Yannis Schumann
| Snapshot Date: 2024-10-09 13:40 -0400 (Wed, 09 Oct 2024) |
| git_url: https://git.bioconductor.org/packages/BERT |
| git_branch: devel |
| git_last_commit: aaedecb |
| git_last_commit_date: 2024-07-22 10:00:51 -0400 (Mon, 22 Jul 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-10-10 11:43 -0400 (Thu, 10 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4468 |
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4715 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4473 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4504 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4452 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4452 |
| 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 159/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BERT 1.1.2 (landing page) Yannis Schumann
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BERT package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BERT.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BERT |
| Version: 1.1.2 |
| Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BERT_1.1.2.tar.gz |
| StartedAt: 2024-10-09 22:25:47 -0400 (Wed, 09 Oct 2024) |
| EndedAt: 2024-10-09 22:27:58 -0400 (Wed, 09 Oct 2024) |
| EllapsedTime: 131.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BERT.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BERT.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BERT_1.1.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/BERT.Rcheck'
* using R version 4.4.1 (2024-06-14 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 '1.1.2'
* 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 7.88 0.53 16.81
* 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-3.20-bioc\R\bin\R.exe CMD INSTALL BERT ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-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 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
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")
2024-10-09 22:26:46.409457 INFO::Formatting Data.
2024-10-09 22:26:46.412464 INFO::Replacing NaNs with NAs.
2024-10-09 22:26:46.42848 INFO::Removing potential empty rows and columns
2024-10-09 22:26:46.638764 INFO::Found 0 missing values.
2024-10-09 22:26:46.641833 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-09 22:26:46.642649 INFO::Done
2024-10-09 22:26:46.643343 INFO::Acquiring quality metrics before batch effect correction.
2024-10-09 22:26:46.656373 INFO::Starting hierarchical adjustment
2024-10-09 22:26:46.657381 INFO::Found 3 batches.
2024-10-09 22:26:46.65809 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-09 22:26:46.659373 INFO::Using default BPPARAM
2024-10-09 22:26:46.660079 INFO::Processing subtree level 1
2024-10-09 22:26:49.380408 INFO::Adjusting the last 1 batches sequentially
2024-10-09 22:26:49.382467 INFO::Done
2024-10-09 22:26:49.383707 INFO::Acquiring quality metrics after batch effect correction.
2024-10-09 22:26:49.386748 INFO::ASW Batch was -0.0461855056590869 prior to batch effect correction and is now -0.0461855056590869 .
2024-10-09 22:26:49.38839 INFO::Total function execution time is 2.97966814041138 s and adjustment time is 2.72521686553955 s ( 91.46 )
2024-10-09 22:26:49.411282 INFO::Formatting Data.
2024-10-09 22:26:49.412784 INFO::Replacing NaNs with NAs.
2024-10-09 22:26:49.41447 INFO::Removing potential empty rows and columns
2024-10-09 22:26:49.416024 INFO::Found 0 missing values.
2024-10-09 22:26:49.417658 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.
2024-10-09 22:26:49.429445 INFO::Formatting Data.
2024-10-09 22:26:49.43072 INFO::Replacing NaNs with NAs.
2024-10-09 22:26:49.432177 INFO::Removing potential empty rows and columns
2024-10-09 22:26:49.433784 INFO::Found 0 missing values.
2024-10-09 22:26:49.434814 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.
2024-10-09 22:26:49.459984 INFO::Formatting Data.
2024-10-09 22:26:49.461463 INFO::Replacing NaNs with NAs.
2024-10-09 22:26:49.46313 INFO::Removing potential empty rows and columns
2024-10-09 22:26:49.464912 INFO::Found 0 missing values.
2024-10-09 22:26:49.466575 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.
2024-10-09 22:26:49.472632 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-09 22:26:49.473834 INFO::Done
2024-10-09 22:26:49.474983 INFO::Acquiring quality metrics before batch effect correction.
2024-10-09 22:26:49.478114 INFO::Starting hierarchical adjustment
2024-10-09 22:26:49.479486 INFO::Found 2 batches.
2024-10-09 22:26:49.480688 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-09 22:26:49.481909 INFO::Using default BPPARAM
2024-10-09 22:26:49.483012 INFO::Adjusting the last 2 batches sequentially
2024-10-09 22:26:49.484714 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-09 22:26:49.507334 INFO::Done
2024-10-09 22:26:49.508162 INFO::Acquiring quality metrics after batch effect correction.
2024-10-09 22:26:49.511103 INFO::ASW Batch was 0.0145774653315244 prior to batch effect correction and is now -0.126090853740393 .
2024-10-09 22:26:49.512248 INFO::Total function execution time is 0.0524249076843262 s and adjustment time is 0.0280628204345703 s ( 53.53 )
2024-10-09 22:26:49.515332 INFO::Formatting Data.
2024-10-09 22:26:49.516213 INFO::Replacing NaNs with NAs.
2024-10-09 22:26:49.523247 INFO::Formatting Data.
2024-10-09 22:26:49.524109 INFO::Replacing NaNs with NAs.
2024-10-09 22:26:49.525179 INFO::Removing potential empty rows and columns
2024-10-09 22:26:49.526248 INFO::Found 0 missing values.
2024-10-09 22:26:49.528621 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-09 22:26:49.529305 INFO::Done
2024-10-09 22:26:49.529967 INFO::Acquiring quality metrics before batch effect correction.
2024-10-09 22:26:49.531971 INFO::Starting hierarchical adjustment
2024-10-09 22:26:49.532809 INFO::Found 2 batches.
2024-10-09 22:26:49.533475 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-09 22:26:49.534206 INFO::Using default BPPARAM
2024-10-09 22:26:49.535146 INFO::Adjusting the last 2 batches sequentially
2024-10-09 22:26:49.53682 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-09 22:26:49.556731 INFO::Done
2024-10-09 22:26:49.558089 INFO::Acquiring quality metrics after batch effect correction.
2024-10-09 22:26:49.56134 INFO::ASW Batch was 0.0239341265273443 prior to batch effect correction and is now -0.111753161367719 .
2024-10-09 22:26:49.562847 INFO::Total function execution time is 0.0395650863647461 s and adjustment time is 0.0239760875701904 s ( 60.6 )
2024-10-09 22:26:49.564734 INFO::Formatting Data.
2024-10-09 22:26:49.565996 INFO::Replacing NaNs with NAs.
2024-10-09 22:26:49.56759 INFO::Removing potential empty rows and columns
2024-10-09 22:26:49.569266 INFO::Found 0 missing values.
2024-10-09 22:26:49.573439 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-09 22:26:49.574492 INFO::Done
2024-10-09 22:26:49.575619 INFO::Acquiring quality metrics before batch effect correction.
2024-10-09 22:26:49.578864 INFO::Starting hierarchical adjustment
2024-10-09 22:26:49.580267 INFO::Found 2 batches.
2024-10-09 22:26:49.581384 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-09 22:26:49.582542 INFO::Using default BPPARAM
2024-10-09 22:26:49.583699 INFO::Adjusting the last 2 batches sequentially
2024-10-09 22:26:49.585399 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-09 22:26:49.605393 INFO::Done
2024-10-09 22:26:49.606749 INFO::Acquiring quality metrics after batch effect correction.
2024-10-09 22:26:49.610008 INFO::ASW Batch was 0.0239341265273443 prior to batch effect correction and is now -0.111753161367719 .
2024-10-09 22:26:49.611501 INFO::Total function execution time is 0.0467610359191895 s and adjustment time is 0.0253288745880127 s ( 54.17 )
2024-10-09 22:26:52.230042 INFO::Formatting Data.
2024-10-09 22:26:52.231492 INFO::Recognized SummarizedExperiment
2024-10-09 22:26:52.232724 INFO::Typecasting input to dataframe.
2024-10-09 22:26:52.280285 INFO::Replacing NaNs with NAs.
2024-10-09 22:26:52.282608 INFO::Removing potential empty rows and columns
2024-10-09 22:26:52.287972 INFO::Found 0 missing values.
2024-10-09 22:26:52.297681 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-09 22:26:52.299061 INFO::Done
2024-10-09 22:26:52.300287 INFO::Acquiring quality metrics before batch effect correction.
2024-10-09 22:26:52.306214 INFO::Starting hierarchical adjustment
2024-10-09 22:26:52.307639 INFO::Found 2 batches.
2024-10-09 22:26:52.308741 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-09 22:26:52.31051 INFO::Using default BPPARAM
2024-10-09 22:26:52.311606 INFO::Adjusting the last 2 batches sequentially
2024-10-09 22:26:52.313415 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-09 22:26:52.381897 INFO::Done
2024-10-09 22:26:52.383301 INFO::Acquiring quality metrics after batch effect correction.
2024-10-09 22:26:52.389315 INFO::ASW Batch was -0.0141332883963234 prior to batch effect correction and is now -0.0888688918158313 .
2024-10-09 22:26:52.390979 INFO::Total function execution time is 0.1613450050354 s and adjustment time is 0.0744202136993408 s ( 46.12 )
2024-10-09 22:26:53.093389 INFO::Formatting Data.
2024-10-09 22:26:53.09473 INFO::Recognized SummarizedExperiment
2024-10-09 22:26:53.095995 INFO::Typecasting input to dataframe.
2024-10-09 22:26:53.107708 INFO::Replacing NaNs with NAs.
2024-10-09 22:26:53.109635 INFO::Removing potential empty rows and columns
2024-10-09 22:26:53.114066 INFO::Found 0 missing values.
2024-10-09 22:26:53.122194 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-09 22:26:53.12344 INFO::Done
2024-10-09 22:26:53.124558 INFO::Acquiring quality metrics before batch effect correction.
2024-10-09 22:26:53.130031 INFO::Starting hierarchical adjustment
2024-10-09 22:26:53.131351 INFO::Found 2 batches.
2024-10-09 22:26:53.132421 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-09 22:26:53.133581 INFO::Using default BPPARAM
2024-10-09 22:26:53.13463 INFO::Adjusting the last 2 batches sequentially
2024-10-09 22:26:53.13633 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-09 22:26:53.164813 INFO::Done
2024-10-09 22:26:53.16612 INFO::Acquiring quality metrics after batch effect correction.
2024-10-09 22:26:53.171819 INFO::ASW Batch was -0.00295959470912401 prior to batch effect correction and is now -0.00295959470912401 .
2024-10-09 22:26:53.173396 INFO::Total function execution time is 0.0799579620361328 s and adjustment time is 0.0336089134216309 s ( 42.03 )
2024-10-09 22:26:53.202445 INFO::Formatting Data.
2024-10-09 22:26:53.203923 INFO::Replacing NaNs with NAs.
2024-10-09 22:26:53.205483 INFO::Removing potential empty rows and columns
2024-10-09 22:26:53.207136 INFO::Found 0 missing values.
2024-10-09 22:26:53.211017 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-09 22:26:53.212146 INFO::Done
2024-10-09 22:26:53.213244 INFO::Acquiring quality metrics before batch effect correction.
2024-10-09 22:26:53.216294 INFO::Starting hierarchical adjustment
2024-10-09 22:26:53.217579 INFO::Found 3 batches.
2024-10-09 22:26:53.218633 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-09 22:26:53.219808 INFO::Using default BPPARAM
2024-10-09 22:26:53.220869 INFO::Processing subtree level 1
2024-10-09 22:27:04.843163 INFO::Adjusting the last 1 batches sequentially
2024-10-09 22:27:04.84534 INFO::Done
2024-10-09 22:27:04.846601 INFO::Acquiring quality metrics after batch effect correction.
2024-10-09 22:27:04.849608 INFO::ASW Batch was -0.0709928152200938 prior to batch effect correction and is now -0.167141888521307 .
2024-10-09 22:27:04.851026 INFO::Total function execution time is 11.6486709117889 s and adjustment time is 11.6279280185699 s ( 99.82 )
2024-10-09 22:27:04.872957 INFO::Skipping initial DF formatting
2024-10-09 22:27:04.874213 INFO::Acquiring quality metrics before batch effect correction.
2024-10-09 22:27:04.880393 INFO::Starting hierarchical adjustment
2024-10-09 22:27:04.881756 INFO::Found 5 batches.
2024-10-09 22:27:04.882808 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-09 22:27:04.883895 INFO::Using default BPPARAM
2024-10-09 22:27:04.88488 INFO::Processing subtree level 1
2024-10-09 22:27:08.475923 INFO::Adjusting the last 2 batches sequentially
2024-10-09 22:27:08.47775 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-09 22:27:08.493159 INFO::Done
2024-10-09 22:27:08.494199 INFO::Acquiring quality metrics after batch effect correction.
2024-10-09 22:27:08.498522 INFO::ASW Batch was 0.539352118374535 prior to batch effect correction and is now 0.539352118374535 .
2024-10-09 22:27:08.499334 INFO::ASW Label was 0.35872766372516 prior to batch effect correction and is now 0.35872766372516 .
2024-10-09 22:27:08.500275 INFO::Total function execution time is 3.62748193740845 s and adjustment time is 3.61162281036377 s ( 99.56 )
2024-10-09 22:27:08.518326 INFO::Formatting Data.
2024-10-09 22:27:08.519253 INFO::Replacing NaNs with NAs.
2024-10-09 22:27:08.520285 INFO::Removing potential empty rows and columns
2024-10-09 22:27:08.521333 INFO::Found 0 missing values.
2024-10-09 22:27:08.524821 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-09 22:27:08.52553 INFO::Done
2024-10-09 22:27:08.526203 INFO::Acquiring quality metrics before batch effect correction.
2024-10-09 22:27:08.52924 INFO::Starting hierarchical adjustment
2024-10-09 22:27:08.530117 INFO::Found 5 batches.
2024-10-09 22:27:08.530799 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-09 22:27:08.531537 INFO::Using default BPPARAM
2024-10-09 22:27:08.532207 INFO::Processing subtree level 1
2024-10-09 22:27:11.439688 INFO::Adjusting the last 2 batches sequentially
2024-10-09 22:27:11.441138 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-09 22:27:11.45288 INFO::Done
2024-10-09 22:27:11.453705 INFO::Acquiring quality metrics after batch effect correction.
2024-10-09 22:27:11.456547 INFO::ASW Batch was 0.265735066828727 prior to batch effect correction and is now 0.0100005934982476 .
2024-10-09 22:27:11.45728 INFO::ASW Label was 0.470402942753597 prior to batch effect correction and is now 0.74205192648764 .
2024-10-09 22:27:11.458159 INFO::Total function execution time is 2.93992781639099 s and adjustment time is 2.92288088798523 s ( 99.42 )
2024-10-09 22:27:11.459072 INFO::Formatting Data.
2024-10-09 22:27:11.45981 INFO::Replacing NaNs with NAs.
2024-10-09 22:27:11.460758 INFO::Removing potential empty rows and columns
2024-10-09 22:27:11.461789 INFO::Found 0 missing values.
2024-10-09 22:27:11.4651 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-09 22:27:11.46582 INFO::Done
2024-10-09 22:27:11.466477 INFO::Acquiring quality metrics before batch effect correction.
2024-10-09 22:27:11.46948 INFO::Starting hierarchical adjustment
2024-10-09 22:27:11.470325 INFO::Found 5 batches.
2024-10-09 22:27:11.470987 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-09 22:27:11.471722 INFO::Using default BPPARAM
2024-10-09 22:27:11.472378 INFO::Processing subtree level 1
2024-10-09 22:27:14.273433 INFO::Adjusting the last 2 batches sequentially
2024-10-09 22:27:14.27532 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-09 22:27:14.293384 INFO::Done
2024-10-09 22:27:14.294676 INFO::Acquiring quality metrics after batch effect correction.
2024-10-09 22:27:14.299284 INFO::ASW Batch was 0.265735066828727 prior to batch effect correction and is now 0.0100005934982476 .
2024-10-09 22:27:14.300505 INFO::ASW Label was 0.470402942753597 prior to batch effect correction and is now 0.74205192648764 .
2024-10-09 22:27:14.301998 INFO::Total function execution time is 2.8428521156311 s and adjustment time is 2.8231098651886 s ( 99.31 )
2024-10-09 22:27:14.3264 INFO::Formatting Data.
2024-10-09 22:27:14.327976 INFO::Replacing NaNs with NAs.
2024-10-09 22:27:14.329802 INFO::Removing potential empty rows and columns
2024-10-09 22:27:14.331692 INFO::Found 0 missing values.
2024-10-09 22:27:14.337438 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-09 22:27:14.33877 INFO::Done
2024-10-09 22:27:14.33992 INFO::Acquiring quality metrics before batch effect correction.
2024-10-09 22:27:14.344932 INFO::Starting hierarchical adjustment
2024-10-09 22:27:14.346425 INFO::Found 5 batches.
2024-10-09 22:27:14.347719 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-09 22:27:14.348958 INFO::Using default BPPARAM
2024-10-09 22:27:14.350078 INFO::Processing subtree level 1
2024-10-09 22:27:17.404217 INFO::Adjusting the last 2 batches sequentially
2024-10-09 22:27:17.406145 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-09 22:27:17.424132 INFO::Done
2024-10-09 22:27:17.42541 INFO::Acquiring quality metrics after batch effect correction.
2024-10-09 22:27:17.429783 INFO::ASW Batch was 0.282416274185511 prior to batch effect correction and is now -0.0642381658280559 .
2024-10-09 22:27:17.430948 INFO::ASW Label was 0.466192615931842 prior to batch effect correction and is now 0.89210668807824 .
2024-10-09 22:27:17.432361 INFO::Total function execution time is 3.1060619354248 s and adjustment time is 3.07793092727661 s ( 99.09 )
2024-10-09 22:27:17.433752 INFO::Formatting Data.
2024-10-09 22:27:17.434931 INFO::Replacing NaNs with NAs.
2024-10-09 22:27:17.436414 INFO::Removing potential empty rows and columns
2024-10-09 22:27:17.437962 INFO::Found 0 missing values.
2024-10-09 22:27:17.443465 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-09 22:27:17.444641 INFO::Done
2024-10-09 22:27:17.44575 INFO::Acquiring quality metrics before batch effect correction.
2024-10-09 22:27:17.450162 INFO::Starting hierarchical adjustment
2024-10-09 22:27:17.451526 INFO::Found 5 batches.
2024-10-09 22:27:17.452619 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-09 22:27:17.453777 INFO::Using default BPPARAM
2024-10-09 22:27:17.454819 INFO::Processing subtree level 1
2024-10-09 22:27:20.467259 INFO::Adjusting the last 2 batches sequentially
2024-10-09 22:27:20.469178 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-09 22:27:20.487039 INFO::Done
2024-10-09 22:27:20.488367 INFO::Acquiring quality metrics after batch effect correction.
2024-10-09 22:27:20.492937 INFO::ASW Batch was 0.282416274185511 prior to batch effect correction and is now -0.0642381658280559 .
2024-10-09 22:27:20.49419 INFO::ASW Label was 0.466192615931842 prior to batch effect correction and is now 0.89210668807824 .
2024-10-09 22:27:20.495668 INFO::Total function execution time is 3.06193900108337 s and adjustment time is 3.03569388389587 s ( 99.14 )
2024-10-09 22:27:20.518096 INFO::Formatting Data.
2024-10-09 22:27:20.51954 INFO::Replacing NaNs with NAs.
2024-10-09 22:27:20.521178 INFO::Removing potential empty rows and columns
2024-10-09 22:27:20.522943 INFO::Found 0 missing values.
2024-10-09 22:27:20.526607 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-09 22:27:20.527732 INFO::Done
2024-10-09 22:27:20.528808 INFO::Acquiring quality metrics before batch effect correction.
2024-10-09 22:27:20.53294 INFO::Starting hierarchical adjustment
2024-10-09 22:27:20.534253 INFO::Found 2 batches.
2024-10-09 22:27:20.535331 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-09 22:27:20.536479 INFO::Using default BPPARAM
2024-10-09 22:27:20.537548 INFO::Adjusting the last 2 batches sequentially
2024-10-09 22:27:20.539182 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-09 22:27:20.557109 INFO::Done
2024-10-09 22:27:20.558432 INFO::Acquiring quality metrics after batch effect correction.
2024-10-09 22:27:20.562817 INFO::ASW Batch was 0.69490148852877 prior to batch effect correction and is now -0.0279028688992641 .
2024-10-09 22:27:20.564028 INFO::ASW Label was 0.307358616989916 prior to batch effect correction and is now 0.859965994386877 .
2024-10-09 22:27:20.565452 INFO::Total function execution time is 0.0474441051483154 s and adjustment time is 0.0230050086975098 s ( 48.49 )
2024-10-09 22:27:20.56685 INFO::Formatting Data.
2024-10-09 22:27:20.56808 INFO::Replacing NaNs with NAs.
2024-10-09 22:27:20.569642 INFO::Removing potential empty rows and columns
2024-10-09 22:27:20.571175 INFO::Found 0 missing values.
2024-10-09 22:27:20.574845 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-09 22:27:20.575888 INFO::Done
2024-10-09 22:27:20.576956 INFO::Acquiring quality metrics before batch effect correction.
2024-10-09 22:27:20.581315 INFO::Starting hierarchical adjustment
2024-10-09 22:27:20.582534 INFO::Found 2 batches.
2024-10-09 22:27:20.583254 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-09 22:27:20.584006 INFO::Using default BPPARAM
2024-10-09 22:27:20.584675 INFO::Adjusting the last 2 batches sequentially
2024-10-09 22:27:20.585767 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-09 22:27:20.601356 INFO::Done
2024-10-09 22:27:20.602609 INFO::Acquiring quality metrics after batch effect correction.
2024-10-09 22:27:20.607311 INFO::ASW Batch was 0.69490148852877 prior to batch effect correction and is now -0.0279028688992641 .
2024-10-09 22:27:20.608627 INFO::ASW Label was 0.307358616989916 prior to batch effect correction and is now 0.859965994386877 .
2024-10-09 22:27:20.610144 INFO::Total function execution time is 0.0432839393615723 s and adjustment time is 0.0190160274505615 s ( 43.93 )
2024-10-09 22:27:20.631826 INFO::Formatting Data.
2024-10-09 22:27:20.633324 INFO::Replacing NaNs with NAs.
2024-10-09 22:27:20.634932 INFO::Removing potential empty rows and columns
2024-10-09 22:27:20.636544 INFO::Found 0 missing values.
2024-10-09 22:27:20.639799 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-09 22:27:20.640959 INFO::Done
2024-10-09 22:27:20.642059 INFO::Acquiring quality metrics before batch effect correction.
2024-10-09 22:27:20.644999 INFO::Starting hierarchical adjustment
2024-10-09 22:27:20.6463 INFO::Found 2 batches.
2024-10-09 22:27:20.647349 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-09 22:27:20.648559 INFO::Using default BPPARAM
2024-10-09 22:27:20.649606 INFO::Adjusting the last 2 batches sequentially
2024-10-09 22:27:20.651205 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-09 22:27:20.689464 INFO::Done
2024-10-09 22:27:20.690759 INFO::Acquiring quality metrics after batch effect correction.
2024-10-09 22:27:20.693785 INFO::ASW Batch was -0.103739077014922 prior to batch effect correction and is now -0.1439754468814 .
2024-10-09 22:27:20.695258 INFO::Total function execution time is 0.0635049343109131 s and adjustment time is 0.0433371067047119 s ( 68.24 )
2024-10-09 22:27:20.715144 INFO::Formatting Data.
2024-10-09 22:27:20.716074 INFO::Replacing NaNs with NAs.
2024-10-09 22:27:20.717121 INFO::Removing potential empty rows and columns
2024-10-09 22:27:20.718237 INFO::Found 0 missing values.
2024-10-09 22:27:20.719435 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.
2024-10-09 22:27:20.723448 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-09 22:27:20.724167 INFO::Done
2024-10-09 22:27:20.724852 INFO::Acquiring quality metrics before batch effect correction.
2024-10-09 22:27:20.727895 INFO::Starting hierarchical adjustment
2024-10-09 22:27:20.728768 INFO::Found 2 batches.
2024-10-09 22:27:20.729496 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-09 22:27:20.730254 INFO::Using default BPPARAM
2024-10-09 22:27:20.730921 INFO::Adjusting the last 2 batches sequentially
2024-10-09 22:27:20.731993 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-09 22:27:20.74573 INFO::Done
2024-10-09 22:27:20.746596 INFO::Acquiring quality metrics after batch effect correction.
2024-10-09 22:27:20.749564 INFO::ASW Batch was 0.673162669893811 prior to batch effect correction and is now 0.204298216845898 .
2024-10-09 22:27:20.750326 INFO::ASW Label was 0.439570987639357 prior to batch effect correction and is now 0.738682345517953 .
2024-10-09 22:27:20.751249 INFO::Total function execution time is 0.0361888408660889 s and adjustment time is 0.0170769691467285 s ( 47.19 )
2024-10-09 22:27:20.752173 INFO::Formatting Data.
2024-10-09 22:27:20.752931 INFO::Replacing NaNs with NAs.
2024-10-09 22:27:20.753966 INFO::Removing potential empty rows and columns
2024-10-09 22:27:20.75507 INFO::Found 0 missing values.
2024-10-09 22:27:20.756133 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.
2024-10-09 22:27:20.760206 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-09 22:27:20.760939 INFO::Done
2024-10-09 22:27:20.761631 INFO::Acquiring quality metrics before batch effect correction.
2024-10-09 22:27:20.764554 INFO::Starting hierarchical adjustment
2024-10-09 22:27:20.765413 INFO::Found 2 batches.
2024-10-09 22:27:20.766092 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-09 22:27:20.766849 INFO::Using default BPPARAM
2024-10-09 22:27:20.767529 INFO::Adjusting the last 2 batches sequentially
2024-10-09 22:27:20.768619 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-09 22:27:20.783241 INFO::Done
2024-10-09 22:27:20.784157 INFO::Acquiring quality metrics after batch effect correction.
2024-10-09 22:27:20.787472 INFO::ASW Batch was 0.673162669893811 prior to batch effect correction and is now 0.204298216845898 .
2024-10-09 22:27:20.788327 INFO::ASW Label was 0.439570987639357 prior to batch effect correction and is now 0.738682345517953 .
2024-10-09 22:27:20.789426 INFO::Total function execution time is 0.0372490882873535 s and adjustment time is 0.0179190635681152 s ( 48.11 )
2024-10-09 22:27:21.021015 INFO::Formatting Data.
2024-10-09 22:27:21.022648 INFO::Replacing NaNs with NAs.
2024-10-09 22:27:21.024659 INFO::Removing potential empty rows and columns
2024-10-09 22:27:21.026648 INFO::Found 0 missing values.
2024-10-09 22:27:21.031873 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-09 22:27:21.033291 INFO::Done
2024-10-09 22:27:21.034603 INFO::Acquiring quality metrics before batch effect correction.
2024-10-09 22:27:21.038183 INFO::Starting hierarchical adjustment
2024-10-09 22:27:21.039729 INFO::Found 3 batches.
2024-10-09 22:27:21.040922 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-09 22:27:21.042251 INFO::Using default BPPARAM
2024-10-09 22:27:21.043482 INFO::Processing subtree level 1
2024-10-09 22:27:23.860279 INFO::Adjusting the last 1 batches sequentially
2024-10-09 22:27:23.862306 INFO::Done
2024-10-09 22:27:23.863515 INFO::Acquiring quality metrics after batch effect correction.
2024-10-09 22:27:23.86653 INFO::ASW Batch was -0.0562759942261042 prior to batch effect correction and is now -0.0562759942261042 .
2024-10-09 22:27:23.867974 INFO::Total function execution time is 2.84710788726807 s and adjustment time is 2.82280802726746 s ( 99.15 )
2024-10-09 22:27:23.869562 INFO::Formatting Data.
2024-10-09 22:27:23.87074 INFO::Typecasting input to dataframe.
2024-10-09 22:27:23.872051 INFO::Replacing NaNs with NAs.
2024-10-09 22:27:23.873528 INFO::Removing potential empty rows and columns
2024-10-09 22:27:23.875116 INFO::Found 0 missing values.
2024-10-09 22:27:23.879162 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-09 22:27:23.880236 INFO::Done
2024-10-09 22:27:23.881253 INFO::Acquiring quality metrics before batch effect correction.
2024-10-09 22:27:23.884173 INFO::Starting hierarchical adjustment
2024-10-09 22:27:23.885407 INFO::Found 3 batches.
2024-10-09 22:27:23.886423 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-09 22:27:23.887546 INFO::Using default BPPARAM
2024-10-09 22:27:23.888572 INFO::Processing subtree level 1
2024-10-09 22:27:26.724426 INFO::Adjusting the last 1 batches sequentially
2024-10-09 22:27:26.726495 INFO::Done
2024-10-09 22:27:26.727432 INFO::Acquiring quality metrics after batch effect correction.
2024-10-09 22:27:26.729538 INFO::ASW Batch was -0.0562759942261042 prior to batch effect correction and is now -0.0562759942261042 .
2024-10-09 22:27:26.730493 INFO::Total function execution time is 2.86101698875427 s and adjustment time is 2.84125900268555 s ( 99.31 )
2024-10-09 22:27:26.745006 INFO::Formatting Data.
2024-10-09 22:27:26.745898 INFO::Typecasting input to dataframe.
2024-10-09 22:27:26.746829 INFO::Replacing NaNs with NAs.
2024-10-09 22:27:26.747803 INFO::Removing potential empty rows and columns
2024-10-09 22:27:26.748889 INFO::Found 0 missing values.
2024-10-09 22:27:26.751348 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-09 22:27:26.75202 INFO::Done
2024-10-09 22:27:26.752669 INFO::Acquiring quality metrics before batch effect correction.
2024-10-09 22:27:26.754613 INFO::Starting hierarchical adjustment
2024-10-09 22:27:26.755427 INFO::Found 3 batches.
2024-10-09 22:27:26.756082 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-09 22:27:26.75682 INFO::Using default BPPARAM
2024-10-09 22:27:26.757489 INFO::Processing subtree level 1
2024-10-09 22:27:29.716657 INFO::Adjusting the last 1 batches sequentially
2024-10-09 22:27:29.718765 INFO::Done
2024-10-09 22:27:29.719937 INFO::Acquiring quality metrics after batch effect correction.
2024-10-09 22:27:29.722821 INFO::ASW Batch was -0.16306585810588 prior to batch effect correction and is now -0.16306585810588 .
2024-10-09 22:27:29.724174 INFO::Total function execution time is 2.97918701171875 s and adjustment time is 2.96341300010681 s ( 99.47 )
2024-10-09 22:27:32.589468 INFO::Formatting Data.
2024-10-09 22:27:32.591046 INFO::Replacing NaNs with NAs.
2024-10-09 22:27:32.592984 INFO::Removing potential empty rows and columns
2024-10-09 22:27:32.596555 INFO::Found 1000 missing values.
2024-10-09 22:27:32.619287 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-09 22:27:32.62068 INFO::Done
2024-10-09 22:27:32.621949 INFO::Acquiring quality metrics before batch effect correction.
2024-10-09 22:27:32.632035 INFO::Starting hierarchical adjustment
2024-10-09 22:27:32.633666 INFO::Found 10 batches.
2024-10-09 22:27:32.634869 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-09 22:27:32.636153 INFO::Using default BPPARAM
2024-10-09 22:27:32.637345 INFO::Processing subtree level 1
2024-10-09 22:27:35.779201 INFO::Processing subtree level 2
2024-10-09 22:27:38.587104 INFO::Adjusting the last 1 batches sequentially
2024-10-09 22:27:38.589396 INFO::Done
2024-10-09 22:27:38.590551 INFO::Acquiring quality metrics after batch effect correction.
2024-10-09 22:27:38.598927 INFO::ASW Batch was 0.535521104480705 prior to batch effect correction and is now 0.535521104480705 .
2024-10-09 22:27:38.600153 INFO::ASW Label was 0.291786575919817 prior to batch effect correction and is now 0.291786575919817 .
2024-10-09 22:27:38.601669 INFO::Total function execution time is 6.0123279094696 s and adjustment time is 5.95601487159729 s ( 99.06 )
2024-10-09 22:27:38.602996 INFO::Formatting Data.
2024-10-09 22:27:38.604117 INFO::Replacing NaNs with NAs.
2024-10-09 22:27:38.6058 INFO::Removing potential empty rows and columns
2024-10-09 22:27:38.608438 INFO::Found 1000 missing values.
2024-10-09 22:27:38.623488 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-09 22:27:38.624367 INFO::Done
2024-10-09 22:27:38.625079 INFO::Acquiring quality metrics before batch effect correction.
2024-10-09 22:27:38.631397 INFO::Starting hierarchical adjustment
2024-10-09 22:27:38.632398 INFO::Found 10 batches.
2024-10-09 22:27:39.340647 INFO::Set up parallel execution backend with 2 workers
2024-10-09 22:27:39.341593 INFO::Processing subtree level 1 with 10 batches using 2 cores.
2024-10-09 22:27:42.161619 INFO::Adjusting the last 2 batches sequentially
2024-10-09 22:27:42.16378 INFO::Adjusting sequential tree level 1 with 2 batches
2024-10-09 22:27:42.188405 INFO::Done
2024-10-09 22:27:42.189757 INFO::Acquiring quality metrics after batch effect correction.
2024-10-09 22:27:42.199162 INFO::ASW Batch was 0.535521104480705 prior to batch effect correction and is now 0.535521104480705 .
2024-10-09 22:27:42.200534 INFO::ASW Label was 0.291786575919817 prior to batch effect correction and is now 0.291786575919817 .
2024-10-09 22:27:42.202108 INFO::Total function execution time is 3.5990948677063 s and adjustment time is 3.55608105659485 s ( 98.8 )
2024-10-09 22:27:44.999626 INFO::Formatting Data.
2024-10-09 22:27:45.000894 INFO::Replacing NaNs with NAs.
2024-10-09 22:27:45.002354 INFO::Removing potential empty rows and columns
2024-10-09 22:27:45.003909 INFO::Found 0 missing values.
2024-10-09 22:27:45.007063 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-09 22:27:45.007782 INFO::Done
2024-10-09 22:27:45.008448 INFO::Acquiring quality metrics before batch effect correction.
2024-10-09 22:27:45.011037 INFO::Starting hierarchical adjustment
2024-10-09 22:27:45.011855 INFO::Found 3 batches.
2024-10-09 22:27:45.012526 INFO::Cores argument is not defined or BPPARAM has been specified. Argument corereduction will not be used.
2024-10-09 22:27:45.013277 INFO::Using default BPPARAM
2024-10-09 22:27:45.01397 INFO::Processing subtree level 1
2024-10-09 22:27:48.019952 INFO::Adjusting the last 1 batches sequentially
2024-10-09 22:27:48.022005 INFO::Done
2024-10-09 22:27:48.023138 INFO::Acquiring quality metrics after batch effect correction.
2024-10-09 22:27:48.026697 INFO::ASW Batch was 0.208165992939658 prior to batch effect correction and is now -0.192915197576096 .
2024-10-09 22:27:48.027771 INFO::ASW Label was -0.148475273152933 prior to batch effect correction and is now 0.0417400277679851 .
2024-10-09 22:27:48.029116 INFO::Total function execution time is 3.0295889377594 s and adjustment time is 3.01023316383362 s ( 99.36 )
2024-10-09 22:27:48.225973 INFO::Formatting Data.
2024-10-09 22:27:48.22742 INFO::Replacing NaNs with NAs.
2024-10-09 22:27:48.229016 INFO::Removing potential empty rows and columns
2024-10-09 22:27:48.230668 INFO::Found 2 missing values.
2024-10-09 22:27:48.234754 INFO::Introduced 1 missing values due to singular proteins at batch/covariate level.
2024-10-09 22:27:48.235883 INFO::Done
2024-10-09 22:27:48.290791 INFO::Found NA in Reference column
2024-10-09 22:27:48.305689 INFO::Require at least two references per batch.
2024-10-09 22:27:48.32617 INFO::Formatting Data.
2024-10-09 22:27:48.327095 INFO::Recognized SummarizedExperiment
2024-10-09 22:27:48.327798 INFO::Typecasting input to dataframe.
2024-10-09 22:27:48.33563 INFO::Replacing NaNs with NAs.
2024-10-09 22:27:48.336923 INFO::Removing potential empty rows and columns
2024-10-09 22:27:48.339598 INFO::Found 0 missing values.
2024-10-09 22:27:48.344644 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-09 22:27:48.345439 INFO::Done
2024-10-09 22:27:48.359221 INFO::Formatting Data.
2024-10-09 22:27:48.360129 INFO::Recognized SummarizedExperiment
2024-10-09 22:27:48.360818 INFO::Typecasting input to dataframe.
2024-10-09 22:27:48.375627 INFO::Replacing NaNs with NAs.
2024-10-09 22:27:48.376949 INFO::Removing potential empty rows and columns
2024-10-09 22:27:48.379734 INFO::Found 0 missing values.
2024-10-09 22:27:48.38741 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-09 22:27:48.388271 INFO::Done
2024-10-09 22:27:48.402516 INFO::Formatting Data.
2024-10-09 22:27:48.403475 INFO::Recognized SummarizedExperiment
2024-10-09 22:27:48.404226 INFO::Typecasting input to dataframe.
2024-10-09 22:27:48.419246 INFO::Replacing NaNs with NAs.
2024-10-09 22:27:48.420418 INFO::Removing potential empty rows and columns
2024-10-09 22:27:48.42161 INFO::Found 0 missing values.
2024-10-09 22:27:48.422719 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.
2024-10-09 22:27:48.426441 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-09 22:27:48.427186 INFO::Done
2024-10-09 22:27:48.441196 INFO::Formatting Data.
2024-10-09 22:27:48.442167 INFO::Replacing NaNs with NAs.
2024-10-09 22:27:48.443186 INFO::Removing potential empty rows and columns
2024-10-09 22:27:48.444278 INFO::Found 0 missing values.
2024-10-09 22:27:48.44686 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-09 22:27:48.447563 INFO::Done
2024-10-09 22:27:48.462982 INFO::Formatting Data.
2024-10-09 22:27:48.46448 INFO::Replacing NaNs with NAs.
2024-10-09 22:27:48.466217 INFO::Removing potential empty rows and columns
2024-10-09 22:27:48.468126 INFO::Found 0 missing values.
2024-10-09 22:27:48.472765 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-09 22:27:48.474038 INFO::Done
2024-10-09 22:27:48.532706 INFO::Formatting Data.
2024-10-09 22:27:48.534137 INFO::Replacing NaNs with NAs.
2024-10-09 22:27:48.535927 INFO::Removing potential empty rows and columns
2024-10-09 22:27:48.537827 INFO::Found 1 missing values.
2024-10-09 22:27:48.541511 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-09 22:27:48.542654 INFO::Done
2024-10-09 22:27:48.580851 INFO::Formatting Data.
2024-10-09 22:27:48.582345 INFO::Replacing NaNs with NAs.
2024-10-09 22:27:48.584008 INFO::Removing potential empty rows and columns
2024-10-09 22:27:48.585736 INFO::Found 2 missing values.
2024-10-09 22:27:48.58749 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.
2024-10-09 22:27:48.590952 INFO::Introduced 4 missing values due to singular proteins at batch/covariate level.
2024-10-09 22:27:48.592041 INFO::Done
2024-10-09 22:27:48.613074 INFO::Formatting Data.
2024-10-09 22:27:48.614532 INFO::Replacing NaNs with NAs.
2024-10-09 22:27:48.616209 INFO::Removing potential empty rows and columns
2024-10-09 22:27:48.617969 INFO::Found 2 missing values.
2024-10-09 22:27:48.620599 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-09 22:27:48.621722 INFO::Done
2024-10-09 22:27:48.643153 INFO::Formatting Data.
2024-10-09 22:27:48.644675 INFO::Typecasting input to dataframe.
2024-10-09 22:27:48.646344 INFO::Replacing NaNs with NAs.
2024-10-09 22:27:48.64801 INFO::Removing potential empty rows and columns
2024-10-09 22:27:48.64978 INFO::Found 0 missing values.
2024-10-09 22:27:48.654084 INFO::Introduced 0 missing values due to singular proteins at batch/covariate level.
2024-10-09 22:27:48.655278 INFO::Done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 134 ]
>
> proc.time()
user system elapsed
28.64 1.65 76.78
BERT.Rcheck/BERT-Ex.timings
| name | user | system | elapsed | |
| BERT | 7.88 | 0.53 | 16.81 | |
| compute_asw | 0.03 | 0.00 | 0.03 | |
| count_existing | 0.01 | 0.00 | 0.02 | |
| generate_data_covariables | 0.00 | 0.02 | 0.01 | |
| generate_dataset | 0.02 | 0.00 | 0.02 | |