23:22:35.635345 INFO::Total function execution time is 3.2504301071167 s and adjustment time is 3.22728395462036 s ( 99.29 )
2024-05-21 23:22:35.678515 INFO::Formatting Data.
2024-05-21 23:22:35.747333 INFO::Replacing NaNs with NAs.
2024-05-21 23:22:35.749567 INFO::Removing potential empty rows and columns
2024-05-21 23:22:35.751601 INFO::Found 0 missing values.
2024-05-21 23:22:35.758312 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-21 23:22:35.759841 INFO::Done
2024-05-21 23:22:35.761161 INFO::Acquiring quality metrics before batch effect correction.
2024-05-21 23:22:35.766262 INFO::Starting hierarchical adjustment
2024-05-21 23:22:35.76779 INFO::Found 5 batches.
2024-05-21 23:22:35.769071 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-21 23:22:35.770418 INFO::Using default BPPARAM
2024-05-21 23:22:35.77166 INFO::Processing subtree level 1
2024-05-21 23:22:38.678369 INFO::Adjusting the last 2 batches sequentially
2024-05-21 23:22:38.680542 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-21 23:22:38.698372 INFO::Done
2024-05-21 23:22:38.699435 INFO::Acquiring quality metrics after batch effect correction.
2024-05-21 23:22:38.702598 INFO::ASW Batch was 0.526237895099794 prior to batch effect correction and is now -0.0913547563392133 .
2024-05-21 23:22:38.703429 INFO::ASW Label was 0.316492421856159 prior to batch effect correction and is now 0.787165176813365 .
2024-05-21 23:22:38.704394 INFO::Total function execution time is 3.02628087997437 s and adjustment time is 2.9307279586792 s ( 96.84 )
2024-05-21 23:22:38.705361 INFO::Formatting Data.
2024-05-21 23:22:38.706165 INFO::Replacing NaNs with NAs.
2024-05-21 23:22:38.707188 INFO::Removing potential empty rows and columns
2024-05-21 23:22:38.708279 INFO::Found 0 missing values.
2024-05-21 23:22:38.711703 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-21 23:22:38.712435 INFO::Done
2024-05-21 23:22:38.713157 INFO::Acquiring quality metrics before batch effect correction.
2024-05-21 23:22:38.716168 INFO::Starting hierarchical adjustment
2024-05-21 23:22:38.717071 INFO::Found 5 batches.
2024-05-21 23:22:38.717795 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-21 23:22:38.718567 INFO::Using default BPPARAM
2024-05-21 23:22:38.719275 INFO::Processing subtree level 1
2024-05-21 23:22:41.922092 INFO::Adjusting the last 2 batches sequentially
2024-05-21 23:22:41.924126 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-21 23:22:41.943323 INFO::Done
2024-05-21 23:22:41.944764 INFO::Acquiring quality metrics after batch effect correction.
2024-05-21 23:22:41.950006 INFO::ASW Batch was 0.526237895099794 prior to batch effect correction and is now -0.0913547563392133 .
2024-05-21 23:22:41.951301 INFO::ASW Label was 0.316492421856159 prior to batch effect correction and is now 0.787165176813365 .
2024-05-21 23:22:41.952937 INFO::Total function execution time is 3.24750208854675 s and adjustment time is 3.22630405426025 s ( 99.35 )
2024-05-21 23:22:41.979252 INFO::Formatting Data.
2024-05-21 23:22:41.980811 INFO::Replacing NaNs with NAs.
2024-05-21 23:22:41.981989 INFO::Removing potential empty rows and columns
2024-05-21 23:22:41.983111 INFO::Found 0 missing values.
2024-05-21 23:22:41.985769 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-21 23:22:41.986707 INFO::Done
2024-05-21 23:22:41.987443 INFO::Acquiring quality metrics before batch effect correction.
2024-05-21 23:22:41.990484 INFO::Starting hierarchical adjustment
2024-05-21 23:22:41.991365 INFO::Found 2 batches.
2024-05-21 23:22:41.992077 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-21 23:22:41.992848 INFO::Using default BPPARAM
2024-05-21 23:22:41.993548 INFO::Adjusting the last 2 batches sequentially
2024-05-21 23:22:41.994638 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-21 23:22:42.006316 INFO::Done
2024-05-21 23:22:42.007279 INFO::Acquiring quality metrics after batch effect correction.
2024-05-21 23:22:42.010243 INFO::ASW Batch was 0.491073108094712 prior to batch effect correction and is now 0.00152433819744914 .
2024-05-21 23:22:42.011039 INFO::ASW Label was 0.597885133113203 prior to batch effect correction and is now 0.919431406102299 .
2024-05-21 23:22:42.012015 INFO::Total function execution time is 0.0329539775848389 s and adjustment time is 0.0150771141052246 s ( 45.75 )
2024-05-21 23:22:42.0131 INFO::Formatting Data.
2024-05-21 23:22:42.013894 INFO::Replacing NaNs with NAs.
2024-05-21 23:22:42.014895 INFO::Removing potential empty rows and columns
2024-05-21 23:22:42.015974 INFO::Found 0 missing values.
2024-05-21 23:22:42.01842 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-21 23:22:42.019151 INFO::Done
2024-05-21 23:22:42.019849 INFO::Acquiring quality metrics before batch effect correction.
2024-05-21 23:22:42.022784 INFO::Starting hierarchical adjustment
2024-05-21 23:22:42.023662 INFO::Found 2 batches.
2024-05-21 23:22:42.024374 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-21 23:22:42.025211 INFO::Using default BPPARAM
2024-05-21 23:22:42.025928 INFO::Adjusting the last 2 batches sequentially
2024-05-21 23:22:42.027077 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-21 23:22:42.039327 INFO::Done
2024-05-21 23:22:42.040147 INFO::Acquiring quality metrics after batch effect correction.
2024-05-21 23:22:42.043187 INFO::ASW Batch was 0.491073108094712 prior to batch effect correction and is now 0.00152433819744914 .
2024-05-21 23:22:42.04406 INFO::ASW Label was 0.597885133113203 prior to batch effect correction and is now 0.919431406102299 .
2024-05-21 23:22:42.045016 INFO::Total function execution time is 0.0319259166717529 s and adjustment time is 0.0157890319824219 s ( 49.46 )
2024-05-21 23:22:42.064704 INFO::Formatting Data.
2024-05-21 23:22:42.065717 INFO::Replacing NaNs with NAs.
2024-05-21 23:22:42.06687 INFO::Removing potential empty rows and columns
2024-05-21 23:22:42.068084 INFO::Found 0 missing values.
2024-05-21 23:22:42.070143 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-21 23:22:42.070891 INFO::Done
2024-05-21 23:22:42.071589 INFO::Acquiring quality metrics before batch effect correction.
2024-05-21 23:22:42.074265 INFO::Starting hierarchical adjustment
2024-05-21 23:22:42.075348 INFO::Found 2 batches.
2024-05-21 23:22:42.076175 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-21 23:22:42.077068 INFO::Using default BPPARAM
2024-05-21 23:22:42.078001 INFO::Adjusting the last 2 batches sequentially
2024-05-21 23:22:42.079312 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-21 23:22:42.105121 INFO::Done
2024-05-21 23:22:42.106001 INFO::Acquiring quality metrics after batch effect correction.
2024-05-21 23:22:42.108263 INFO::ASW Batch was -0.0272287932043422 prior to batch effect correction and is now -0.0971522523806405 .
2024-05-21 23:22:42.109237 INFO::Total function execution time is 0.0446438789367676 s and adjustment time is 0.0299179553985596 s ( 67.01 )
2024-05-21 23:22:42.125023 INFO::Formatting Data.
2024-05-21 23:22:42.125957 INFO::Replacing NaNs with NAs.
2024-05-21 23:22:42.126995 INFO::Removing potential empty rows and columns
2024-05-21 23:22:42.128179 INFO::Found 0 missing values.
2024-05-21 23:22:42.129681 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.
2024-05-21 23:22:42.133582 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-21 23:22:42.134664 INFO::Done
2024-05-21 23:22:42.135939 INFO::Acquiring quality metrics before batch effect correction.
2024-05-21 23:22:42.140925 INFO::Starting hierarchical adjustment
2024-05-21 23:22:42.142484 INFO::Found 2 batches.
2024-05-21 23:22:42.143752 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-21 23:22:42.145098 INFO::Using default BPPARAM
2024-05-21 23:22:42.146329 INFO::Adjusting the last 2 batches sequentially
2024-05-21 23:22:42.148167 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-21 23:22:42.171203 INFO::Done
2024-05-21 23:22:42.172698 INFO::Acquiring quality metrics after batch effect correction.
2024-05-21 23:22:42.177769 INFO::ASW Batch was 0.558615097609818 prior to batch effect correction and is now 0.0173309017961738 .
2024-05-21 23:22:42.179279 INFO::ASW Label was 0.529555584387222 prior to batch effect correction and is now 0.891159643400767 .
2024-05-21 23:22:42.180924 INFO::Total function execution time is 0.0558969974517822 s and adjustment time is 0.0288820266723633 s ( 51.67 )
2024-05-21 23:22:42.182548 INFO::Formatting Data.
2024-05-21 23:22:42.183935 INFO::Replacing NaNs with NAs.
2024-05-21 23:22:42.185822 INFO::Removing potential empty rows and columns
2024-05-21 23:22:42.187724 INFO::Found 0 missing values.
2024-05-21 23:22:42.189612 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.
2024-05-21 23:22:42.19619 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-21 23:22:42.197496 INFO::Done
2024-05-21 23:22:42.198742 INFO::Acquiring quality metrics before batch effect correction.
2024-05-21 23:22:42.203853 INFO::Starting hierarchical adjustment
2024-05-21 23:22:42.205387 INFO::Found 2 batches.
2024-05-21 23:22:42.206641 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-21 23:22:42.207997 INFO::Using default BPPARAM
2024-05-21 23:22:42.209396 INFO::Adjusting the last 2 batches sequentially
2024-05-21 23:22:42.211301 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-21 23:22:42.235087 INFO::Done
2024-05-21 23:22:42.236613 INFO::Acquiring quality metrics after batch effect correction.
2024-05-21 23:22:42.241863 INFO::ASW Batch was 0.558615097609818 prior to batch effect correction and is now 0.0173309017961738 .
2024-05-21 23:22:42.243243 INFO::ASW Label was 0.529555584387222 prior to batch effect correction and is now 0.891159643400767 .
2024-05-21 23:22:42.244915 INFO::Total function execution time is 0.0623681545257568 s and adjustment time is 0.0297901630401611 s ( 47.77 )
2024-05-21 23:22:42.504457 INFO::Formatting Data.
2024-05-21 23:22:42.505565 INFO::Replacing NaNs with NAs.
2024-05-21 23:22:42.506756 INFO::Removing potential empty rows and columns
2024-05-21 23:22:42.508037 INFO::Found 0 missing values.
2024-05-21 23:22:42.511348 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-21 23:22:42.512145 INFO::Done
2024-05-21 23:22:42.512935 INFO::Acquiring quality metrics before batch effect correction.
2024-05-21 23:22:42.515604 INFO::Starting hierarchical adjustment
2024-05-21 23:22:42.516639 INFO::Found 3 batches.
2024-05-21 23:22:42.517473 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-21 23:22:42.518363 INFO::Using default BPPARAM
2024-05-21 23:22:42.519165 INFO::Processing subtree level 1
2024-05-21 23:22:45.193151 INFO::Adjusting the last 1 batches sequentially
2024-05-21 23:22:45.195386 INFO::Done
2024-05-21 23:22:45.196638 INFO::Acquiring quality metrics after batch effect correction.
2024-05-21 23:22:45.199664 INFO::ASW Batch was 0.0151431017446726 prior to batch effect correction and is now 0.0151431017446726 .
2024-05-21 23:22:45.20115 INFO::Total function execution time is 2.69675302505493 s and adjustment time is 2.67891192436218 s ( 99.34 )
2024-05-21 23:22:45.202785 INFO::Formatting Data.
2024-05-21 23:22:45.204009 INFO::Typecasting input to dataframe.
2024-05-21 23:22:45.205362 INFO::Replacing NaNs with NAs.
2024-05-21 23:22:45.206885 INFO::Removing potential empty rows and columns
2024-05-21 23:22:45.20855 INFO::Found 0 missing values.
2024-05-21 23:22:45.212567 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-21 23:22:45.213679 INFO::Done
2024-05-21 23:22:45.214804 INFO::Acquiring quality metrics before batch effect correction.
2024-05-21 23:22:45.217299 INFO::Starting hierarchical adjustment
2024-05-21 23:22:45.218324 INFO::Found 3 batches.
2024-05-21 23:22:45.219113 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-21 23:22:45.219977 INFO::Using default BPPARAM
2024-05-21 23:22:45.220754 INFO::Processing subtree level 1
2024-05-21 23:22:48.152749 INFO::Adjusting the last 1 batches sequentially
2024-05-21 23:22:48.155066 INFO::Done
2024-05-21 23:22:48.156325 INFO::Acquiring quality metrics after batch effect correction.
2024-05-21 23:22:48.159412 INFO::ASW Batch was 0.0151431017446726 prior to batch effect correction and is now 0.0151431017446726 .
2024-05-21 23:22:48.160894 INFO::Total function execution time is 2.95811104774475 s and adjustment time is 2.93683385848999 s ( 99.28 )
2024-05-21 23:22:48.180954 INFO::Formatting Data.
2024-05-21 23:22:48.181932 INFO::Typecasting input to dataframe.
2024-05-21 23:22:48.182916 INFO::Replacing NaNs with NAs.
2024-05-21 23:22:48.183952 INFO::Removing potential empty rows and columns
2024-05-21 23:22:48.185164 INFO::Found 0 missing values.
2024-05-21 23:22:48.18786 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-21 23:22:48.188615 INFO::Done
2024-05-21 23:22:48.189395 INFO::Acquiring quality metrics before batch effect correction.
2024-05-21 23:22:48.191649 INFO::Starting hierarchical adjustment
2024-05-21 23:22:48.192508 INFO::Found 3 batches.
2024-05-21 23:22:48.193203 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-21 23:22:48.193973 INFO::Using default BPPARAM
2024-05-21 23:22:48.194685 INFO::Processing subtree level 1
2024-05-21 23:22:50.917248 INFO::Adjusting the last 1 batches sequentially
2024-05-21 23:22:50.91879 INFO::Done
2024-05-21 23:22:50.919715 INFO::Acquiring quality metrics after batch effect correction.
2024-05-21 23:22:50.921901 INFO::ASW Batch was -0.0556490849177486 prior to batch effect correction and is now -0.0556490849177486 .
2024-05-21 23:22:50.922886 INFO::Total function execution time is 2.74204087257385 s and adjustment time is 2.72639298439026 s ( 99.43 )
2024-05-21 23:22:53.681864 INFO::Formatting Data.
2024-05-21 23:22:53.683276 INFO::Replacing NaNs with NAs.
2024-05-21 23:22:53.685106 INFO::Removing potential empty rows and columns
2024-05-21 23:22:53.68847 INFO::Found 1000 missing values.
2024-05-21 23:22:53.704809 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-21 23:22:53.705762 INFO::Done
2024-05-21 23:22:53.706514 INFO::Acquiring quality metrics before batch effect correction.
2024-05-21 23:22:53.715412 INFO::Starting hierarchical adjustment
2024-05-21 23:22:53.717089 INFO::Found 10 batches.
2024-05-21 23:22:53.718388 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-21 23:22:53.719774 INFO::Using default BPPARAM
2024-05-21 23:22:53.720942 INFO::Processing subtree level 1
2024-05-21 23:22:56.890453 INFO::Processing subtree level 2
2024-05-21 23:22:59.715399 INFO::Adjusting the last 1 batches sequentially
2024-05-21 23:22:59.717819 INFO::Done
2024-05-21 23:22:59.719116 INFO::Acquiring quality metrics after batch effect correction.
2024-05-21 23:22:59.727634 INFO::ASW Batch was 0.485091342846742 prior to batch effect correction and is now 0.485091342846742 .
2024-05-21 23:22:59.728892 INFO::ASW Label was 0.350940261701474 prior to batch effect correction and is now 0.350940261701474 .
2024-05-21 23:22:59.732542 INFO::Total function execution time is 6.05077004432678 s and adjustment time is 6.00099301338196 s ( 99.18 )
2024-05-21 23:22:59.733983 INFO::Formatting Data.
2024-05-21 23:22:59.73517 INFO::Replacing NaNs with NAs.
2024-05-21 23:22:59.736961 INFO::Removing potential empty rows and columns
2024-05-21 23:22:59.740475 INFO::Found 1000 missing values.
2024-05-21 23:22:59.75445 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-21 23:22:59.755395 INFO::Done
2024-05-21 23:22:59.756204 INFO::Acquiring quality metrics before batch effect correction.
2024-05-21 23:22:59.762532 INFO::Starting hierarchical adjustment
2024-05-21 23:22:59.763494 INFO::Found 10 batches.
2024-05-21 23:23:00.535215 INFO::Set up parallel execution backend with 2 workers
2024-05-21 23:23:00.53675 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-05-21 23:23:03.76127 INFO::Adjusting the last 2 batches sequentially
2024-05-21 23:23:03.763672 INFO::Adjusting sequential tree level 1 with 2 batches
2024-05-21 23:23:03.779287 INFO::Done
2024-05-21 23:23:03.780243 INFO::Acquiring quality metrics after batch effect correction.
2024-05-21 23:23:03.786162 INFO::ASW Batch was 0.485091342846742 prior to batch effect correction and is now 0.485091342846742 .
2024-05-21 23:23:03.787025 INFO::ASW Label was 0.350940261701474 prior to batch effect correction and is now 0.350940261701474 .
2024-05-21 23:23:03.788047 INFO::Total function execution time is 4.05414390563965 s and adjustment time is 4.01588106155396 s ( 99.06 )
2024-05-21 23:23:06.932302 INFO::Formatting Data.
2024-05-21 23:23:06.933429 INFO::Replacing NaNs with NAs.
2024-05-21 23:23:06.934749 INFO::Removing potential empty rows and columns
2024-05-21 23:23:06.936453 INFO::Found 0 missing values.
2024-05-21 23:23:06.94141 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-21 23:23:06.942795 INFO::Done
2024-05-21 23:23:06.944115 INFO::Acquiring quality metrics before batch effect correction.
2024-05-21 23:23:06.948785 INFO::Starting hierarchical adjustment
2024-05-21 23:23:06.950447 INFO::Found 3 batches.
2024-05-21 23:23:06.951994 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-05-21 23:23:06.952942 INFO::Using default BPPARAM
2024-05-21 23:23:06.953678 INFO::Processing subtree level 1
2024-05-21 23:23:09.818372 INFO::Adjusting the last 1 batches sequentially
2024-05-21 23:23:09.820636 INFO::Done
2024-05-21 23:23:09.821912 INFO::Acquiring quality metrics after batch effect correction.
2024-05-21 23:23:09.826062 INFO::ASW Batch was 0.167132689352603 prior to batch effect correction and is now -0.162189727496116 .
2024-05-21 23:23:09.827318 INFO::ASW Label was -0.205175751437916 prior to batch effect correction and is now 0.00959560276355129 .
2024-05-21 23:23:09.828776 INFO::Total function execution time is 2.89653301239014 s and adjustment time is 2.87045288085938 s ( 99.1 )
2024-05-21 23:23:09.991543 INFO::Formatting Data.
2024-05-21 23:23:09.992578 INFO::Replacing NaNs with NAs.
2024-05-21 23:23:09.993642 INFO::Removing potential empty rows and columns
2024-05-21 23:23:09.994746 INFO::Found 2 missing values.
2024-05-21 23:23:09.997549 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-05-21 23:23:09.998302 INFO::Done
2024-05-21 23:23:10.04064 INFO::Found NA in Reference column
2024-05-21 23:23:10.055166 INFO::Require at least two references per batch.
2024-05-21 23:23:10.077298 INFO::Formatting Data.
2024-05-21 23:23:10.078445 INFO::Recognized SummarizedExperiment
2024-05-21 23:23:10.079212 INFO::Typecasting input to dataframe.
2024-05-21 23:23:10.087413 INFO::Replacing NaNs with NAs.
2024-05-21 23:23:10.088895 INFO::Removing potential empty rows and columns
2024-05-21 23:23:10.091672 INFO::Found 0 missing values.
2024-05-21 23:23:10.096715 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-21 23:23:10.097617 INFO::Done
2024-05-21 23:23:10.112328 INFO::Formatting Data.
2024-05-21 23:23:10.113304 INFO::Recognized SummarizedExperiment
2024-05-21 23:23:10.114332 INFO::Typecasting input to dataframe.
2024-05-21 23:23:10.130465 INFO::Replacing NaNs with NAs.
2024-05-21 23:23:10.131943 INFO::Removing potential empty rows and columns
2024-05-21 23:23:10.134811 INFO::Found 0 missing values.
2024-05-21 23:23:10.142724 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-21 23:23:10.143583 INFO::Done
2024-05-21 23:23:10.158524 INFO::Formatting Data.
2024-05-21 23:23:10.159645 INFO::Recognized SummarizedExperiment
2024-05-21 23:23:10.160418 INFO::Typecasting input to dataframe.
2024-05-21 23:23:10.175077 INFO::Replacing NaNs with NAs.
2024-05-21 23:23:10.176356 INFO::Removing potential empty rows and columns
2024-05-21 23:23:10.177652 INFO::Found 0 missing values.
2024-05-21 23:23:10.17878 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.
2024-05-21 23:23:10.184174 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-21 23:23:10.184962 INFO::Done
2024-05-21 23:23:10.200634 INFO::Formatting Data.
2024-05-21 23:23:10.201669 INFO::Replacing NaNs with NAs.
2024-05-21 23:23:10.202753 INFO::Removing potential empty rows and columns
2024-05-21 23:23:10.203902 INFO::Found 0 missing values.
2024-05-21 23:23:10.206596 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-21 23:23:10.207335 INFO::Done
2024-05-21 23:23:10.223108 INFO::Formatting Data.
2024-05-21 23:23:10.224247 INFO::Replacing NaNs with NAs.
2024-05-21 23:23:10.225387 INFO::Removing potential empty rows and columns
2024-05-21 23:23:10.226538 INFO::Found 0 missing values.
2024-05-21 23:23:10.229258 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-21 23:23:10.230151 INFO::Done
2024-05-21 23:23:10.272536 INFO::Formatting Data.
2024-05-21 23:23:10.273595 INFO::Replacing NaNs with NAs.
2024-05-21 23:23:10.274811 INFO::Removing potential empty rows and columns
2024-05-21 23:23:10.276061 INFO::Found 1 missing values.
2024-05-21 23:23:10.278548 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-21 23:23:10.27928 INFO::Done
2024-05-21 23:23:10.306492 INFO::Formatting Data.
2024-05-21 23:23:10.307509 INFO::Replacing NaNs with NAs.
2024-05-21 23:23:10.308601 INFO::Removing potential empty rows and columns
2024-05-21 23:23:10.309668 INFO::Found 2 missing values.
2024-05-21 23:23:10.310733 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.
2024-05-21 23:23:10.312947 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-05-21 23:23:10.313673 INFO::Done
2024-05-21 23:23:10.3291 INFO::Formatting Data.
2024-05-21 23:23:10.330108 INFO::Replacing NaNs with NAs.
2024-05-21 23:23:10.33116 INFO::Removing potential empty rows and columns
2024-05-21 23:23:10.332336 INFO::Found 2 missing values.
2024-05-21 23:23:10.334009 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-21 23:23:10.334735 INFO::Done
2024-05-21 23:23:10.353553 INFO::Formatting Data.
2024-05-21 23:23:10.355078 INFO::Typecasting input to dataframe.
2024-05-21 23:23:10.356124 INFO::Replacing NaNs with NAs.
2024-05-21 23:23:10.357186 INFO::Removing potential empty rows and columns
2024-05-21 23:23:10.358329 INFO::Found 0 missing values.
2024-05-21 23:23:10.360905 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-05-21 23:23:10.361637 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
29.48 1.45 75.39
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 8.81 | 0.48 | 18.52 | |
| compute_asw | 0.03 | 0.00 | 0.03 | |
| count_existing | 0.03 | 0.00 | 0.03 | |
| generate_data_covariables | 0.02 | 0.00 | 0.02 | |
| generate_dataset | 0.01 | 0.00 | 0.02 | |